Refactor of thread management in neuronavigation (#242)

* ADD: Initial support for real time tracts visualization during navigation * ENH: Improved affine transformations for importing external polydata in world coordinates * ENH: Tracts visualization with cross move started * Create Trekker thread * Tracts style working and save and load project with affine * Tract computing incorporated to navigation pipeline * Add offset to coil normal to get coordinate inside brain * ADD: Pipeline for navigation with tract visualiztion and better debug tracker * ENH: Refactor the cross update feature * FIX: Fixed update cross during navigation and improved tract visualization * FIX: Seed flip when applying offset and added list to offset user control * ADD: Brain surface texture mapping with peeling depth * Improved sleep for navigation with tractography * ENH: Tract computation speed doubled and tracts colors fixed * ENH: Print removed in tract coloring * ENH: Improved visualization of tracts * ENH: Divide tract computation in chuncks * ADD: Threads using Queue for navigation * ADD: Thread computing with class and pipeline * ENH: Navigation working with separate threads and lock * ENH: Navigation with tracts running in producer-consumer method with locks * ENH: Refactoring tracts threads * Update tractography data exchange * ENH: Improved Trekker GUI and tractography navigation working * Update optimal Trekker parameters * ADD: Dialog to adjust Trekker parameters * ENH: Dialog to load Trekker JSON configuration file * ENH: Replaced Trekker default list by dictionary with values[C * ENH: Remove tract code comments and refactor navigation pipeline * ENH: Replaced dialog warnings for message box in navigation tab * ENH: Split the removal and update of tracts * ENH: Major changes in navigation array management and tracts cleaning - Replaced all matrix to array, now using python matrix operator - Refactored flip_x function - Improved cleaning of tracts * ENH: Tract visualization enabled in cross function and matrix operations replaced by arrays - Additional code cleaning and commenting - Refactoring of tip offset snippet * ADD: Control of brain mask opacity * FIX: Remove brain surface when closing project * ENH: Update trekker parameters after loading files and major refactor in flip_x - Additional refactor of FRE computation and use of base_creation * ENH: Improved object load dialog, OnNavigate pipeline and better tracts cleaning * FIX: Navigation with tractography working - Improved offset computation for seed - Improved flip_x. No need to use a function, only multiply Y coordinate by -1 * Refactored compute_seed, affine_to_vtk, and set_message for tracts computation - Cleaned unecessary comments - Providing m_img already flip_x while set_message * FIX: Tract removal with update cross position was disabled * ENH: Threading of navigation replaced to LifoQueue, working with dev_tracker but not tested in real tracker * ENH: Tractography running with new limited Queue and nowait - Tracts actors are computed all at once, no optimization for computing blocks * FIX: Update pubsub in tracker - Navgation with tractography running * ENH: Multiblock tract computation and fixed tract cleaning - Tractography navigation working at 0.1-s sleep * ENH: Documented tractography computation and cleaned code * FIX: Navigation was not running if tracts were not found - created thread in new format for trigger - removed comments of unused pipelines and threading - removed commented old FRE base creation * FIX: Generalize new navigation to objects even without tracts - Navigation with object working seamless with and without tracts - Navigation in other modes (single ref, no object) not working - Added one extra queue to generalize the pipeline in navigation * FIX: Static object navigation working and refactor navigation pipeline - Object corregistration split in functions - Cleaned comments on reference computation * FIX: Tractography navigation working with and without coil - Applied the new threading to the non-object navigations - Improved visualization of the offset marker for tractography - Cleaned commented code * ENH: Clean solved TODOs and commented unused navigation code * FIX: Fixed open and save dialogs for navigation purposes * FIX: Reading affine from old projects and replaced affine function form transformation * UPD: Removed surface back culling prints * DEL: Hided tractography panel and removed brain mesh mask

Refactor of thread management in neuronavigation (#242)
* ADD: Initial support for real time tracts visualization during navigation * ENH: Improved affine transformations for importing external polydata in world coordinates * ENH: Tracts visualization with cross move started * Create Trekker thread * Tracts style working and save and load project with affine * Tract computing incorporated to navigation pipeline * Add offset to coil normal to get coordinate inside brain * ADD: Pipeline for navigation with tract visualiztion and better debug tracker * ENH: Refactor the cross update feature * FIX: Fixed update cross during navigation and improved tract visualization * FIX: Seed flip when applying offset and added list to offset user control * ADD: Brain surface texture mapping with peeling depth * Improved sleep for navigation with tractography * ENH: Tract computation speed doubled and tracts colors fixed * ENH: Print removed in tract coloring * ENH: Improved visualization of tracts * ENH: Divide tract computation in chuncks * ADD: Threads using Queue for navigation * ADD: Thread computing with class and pipeline * ENH: Navigation working with separate threads and lock * ENH: Navigation with tracts running in producer-consumer method with locks * ENH: Refactoring tracts threads * Update tractography data exchange * ENH: Improved Trekker GUI and tractography navigation working * Update optimal Trekker parameters * ADD: Dialog to adjust Trekker parameters * ENH: Dialog to load Trekker JSON configuration file * ENH: Replaced Trekker default list by dictionary with values[C * ENH: Remove tract code comments and refactor navigation pipeline * ENH: Replaced dialog warnings for message box in navigation tab * ENH: Split the removal and update of tracts * ENH: Major changes in navigation array management and tracts cleaning - Replaced all matrix to array, now using python matrix operator - Refactored flip_x function - Improved cleaning of tracts * ENH: Tract visualization enabled in cross function and matrix operations replaced by arrays - Additional code cleaning and commenting - Refactoring of tip offset snippet * ADD: Control of brain mask opacity * FIX: Remove brain surface when closing project * ENH: Update trekker parameters after loading files and major refactor in flip_x - Additional refactor of FRE computation and use of base_creation * ENH: Improved object load dialog, OnNavigate pipeline and better tracts cleaning * FIX: Navigation with tractography working - Improved offset computation for seed - Improved flip_x. No need to use a function, only multiply Y coordinate by -1 * Refactored compute_seed, affine_to_vtk, and set_message for tracts computation - Cleaned unecessary comments - Providing m_img already flip_x while set_message * FIX: Tract removal with update cross position was disabled * ENH: Threading of navigation replaced to LifoQueue, working with dev_tracker but not tested in real tracker * ENH: Tractography running with new limited Queue and nowait - Tracts actors are computed all at once, no optimization for computing blocks * FIX: Update pubsub in tracker - Navgation with tractography running * ENH: Multiblock tract computation and fixed tract cleaning - Tractography navigation working at 0.1-s sleep * ENH: Documented tractography computation and cleaned code * FIX: Navigation was not running if tracts were not found - created thread in new format for trigger - removed comments of unused pipelines and threading - removed commented old FRE base creation * FIX: Generalize new navigation to objects even without tracts - Navigation with object working seamless with and without tracts - Navigation in other modes (single ref, no object) not working - Added one extra queue to generalize the pipeline in navigation * FIX: Static object navigation working and refactor navigation pipeline - Object corregistration split in functions - Cleaned comments on reference computation * FIX: Tractography navigation working with and without coil - Applied the new threading to the non-object navigations - Improved visualization of the offset marker for tractography - Cleaned commented code * ENH: Clean solved TODOs and commented unused navigation code * FIX: Fixed open and save dialogs for navigation purposes * FIX: Reading affine from old projects and replaced affine function form transformation * UPD: Removed surface back culling prints * DEL: Hided tractography panel and removed brain mesh mask
Victor Hugo Souza · GitHub
1 parent b7470270
Showing 20 changed files with 2711 additions and 1011 deletions Show diff stats
invesalius/constants.py
invesalius/control.py
invesalius/data/bases.py
invesalius/data/coordinates.py
invesalius/data/coregistration.py
invesalius/data/imagedata_utils.py
invesalius/data/record_coords.py
invesalius/data/slice_.py
invesalius/data/styles.py
invesalius/data/surface.py
invesalius/data/trackers.py
invesalius/data/tractography.py
invesalius/data/trigger.py
invesalius/data/viewer_slice.py
invesalius/data/viewer_volume.py
invesalius/data/vtk_utils.py
invesalius/gui/dialogs.py
invesalius/gui/frame.py
invesalius/gui/task_navigator.py
invesalius/project.py
@@ -19,6 +19,7 @@
 import os.path
 import platform
+import psutil
 import sys
 import wx
 import itertools
@@ -521,6 +522,11 @@ ID_GOTO_COORD = wx.NewId()
 ID_MANUAL_WWWL = wx.NewId()
+# Tractography with Trekker
+ID_TREKKER_MASK = wx.NewId()
+ID_TREKKER_IMG = wx.NewId()
+ID_TREKKER_FOD = wx.NewId()
+
 #---------------------------------------------------------
 STATE_DEFAULT = 1000
 STATE_WL = 1001
@@ -545,6 +551,7 @@ SLICE_STATE_REMOVE_MASK_PARTS = 3012
 SLICE_STATE_SELECT_MASK_PARTS = 3013
 SLICE_STATE_FFILL_SEGMENTATION = 3014
 SLICE_STATE_CROP_MASK = 3015
+SLICE_STATE_TRACTS = 3016
 VOLUME_STATE_SEED = 2001
 #  STATE_LINEAR_MEASURE = 3001
@@ -559,7 +566,7 @@ TOOL_STATES = [STATE_WL, STATE_SPIN, STATE_ZOOM,
 TOOL_SLICE_STATES = [SLICE_STATE_CROSS, SLICE_STATE_SCROLL,
-                     SLICE_STATE_REORIENT]
+                     SLICE_STATE_REORIENT, SLICE_STATE_TRACTS]
 SLICE_STYLES = TOOL_STATES + TOOL_SLICE_STATES
@@ -651,6 +658,8 @@ BOOLEAN_XOR = 4
 #------------ Navigation defaults -------------------
+MARKER_COLOUR = (1.0, 1.0, 0.)
+MARKER_SIZE = 2
 SELECT = 0
 MTC = 1
 FASTRAK = 2
@@ -738,3 +747,17 @@ COIL_COORD_THRESHOLD = 3
 TIMESTAMP = 2.0
 CAM_MODE = True
+
+# Tractography visualization
+N_TRACTS = 100
+PEEL_DEPTH = 5
+MAX_PEEL_DEPTH = 30
+SEED_OFFSET = 15
+SEED_RADIUS = 1.5
+SLEEP_NAVIGATION = 0.1
+BRAIN_OPACITY = 0.5
+N_CPU = psutil.cpu_count()
+TREKKER_CONFIG = {'seed_max': 1, 'step_size': 0.1, 'min_fod': 0.1, 'probe_quality': 3,
+                  'max_interval': 1, 'min_radius_curv': 0.8, 'probe_length': 0.4,
+                  'write_interval': 50, 'numb_threads': '', 'max_lenth': 200,
+                  'min_lenth': 20, 'max_sampling_step': 100}
@@ -32,6 +32,7 @@ import invesalius.data.mask as msk
 import invesalius.data.measures as measures
 import invesalius.data.slice_ as sl
 import invesalius.data.surface as srf
+import invesalius.data.transformations as tr
 import invesalius.data.volume as volume
 import invesalius.gui.dialogs as dialog
 import invesalius.project as prj
@@ -57,7 +58,6 @@ class Controller():
     def __init__(self, frame):
         self.surface_manager = srf.SurfaceManager()
         self.volume = volume.Volume()
-        self.plugin_manager = plugins.PluginManager()
         self.__bind_events()
         self.frame = frame
         self.progress_dialog = None
@@ -76,12 +76,9 @@ class Controller():
         Publisher.sendMessage('Load Preferences')
-        self.plugin_manager.find_plugins()
-
     def __bind_events(self):
         Publisher.subscribe(self.OnImportMedicalImages, 'Import directory')
         Publisher.subscribe(self.OnImportGroup, 'Import group')
-        Publisher.subscribe(self.OnImportFolder, 'Import folder')
         Publisher.subscribe(self.OnShowDialogImportDirectory,
                                  'Show import directory dialog')
         Publisher.subscribe(self.OnShowDialogImportOtherFiles,
@@ -123,8 +120,6 @@ class Controller():
         Publisher.subscribe(self.Send_affine, 'Get affine matrix')
-        Publisher.subscribe(self.create_project_from_matrix, 'Create project from matrix')
-
     def SetBitmapSpacing(self, spacing):
         proj = prj.Project()
         proj.spacing = spacing
@@ -336,6 +331,10 @@ class Controller():
         self.Slice.window_level = proj.level
         self.Slice.window_width = proj.window
+        if proj.affine:
+            self.Slice.affine = np.asarray(proj.affine).reshape(4, 4)
+        else:
+            self.Slice.affine = None
         Publisher.sendMessage('Update threshold limits list',
                               threshold_range=proj.threshold_range)
@@ -504,32 +503,7 @@ class Controller():
         self.LoadProject()
         Publisher.sendMessage("Enable state project", state=True)
-    def OnImportFolder(self, folder):
-        Publisher.sendMessage('Begin busy cursor')
-        folder = os.path.abspath(folder)
-
-        proj = prj.Project()
-        proj.load_from_folder(folder)
-
-        self.Slice = sl.Slice()
-        self.Slice._open_image_matrix(proj.matrix_filename,
-                                      tuple(proj.matrix_shape),
-                                      proj.matrix_dtype)
-
-        self.Slice.window_level = proj.level
-        self.Slice.window_width = proj.window
-
-        Publisher.sendMessage('Update threshold limits list',
-                              threshold_range=proj.threshold_range)
-
-        session = ses.Session()
-        filename = proj.name+".inv3"
-        filename = filename.replace("/", "") #Fix problem case other/Skull_DICOM
-        dirpath = session.CreateProject(filename)
-        self.LoadProject()
-        Publisher.sendMessage("Enable state project", state=True)
-
-        Publisher.sendMessage('End busy cursor')
+    #-------------------------------------------------------------------------------------
     def LoadProject(self):
         proj = prj.Project()
@@ -688,6 +662,9 @@ class Controller():
         proj.matrix_dtype = matrix.dtype.name
         proj.matrix_filename = matrix_filename
+        if self.affine is not None:
+            proj.affine = self.affine.tolist()
+
         # Orientation must be CORONAL in order to as_closes_canonical and
         # swap axis in img2memmap to work in a standardized way.
         # TODO: Create standard import image for all acquisition orientations
@@ -700,7 +677,6 @@ class Controller():
         proj.level = self.Slice.window_level
         proj.threshold_range = int(matrix.min()), int(matrix.max())
         proj.spacing = self.Slice.spacing
-        proj.affine = self.affine.tolist()
         ######
         session = ses.Session()
@@ -872,11 +848,13 @@ class Controller():
     def OnOpenOtherFiles(self, filepath):
         filepath = utils.decode(filepath, const.FS_ENCODE)
         if not(filepath) == None:
-            name = os.path.basename(filepath).split(".")[0]
+            name = filepath.rpartition('\\')[-1].split('.')
+
             group = oth.ReadOthers(filepath)
+            
             if group:
                 matrix, matrix_filename = self.OpenOtherFiles(group)
-                self.CreateOtherProject(name, matrix, matrix_filename)
+                self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
                 self.LoadProject()
                 Publisher.sendMessage("Enable state project", state=True)
             else:
@@ -981,10 +959,10 @@ class Controller():
         self.matrix, scalar_range, self.filename = image_utils.img2memmap(group)
         hdr = group.header
-        if group.affine.any():
-            self.affine = group.affine
-            Publisher.sendMessage('Update affine matrix',
-                                  affine=self.affine, status=True)
+        # if group.affine.any():
+        #     self.affine = group.affine
+        #     Publisher.sendMessage('Update affine matrix',
+        #                           affine=self.affine, status=True)
         hdr.set_data_dtype('int16')
         dims = hdr.get_zooms()
         dimsf = tuple([float(s) for s in dims])
@@ -1000,6 +978,18 @@ class Controller():
         self.Slice.window_level = wl
         self.Slice.window_width = ww
+        if group.affine.any():
+            # TODO: replace the inverse of the affine by the actual affine in the whole code
+            # remove scaling factor for non-unitary voxel dimensions
+            # self.affine = image_utils.world2invspace(affine=group.affine)
+            scale, shear, angs, trans, persp = tr.decompose_matrix(group.affine)
+            self.affine = np.linalg.inv(tr.compose_matrix(scale=None, shear=shear,
+                                                          angles=angs, translate=trans, perspective=persp))
+            # print("repos_img: {}".format(repos_img))
+            self.Slice.affine = self.affine
+            Publisher.sendMessage('Update affine matrix',
+                                  affine=self.affine, status=True)
+
         scalar_range = int(scalar_range[0]), int(scalar_range[1])
         Publisher.sendMessage('Update threshold limits list',
                               threshold_range=scalar_range)
@@ -1066,24 +1056,3 @@ class Controller():
     def ApplyReorientation(self):
         self.Slice.apply_reorientation()
-
-    def start_new_inv_instance(self, image, name, spacing, modality, orientation, window_width, window_level):
-        p = prj.Project()
-        project_folder = tempfile.mkdtemp()
-        p.create_project_file(name, spacing, modality, orientation, window_width, window_level, image, folder=project_folder)
-        err_msg = ''
-        try:
-            sp = subprocess.Popen([sys.executable, sys.argv[0], '--import-folder', project_folder],
-                                  stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=os.getcwd())
-        except Exception as err:
-            err_msg = str(err)
-        else:
-            try:
-                if sp.wait(2):
-                    err_msg = sp.stderr.read().decode('utf8')
-                    sp.terminate()
-            except subprocess.TimeoutExpired:
-                pass
-
-        if err_msg:
-            dialog.MessageBox(None, "It was not possible to launch new instance of InVesalius3 dsfa dfdsfa sdfas fdsaf asdfasf dsaa", err_msg)
-from math import sqrt, pi
 import numpy as np
 import invesalius.data.coordinates as dco
 import invesalius.data.transformations as tr
@@ -23,8 +22,7 @@ def angle_calculation(ap_axis, coil_axis):
 def base_creation_old(fiducials):
     """
-    Calculate the origin and matrix for coordinate system
-    transformation.
+    Calculate the origin and matrix for coordinate system transformation.
     q: origin of coordinate system
     g1, g2, g3: orthogonal vectors of coordinate system
@@ -49,9 +47,9 @@ def base_creation_old(fiducials):
     g3 = np.cross(g2, g1)
-    g1 = g1/sqrt(np.dot(g1, g1))
-    g2 = g2/sqrt(np.dot(g2, g2))
-    g3 = g3/sqrt(np.dot(g3, g3))
+    g1 = g1/np.sqrt(np.dot(g1, g1))
+    g2 = g2/np.sqrt(np.dot(g2, g2))
+    g3 = g3/np.sqrt(np.dot(g3, g3))
     m = np.matrix([[g1[0], g1[1], g1[2]],
                    [g2[0], g2[1], g2[2]],
@@ -79,7 +77,7 @@ def base_creation(fiducials):
     sub1 = p2 - p1
     sub2 = p3 - p1
-    lamb = (sub1[0]*sub2[0]+sub1[1]*sub2[1]+sub1[2]*sub2[2])/np.dot(sub1, sub1)
+    lamb = np.dot(sub1, sub2)/np.dot(sub1, sub1)
     q = p1 + lamb*sub1
     g1 = p3 - q
@@ -90,20 +88,52 @@ def base_creation(fiducials):
     g3 = np.cross(g1, g2)
-    g1 = g1/sqrt(np.dot(g1, g1))
-    g2 = g2/sqrt(np.dot(g2, g2))
-    g3 = g3/sqrt(np.dot(g3, g3))
-
-    m = np.matrix([[g1[0], g2[0], g3[0]],
-                   [g1[1], g2[1], g3[1]],
-                   [g1[2], g2[2], g3[2]]])
-
-    m_inv = m.I
-
-    return m, q, m_inv
-
-
-def calculate_fre(fiducials, minv, n, q, o):
+    g1 = g1/np.sqrt(np.dot(g1, g1))
+    g2 = g2/np.sqrt(np.dot(g2, g2))
+    g3 = g3/np.sqrt(np.dot(g3, g3))
+
+    m = np.zeros([3, 3])
+    m[:, 0] = g1/np.sqrt(np.dot(g1, g1))
+    m[:, 1] = g2/np.sqrt(np.dot(g2, g2))
+    m[:, 2] = g3/np.sqrt(np.dot(g3, g3))
+
+    return m, q
+
+
+# def calculate_fre(fiducials, minv, n, q, o):
+#     """
+#     Calculate the Fiducial Registration Error for neuronavigation.
+#
+#     :param fiducials: array of 6 rows (image and tracker fiducials) and 3 columns (x, y, z) with coordinates
+#     :param minv: inverse matrix given by base creation
+#     :param n: base change matrix given by base creation
+#     :param q: origin of first base
+#     :param o: origin of second base
+#     :return: float number of fiducial registration error
+#     """
+#
+#     img = np.zeros([3, 3])
+#     dist = np.zeros([3, 1])
+#
+#     q1 = np.mat(q).reshape(3, 1)
+#     q2 = np.mat(o).reshape(3, 1)
+#
+#     p1 = np.mat(fiducials[3, :]).reshape(3, 1)
+#     p2 = np.mat(fiducials[4, :]).reshape(3, 1)
+#     p3 = np.mat(fiducials[5, :]).reshape(3, 1)
+#
+#     img[0, :] = np.asarray((q1 + (minv * n) * (p1 - q2)).reshape(1, 3))
+#     img[1, :] = np.asarray((q1 + (minv * n) * (p2 - q2)).reshape(1, 3))
+#     img[2, :] = np.asarray((q1 + (minv * n) * (p3 - q2)).reshape(1, 3))
+#
+#     dist[0] = np.sqrt(np.sum(np.power((img[0, :] - fiducials[0, :]), 2)))
+#     dist[1] = np.sqrt(np.sum(np.power((img[1, :] - fiducials[1, :]), 2)))
+#     dist[2] = np.sqrt(np.sum(np.power((img[2, :] - fiducials[2, :]), 2)))
+#
+#     return float(np.sqrt(np.sum(dist ** 2) / 3))
+
+
+def calculate_fre_m(fiducials):
     """
     Calculate the Fiducial Registration Error for neuronavigation.
@@ -115,19 +145,29 @@ def calculate_fre(fiducials, minv, n, q, o):
     :return: float number of fiducial registration error
     """
+    m, q1, minv = base_creation_old(fiducials[:3, :])
+    n, q2, ninv = base_creation_old(fiducials[3:, :])
+
+    # TODO: replace the old by the new base creation
+    # the values differ greatly if FRE is computed using the old or new base_creation
+    # check the reason for the difference, because they should be the same
+    # m, q1 = base_creation(fiducials[:3, :])
+    # n, q2 = base_creation(fiducials[3:, :])
+    # minv = np.linalg.inv(m)
+
     img = np.zeros([3, 3])
     dist = np.zeros([3, 1])
-    q1 = np.mat(q).reshape(3, 1)
-    q2 = np.mat(o).reshape(3, 1)
+    q1 = q1.reshape(3, 1)
+    q2 = q2.reshape(3, 1)
-    p1 = np.mat(fiducials[3, :]).reshape(3, 1)
-    p2 = np.mat(fiducials[4, :]).reshape(3, 1)
-    p3 = np.mat(fiducials[5, :]).reshape(3, 1)
+    p1 = fiducials[3, :].reshape(3, 1)
+    p2 = fiducials[4, :].reshape(3, 1)
+    p3 = fiducials[5, :].reshape(3, 1)
-    img[0, :] = np.asarray((q1 + (minv * n) * (p1 - q2)).reshape(1, 3))
-    img[1, :] = np.asarray((q1 + (minv * n) * (p2 - q2)).reshape(1, 3))
-    img[2, :] = np.asarray((q1 + (minv * n) * (p3 - q2)).reshape(1, 3))
+    img[0, :] = (q1 + (minv @ n) * (p1 - q2)).reshape(1, 3)
+    img[1, :] = (q1 + (minv @ n) * (p2 - q2)).reshape(1, 3)
+    img[2, :] = (q1 + (minv @ n) * (p3 - q2)).reshape(1, 3)
     dist[0] = np.sqrt(np.sum(np.power((img[0, :] - fiducials[0, :]), 2)))
     dist[1] = np.sqrt(np.sum(np.power((img[1, :] - fiducials[1, :]), 2)))
@@ -136,44 +176,68 @@ def calculate_fre(fiducials, minv, n, q, o):
     return float(np.sqrt(np.sum(dist ** 2) / 3))
-def flip_x(point):
-    """
-    Flip coordinates of a vector according to X axis
-    Coronal Images do not require this transformation - 1 tested
-    and for this case, at navigation, the z axis is inverted
-
-    It's necessary to multiply the z coordinate by (-1). Possibly
-    because the origin of coordinate system of imagedata is
-    located in superior left corner and the origin of VTK scene coordinate
-    system (polygonal surface) is in the interior left corner. Second
-    possibility is the order of slice stacking
-
-    :param point: list of coordinates x, y and z
-    :return: flipped coordinates
-    """
-
-    # TODO: check if the Flip function is related to the X or Y axis
-
-    point = np.matrix(point + (0,))
-    point[0, 2] = -point[0, 2]
-
-    m_rot = np.matrix([[1.0, 0.0, 0.0, 0.0],
-                      [0.0, -1.0, 0.0, 0.0],
-                      [0.0, 0.0, -1.0, 0.0],
-                      [0.0, 0.0, 0.0, 1.0]])
-    m_trans = np.matrix([[1.0, 0, 0, -point[0, 0]],
-                        [0.0, 1.0, 0, -point[0, 1]],
-                        [0.0, 0.0, 1.0, -point[0, 2]],
-                        [0.0, 0.0, 0.0, 1.0]])
-    m_trans_return = np.matrix([[1.0, 0, 0, point[0, 0]],
-                               [0.0, 1.0, 0, point[0, 1]],
-                               [0.0, 0.0, 1.0, point[0, 2]],
-                               [0.0, 0.0, 0.0, 1.0]])
-        
-    point_rot = point*m_trans*m_rot*m_trans_return
-    x, y, z = point_rot.tolist()[0][:3]
-
-    return x, y, z
+# def flip_x(point):
+#     """
+#     Flip coordinates of a vector according to X axis
+#     Coronal Images do not require this transformation - 1 tested
+#     and for this case, at navigation, the z axis is inverted
+#
+#     It's necessary to multiply the z coordinate by (-1). Possibly
+#     because the origin of coordinate system of imagedata is
+#     located in superior left corner and the origin of VTK scene coordinate
+#     system (polygonal surface) is in the interior left corner. Second
+#     possibility is the order of slice stacking
+#
+#     :param point: list of coordinates x, y and z
+#     :return: flipped coordinates
+#     """
+#
+#     # TODO: check if the Flip function is related to the X or Y axis
+#
+#     point = np.matrix(point + (0,))
+#     point[0, 2] = -point[0, 2]
+#
+#     m_rot = np.matrix([[1.0, 0.0, 0.0, 0.0],
+#                       [0.0, -1.0, 0.0, 0.0],
+#                       [0.0, 0.0, -1.0, 0.0],
+#                       [0.0, 0.0, 0.0, 1.0]])
+#     m_trans = np.matrix([[1.0, 0, 0, -point[0, 0]],
+#                         [0.0, 1.0, 0, -point[0, 1]],
+#                         [0.0, 0.0, 1.0, -point[0, 2]],
+#                         [0.0, 0.0, 0.0, 1.0]])
+#     m_trans_return = np.matrix([[1.0, 0, 0, point[0, 0]],
+#                                [0.0, 1.0, 0, point[0, 1]],
+#                                [0.0, 0.0, 1.0, point[0, 2]],
+#                                [0.0, 0.0, 0.0, 1.0]])
+#
+#     point_rot = point*m_trans*m_rot*m_trans_return
+#     x, y, z = point_rot.tolist()[0][:3]
+#
+#     return x, y, z
+
+
+# def flip_x_m(point):
+#     """
+#     Rotate coordinates of a vector by pi around X axis in static reference frame.
+#
+#     InVesalius also require to multiply the z coordinate by (-1). Possibly
+#     because the origin of coordinate system of imagedata is
+#     located in superior left corner and the origin of VTK scene coordinate
+#     system (polygonal surface) is in the interior left corner. Second
+#     possibility is the order of slice stacking
+#
+#     :param point: list of coordinates x, y and z
+#     :return: rotated coordinates
+#     """
+#
+#     point_4 = np.hstack((point, 1.)).reshape([4, 1])
+#     point_4[2, 0] = -point_4[2, 0]
+#
+#     m_rot = tr.euler_matrix(pi, 0, 0)
+#
+#     point_rot = m_rot @ point_4
+#
+#     return point_rot[0, 0], point_rot[1, 0], point_rot[2, 0]
 def flip_x_m(point):
@@ -190,14 +254,14 @@ def flip_x_m(point):
     :return: rotated coordinates
     """
-    point_4 = np.hstack((point, 1.)).reshape([4, 1])
+    point_4 = np.hstack((point, 1.)).reshape(4, 1)
     point_4[2, 0] = -point_4[2, 0]
-    m_rot = np.asmatrix(tr.euler_matrix(pi, 0, 0))
+    m_rot = tr.euler_matrix(np.pi, 0, 0)
-    point_rot = m_rot*point_4
+    point_rot = m_rot @ point_4
-    return point_rot[0, 0], point_rot[1, 0], point_rot[2, 0]
+    return point_rot
 def object_registration(fiducials, orients, coord_raw, m_change):
@@ -224,48 +288,48 @@ def object_registration(fiducials, orients, coord_raw, m_change):
         fids_raw[ic, :] = dco.dynamic_reference_m2(coords[ic, :], coords[3, :])[:3]
     # compute initial alignment of probe fixed in the object in source frame
-    t_s0_raw = np.asmatrix(tr.translation_matrix(coords[3, :3]))
-    r_s0_raw = np.asmatrix(tr.euler_matrix(np.radians(coords[3, 3]), np.radians(coords[3, 4]),
-                             np.radians(coords[3, 5]), 'rzyx'))
-    s0_raw = np.asmatrix(tr.concatenate_matrices(t_s0_raw, r_s0_raw))
+    t_s0_raw = tr.translation_matrix(coords[3, :3])
+    r_s0_raw = tr.euler_matrix(np.radians(coords[3, 3]), np.radians(coords[3, 4]),
+                             np.radians(coords[3, 5]), 'rzyx')
+    s0_raw = tr.concatenate_matrices(t_s0_raw, r_s0_raw)
     # compute change of basis for object fiducials in source frame
-    base_obj_raw, q_obj_raw, base_inv_obj_raw = base_creation(fids_raw[:3, :3])
-    r_obj_raw = np.asmatrix(np.identity(4))
+    base_obj_raw, q_obj_raw = base_creation(fids_raw[:3, :3])
+    r_obj_raw = np.identity(4)
     r_obj_raw[:3, :3] = base_obj_raw[:3, :3]
-    t_obj_raw = np.asmatrix(tr.translation_matrix(q_obj_raw))
-    m_obj_raw = np.asmatrix(tr.concatenate_matrices(t_obj_raw, r_obj_raw))
+    t_obj_raw = tr.translation_matrix(q_obj_raw)
+    m_obj_raw = tr.concatenate_matrices(t_obj_raw, r_obj_raw)
     for ic in range(0, 4):
         if coord_raw.any():
             # compute object fiducials in reference frame
             fids_dyn[ic, :] = dco.dynamic_reference_m2(coords[ic, :], coord_raw[1, :])
-            fids_dyn[ic, 2] = -fids_dyn[ic, 2]
         else:
             # compute object fiducials in source frame
             fids_dyn[ic, :] = coords[ic, :]
+        fids_dyn[ic, 2] = -fids_dyn[ic, 2]
         # compute object fiducials in vtk head frame
         a, b, g = np.radians(fids_dyn[ic, 3:])
         T_p = tr.translation_matrix(fids_dyn[ic, :3])
         R_p = tr.euler_matrix(a, b, g, 'rzyx')
-        M_p = np.asmatrix(tr.concatenate_matrices(T_p, R_p))
-        M_img = np.asmatrix(m_change) * M_p
+        M_p = tr.concatenate_matrices(T_p, R_p)
+        M_img = m_change @ M_p
         angles_img = np.degrees(np.asarray(tr.euler_from_matrix(M_img, 'rzyx')))
-        coord_img = np.asarray(flip_x_m(tr.translation_from_matrix(M_img)))
+        coord_img = flip_x_m(tr.translation_from_matrix(M_img))
-        fids_img[ic, :] = np.hstack((coord_img, angles_img))
+        fids_img[ic, :] = np.hstack((coord_img[:3, 0], angles_img))
     # compute object base change in vtk head frame
-    base_obj_img, q_obj_img, base_inv_obj_img = base_creation(fids_img[:3, :3])
-    r_obj_img = np.asmatrix(np.identity(4))
+    base_obj_img, _ = base_creation(fids_img[:3, :3])
+    r_obj_img = np.identity(4)
     r_obj_img[:3, :3] = base_obj_img[:3, :3]
     # compute initial alignment of probe fixed in the object in reference (or static) frame
-    s0_trans_dyn = np.asmatrix(tr.translation_matrix(fids_dyn[3, :3]))
-    s0_rot_dyn = np.asmatrix(tr.euler_matrix(np.radians(fids_dyn[3, 3]), np.radians(fids_dyn[3, 4]),
-                                             np.radians(fids_dyn[3, 5]), 'rzyx'))
-    s0_dyn = np.asmatrix(tr.concatenate_matrices(s0_trans_dyn, s0_rot_dyn))
+    s0_trans_dyn = tr.translation_matrix(fids_dyn[3, :3])
+    s0_rot_dyn = tr.euler_matrix(np.radians(fids_dyn[3, 3]), np.radians(fids_dyn[3, 4]),
+                                             np.radians(fids_dyn[3, 5]), 'rzyx')
+    s0_dyn = tr.concatenate_matrices(s0_trans_dyn, s0_rot_dyn)
     return t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img
@@ -20,6 +20,7 @@
 from math import sin, cos
 import numpy as np
+import invesalius.data.bases as db
 import invesalius.data.transformations as tr
 import invesalius.constants as const
@@ -74,7 +75,7 @@ def PolarisCoord(trck_init, trck_id, ref_mode):
     coord3 = np.hstack((trans_obj, angles_obj))
     coord = np.vstack([coord1, coord2, coord3])
-    Publisher.sendMessage('Sensors ID', probe_id=trck.probeID, ref_id=trck.refID, obj_id=trck.objID)
+    # Publisher.sendMessage('Sensors ID', probe_id=trck.probeID, ref_id=trck.refID, obj_id=trck.objID)
     return coord
@@ -232,19 +233,45 @@ def DebugCoord(trk_init, trck_id, ref_mode):
     :return: six coordinates x, y, z, alfa, beta and gama
     """
-    sleep(0.05)
+    # Started to take a more reasonable, limited random coordinate generator based on
+    # the collected fiducials, but it is more complicated than this. It should account for the
+    # dynamic reference computation
+    # if trk_init:
+    #     fiducials = trk_init[3:, :]
+    #     fids_max = fiducials.max(axis=0)
+    #     fids_min = fiducials.min(axis=0)
+    #     fids_lim = np.hstack((fids_min[np.newaxis, :].T, fids_max[np.newaxis, :].T))
+    #
+    #     dx = fids_max[]
+    #     dt = [-180, 180]
+    #
+    # else:
-    coord1 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
-                      uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    dx = [-70, 70]
+    dt = [-180, 180]
-    coord2 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
-                       uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    coord1 = np.array([uniform(*dx), uniform(*dx), uniform(*dx),
+                      uniform(*dt), uniform(*dt), uniform(*dt)])
+    coord2 = np.array([uniform(*dx), uniform(*dx), uniform(*dx),
+                      uniform(*dt), uniform(*dt), uniform(*dt)])
+    coord3 = np.array([uniform(*dx), uniform(*dx), uniform(*dx),
+                       uniform(*dt), uniform(*dt), uniform(*dt)])
+    coord4 = np.array([uniform(*dx), uniform(*dx), uniform(*dx),
+                       uniform(*dt), uniform(*dt), uniform(*dt)])
-    coord3 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
-                       uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    sleep(0.05)
-    coord4 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
-                       uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    # coord1 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+    #                    uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    #
+    # coord2 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+    #                    uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    #
+    # coord3 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+    #                    uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+    #
+    # coord4 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+    #                    uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
     Publisher.sendMessage('Sensors ID', probe_id=int(uniform(0, 5)), ref_id=int(uniform(0, 5)), obj_id=int(uniform(0, 5)))
@@ -297,19 +324,20 @@ def dynamic_reference_m(probe, reference):
     :param reference: sensor two defined as reference
     :return: rotated and translated coordinates
     """
-
     a, b, g = np.radians(reference[3:6])
-    T = tr.translation_matrix(reference[:3])
-    R = tr.euler_matrix(a, b, g, 'rzyx')
-    M = np.asmatrix(tr.concatenate_matrices(T, R))
-    # M = tr.compose_matrix(angles=np.radians(reference[3:6]), translate=reference[:3])
-    # print M
-    probe_4 = np.vstack((np.asmatrix(probe[:3]).reshape([3, 1]), 1.))
-    coord_rot = M.I * probe_4
-    coord_rot = np.squeeze(np.asarray(coord_rot))
+    trans = tr.translation_matrix(reference[:3])
+    rot = tr.euler_matrix(a, b, g, 'rzyx')
+    affine = tr.concatenate_matrices(trans, rot)
+    probe_4 = np.vstack((probe[:3].reshape([3, 1]), 1.))
+    coord_rot = np.linalg.inv(affine) @ probe_4
+    # minus sign to the z coordinate
+    coord_rot[2, 0] = -coord_rot[2, 0]
+    coord_rot = coord_rot[:3, 0].tolist()
+    coord_rot.extend(probe[3:])
+
+    return coord_rot
-    return coord_rot[0], coord_rot[1], -coord_rot[2], probe[3], probe[4], probe[5]
 def dynamic_reference_m2(probe, reference):
     """
@@ -331,70 +359,18 @@ def dynamic_reference_m2(probe, reference):
     T_p = tr.translation_matrix(probe[:3])
     R = tr.euler_matrix(a, b, g, 'rzyx')
     R_p = tr.euler_matrix(a_p, b_p, g_p, 'rzyx')
-    M = np.asmatrix(tr.concatenate_matrices(T, R))
-    M_p = np.asmatrix(tr.concatenate_matrices(T_p, R_p))
-    # M = tr.compose_matrix(angles=np.radians(reference[3:6]), translate=reference[:3])
-    # print M
+    M = tr.concatenate_matrices(T, R)
+    M_p = tr.concatenate_matrices(T_p, R_p)
-    M_dyn = M.I * M_p
+    M_dyn = np.linalg.inv(M) @ M_p
     al, be, ga = tr.euler_from_matrix(M_dyn, 'rzyx')
     coord_rot = tr.translation_from_matrix(M_dyn)
     coord_rot = np.squeeze(coord_rot)
-    # probe_4 = np.vstack((np.asmatrix(probe[:3]).reshape([3, 1]), 1.))
-    # coord_rot_test = M.I * probe_4
-    # coord_rot_test = np.squeeze(np.asarray(coord_rot_test))
-    #
-    # print "coord_rot: ", coord_rot
-    # print "coord_rot_test: ", coord_rot_test
-    # print "test: ", np.allclose(coord_rot, coord_rot_test[:3])
-
     return coord_rot[0], coord_rot[1], coord_rot[2], np.degrees(al), np.degrees(be), np.degrees(ga)
-# def dynamic_reference_m3(probe, reference):
-#     """
-#     Apply dynamic reference correction to probe coordinates. Uses the alpha, beta and gama
-#     rotation angles of reference to rotate the probe coordinate and returns the x, y, z
-#     difference between probe and reference. Angles sequences and equation was extracted from
-#     Polhemus manual and Attitude matrix in Wikipedia.
-#     General equation is:
-#     coord = Mrot * (probe - reference)
-#     :param probe: sensor one defined as probe
-#     :param reference: sensor two defined as reference
-#     :return: rotated and translated coordinates
-#     """
-#
-#     a, b, g = np.radians(reference[3:6])
-#     a_p, b_p, g_p = np.radians(probe[3:6])
-#
-#     T = tr.translation_matrix(reference[:3])
-#     T_p = tr.translation_matrix(probe[:3])
-#     R = tr.euler_matrix(a, b, g, 'rzyx')
-#     R_p = tr.euler_matrix(a_p, b_p, g_p, 'rzyx')
-#     M = np.asmatrix(tr.concatenate_matrices(T, R))
-#     M_p = np.asmatrix(tr.concatenate_matrices(T_p, R_p))
-#     # M = tr.compose_matrix(angles=np.radians(reference[3:6]), translate=reference[:3])
-#     # print M
-#
-#     M_dyn = M.I * M_p
-#
-#     # al, be, ga = tr.euler_from_matrix(M_dyn, 'rzyx')
-#     # coord_rot = tr.translation_from_matrix(M_dyn)
-#     #
-#     # coord_rot = np.squeeze(coord_rot)
-#
-#     # probe_4 = np.vstack((np.asmatrix(probe[:3]).reshape([3, 1]), 1.))
-#     # coord_rot_test = M.I * probe_4
-#     # coord_rot_test = np.squeeze(np.asarray(coord_rot_test))
-#     #
-#     # print "coord_rot: ", coord_rot
-#     # print "coord_rot_test: ", coord_rot_test
-#     # print "test: ", np.allclose(coord_rot, coord_rot_test[:3])
-#
-#     return M_dyn
-
 def str2float(data):
     """
@@ -414,3 +390,15 @@ def str2float(data):
     data = [float(s) for s in data[1:len(data)]]
     return data
+
+
+def offset_coordinate(p_old, norm_vec, offset):
+    """
+    Translate the coordinates of a point along a vector
+    :param p_old: (x, y, z) array with current point coordinates
+    :param norm_vec: (vx, vy, vz) array with normal vector coordinates
+    :param offset: double representing the magnitude of offset
+    :return: (x_new, y_new, z_new) array of offset coordinates
+    """
+    p_offset = p_old - offset * norm_vec
+    return p_offset
@@ -17,347 +17,620 @@
 #    detalhes.
 #--------------------------------------------------------------------------
+import numpy as np
+import queue
 import threading
 from time import sleep
-from numpy import asmatrix, mat, degrees, radians, identity
-import wx
-from pubsub import pub as Publisher
-
 import invesalius.data.coordinates as dco
 import invesalius.data.transformations as tr
-# TODO: Optimize navigation thread. Remove the infinite loop and optimize sleep.
-
-class CoregistrationStatic(threading.Thread):
-    """
-    Thread to update the coordinates with the fiducial points
-    co-registration method while the Navigation Button is pressed.
-    Sleep function in run method is used to avoid blocking GUI and
-    for better real-time navigation
+# TODO: Replace the use of degrees by radians in every part of the navigation pipeline
+
+def object_marker_to_center(coord_raw, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw):
+    """Translate and rotate the raw coordinate given by the tracking device to the reference system created during
+    the object registration.
+
+    :param coord_raw: Coordinates returned by the tracking device
+    :type coord_raw: numpy.ndarray
+    :param obj_ref_mode:
+    :type obj_ref_mode: int
+    :param t_obj_raw:
+    :type t_obj_raw: numpy.ndarray
+    :param s0_raw:
+    :type s0_raw: numpy.ndarray
+    :param r_s0_raw: rotation transformation from marker to object basis
+    :type r_s0_raw: numpy.ndarray
+    :return: 4 x 4 numpy double array
+    :rtype: numpy.ndarray
     """
-    def __init__(self, coreg_data, nav_id, trck_info):
-        threading.Thread.__init__(self)
-        self.coreg_data = coreg_data
-        self.nav_id = nav_id
-        self.trck_info = trck_info
-        self._pause_ = False
-        self.start()
-
-    def stop(self):
-        self._pause_ = True
-
-    def run(self):
-        # m_change = self.coreg_data[0]
-        # obj_ref_mode = self.coreg_data[2]
-        #
-        # trck_init = self.trck_info[0]
-        # trck_id = self.trck_info[1]
-        # trck_mode = self.trck_info[2]
-
-        m_change, obj_ref_mode = self.coreg_data
-        trck_init, trck_id, trck_mode = self.trck_info
-
-        while self.nav_id:
-            coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
-
-            psi, theta, phi = coord_raw[obj_ref_mode, 3:]
-            t_probe_raw = asmatrix(tr.translation_matrix(coord_raw[obj_ref_mode, :3]))
+    as1, bs1, gs1 = np.radians(coord_raw[obj_ref_mode, 3:])
+    r_probe = tr.euler_matrix(as1, bs1, gs1, 'rzyx')
+    t_probe_raw = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
+    t_offset_aux = np.linalg.inv(r_s0_raw) @ r_probe @ t_obj_raw
+    t_offset = np.identity(4)
+    t_offset[:, -1] = t_offset_aux[:, -1]
+    t_probe = s0_raw @ t_offset @ np.linalg.inv(s0_raw) @ t_probe_raw
+    m_probe = tr.concatenate_matrices(t_probe, r_probe)
-            t_probe_raw[2, -1] = -t_probe_raw[2, -1]
+    return m_probe
-            m_img = m_change * t_probe_raw
-            coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], psi, theta, phi
+def object_to_reference(coord_raw, m_probe):
+    """Compute affine transformation matrix to the reference basis
-            wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
-
-            # TODO: Optimize the value of sleep for each tracking device.
-            sleep(0.175)
-
-            if self._pause_:
-                return
-
-
-class CoregistrationDynamic(threading.Thread):
-    """
-    Thread to update the coordinates with the fiducial points
-    co-registration method while the Navigation Button is pressed.
-    Sleep function in run method is used to avoid blocking GUI and
-    for better real-time navigation
+    :param coord_raw: Coordinates returned by the tracking device
+    :type coord_raw: numpy.ndarray
+    :param m_probe: Probe coordinates
+    :type m_probe: numpy.ndarray
+    :return: 4 x 4 numpy double array
+    :rtype: numpy.ndarray
     """
-    def __init__(self, coreg_data, nav_id, trck_info):
-        threading.Thread.__init__(self)
-        self.coreg_data = coreg_data
-        self.nav_id = nav_id
-        self.trck_info = trck_info
-        self._pause_ = False
-        self.start()
-
-    def stop(self):
-        self._pause_ = True
-
-    def run(self):
-        m_change, obj_ref_mode = self.coreg_data
-        trck_init, trck_id, trck_mode = self.trck_info
-
-        while self.nav_id:
-            coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
-
-            psi, theta, phi = radians(coord_raw[obj_ref_mode, 3:])
-            r_probe = tr.euler_matrix(psi, theta, phi, 'rzyx')
-            t_probe = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
-            m_probe = asmatrix(tr.concatenate_matrices(t_probe, r_probe))
-
-            psi_ref, theta_ref, phi_ref = radians(coord_raw[1, 3:])
-            r_ref = tr.euler_matrix(psi_ref, theta_ref, phi_ref, 'rzyx')
-            t_ref = tr.translation_matrix(coord_raw[1, :3])
-            m_ref = asmatrix(tr.concatenate_matrices(t_ref, r_ref))
-
-            m_dyn = m_ref.I * m_probe
-            m_dyn[2, -1] = -m_dyn[2, -1]
-
-            m_img = m_change * m_dyn
-
-            scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
-
-            coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \
-                    degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
-
-            wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
-
-            # TODO: Optimize the value of sleep for each tracking device.
-            sleep(0.175)
-
-            if self._pause_:
-                return
-
-
-class CoregistrationDynamic_old(threading.Thread):
-    """
-    Thread to update the coordinates with the fiducial points
-    co-registration method while the Navigation Button is pressed.
-    Sleep function in run method is used to avoid blocking GUI and
-    for better real-time navigation
+    a, b, g = np.radians(coord_raw[1, 3:])
+    r_ref = tr.euler_matrix(a, b, g, 'rzyx')
+    t_ref = tr.translation_matrix(coord_raw[1, :3])
+    m_ref = tr.concatenate_matrices(t_ref, r_ref)
+
+    m_dyn = np.linalg.inv(m_ref) @ m_probe
+    return m_dyn
+
+
+def tracker_to_image(m_change, m_probe_ref, r_obj_img, m_obj_raw, s0_dyn):
+    """Compute affine transformation matrix to the reference basis
+
+    :param m_change: Corregistration transformation obtained from fiducials
+    :type m_change: numpy.ndarray
+    :param m_probe_ref: Object or probe in reference coordinate system
+    :type m_probe_ref: numpy.ndarray
+    :param r_obj_img: Object coordinate system in image space (3d model)
+    :type r_obj_img: numpy.ndarray
+    :param m_obj_raw: Object basis in raw coordinates from tacker
+    :type m_obj_raw: numpy.ndarray
+    :param s0_dyn:
+    :type s0_dyn: numpy.ndarray
+    :return: 4 x 4 numpy double array
+    :rtype: numpy.ndarray
     """
-    def __init__(self, bases, nav_id, trck_info):
-        threading.Thread.__init__(self)
-        self.bases = bases
-        self.nav_id = nav_id
+    m_img = m_change @ m_probe_ref
+    r_obj = r_obj_img @ np.linalg.inv(m_obj_raw) @ np.linalg.inv(s0_dyn) @ m_probe_ref @ m_obj_raw
+    m_img[:3, :3] = r_obj[:3, :3]
+    return m_img
+
+
+def corregistrate_object_dynamic(inp, coord_raw, ref_mode_id):
+
+    m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
+
+    # transform raw marker coordinate to object center
+    m_probe = object_marker_to_center(coord_raw, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw)
+    # transform object center to reference marker if specified as dynamic reference
+    if ref_mode_id:
+        m_probe_ref = object_to_reference(coord_raw, m_probe)
+    else:
+        m_probe_ref = m_probe
+    # invert y coordinate
+    m_probe_ref[2, -1] = -m_probe_ref[2, -1]
+    # corregistrate from tracker to image space
+    m_img = tracker_to_image(m_change, m_probe_ref, r_obj_img, m_obj_raw, s0_dyn)
+    # compute rotation angles
+    _, _, angles, _, _ = tr.decompose_matrix(m_img)
+    # create output coordiante list
+    coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \
+            np.degrees(angles[0]), np.degrees(angles[1]), np.degrees(angles[2])
+
+    return coord, m_img
+
+
+def compute_marker_transformation(coord_raw, obj_ref_mode):
+    psi, theta, phi = np.radians(coord_raw[obj_ref_mode, 3:])
+    r_probe = tr.euler_matrix(psi, theta, phi, 'rzyx')
+    t_probe = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
+    m_probe = tr.concatenate_matrices(t_probe, r_probe)
+    return m_probe
+
+
+def corregistrate_dynamic(inp, coord_raw, ref_mode_id):
+
+    m_change, obj_ref_mode = inp
+
+    # transform raw marker coordinate to object center
+    m_probe = compute_marker_transformation(coord_raw, obj_ref_mode)
+    # transform object center to reference marker if specified as dynamic reference
+    if ref_mode_id:
+        m_ref = compute_marker_transformation(coord_raw, 1)
+        m_probe_ref = np.linalg.inv(m_ref) @ m_probe
+    else:
+        m_probe_ref = m_probe
+
+    # invert y coordinate
+    m_probe_ref[2, -1] = -m_probe_ref[2, -1]
+    # corregistrate from tracker to image space
+    m_img = m_change @ m_probe_ref
+    # compute rotation angles
+    _, _, angles, _, _ = tr.decompose_matrix(m_img)
+    # create output coordiante list
+    coord = m_img[0, -1], m_img[1, -1], m_img[2, -1],\
+            np.degrees(angles[0]), np.degrees(angles[1]), np.degrees(angles[2])
+
+    return coord, m_img
+
+
+class CoordinateCorregistrate(threading.Thread):
+    def __init__(self, ref_mode_id, trck_info, coreg_data, coord_queue, view_tracts, coord_tracts_queue, event, sle):
+        threading.Thread.__init__(self, name='CoordCoregObject')
+        self.ref_mode_id = ref_mode_id
         self.trck_info = trck_info
-        self._pause_ = False
-        self.start()
-
-    def stop(self):
-        self._pause_ = True
-
-    def run(self):
-        m_inv = self.bases[0]
-        n = self.bases[1]
-        q1 = self.bases[2]
-        q2 = self.bases[3]
-        trck_init = self.trck_info[0]
-        trck_id = self.trck_info[1]
-        trck_mode = self.trck_info[2]
-
-        while self.nav_id:
-            # trck_coord, probe, reference = dco.GetCoordinates(trck_init, trck_id, trck_mode)
-            coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
-
-            trck_coord = dco.dynamic_reference(coord_raw[0, :], coord_raw[1, :])
-
-            trck_xyz = mat([[trck_coord[0]], [trck_coord[1]], [trck_coord[2]]])
-            img = q1 + (m_inv * n) * (trck_xyz - q2)
-
-            coord = (float(img[0]), float(img[1]), float(img[2]), trck_coord[3],
-                     trck_coord[4], trck_coord[5])
-            angles = coord_raw[0, 3:6]
-
-            # Tried several combinations and different locations to send the messages,
-            # however only this one does not block the GUI during navigation.
-            wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=None, position=coord)
-            wx.CallAfter(Publisher.sendMessage, 'Set camera in volume', coord)
-            wx.CallAfter(Publisher.sendMessage, 'Update tracker angles', angles)
-
-            # TODO: Optimize the value of sleep for each tracking device.
-            # Debug tracker is not working with 0.175 so changed to 0.2
-            # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
-            # sleep(.3)
-            sleep(0.175)
-
-            if self._pause_:
-                return
-
-
-class CoregistrationObjectStatic(threading.Thread):
-    """
-    Thread to update the coordinates with the fiducial points
-    co-registration method while the Navigation Button is pressed.
-    Sleep function in run method is used to avoid blocking GUI and
-    for better real-time navigation
-    """
-
-    def __init__(self, coreg_data, nav_id, trck_info):
-        threading.Thread.__init__(self)
         self.coreg_data = coreg_data
-        self.nav_id = nav_id
-        self.trck_info = trck_info
-        self._pause_ = False
-        self.start()
-
-    def stop(self):
-        self._pause_ = True
+        self.coord_queue = coord_queue
+        self.view_tracts = view_tracts
+        self.coord_tracts_queue = coord_tracts_queue
+        self.event = event
+        self.sle = sle
     def run(self):
-        # m_change = self.coreg_data[0]
-        # t_obj_raw = self.coreg_data[1]
-        # s0_raw = self.coreg_data[2]
-        # r_s0_raw = self.coreg_data[3]
-        # s0_dyn = self.coreg_data[4]
-        # m_obj_raw = self.coreg_data[5]
-        # r_obj_img = self.coreg_data[6]
-        # obj_ref_mode = self.coreg_data[7]
-        #
-        # trck_init = self.trck_info[0]
-        # trck_id = self.trck_info[1]
-        # trck_mode = self.trck_info[2]
-
-        m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = self.coreg_data
-        trck_init, trck_id, trck_mode = self.trck_info
-
-        while self.nav_id:
-            coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
-
-            as1, bs1, gs1 = radians(coord_raw[obj_ref_mode, 3:])
-            r_probe = asmatrix(tr.euler_matrix(as1, bs1, gs1, 'rzyx'))
-            t_probe_raw = asmatrix(tr.translation_matrix(coord_raw[obj_ref_mode, :3]))
-            t_offset_aux = r_s0_raw.I * r_probe * t_obj_raw
-            t_offset = asmatrix(identity(4))
-            t_offset[:, -1] = t_offset_aux[:, -1]
-            t_probe = s0_raw * t_offset * s0_raw.I * t_probe_raw
-            m_probe = asmatrix(tr.concatenate_matrices(t_probe, r_probe))
-
-            m_probe[2, -1] = -m_probe[2, -1]
-
-            m_img = m_change * m_probe
-            r_obj = r_obj_img * m_obj_raw.I * s0_dyn.I * m_probe * m_obj_raw
-
-            m_img[:3, :3] = r_obj[:3, :3]
-
-            scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
-
-            coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \
-                    degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
-
-            wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
-            wx.CallAfter(Publisher.sendMessage, 'Update object matrix', m_img=m_img, coord=coord)
-
-            # TODO: Optimize the value of sleep for each tracking device.
-            sleep(0.175)
-
-            # Debug tracker is not working with 0.175 so changed to 0.2
-            # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
-            # sleep(.3)
-
-            # partially working for translate and offset,
-            # but offset is kept always in same axis, have to fix for rotation
-            # M_dyn = M_reference.I * T_stylus
-            # M_dyn[2, -1] = -M_dyn[2, -1]
-            # M_dyn_ch = M_change * M_dyn
-            # ddd = M_dyn_ch[0, -1], M_dyn_ch[1, -1], M_dyn_ch[2, -1]
-            # M_dyn_ch[:3, -1] = asmatrix(db.flip_x_m(ddd)).reshape([3, 1])
-            # M_final = S0 * M_obj_trans_0 * S0.I * M_dyn_ch
-
-            # this works for static reference object rotation
-            # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_raw.I * R_stylus * M_obj_rot_raw
-            # this works for dynamic reference in rotation but not in translation
-            # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_dyn.I * R_reference.I * R_stylus * M_obj_rot_raw
-
-            if self._pause_:
-                return
-
-
-class CoregistrationObjectDynamic(threading.Thread):
-    """
-    Thread to update the coordinates with the fiducial points
-    co-registration method while the Navigation Button is pressed.
-    Sleep function in run method is used to avoid blocking GUI and
-    for better real-time navigation
-    """
-
-    def __init__(self, coreg_data, nav_id, trck_info):
-        threading.Thread.__init__(self)
-        self.coreg_data = coreg_data
-        self.nav_id = nav_id
+        trck_info = self.trck_info
+        coreg_data = self.coreg_data
+        view_obj = 1
+
+        trck_init, trck_id, trck_mode = trck_info
+        # print('CoordCoreg: event {}'.format(self.event.is_set()))
+        while not self.event.is_set():
+            try:
+                # print(f"Set the coordinate")
+                coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+                coord, m_img = corregistrate_object_dynamic(coreg_data, coord_raw, self.ref_mode_id)
+                m_img_flip = m_img.copy()
+                m_img_flip[1, -1] = -m_img_flip[1, -1]
+                # self.pipeline.set_message(m_img_flip)
+                self.coord_queue.put_nowait([coord, m_img, view_obj])
+                # print('CoordCoreg: put {}'.format(count))
+                # count += 1
+
+                if self.view_tracts:
+                    self.coord_tracts_queue.put_nowait(m_img_flip)
+
+                # The sleep has to be in both threads
+                sleep(self.sle)
+            except queue.Full:
+                pass
+
+
+class CoordinateCorregistrateNoObject(threading.Thread):
+    def __init__(self, ref_mode_id, trck_info, coreg_data, coord_queue, view_tracts, coord_tracts_queue, event, sle):
+        threading.Thread.__init__(self, name='CoordCoregNoObject')
+        self.ref_mode_id = ref_mode_id
         self.trck_info = trck_info
-        self._pause_ = False
-        self.start()
-
-    def stop(self):
-        self._pause_ = True
+        self.coreg_data = coreg_data
+        self.coord_queue = coord_queue
+        self.view_tracts = view_tracts
+        self.coord_tracts_queue = coord_tracts_queue
+        self.event = event
+        self.sle = sle
     def run(self):
+        trck_info = self.trck_info
+        coreg_data = self.coreg_data
+        view_obj = 0
+
+        trck_init, trck_id, trck_mode = trck_info
+        # print('CoordCoreg: event {}'.format(self.event.is_set()))
+        while not self.event.is_set():
+            try:
+                # print(f"Set the coordinate")
+                coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+                coord, m_img = corregistrate_dynamic(coreg_data, coord_raw, self.ref_mode_id)
+                # print("Coord: ", coord)
+                m_img_flip = m_img.copy()
+                m_img_flip[1, -1] = -m_img_flip[1, -1]
+                self.coord_queue.put_nowait([coord, m_img, view_obj])
+
+                if self.view_tracts:
+                    self.coord_tracts_queue.put_nowait(m_img_flip)
+
+                # The sleep has to be in both threads
+                sleep(self.sle)
+            except queue.Full:
+                pass
+
+
+# class CoregistrationStatic(threading.Thread):
+#     """
+#     Thread to update the coordinates with the fiducial points
+#     co-registration method while the Navigation Button is pressed.
+#     Sleep function in run method is used to avoid blocking GUI and
+#     for better real-time navigation
+#     """
+#
+#     def __init__(self, coreg_data, nav_id, trck_info):
+#         threading.Thread.__init__(self)
+#         self.coreg_data = coreg_data
+#         self.nav_id = nav_id
+#         self.trck_info = trck_info
+#         self._pause_ = False
+#         self.start()
+#
+#     def stop(self):
+#         self._pause_ = True
+#
+#     def run(self):
+#         # m_change = self.coreg_data[0]
+#         # obj_ref_mode = self.coreg_data[2]
+#         #
+#         # trck_init = self.trck_info[0]
+#         # trck_id = self.trck_info[1]
+#         # trck_mode = self.trck_info[2]
+#
+#         m_change, obj_ref_mode = self.coreg_data
+#         trck_init, trck_id, trck_mode = self.trck_info
+#
+#         while self.nav_id:
+#             coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+#
+#             psi, theta, phi = coord_raw[obj_ref_mode, 3:]
+#             t_probe_raw = asmatrix(tr.translation_matrix(coord_raw[obj_ref_mode, :3]))
+#
+#             t_probe_raw[2, -1] = -t_probe_raw[2, -1]
+#
+#             m_img = m_change * t_probe_raw
+#
+#             coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], psi, theta, phi
+#
+#             wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
+#
+#             # TODO: Optimize the value of sleep for each tracking device.
+#             sleep(0.175)
+#
+#             if self._pause_:
+#                 return
+#
+#
+# class CoregistrationDynamic(threading.Thread):
+#     """
+#     Thread to update the coordinates with the fiducial points
+#     co-registration method while the Navigation Button is pressed.
+#     Sleep function in run method is used to avoid blocking GUI and
+#     for better real-time navigation
+#     """
+#
+#     def __init__(self, coreg_data, nav_id, trck_info):
+#         threading.Thread.__init__(self)
+#         self.coreg_data = coreg_data
+#         self.nav_id = nav_id
+#         self.trck_info = trck_info
+#         # self.tracts_info = tracts_info
+#         # self.tracts = None
+#         self._pause_ = False
+#         # self.start()
+#
+#     def stop(self):
+#         # self.tracts.stop()
+#         self._pause_ = True
+#
+#     def run(self):
+#         m_change, obj_ref_mode = self.coreg_data
+#         trck_init, trck_id, trck_mode = self.trck_info
+#         # seed, tracker, affine, affine_vtk = self.tracts_info
+#
+#         while self.nav_id:
+#             coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+#
+#             psi, theta, phi = radians(coord_raw[obj_ref_mode, 3:])
+#             r_probe = tr.euler_matrix(psi, theta, phi, 'rzyx')
+#             t_probe = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
+#             m_probe = asmatrix(tr.concatenate_matrices(t_probe, r_probe))
+#
+#             psi_ref, theta_ref, phi_ref = radians(coord_raw[1, 3:])
+#             r_ref = tr.euler_matrix(psi_ref, theta_ref, phi_ref, 'rzyx')
+#             t_ref = tr.translation_matrix(coord_raw[1, :3])
+#             m_ref = asmatrix(tr.concatenate_matrices(t_ref, r_ref))
+#
+#             m_dyn = m_ref.I * m_probe
+#             m_dyn[2, -1] = -m_dyn[2, -1]
+#
+#             m_img = m_change * m_dyn
+#
+#             scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
+#
+#             coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \
+#                     degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
+#
+#             # pos_world_aux = np.ones([4, 1])
+#             # pos_world_aux[:3, -1] = db.flip_x((m_img[0, -1], m_img[1, -1], m_img[2, -1]))[:3]
+#             # pos_world = np.linalg.inv(affine) @ pos_world_aux
+#             # seed_aux = pos_world.reshape([1, 4])[0, :3]
+#             # seed = seed_aux[np.newaxis, :]
+#             #
+#             # self.tracts = dtr.compute_tracts(tracker, seed, affine_vtk, True)
+#
+#             # wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
+#             wx.CallAfter(Publisher.sendMessage, 'Update cross position', arg=m_img, position=coord)
+#
+#             # TODO: Optimize the value of sleep for each tracking device.
+#             sleep(3.175)
+#
+#             if self._pause_:
+#                 return
+#
+#
+# class CoregistrationDynamic_old(threading.Thread):
+#     """
+#     Thread to update the coordinates with the fiducial points
+#     co-registration method while the Navigation Button is pressed.
+#     Sleep function in run method is used to avoid blocking GUI and
+#     for better real-time navigation
+#     """
+#
+#     def __init__(self, bases, nav_id, trck_info):
+#         threading.Thread.__init__(self)
+#         self.bases = bases
+#         self.nav_id = nav_id
+#         self.trck_info = trck_info
+#         self._pause_ = False
+#         self.start()
+#
+#     def stop(self):
+#         self._pause_ = True
+#
+#     def run(self):
+#         m_inv = self.bases[0]
+#         n = self.bases[1]
+#         q1 = self.bases[2]
+#         q2 = self.bases[3]
+#         trck_init = self.trck_info[0]
+#         trck_id = self.trck_info[1]
+#         trck_mode = self.trck_info[2]
+#
+#         while self.nav_id:
+#             # trck_coord, probe, reference = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+#             coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+#
+#             trck_coord = dco.dynamic_reference(coord_raw[0, :], coord_raw[1, :])
+#
+#             trck_xyz = mat([[trck_coord[0]], [trck_coord[1]], [trck_coord[2]]])
+#             img = q1 + (m_inv * n) * (trck_xyz - q2)
+#
+#             coord = (float(img[0]), float(img[1]), float(img[2]), trck_coord[3],
+#                      trck_coord[4], trck_coord[5])
+#             angles = coord_raw[0, 3:6]
+#
+#             # Tried several combinations and different locations to send the messages,
+#             # however only this one does not block the GUI during navigation.
+#             wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=None, position=coord)
+#             wx.CallAfter(Publisher.sendMessage, 'Set camera in volume', coord)
+#             wx.CallAfter(Publisher.sendMessage, 'Update tracker angles', angles)
+#
+#             # TODO: Optimize the value of sleep for each tracking device.
+#             # Debug tracker is not working with 0.175 so changed to 0.2
+#             # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
+#             # sleep(.3)
+#             sleep(0.175)
+#
+#             if self._pause_:
+#                 return
+#
+#
+# class CoregistrationObjectStatic(threading.Thread):
+#     """
+#     Thread to update the coordinates with the fiducial points
+#     co-registration method while the Navigation Button is pressed.
+#     Sleep function in run method is used to avoid blocking GUI and
+#     for better real-time navigation
+#     """
+#
+#     def __init__(self, coreg_data, nav_id, trck_info):
+#         threading.Thread.__init__(self)
+#         self.coreg_data = coreg_data
+#         self.nav_id = nav_id
+#         self.trck_info = trck_info
+#         self._pause_ = False
+#         self.start()
+#
+#     def stop(self):
+#         self._pause_ = True
+#
+#     def run(self):
+#         # m_change = self.coreg_data[0]
+#         # t_obj_raw = self.coreg_data[1]
+#         # s0_raw = self.coreg_data[2]
+#         # r_s0_raw = self.coreg_data[3]
+#         # s0_dyn = self.coreg_data[4]
+#         # m_obj_raw = self.coreg_data[5]
+#         # r_obj_img = self.coreg_data[6]
+#         # obj_ref_mode = self.coreg_data[7]
+#         #
+#         # trck_init = self.trck_info[0]
+#         # trck_id = self.trck_info[1]
+#         # trck_mode = self.trck_info[2]
+#
+#         m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = self.coreg_data
+#         trck_init, trck_id, trck_mode = self.trck_info
+#
+#         while self.nav_id:
+#             coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+#
+#             as1, bs1, gs1 = radians(coord_raw[obj_ref_mode, 3:])
+#             r_probe = asmatrix(tr.euler_matrix(as1, bs1, gs1, 'rzyx'))
+#             t_probe_raw = asmatrix(tr.translation_matrix(coord_raw[obj_ref_mode, :3]))
+#             t_offset_aux = r_s0_raw.I * r_probe * t_obj_raw
+#             t_offset = asmatrix(identity(4))
+#             t_offset[:, -1] = t_offset_aux[:, -1]
+#             t_probe = s0_raw * t_offset * s0_raw.I * t_probe_raw
+#             m_probe = asmatrix(tr.concatenate_matrices(t_probe, r_probe))
+#
+#             m_probe[2, -1] = -m_probe[2, -1]
+#
+#             m_img = m_change * m_probe
+#             r_obj = r_obj_img * m_obj_raw.I * s0_dyn.I * m_probe * m_obj_raw
+#
+#             m_img[:3, :3] = r_obj[:3, :3]
+#
+#             scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
+#
+#             coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \
+#                     degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
+#
+#             wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
+#             wx.CallAfter(Publisher.sendMessage, 'Update object matrix', m_img=m_img, coord=coord)
+#
+#             # TODO: Optimize the value of sleep for each tracking device.
+#             sleep(0.175)
+#
+#             # Debug tracker is not working with 0.175 so changed to 0.2
+#             # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
+#             # sleep(.3)
+#
+#             # partially working for translate and offset,
+#             # but offset is kept always in same axis, have to fix for rotation
+#             # M_dyn = M_reference.I * T_stylus
+#             # M_dyn[2, -1] = -M_dyn[2, -1]
+#             # M_dyn_ch = M_change * M_dyn
+#             # ddd = M_dyn_ch[0, -1], M_dyn_ch[1, -1], M_dyn_ch[2, -1]
+#             # M_dyn_ch[:3, -1] = asmatrix(db.flip_x_m(ddd)).reshape([3, 1])
+#             # M_final = S0 * M_obj_trans_0 * S0.I * M_dyn_ch
+#
+#             # this works for static reference object rotation
+#             # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_raw.I * R_stylus * M_obj_rot_raw
+#             # this works for dynamic reference in rotation but not in translation
+#             # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_dyn.I * R_reference.I * R_stylus * M_obj_rot_raw
+#
+#             if self._pause_:
+#                 return
+#
+#
+# class CoregistrationObjectDynamic(threading.Thread):
+#     """
+#     Thread to update the coordinates with the fiducial points
+#     co-registration method while the Navigation Button is pressed.
+#     Sleep function in run method is used to avoid blocking GUI and
+#     for better real-time navigation
+#     """
+#
+#     def __init__(self, coreg_data, nav_id, trck_info, tracts_info):
+#         threading.Thread.__init__(self)
+#         self.coreg_data = coreg_data
+#         self.nav_id = nav_id
+#         self.trck_info = trck_info
+#         # self.tracts_info = tracts_info
+#         # self.tracts = None
+#         self._pause_ = False
+#         self.start()
+#
+#     def stop(self):
+#         # self.tracts.stop()
+#         self._pause_ = True
+#
+#     def run(self):
+#
+#         m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = self.coreg_data
+#         trck_init, trck_id, trck_mode = self.trck_info
+#         # seed, tracker, affine, affine_vtk = self.tracts_info
+#
+#         while self.nav_id:
+#             coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+#
+#             as1, bs1, gs1 = radians(coord_raw[obj_ref_mode, 3:])
+#             r_probe = asmatrix(tr.euler_matrix(as1, bs1, gs1, 'rzyx'))
+#             t_probe_raw = asmatrix(tr.translation_matrix(coord_raw[obj_ref_mode, :3]))
+#             t_offset_aux = r_s0_raw.I * r_probe * t_obj_raw
+#             t_offset = asmatrix(identity(4))
+#             t_offset[:, -1] = t_offset_aux[:, -1]
+#             t_probe = s0_raw * t_offset * s0_raw.I * t_probe_raw
+#             m_probe = asmatrix(tr.concatenate_matrices(t_probe, r_probe))
+#
+#             a, b, g = radians(coord_raw[1, 3:])
+#             r_ref = tr.euler_matrix(a, b, g, 'rzyx')
+#             t_ref = tr.translation_matrix(coord_raw[1, :3])
+#             m_ref = asmatrix(tr.concatenate_matrices(t_ref, r_ref))
+#
+#             m_dyn = m_ref.I * m_probe
+#             m_dyn[2, -1] = -m_dyn[2, -1]
+#
+#             m_img = m_change * m_dyn
+#             r_obj = r_obj_img * m_obj_raw.I * s0_dyn.I * m_dyn * m_obj_raw
+#
+#             m_img[:3, :3] = r_obj[:3, :3]
+#
+#             scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
+#
+#             coord = m_img[0, -1], m_img[1, -1], m_img[2, -1],\
+#                     degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
+#
+#             # norm_vec = m_img[:3, 2].reshape([1, 3]).tolist()
+#             # p0 = m_img[:3, -1].reshape([1, 3]).tolist()
+#             # p2 = [x - 30 * y for x, y in zip(p0[0], norm_vec[0])]
+#             # m_tract = m_img.copy()
+#             # m_tract[:3, -1] = np.reshape(np.asarray(p2)[np.newaxis, :], [3, 1])
+#
+#             # pos_world_aux = np.ones([4, 1])
+#             # pos_world_aux[:3, -1] = db.flip_x((p2[0], p2[1], p2[2]))[:3]
+#             # pos_world = np.linalg.inv(affine) @ pos_world_aux
+#             # seed_aux = pos_world.reshape([1, 4])[0, :3]
+#             # seed = seed_aux[np.newaxis, :]
+#
+#             # self.tracts = dtr.compute_tracts(tracker, seed, affine_vtk, True)
+#
+#             # wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
+#             wx.CallAfter(Publisher.sendMessage, 'Update cross position', arg=m_img, position=coord)
+#             wx.CallAfter(Publisher.sendMessage, 'Update object matrix', m_img=m_img, coord=coord)
+#
+#             # TODO: Optimize the value of sleep for each tracking device.
+#             #sleep(2.175)
+#             sleep(0.175)
+#
+#             # Debug tracker is not working with 0.175 so changed to 0.2
+#             # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
+#             # sleep(.3)
+#
+#             # partially working for translate and offset,
+#             # but offset is kept always in same axis, have to fix for rotation
+#             # M_dyn = M_reference.I * T_stylus
+#             # M_dyn[2, -1] = -M_dyn[2, -1]
+#             # M_dyn_ch = M_change * M_dyn
+#             # ddd = M_dyn_ch[0, -1], M_dyn_ch[1, -1], M_dyn_ch[2, -1]
+#             # M_dyn_ch[:3, -1] = asmatrix(db.flip_x_m(ddd)).reshape([3, 1])
+#             # M_final = S0 * M_obj_trans_0 * S0.I * M_dyn_ch
+#
+#             # this works for static reference object rotation
+#             # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_raw.I * R_stylus * M_obj_rot_raw
+#             # this works for dynamic reference in rotation but not in translation
+#             # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_dyn.I * R_reference.I * R_stylus * M_obj_rot_raw
+#
+#             if self._pause_:
+#                 return
+#
+#
+# def corregistrate_object(inp, coord_raw):
+#     m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = inp
+#     as1, bs1, gs1 = radians(coord_raw[obj_ref_mode, 3:])
+#     r_probe = tr.euler_matrix(as1, bs1, gs1, 'rzyx')
+#     t_probe_raw = tr.translation_matrix(coord_raw[obj_ref_mode, :3])
+#     t_offset_aux = np.linalg.inv(r_s0_raw) @ r_probe @ t_obj_raw
+#     t_offset = identity(4)
+#     t_offset[:, -1] = t_offset_aux[:, -1]
+#     t_probe = s0_raw @ t_offset @ np.linalg.inv(s0_raw) @ t_probe_raw
+#     m_probe = tr.concatenate_matrices(t_probe, r_probe)
+#
+#     a, b, g = radians(coord_raw[1, 3:])
+#     r_ref = tr.euler_matrix(a, b, g, 'rzyx')
+#     t_ref = tr.translation_matrix(coord_raw[1, :3])
+#     m_ref = tr.concatenate_matrices(t_ref, r_ref)
+#
+#     m_dyn = np.linalg.inv(m_ref) @ m_probe
+#     m_dyn[2, -1] = -m_dyn[2, -1]
+#
+#     m_img = m_change @ m_dyn
+#     r_obj = r_obj_img @ np.linalg.inv(m_obj_raw) @ np.linalg.inv(s0_dyn) @ m_dyn @ m_obj_raw
+#
+#     m_img[:3, :3] = r_obj[:3, :3]
+#
+#     scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
+#
+#     coord = m_img[0, -1], m_img[1, -1], m_img[2, -1], \
+#             degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
+#
+#     return coord, m_img
-        m_change, obj_ref_mode, t_obj_raw, s0_raw, r_s0_raw, s0_dyn, m_obj_raw, r_obj_img = self.coreg_data
-        trck_init, trck_id, trck_mode = self.trck_info
-
-        while self.nav_id:
-            coord_raw = dco.GetCoordinates(trck_init, trck_id, trck_mode)
-
-            as1, bs1, gs1 = radians(coord_raw[obj_ref_mode, 3:])
-            r_probe = asmatrix(tr.euler_matrix(as1, bs1, gs1, 'rzyx'))
-            t_probe_raw = asmatrix(tr.translation_matrix(coord_raw[obj_ref_mode, :3]))
-            t_offset_aux = r_s0_raw.I * r_probe * t_obj_raw
-            t_offset = asmatrix(identity(4))
-            t_offset[:, -1] = t_offset_aux[:, -1]
-            t_probe = s0_raw * t_offset * s0_raw.I * t_probe_raw
-            m_probe = asmatrix(tr.concatenate_matrices(t_probe, r_probe))
-
-            a, b, g = radians(coord_raw[1, 3:])
-            r_ref = tr.euler_matrix(a, b, g, 'rzyx')
-            t_ref = tr.translation_matrix(coord_raw[1, :3])
-            m_ref = asmatrix(tr.concatenate_matrices(t_ref, r_ref))
-
-            m_dyn = m_ref.I * m_probe
-            m_dyn[2, -1] = -m_dyn[2, -1]
-
-            m_img = m_change * m_dyn
-            r_obj = r_obj_img * m_obj_raw.I * s0_dyn.I * m_dyn * m_obj_raw
-
-            m_img[:3, :3] = r_obj[:3, :3]
-
-            scale, shear, angles, trans, persp = tr.decompose_matrix(m_img)
-
-            coord = m_img[0, -1], m_img[1, -1], m_img[2, -1],\
-                    degrees(angles[0]), degrees(angles[1]), degrees(angles[2])
-
-            wx.CallAfter(Publisher.sendMessage, 'Co-registered points', arg=m_img, position=coord)
-            wx.CallAfter(Publisher.sendMessage, 'Update object matrix', m_img=m_img, coord=coord)
-
-            # TODO: Optimize the value of sleep for each tracking device.
-            sleep(0.175)
-
-            # Debug tracker is not working with 0.175 so changed to 0.2
-            # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
-            # sleep(.3)
-
-            # partially working for translate and offset,
-            # but offset is kept always in same axis, have to fix for rotation
-            # M_dyn = M_reference.I * T_stylus
-            # M_dyn[2, -1] = -M_dyn[2, -1]
-            # M_dyn_ch = M_change * M_dyn
-            # ddd = M_dyn_ch[0, -1], M_dyn_ch[1, -1], M_dyn_ch[2, -1]
-            # M_dyn_ch[:3, -1] = asmatrix(db.flip_x_m(ddd)).reshape([3, 1])
-            # M_final = S0 * M_obj_trans_0 * S0.I * M_dyn_ch
-
-            # this works for static reference object rotation
-            # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_raw.I * R_stylus * M_obj_rot_raw
-            # this works for dynamic reference in rotation but not in translation
-            # R_dyn = M_vtk * M_obj_rot_raw.I * S0_rot_dyn.I * R_reference.I * R_stylus * M_obj_rot_raw
-
-            if self._pause_:
-                return
@@ -37,6 +37,8 @@ from invesalius.data import vtk_utils as vtk_utils
 import invesalius.reader.bitmap_reader as bitmap_reader
 import invesalius.utils as utils
 import invesalius.data.converters as converters
+import invesalius.data.slice_ as sl
+import invesalius.data.transformations as tr
 from invesalius import inv_paths
@@ -516,3 +518,67 @@ def image_normalize(image, min_=0.0, max_=1.0, output_dtype=np.int16):
     imin, imax = image.min(), image.max()
     output[:] = (image - imin) * ((max_ - min_) / (imax - imin)) + min_
     return output
+
+
+def world2invspace(affine=None):
+    """
+    Normalize image pixel intensity for int16 gray scale values.
+
+    :param repos: list of translation and rotation [trans_x, trans_y, trans_z, rot_x, rot_y, rot_z] to reposition the
+    vtk object prior to applying the affine matrix transformation. Note: rotation given in degrees
+    :param user_matrix: affine matrix from image header, prefered QForm matrix
+    :return: vtk transform filter for repositioning the polydata and affine matrix to be used as SetUserMatrix in actor
+    """
+
+    # remove scaling factor for non-unitary voxel dimensions
+    scale, shear, angs, trans, persp = tr.decompose_matrix(affine)
+    affine_noscale = tr.compose_matrix(scale=None, shear=shear, angles=angs, translate=trans, perspective=persp)
+    # repos_img = [0.] * 6
+    # repos_img[1] = -float(shape[1])
+    #
+    # repos_mat = np.identity(4)
+    # # translation
+    # repos_mat[:3, -1] = repos_img[:3]
+    # # rotation (in principle for invesalius space no rotation is needed)
+    # repos_mat[:3, :3] = tr.euler_matrix(*np.deg2rad(repos_img[3:]), axes='sxyz')[:3, :3]
+
+    # if repos:
+    #     transx, transy, transz, rotx, roty, rotz = repos
+    #     # create a transform that rotates the stl source
+    #     transform = vtk.vtkTransform()
+    #     transform.PostMultiply()
+    #     transform.RotateX(rotx)
+    #     transform.RotateY(roty)
+    #     transform.RotateZ(rotz)
+    #     transform.Translate(transx, transy, transz)
+    #
+    #     transform_filt = vtk.vtkTransformPolyDataFilter()
+    #     transform_filt.SetTransform(transform)
+    #     transform_filt.Update()
+
+    # assuming vtk default transformation order is PreMultiply, the user matrix is set so:
+    # 1. Replace the object -> 2. Transform the object to desired position/orientation
+    # PreMultiplty: M = M*A where M is current transformation and A is applied transformation
+    # user_matrix = np.linalg.inv(user_matrix) @ repos_mat
+
+    return np.linalg.inv(affine_noscale)
+
+
+def convert_world_to_voxel(xyz, affine):
+    """
+    Convert a coordinate from the world space ((x, y, z); scanner space; millimeters) to the
+    voxel space ((i, j, k)). This is achieved by multiplying a coordinate by the inverse
+    of the affine transformation.
+    More information: https://nipy.org/nibabel/coordinate_systems.html
+    :param xyz: a list or array of 3 coordinates (x, y, z) in the world coordinates
+    :param affine: a 4x4 array containing the image affine transformation in homogeneous coordinates
+    :return: a 1x3 array with the point coordinates in image space (i, j, k)
+    """
+
+    # print("xyz: ", xyz, "\naffine", affine)
+    # convert xyz coordinate to 1x4 homogeneous coordinates array
+    xyz_homo = np.hstack((xyz, 1.)).reshape([4, 1])
+    ijk_homo = np.linalg.inv(affine) @ xyz_homo
+    ijk = ijk_homo.T[np.newaxis, 0, :3]
+
+    return ijk
@@ -42,7 +42,8 @@ class Record(threading.Thread):
         self.start()
     def __bind_events(self):
-        Publisher.subscribe(self.UpdateCurrentCoords, 'Co-registered points')
+        # Publisher.subscribe(self.UpdateCurrentCoords, 'Co-registered points')
+        Publisher.subscribe(self.UpdateCurrentCoords, 'Update cross position')
     def UpdateCurrentCoords(self, arg, position):
         self.coord = asarray(position)
@@ -50,7 +51,10 @@ class Record(threading.Thread):
     def stop(self):
         self._pause_ = True
         #save coords dialog
-        filename = dlg.ShowSaveCoordsDialog("coords.csv")
+        filename = dlg.ShowLoadSaveDialog(message=_(u"Save coords as..."),
+                                          wildcard=_("Coordinates files (*.csv)|*.csv"),
+                                          style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
+                                          default_filename="coords.csv", save_ext="csv")
         if filename:
             savetxt(filename, self.coord_list, delimiter=',', fmt='%.4f', header="time, x, y, z, a, b, g", comments="")
@@ -82,6 +82,9 @@ class Slice(metaclass=utils.Singleton):
         self.blend_filter = None
         self.histogram = None
         self._matrix = None
+        self._affine = np.identity(4)
+        self._n_tracts = 0
+        self._tracker = None
         self.aux_matrices = {}
         self.aux_matrices_colours = {}
         self.state = const.STATE_DEFAULT
@@ -144,6 +147,30 @@ class Slice(metaclass=utils.Singleton):
             (s * d / 2.0) for (d, s) in zip(self.matrix.shape[::-1], self.spacing)
         ]
+    @property
+    def affine(self):
+        return self._affine
+
+    @affine.setter
+    def affine(self, value):
+        self._affine = value
+
+    @property
+    def n_tracts(self):
+        return self._n_tracts
+
+    @n_tracts.setter
+    def n_tracts(self, value):
+        self._n_tracts = value
+
+    @property
+    def tracker(self):
+        return self._tracker
+
+    @tracker.setter
+    def tracker(self, value):
+        self._tracker = value
+
     def __bind_events(self):
         # General slice control
         Publisher.subscribe(self.CreateSurfaceFromIndex, "Create surface from index")
@@ -47,6 +47,14 @@ from invesalius.data.measures import (CircleDensityMeasure, MeasureData,
 from invesalius_cy import floodfill
+# For tracts
+import invesalius.data.tractography as dtr
+# import invesalius.project as prj
+import invesalius.data.slice_ as sl
+import invesalius.data.bases as bases
+# from time import sleep
+# ---
+
 ORIENTATIONS = {
         "AXIAL": const.AXIAL,
         "CORONAL": const.CORONAL,
@@ -465,6 +473,18 @@ class CrossInteractorStyle(DefaultInteractorStyle):
         self.slice_actor = viewer.slice_data.actor
         self.slice_data = viewer.slice_data
+        # tracts
+        # self.seed = [0., 0., 0.]
+        # slic = sl.Slice()
+        # self.affine = slic.affine
+        # self.tracker = slic.tracker
+        #
+        # self.affine_vtk = vtk.vtkMatrix4x4()
+        # for row in range(0, 4):
+        #     for col in range(0, 4):
+        #         self.affine_vtk.SetElement(row, col, self.affine[row, col])
+        # ---
+
         self.picker = vtk.vtkWorldPointPicker()
         self.AddObserver("MouseMoveEvent", self.OnCrossMove)
@@ -478,6 +498,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
     def CleanUp(self):
         self.viewer._set_cross_visibility(0)
+        Publisher.sendMessage('Remove tracts')
         Publisher.sendMessage('Toggle toolbar item',
                               _id=self.state_code, value=False)
@@ -497,12 +518,20 @@ class CrossInteractorStyle(DefaultInteractorStyle):
         wx, wy, wz = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)
         px, py = self.viewer.get_slice_pixel_coord_by_world_pos(wx, wy, wz)
         coord = self.viewer.calcultate_scroll_position(px, py)
-        Publisher.sendMessage('Update cross position', position=(wx, wy, wz))
+
+        # Tracts
+        # pos_world_aux = np.ones([4, 1])
+        # pos_world_aux[:3, -1] = bases.flip_x((wx, wy, wz))[:3]
+        # pos_world = np.linalg.inv(self.affine) @ pos_world_aux
+        # seed_aux = pos_world.reshape([1, 4])[0, :3]
+        # self.seed = seed_aux[np.newaxis, :]
+        # print("Check the seed: ", self.seed)
+        #
+
+        Publisher.sendMessage('Update cross position', arg=None, position=(wx, wy, wz, 0., 0., 0.))
         self.ScrollSlice(coord)
-        Publisher.sendMessage('Set ball reference position', position=(wx, wy, wz))
-        Publisher.sendMessage('Co-registered points',  arg=None, position=(wx, wy, wz, 0., 0., 0.))
-        iren.Render()
+        # iren.Render()
     def ScrollSlice(self, coord):
         if self.orientation == "AXIAL":
@@ -522,6 +551,92 @@ class CrossInteractorStyle(DefaultInteractorStyle):
                                        index=coord[0])
+class TractsInteractorStyle(CrossInteractorStyle):
+    """
+    Interactor style responsible for tracts visualization.
+    """
+    def __init__(self, viewer):
+        CrossInteractorStyle.__init__(self, viewer)
+
+        # self.state_code = const.SLICE_STATE_TRACTS
+
+        self.viewer = viewer
+        # print("Im fucking brilliant!")
+        self.tracts = None
+
+        # data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
+        # FOD_path = b"sub-P0_dwi_FOD.nii"
+        # full_path = os.path.join(data_dir, FOD_path)
+        # self.tracker = Trekker.tracker(full_path)
+        # self.orientation = viewer.orientation
+        # self.slice_actor = viewer.slice_data.actor
+        # self.slice_data = viewer.slice_data
+
+        # self.picker = vtk.vtkWorldPointPicker()
+
+        self.AddObserver("MouseMoveEvent", self.OnTractsMove)
+        self.AddObserver("LeftButtonPressEvent", self.OnTractsMouseClick)
+        self.AddObserver("LeftButtonReleaseEvent", self.OnTractsReleaseLeftButton)
+
+    # def SetUp(self):
+    #     self.viewer._set_cross_visibility(1)
+    #     Publisher.sendMessage('Toggle toolbar item',
+    #                           _id=self.state_code, value=True)
+
+    # def CleanUp(self):
+    #     self.viewer._set_cross_visibility(0)
+    #     Publisher.sendMessage('Toggle toolbar item',
+    #                           _id=self.state_code, value=False)
+
+    def OnTractsMove(self, obj, evt):
+        # The user moved the mouse with left button pressed
+        if self.left_pressed:
+            # print("OnTractsMove interactor style")
+            # iren = obj.GetInteractor()
+            self.ChangeTracts(True)
+
+    def OnTractsMouseClick(self, obj, evt):
+        # print("Single mouse click")
+        # self.tracts = dtr.compute_tracts(self.tracker, self.seed, self.left_pressed)
+        self.ChangeTracts(True)
+
+    def OnTractsReleaseLeftButton(self, obj, evt):
+        # time.sleep(3.)
+        self.tracts.stop()
+        # self.ChangeCrossPosition(iren)
+
+    def ChangeTracts(self, pressed):
+        # print("Trying to compute tracts")
+        self.tracts = dtr.compute_tracts(self.tracker, self.seed, self.affine_vtk, pressed)
+        # mouse_x, mouse_y = iren.GetEventPosition()
+        # wx, wy, wz = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)
+        # px, py = self.viewer.get_slice_pixel_coord_by_world_pos(wx, wy, wz)
+        # coord = self.viewer.calcultate_scroll_position(px, py)
+        # Publisher.sendMessage('Update cross position', position=(wx, wy, wz))
+        # # self.ScrollSlice(coord)
+        # Publisher.sendMessage('Set ball reference position', position=(wx, wy, wz))
+        # Publisher.sendMessage('Co-registered points',  arg=None, position=(wx, wy, wz, 0., 0., 0.))
+
+        # iren.Render()
+
+    # def ScrollSlice(self, coord):
+    #     if self.orientation == "AXIAL":
+    #         Publisher.sendMessage(('Set scroll position', 'SAGITAL'),
+    #                                    index=coord[0])
+    #         Publisher.sendMessage(('Set scroll position', 'CORONAL'),
+    #                                    index=coord[1])
+    #     elif self.orientation == "SAGITAL":
+    #         Publisher.sendMessage(('Set scroll position', 'AXIAL'),
+    #                                    index=coord[2])
+    #         Publisher.sendMessage(('Set scroll position', 'CORONAL'),
+    #                                    index=coord[1])
+    #     elif self.orientation == "CORONAL":
+    #         Publisher.sendMessage(('Set scroll position', 'AXIAL'),
+    #                                    index=coord[2])
+    #         Publisher.sendMessage(('Set scroll position', 'SAGITAL'),
+    #                                    index=coord[0])
+
+
 class WWWLInteractorStyle(DefaultInteractorStyle):
     """
     Interactor style responsible for Window Level & Width functionality.
@@ -2784,6 +2899,7 @@ class Styles:
         const.SLICE_STATE_SELECT_MASK_PARTS: SelectMaskPartsInteractorStyle,
         const.SLICE_STATE_FFILL_SEGMENTATION: FloodFillSegmentInteractorStyle,
         const.SLICE_STATE_CROP_MASK: CropMaskInteractorStyle,
+        const.SLICE_STATE_TRACTS: TractsInteractorStyle,
     }
     @classmethod
@@ -383,6 +383,7 @@ class SurfaceManager():
         actor = vtk.vtkActor()
         actor.SetMapper(mapper)
+        actor.GetProperty().SetBackfaceCulling(1)
         print("BOunds", actor.GetBounds())
@@ -494,6 +495,7 @@ class SurfaceManager():
             # Represent an object (geometry & properties) in the rendered scene
             actor = vtk.vtkActor()
+            actor.GetProperty().SetBackfaceCulling(1)
             actor.SetMapper(mapper)
             # Set actor colour and transparency
@@ -536,6 +538,7 @@ class SurfaceManager():
         # Represent an object (geometry & properties) in the rendered scene
         actor = vtk.vtkActor()
+        actor.GetProperty().SetBackfaceCulling(1)
         actor.SetMapper(mapper)
         del mapper
         #Create Surface instance
@@ -62,6 +62,7 @@ def DefaultTracker(tracker_id):
     # return tracker initialization variable and type of connection
     return trck_init, 'wrapper'
+
 def PolarisTracker(tracker_id):
     from wx import ID_OK
     trck_init = None
@@ -91,6 +92,7 @@ def PolarisTracker(tracker_id):
     # return tracker initialization variable and type of connection
     return trck_init, lib_mode
+
 def CameraTracker(tracker_id):
     trck_init = None
     try:
@@ -105,6 +107,7 @@ def CameraTracker(tracker_id):
     # return tracker initialization variable and type of connection
     return trck_init, 'wrapper'
+
 def ClaronTracker(tracker_id):
     import invesalius.constants as const
     from invesalius import inv_paths
@@ -0,0 +1,471 @@
+# -*- coding: utf-8 -*-
+
+#--------------------------------------------------------------------------
+# Software:     InVesalius - Software de Reconstrucao 3D de Imagens Medicas
+# Copyright:    (C) 2001  Centro de Pesquisas Renato Archer
+# Homepage:     http://www.softwarepublico.gov.br
+# Contact:      invesalius@cti.gov.br
+# License:      GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
+#--------------------------------------------------------------------------
+#    Este programa e software livre; voce pode redistribui-lo e/ou
+#    modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
+#    publicada pela Free Software Foundation; de acordo com a versao 2
+#    da Licenca.
+#
+#    Este programa eh distribuido na expectativa de ser util, mas SEM
+#    QUALQUER GARANTIA; sem mesmo a garantia implicita de
+#    COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
+#    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
+#    detalhes.
+#--------------------------------------------------------------------------
+
+# Author: Victor Hugo Souza (victorhos-at-hotmail.com)
+# Contributions: Dogu Baran Aydogan
+# Initial date: 8 May 2020
+
+import threading
+import time
+
+import numpy as np
+import queue
+from pubsub import pub as Publisher
+import vtk
+
+import invesalius.constants as const
+import invesalius.data.imagedata_utils as img_utils
+
+# Nice print for arrays
+# np.set_printoptions(precision=2)
+# np.set_printoptions(suppress=True)
+
+
+def compute_directions(trk_n):
+    """Compute direction of a single tract in each point and return as an RGB color
+
+    :param trk_n: nx3 array of doubles (x, y, z) point coordinates composing the tract
+    :type trk_n: numpy.ndarray
+    :return: nx3 array of int (x, y, z) RGB colors in the range 0 - 255
+    :rtype: numpy.ndarray
+    """
+
+    # trk_d = np.diff(trk_n, axis=0, append=2*trk_n[np.newaxis, -1, :])
+    trk_d = np.diff(trk_n, axis=0, append=trk_n[np.newaxis, -2, :])
+    trk_d[-1, :] *= -1
+    # check that linalg norm makes second norm
+    # https://stackoverflow.com/questions/21030391/how-to-normalize-an-array-in-numpy
+    direction = 255 * np.absolute((trk_d / np.linalg.norm(trk_d, axis=1)[:, None]))
+    return direction.astype(int)
+
+
+def compute_tubes(trk, direction):
+    """Compute and assign colors to a vtkTube for visualization of a single tract
+
+    :param trk: nx3 array of doubles (x, y, z) point coordinates composing the tract
+    :type trk: numpy.ndarray
+    :param direction: nx3 array of int (x, y, z) RGB colors in the range 0 - 255
+    :type direction: numpy.ndarray
+    :return: a vtkTubeFilter instance
+    :rtype: vtkTubeFilter
+    """
+
+    numb_points = trk.shape[0]
+    points = vtk.vtkPoints()
+    lines = vtk.vtkCellArray()
+
+    colors = vtk.vtkUnsignedCharArray()
+    colors.SetNumberOfComponents(3)
+
+    k = 0
+    lines.InsertNextCell(numb_points)
+    for j in range(numb_points):
+        points.InsertNextPoint(trk[j, :])
+        colors.InsertNextTuple(direction[j, :])
+        lines.InsertCellPoint(k)
+        k += 1
+
+    trk_data = vtk.vtkPolyData()
+    trk_data.SetPoints(points)
+    trk_data.SetLines(lines)
+    trk_data.GetPointData().SetScalars(colors)
+
+    # make it a tube
+    trk_tube = vtk.vtkTubeFilter()
+    trk_tube.SetRadius(0.5)
+    trk_tube.SetNumberOfSides(4)
+    trk_tube.SetInputData(trk_data)
+    trk_tube.Update()
+
+    return trk_tube
+
+
+def combine_tracts_root(out_list, root, n_block):
+    """Adds a set of tracts to given position in a given vtkMultiBlockDataSet
+
+    :param out_list: List of vtkTubeFilters representing the tracts
+    :type out_list: list
+    :param root: A collection of tracts as a vtkMultiBlockDataSet
+    :type root: vtkMultiBlockDataSet
+    :param n_block: The location in the given vtkMultiBlockDataSet to insert the new tracts
+    :type n_block: int
+    :return: The updated collection of tracts as a vtkMultiBlockDataSet
+    :rtype: vtkMultiBlockDataSet
+    """
+
+    # create tracts only when at least one was computed
+    # print("Len outlist in root: ", len(out_list))
+    if not out_list.count(None) == len(out_list):
+        for n, tube in enumerate(out_list):
+            root.SetBlock(n_block + n, tube.GetOutput())
+
+    return root
+
+
+def combine_tracts_branch(out_list):
+    """Combines a set of tracts in vtkMultiBlockDataSet
+
+    :param out_list: List of vtkTubeFilters representing the tracts
+    :type out_list: list
+    :return: A collection of tracts as a vtkMultiBlockDataSet
+    :rtype: vtkMultiBlockDataSet
+    """
+
+    branch = vtk.vtkMultiBlockDataSet()
+    # create tracts only when at least one was computed
+    # print("Len outlist in root: ", len(out_list))
+    if not out_list.count(None) == len(out_list):
+        for n, tube in enumerate(out_list):
+            branch.SetBlock(n, tube.GetOutput())
+
+    return branch
+
+
+def tracts_computation(trk_list, root, n_tracts):
+    """Convert the list of all computed tracts given by Trekker run and returns a vtkMultiBlockDataSet
+
+    :param trk_list: List of lists containing the computed tracts and corresponding coordinates
+    :type trk_list: list
+    :param root: A collection of tracts as a vtkMultiBlockDataSet
+    :type root: vtkMultiBlockDataSet
+    :param n_tracts:
+    :type n_tracts: int
+    :return: The updated collection of tracts as a vtkMultiBlockDataSet
+    :rtype: vtkMultiBlockDataSet
+    """
+
+    # Transform tracts to array
+    trk_arr = [np.asarray(trk_n).T if trk_n else None for trk_n in trk_list]
+
+    # Compute the directions
+    trk_dir = [compute_directions(trk_n) for trk_n in trk_arr]
+
+    # Compute the vtk tubes
+    out_list = [compute_tubes(trk_arr_n, trk_dir_n) for trk_arr_n, trk_dir_n in zip(trk_arr, trk_dir)]
+
+    root = combine_tracts_root(out_list, root, n_tracts)
+
+    return root
+
+
+def compute_tracts(trekker, position, affine, affine_vtk, n_tracts):
+    """ Compute tractograms using the Trekker library.
+
+    :param trekker: Trekker library instance
+    :type trekker: Trekker.T
+    :param position: 3 double coordinates (x, y, z) in list or array
+    :type position: list
+    :param affine: 4 x 4 numpy double array
+    :type affine: numpy.ndarray
+    :param affine_vtk: vtkMatrix4x4 isntance with affine transformation matrix
+    :type affine_vtk: vtkMatrix4x4
+    :param n_tracts: number of tracts to compute
+    :type n_tracts: int
+    """
+
+    # during neuronavigation, root needs to be initialized outside the while loop so the new tracts
+    # can be appended to the root block set
+    root = vtk.vtkMultiBlockDataSet()
+    # Juuso's
+    # seed = np.array([[-8.49, -8.39, 2.5]])
+    # Baran M1
+    # seed = np.array([[27.53, -77.37, 46.42]])
+    seed_trk = img_utils.convert_world_to_voxel(position, affine)
+    # print("seed example: {}".format(seed_trk))
+    trekker.seed_coordinates(np.repeat(seed_trk, n_tracts, axis=0))
+    # print("trk list len: ", len(trekker.run()))
+    trk_list = trekker.run()
+    if trk_list:
+        root = tracts_computation(trk_list, root, 0)
+        Publisher.sendMessage('Remove tracts')
+        Publisher.sendMessage('Update tracts', flag=True, root=root, affine_vtk=affine_vtk)
+    else:
+        Publisher.sendMessage('Remove tracts')
+
+
+def tracts_computation_branch(trk_list):
+    """Convert the list of all computed tracts given by Trekker run and returns a vtkMultiBlockDataSet
+
+    :param trk_list: List of lists containing the computed tracts and corresponding coordinates
+    :type trk_list: list
+    :return: The collection of tracts as a vtkMultiBlockDataSet
+    :rtype: vtkMultiBlockDataSet
+    """
+    # Transform tracts to array
+    trk_arr = [np.asarray(trk_n).T if trk_n else None for trk_n in trk_list]
+    # Compute the directions
+    trk_dir = [compute_directions(trk_n) for trk_n in trk_arr]
+    # Compute the vtk tubes
+    tube_list = [compute_tubes(trk_arr_n, trk_dir_n) for trk_arr_n, trk_dir_n in zip(trk_arr, trk_dir)]
+    branch = combine_tracts_branch(tube_list)
+
+    return branch
+
+
+class ComputeTractsThread(threading.Thread):
+
+    def __init__(self, inp, affine_vtk, coord_tracts_queue, tracts_queue, event, sle):
+        """Class (threading) to compute real time tractography data for visualization.
+
+        Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
+        For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one
+        vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as
+        bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.
+        Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.
+
+        Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
+
+        :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
+        :type inp: list
+        :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
+        :type affine_vtk: vtkMatrix4x4
+        :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered
+        :type coord_queue: queue.Queue
+        :param visualization_queue: Queue instance that manage coordinates to be visualized
+        :type visualization_queue: queue.Queue
+        :param event: Threading event to coordinate when tasks as done and allow UI release
+        :type event: threading.Event
+        :param sle: Sleep pause in seconds
+        :type sle: float
+        """
+
+        threading.Thread.__init__(self, name='ComputeTractsThread')
+        self.inp = inp
+        self.affine_vtk = affine_vtk
+        # self.coord_queue = coord_queue
+        self.coord_tracts_queue = coord_tracts_queue
+        self.tracts_queue = tracts_queue
+        # self.visualization_queue = visualization_queue
+        self.event = event
+        self.sle = sle
+
+    def run(self):
+
+        trekker, affine, offset, n_tracts_total, seed_radius, n_threads = self.inp
+        # n_threads = n_tracts_total
+        p_old = np.array([[0., 0., 0.]])
+        n_tracts = 0
+
+        # Compute the tracts
+        # print('ComputeTractsThread: event {}'.format(self.event.is_set()))
+        while not self.event.is_set():
+            try:
+                # print("Computing tracts")
+                # get from the queue the coordinates, coregistration transformation matrix, and flipped matrix
+                m_img_flip = self.coord_tracts_queue.get_nowait()
+                # coord, m_img, m_img_flip = self.coord_queue.get_nowait()
+                # print('ComputeTractsThread: get {}'.format(count))
+
+                # 20200402: in this new refactored version the m_img comes different than the position
+                # the new version m_img is already flixped in y, which means that Y is negative
+                # if only the Y is negative maybe no need for the flip_x funtcion at all in the navigation
+                # but check all coord_queue before why now the m_img comes different than position
+                # 20200403: indeed flip_x is just a -1 multiplication to the Y coordinate, remove function flip_x
+                # m_img_flip = m_img.copy()
+                # m_img_flip[1, -1] = -m_img_flip[1, -1]
+
+                # translate the coordinate along the normal vector of the object/coil
+                coord_offset = m_img_flip[:3, -1] - offset * m_img_flip[:3, 2]
+                # coord_offset = np.array([[27.53, -77.37, 46.42]])
+                dist = abs(np.linalg.norm(p_old - np.asarray(coord_offset)))
+                p_old = coord_offset.copy()
+
+                # print("p_new_shape", coord_offset.shape)
+                # print("m_img_flip_shape", m_img_flip.shape)
+                seed_trk = img_utils.convert_world_to_voxel(coord_offset, affine)
+                # Juuso's
+                # seed_trk = np.array([[-8.49, -8.39, 2.5]])
+                # Baran M1
+                # seed_trk = np.array([[27.53, -77.37, 46.42]])
+                # print("Seed: {}".format(seed))
+
+                # set the seeds for trekker, one seed is repeated n_threads times
+                # trekker has internal multiprocessing approach done in C. Here the number of available threads is give,
+                # but in case a large number of tracts is requested, it will compute all in parallel automatically
+                # for a more fluent navigation, better to compute the maximum number the computer handles
+                trekker.seed_coordinates(np.repeat(seed_trk, n_threads, axis=0))
+
+                # run the trekker, this is the slowest line of code, be careful to just use once!
+                trk_list = trekker.run()
+
+                if trk_list:
+                    # print("dist: {}".format(dist))
+                    if dist >= seed_radius:
+                        # when moving the coil further than the seed_radius restart the bundle computation
+                        bundle = vtk.vtkMultiBlockDataSet()
+                        n_branches = 0
+                        branch = tracts_computation_branch(trk_list)
+                        bundle.SetBlock(n_branches, branch)
+                        n_branches += 1
+                        n_tracts = branch.GetNumberOfBlocks()
+
+                    # TODO: maybe keep computing even if reaches the maximum
+                    elif dist < seed_radius and n_tracts < n_tracts_total:
+                        # compute tracts blocks and add to bungle until reaches the maximum number of tracts
+                        branch = tracts_computation_branch(trk_list)
+                        if bundle:
+                            bundle.SetBlock(n_branches, branch)
+                            n_tracts += branch.GetNumberOfBlocks()
+                            n_branches += 1
+
+                else:
+                    bundle = None
+
+                # rethink if this should be inside the if condition, it may lock the thread if no tracts are found
+                # use no wait to ensure maximum speed and avoid visualizing old tracts in the queue, this might
+                # be more evident in slow computer or for heavier tract computations, it is better slow update
+                # than visualizing old data
+                # self.visualization_queue.put_nowait([coord, m_img, bundle])
+                self.tracts_queue.put_nowait((bundle, self.affine_vtk, coord_offset))
+                # print('ComputeTractsThread: put {}'.format(count))
+
+                self.coord_tracts_queue.task_done()
+                # self.coord_queue.task_done()
+                # print('ComputeTractsThread: done {}'.format(count))
+
+                # sleep required to prevent user interface from being unresponsive
+                time.sleep(self.sle)
+            # if no coordinates pass
+            except queue.Empty:
+                # print("Empty queue in tractography")
+                pass
+            # if queue is full mark as done (may not be needed in this new "nowait" method)
+            except queue.Full:
+                # self.coord_queue.task_done()
+                self.coord_tracts_queue.task_done()
+
+
+class ComputeTractsThreadSingleBlock(threading.Thread):
+
+    def __init__(self, inp, affine_vtk, coord_queue, visualization_queue, event, sle):
+        """Class (threading) to compute real time tractography data for visualization in a single loop.
+
+        Different than ComputeTractsThread because it does not keep adding tracts to the bundle until maximum,
+        is reached. It actually compute all requested tracts at once. (Might be deleted in the future)!
+        Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
+        For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one
+        vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as
+        bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.
+        Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.
+
+        Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
+
+        :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
+        :type inp: list
+        :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
+        :type affine_vtk: vtkMatrix4x4
+        :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered
+        :type coord_queue: queue.Queue
+        :param visualization_queue: Queue instance that manage coordinates to be visualized
+        :type visualization_queue: queue.Queue
+        :param event: Threading event to coordinate when tasks as done and allow UI release
+        :type event: threading.Event
+        :param sle: Sleep pause in seconds
+        :type sle: float
+        """
+
+        threading.Thread.__init__(self, name='ComputeTractsThread')
+        self.inp = inp
+        self.affine_vtk = affine_vtk
+        self.coord_queue = coord_queue
+        self.visualization_queue = visualization_queue
+        self.event = event
+        self.sle = sle
+
+    def run(self):
+
+        trekker, affine, offset, n_tracts_total, seed_radius, n_threads = self.inp
+        # as a single block, computes all the maximum number of tracts at once, not optimal for navigation
+        n_threads = n_tracts_total
+        p_old = np.array([[0., 0., 0.]])
+        root = vtk.vtkMultiBlockDataSet()
+
+        # Compute the tracts
+        # print('ComputeTractsThread: event {}'.format(self.event.is_set()))
+        while not self.event.is_set():
+            try:
+                coord, m_img, m_img_flip = self.coord_queue.get_nowait()
+
+                # translate the coordinate along the normal vector of the object/coil
+                coord_offset = m_img_flip[:3, -1] - offset * m_img_flip[:3, 2]
+                # coord_offset = np.array([[27.53, -77.37, 46.42]])
+                dist = abs(np.linalg.norm(p_old - np.asarray(coord_offset)))
+                p_old = coord_offset.copy()
+                seed_trk = img_utils.convert_world_to_voxel(coord_offset, affine)
+                # Juuso's
+                # seed_trk = np.array([[-8.49, -8.39, 2.5]])
+                # Baran M1
+                # seed_trk = np.array([[27.53, -77.37, 46.42]])
+                # print("Seed: {}".format(seed))
+
+                # set the seeds for trekker, one seed is repeated n_threads times
+                # trekker has internal multiprocessing approach done in C. Here the number of available threads is give,
+                # but in case a large number of tracts is requested, it will compute all in parallel automatically
+                # for a more fluent navigation, better to compute the maximum number the computer handles
+                trekker.seed_coordinates(np.repeat(seed_trk, n_threads, axis=0))
+                # run the trekker, this is the slowest line of code, be careful to just use once!
+                trk_list = trekker.run()
+
+                if trk_list:
+                    # if the seed is outside the defined radius, restart the bundle computation
+                    if dist >= seed_radius:
+                        root = tracts_computation(trk_list, root, 0)
+                    self.visualization_queue.put_nowait((coord, m_img, root))
+
+                self.coord_queue.task_done()
+                time.sleep(self.sle)
+            except queue.Empty:
+                pass
+            except queue.Full:
+                self.coord_queue.task_done()
+
+
+def set_trekker_parameters(trekker, params):
+    """Set all user-defined parameters for tractography computation using the Trekker library
+
+    :param trekker: Trekker instance
+    :type trekker: Trekker.T
+    :param params: Dictionary containing the parameters values to set in Trekker. Initial values are in constants.py
+    :type params: dict
+    :return: List containing the Trekker instance and number of threads for parallel processing in the computer
+    :rtype: list
+    """
+    trekker.seed_maxTrials(params['seed_max'])
+    # trekker.stepSize(params['step_size'])
+    trekker.minFODamp(params['min_fod'])
+    # trekker.probeQuality(params['probe_quality'])
+    # trekker.maxEstInterval(params['max_interval'])
+    # trekker.minRadiusOfCurvature(params['min_radius_curv'])
+    # trekker.probeLength(params['probe_length'])
+    trekker.writeInterval(params['write_interval'])
+    trekker.maxLength(params['max_lenth'])
+    trekker.minLength(params['min_lenth'])
+    trekker.maxSamplingPerStep(params['max_sampling_step'])
+
+    # check number if number of cores is valid in configuration file,
+    # otherwise use the maximum number of threads which is usually 2*N_CPUS
+    n_threads = 2 * const.N_CPU
+    if isinstance((params['numb_threads']), int) and params['numb_threads'] <= 2*const.N_CPU:
+        n_threads = params['numb_threads']
+
+    trekker.numberOfThreads(n_threads)
+    # print("Trekker config updated: n_threads, {}; seed_max, {}".format(n_threads, params['seed_max']))
+    return trekker, n_threads
@@ -39,7 +39,7 @@ class Trigger(threading.Thread):
         try:
             import serial
-            self.trigger_init = serial.Serial('COM1', baudrate=9600, timeout=0)
+            self.trigger_init = serial.Serial('COM5', baudrate=115200, timeout=0)
             self.COM = True
         except:
@@ -82,3 +82,91 @@ class Trigger(threading.Thread):
                 if self.trigger_init:
                     self.trigger_init.close()
                 return
+
+
+class TriggerNew(threading.Thread):
+
+    def __init__(self, trigger_queue, event, sle):
+        """Class (threading) to compute real time tractography data for visualization in a single loop.
+
+        Different than ComputeTractsThread because it does not keep adding tracts to the bundle until maximum,
+        is reached. It actually compute all requested tracts at once. (Might be deleted in the future)!
+        Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
+        For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one
+        vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as
+        bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.
+        Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.
+
+        Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
+
+        :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
+        :type inp: list
+        :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
+        :type affine_vtk: vtkMatrix4x4
+        :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered
+        :type coord_queue: queue.Queue
+        :param visualization_queue: Queue instance that manage coordinates to be visualized
+        :type visualization_queue: queue.Queue
+        :param event: Threading event to coordinate when tasks as done and allow UI release
+        :type event: threading.Event
+        :param sle: Sleep pause in seconds
+        :type sle: float
+        """
+
+        threading.Thread.__init__(self, name='Trigger')
+
+        self.trigger_init = None
+        self.stylusplh = False
+        # self.COM = False
+        self.__bind_events()
+        try:
+            import serial
+
+            self.trigger_init = serial.Serial('COM5', baudrate=115200, timeout=0)
+            # self.COM = True
+
+        except:
+            #wx.MessageBox(_('Connection with port COM1 failed'), _('Communication error'), wx.OK | wx.ICON_ERROR)
+            print("Trigger init error: Connection with port COM failed")
+            # self.COM = False
+            pass
+
+        # self.coord_queue = coord_queue
+        self.trigger_queue = trigger_queue
+        self.event = event
+        self.sle = sle
+
+    def run(self):
+
+        while not self.event.is_set():
+            trigger_on = False
+            try:
+                self.trigger_init.write(b'0')
+                sleep(0.3)
+                lines = self.trigger_init.readlines()
+                # Following lines can simulate a trigger in 3 sec repetitions
+                # sleep(3)
+                # lines = True
+                if lines:
+                    trigger_on = True
+                    # wx.CallAfter(Publisher.sendMessage, 'Create marker')
+
+                if self.stylusplh:
+                    trigger_on = True
+                    # wx.CallAfter(Publisher.sendMessage, 'Create marker')
+                    self.stylusplh = False
+
+                self.trigger_queue.put_nowait(trigger_on)
+                sleep(self.sle)
+
+            except:
+                print("Trigger not read, error")
+                pass
+
+            # except queue.Empty:
+            #     pass
+            # except queue.Full:
+            #     self.coord_queue.task_done()
+        else:
+            if self.trigger_init:
+                self.trigger_init.close()
@@ -573,7 +573,7 @@ class Viewer(wx.Panel):
         self.cross.SetFocalPoint((ux, uy, uz))
         self.ScrollSlice(coord)
-        Publisher.sendMessage('Set ball reference position', position=(ux, uy, uz))
+        self.interactor.Render()
     def ScrollSlice(self, coord):
         if self.orientation == "AXIAL":
@@ -817,9 +817,9 @@ class Viewer(wx.Panel):
                                  ('Set scroll position',
                                   self.orientation))
         Publisher.subscribe(self.__update_cross_position,
-                                'Update cross position')
-        Publisher.subscribe(self.UpdateSlicesNavigation,
-                            'Co-registered points')
+                            'Update cross position')
+        # Publisher.subscribe(self.UpdateSlicesNavigation,
+        #                     'Co-registered points')
         ###
         #  Publisher.subscribe(self.ChangeBrushColour,
                                  #  'Add mask')
@@ -1136,8 +1136,9 @@ class Viewer(wx.Panel):
         renderer.AddActor(cross_actor)
-    def __update_cross_position(self, position):
-        self.cross.SetFocalPoint(position)
+    def __update_cross_position(self, arg, position):
+        # self.cross.SetFocalPoint(position[:3])
+        self.UpdateSlicesNavigation(None, position)
     def _set_cross_visibility(self, visibility):
         self.cross_actor.SetVisibility(visibility)
@@ -1296,8 +1297,8 @@ class Viewer(wx.Panel):
         if self.state == const.SLICE_STATE_CROSS:
             # Update other slice's cross according to the new focal point from
             # the actual orientation.
-            focal_point = self.cross.GetFocalPoint()
-            Publisher.sendMessage('Update cross position', position=focal_point)
+            x, y, z = self.cross.GetFocalPoint()
+            Publisher.sendMessage('Update cross position', arg=None, position=(x, y, z, 0., 0., 0.))
             Publisher.sendMessage('Update slice viewer')
         else:
             self.interactor.Render()
@@ -1509,7 +1510,6 @@ class Viewer(wx.Panel):
     def UpdateCross(self, coord):
         self.cross.SetFocalPoint(coord)
-        Publisher.sendMessage('Set ball reference position', position=self.cross.GetFocalPoint())
         Publisher.sendMessage('Co-registered points',  arg=None, position=(coord[0], coord[1], coord[2], 0., 0., 0.))
         self.OnScrollBar()
         self.interactor.Render()
@@ -19,9 +19,10 @@
 #    detalhes.
 #--------------------------------------------------------------------------
-from math import cos, sin
+# from math import cos, sin
 import os
 import sys
+import time
 import numpy as np
 from numpy.core.umath_tests import inner1d
@@ -36,6 +37,7 @@ from imageio import imsave
 import invesalius.constants as const
 import invesalius.data.bases as bases
+import invesalius.data.slice_ as sl
 import invesalius.data.transformations as tr
 import invesalius.data.vtk_utils as vtku
 import invesalius.project as prj
@@ -168,6 +170,10 @@ class Viewer(wx.Panel):
         #self.pTarget = [0., 0., 0.]
         # self.obj_axes = None
+        self.x_actor = None
+        self.y_actor = None
+        self.z_actor = None
+        self.mark_actor = None
         self._mode_cross = False
         self._to_show_ball = 0
@@ -188,12 +194,31 @@ class Viewer(wx.Panel):
         self.anglethreshold = const.COIL_ANGLES_THRESHOLD
         self.distthreshold = const.COIL_COORD_THRESHOLD
+        # for DTI support tests
+        # self.ntimes = False
+        # self._to_show_stream = True
+        # data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
+        # nii_path = b'sub-P0_dwi_FOD.nii'
+        # trk_path = os.path.join(data_dir, nii_path)
+        # self.tracker_FOD = Trekker.tracker(trk_path)
+        # proj = prj.Project()
+        # self.affine = np.identity(4)
+        self.actor_tracts = None
+        self.actor_peel = None
+        self.seed_offset = const.SEED_OFFSET
+        # Publisher.sendMessage('Get affine matrix')
+
+        # initialize Trekker parameters
+        slic = sl.Slice()
+        affine = slic.affine
+        self.affine_vtk = vtku.numpy_to_vtkMatrix4x4(affine)
+
     def __bind_events(self):
         Publisher.subscribe(self.LoadActor,
                                  'Load surface actor into viewer')
         Publisher.subscribe(self.RemoveActor,
                                 'Remove surface actor from viewer')
-        Publisher.subscribe(self.OnShowSurface, 'Show surface')
+        # Publisher.subscribe(self.OnShowSurface, 'Show surface')
         Publisher.subscribe(self.UpdateRender,
                                  'Render volume viewer')
         Publisher.subscribe(self.ChangeBackgroundColour,
@@ -225,7 +250,8 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.LoadSlicePlane, 'Load slice plane')
         Publisher.subscribe(self.ResetCamClippingRange, 'Reset cam clipping range')
-        Publisher.subscribe(self.SetVolumeCamera, 'Co-registered points')
+        # Publisher.subscribe(self.SetVolumeCamera, 'Update cross position')
+        # Publisher.subscribe(self.SetVolumeCamera, 'Co-registered points')
         # Publisher.subscribe(self.SetVolumeCamera, 'Set camera in volume')
         Publisher.subscribe(self.SetVolumeCameraState, 'Update volume camera state')
@@ -255,8 +281,8 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.RemoveVolume, 'Remove Volume')
-        Publisher.subscribe(self.SetBallReferencePosition,
-                            'Set ball reference position')
+        Publisher.subscribe(self.UpdateCameraBallPosition,
+                            'Update cross position')
         Publisher.subscribe(self._check_ball_reference, 'Enable style')
         Publisher.subscribe(self._uncheck_ball_reference, 'Disable style')
@@ -283,11 +309,17 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.OnUpdateObjectTargetGuide, 'Update object matrix')
         Publisher.subscribe(self.OnUpdateTargetCoordinates, 'Update target')
         Publisher.subscribe(self.OnRemoveTarget, 'Disable or enable coil tracker')
-        # Publisher.subscribe(self.UpdateObjectTargetView, 'Co-registered points')
         Publisher.subscribe(self.OnTargetMarkerTransparency, 'Set target transparency')
         Publisher.subscribe(self.OnUpdateAngleThreshold, 'Update angle threshold')
         Publisher.subscribe(self.OnUpdateDistThreshold, 'Update dist threshold')
+        Publisher.subscribe(self.OnUpdateTracts, 'Update tracts')
+        Publisher.subscribe(self.OnRemoveTracts, 'Remove tracts')
+        Publisher.subscribe(self.UpdateSeedOffset, 'Update seed offset')
+        Publisher.subscribe(self.UpdateMarkerOffsetState, 'Update marker offset state')
+        Publisher.subscribe(self.UpdateMarkerOffsetPosition, 'Update marker offset')
+        Publisher.subscribe(self.AddPeeledSurface, 'Update peel')
+
     def SetStereoMode(self, mode):
         ren_win = self.interactor.GetRenderWindow()
@@ -319,13 +351,23 @@ class Viewer(wx.Panel):
     def _check_ball_reference(self, style):
         if style == const.SLICE_STATE_CROSS:
             self._mode_cross = True
-            self._check_and_set_ball_visibility()
+            # self._check_and_set_ball_visibility()
+            self._ball_ref_visibility = True
+            # if self._to_show_ball:
+            if not self.ball_actor:
+                self.CreateBallReference()
+
             self.interactor.Render()
     def _uncheck_ball_reference(self, style):
         if style == const.SLICE_STATE_CROSS:
             self._mode_cross = False
-            self.RemoveBallReference()
+            # self.RemoveBallReference()
+            self._ball_ref_visibility = False
+            if self.ball_actor:
+                self.ren.RemoveActor(self.ball_actor)
+                self.ball_actor = None
+
             self.interactor.Render()
     def OnSensors(self, probe_id, ref_id, obj_id=0):
@@ -385,12 +427,12 @@ class Viewer(wx.Panel):
             self.probe = self.ref = self.obj = False
             self.interactor.Render()
-    def OnShowSurface(self, index, visibility):
-        if visibility:
-            self._to_show_ball += 1
-        else:
-            self._to_show_ball -= 1
-        self._check_and_set_ball_visibility()
+    # def OnShowSurface(self, index, visibility):
+    #     if visibility:
+    #         self._to_show_ball += 1
+    #     else:
+    #         self._to_show_ball -= 1
+    #     self._check_and_set_ball_visibility()
     def OnStartSeed(self):
         self.seed_points = []
@@ -485,8 +527,8 @@ class Viewer(wx.Panel):
         if (volumes.GetNumberOfItems()):
             self.ren.RemoveVolume(volumes.GetLastProp())
             self.interactor.Render()
-            self._to_show_ball -= 1
-            self._check_and_set_ball_visibility()
+            # self._to_show_ball -= 1
+            # self._check_and_set_ball_visibility()
     def RemoveActors(self, actors):
         "Remove a list of actors"
@@ -534,11 +576,11 @@ class Viewer(wx.Panel):
         Markers created by navigation tools and rendered in volume viewer.
         """
         self.ball_id = ball_id
-        x, y, z = bases.flip_x(coord)
+        coord_flip = bases.flip_x_m(coord)[:3, 0]
         ball_ref = vtk.vtkSphereSource()
         ball_ref.SetRadius(size)
-        ball_ref.SetCenter(x, y, z)
+        ball_ref.SetCenter(coord_flip)
         mapper = vtk.vtkPolyDataMapper()
         mapper.SetInputConnection(ball_ref.GetOutputPort())
@@ -557,6 +599,35 @@ class Viewer(wx.Panel):
         #self.UpdateRender()
         self.Refresh()
+    def add_marker(self, coord, color):
+        """Simplified version for creating a spherical marker in the 3D scene
+
+        :param coord:
+        :param color:
+        :return: vtkActor
+        """
+
+        # x, y, z = coord
+
+        ball_ref = vtk.vtkSphereSource()
+        ball_ref.SetRadius(2)
+        ball_ref.SetCenter(coord)
+
+        mapper = vtk.vtkPolyDataMapper()
+        mapper.SetInputConnection(ball_ref.GetOutputPort())
+
+        prop = vtk.vtkProperty()
+        prop.SetColor(color)
+
+        actor = vtk.vtkActor()
+        actor.SetMapper(mapper)
+        actor.SetProperty(prop)
+        actor.GetProperty().SetOpacity(.5)
+
+        # ren.AddActor(actor)
+
+        return actor
+
     def HideAllMarkers(self, indexes):
         ballid = indexes
         for i in range(0, ballid):
@@ -610,7 +681,6 @@ class Viewer(wx.Panel):
         self.staticballs[index].GetProperty().SetColor(color)
         self.Refresh()
-
     def OnTargetMarkerTransparency(self, status, index):
         if status:
             self.staticballs[index].GetProperty().SetOpacity(1)
@@ -1104,7 +1174,6 @@ class Viewer(wx.Panel):
         cam.SetFocalPoint(cam_focus)
         cam.SetPosition(cam_pos)
-
     def CreateBallReference(self):
         """
         Red sphere on volume visualization to reference center of
@@ -1129,31 +1198,14 @@ class Viewer(wx.Panel):
         self.ren.AddActor(self.ball_actor)
-    def ActivateBallReference(self):
-        self._mode_cross = True
-        self._ball_ref_visibility = True
-        if self._to_show_ball:
-            if not self.ball_actor:
-                self.CreateBallReference()
-
-    def RemoveBallReference(self):
-        self._mode_cross = False
-        self._ball_ref_visibility = False
-        if self.ball_actor:
-            self.ren.RemoveActor(self.ball_actor)
-            self.ball_actor = None
+    def UpdateCameraBallPosition(self, arg, position):
+        coord_flip = bases.flip_x_m(position[:3])[:3, 0]
+        self.ball_actor.SetPosition(coord_flip)
+        self.SetVolumeCamera(coord_flip)
     def SetBallReferencePosition(self, position):
-        if self._to_show_ball:
-            if not self.ball_actor:
-                self.ActivateBallReference()
-
-            coord = position
-            x, y, z = bases.flip_x(coord)
-            self.ball_actor.SetPosition(x, y, z)
-
-        else:
-            self.RemoveBallReference()
+        coord_flip = bases.flip_x_m(position[:3])[:3, 0]
+        self.ball_actor.SetPosition(coord_flip)
     def CreateObjectPolyData(self, filename):
         """
@@ -1225,7 +1277,14 @@ class Viewer(wx.Panel):
         self.obj_actor.GetProperty().SetOpacity(.4)
         self.obj_actor.SetVisibility(0)
+        self.x_actor = self.add_line([0., 0., 0.], [1., 0., 0.], color=[.0, .0, 1.0])
+        self.y_actor = self.add_line([0., 0., 0.], [0., 1., 0.], color=[.0, 1.0, .0])
+        self.z_actor = self.add_line([0., 0., 0.], [0., 0., 1.], color=[1.0, .0, .0])
+
         self.ren.AddActor(self.obj_actor)
+        self.ren.AddActor(self.x_actor)
+        self.ren.AddActor(self.y_actor)
+        self.ren.AddActor(self.z_actor)
         # self.obj_axes = vtk.vtkAxesActor()
         # self.obj_axes.SetShaftTypeToCylinder()
@@ -1236,25 +1295,88 @@ class Viewer(wx.Panel):
         # self.ren.AddActor(self.obj_axes)
-    def OnNavigationStatus(self, status):
-        self.nav_status = status
+    def add_line(self, p1, p2, color=[0.0, 0.0, 1.0]):
+        line = vtk.vtkLineSource()
+        line.SetPoint1(p1)
+        line.SetPoint2(p2)
+
+        mapper = vtk.vtkPolyDataMapper()
+        mapper.SetInputConnection(line.GetOutputPort())
+
+        actor = vtk.vtkActor()
+        actor.SetMapper(mapper)
+        actor.GetProperty().SetColor(color)
+
+        return actor
+
+    def AddPeeledSurface(self, flag, actor):
+        if self.actor_peel:
+            self.ren.RemoveActor(self.actor_peel)
+            self.actor_peel = None
+        if flag and actor:
+            self.ren.AddActor(actor)
+            self.actor_peel = actor
+        self.Refresh()
+
+    def OnNavigationStatus(self, nav_status, vis_status):
+        self.nav_status = nav_status
+        self.tracts_status = vis_status[1]
         self.pTarget = self.CenterOfMass()
-        if self.obj_actor and self.nav_status:
-            self.obj_actor.SetVisibility(self.obj_state)
-            if not self.obj_state:
-                self.Refresh()
+
+        if self.nav_status:
+            if self.obj_actor:
+                self.obj_actor.SetVisibility(self.obj_state)
+                self.x_actor.SetVisibility(self.obj_state)
+                self.y_actor.SetVisibility(self.obj_state)
+                self.z_actor.SetVisibility(self.obj_state)
+
+        self.Refresh()
+
+    def UpdateSeedOffset(self, data):
+        self.seed_offset = data
+
+    def UpdateMarkerOffsetState(self, create=False):
+        if create:
+            if not self.mark_actor:
+                self.mark_actor = self.add_marker([0., 0., 0.], color=[0., 1., 1.])
+                self.ren.AddActor(self.mark_actor)
+        else:
+            if self.mark_actor:
+                self.ren.RemoveActor(self.mark_actor)
+                self.mark_actor = None
+        self.Refresh()
+
+    def CreateMarkerOffset(self):
+        self.mark_actor = self.add_marker([0., 0., 0.], color=[0., 1., 1.])
+        self.ren.AddActor(self.mark_actor)
+        self.Refresh()
+
+    def UpdateMarkerOffsetPosition(self, coord_offset):
+        self.mark_actor.SetPosition(coord_offset)
+        self.Refresh()
     def UpdateObjectOrientation(self, m_img, coord):
-        m_img[:3, -1] = np.asmatrix(bases.flip_x_m((m_img[0, -1], m_img[1, -1], m_img[2, -1]))).reshape([3, 1])
+        # print("Update object orientation")
-        m_img_vtk = vtk.vtkMatrix4x4()
+        m_img_flip = m_img.copy()
+        m_img_flip[1, -1] = -m_img_flip[1, -1]
-        for row in range(0, 4):
-            for col in range(0, 4):
-                m_img_vtk.SetElement(row, col, m_img[row, col])
+        # translate coregistered coordinate to display a marker where Trekker seed is computed
+        # coord_offset = m_img_flip[:3, -1] - self.seed_offset * m_img_flip[:3, 2]
+
+        # print("m_img copy in viewer_vol: {}".format(m_img_copy))
+
+        # m_img[:3, 0] is from posterior to anterior direction of the coil
+        # m_img[:3, 1] is from left to right direction of the coil
+        # m_img[:3, 2] is from bottom to up direction of the coil
+
+        m_img_vtk = vtku.numpy_to_vtkMatrix4x4(m_img_flip)
         self.obj_actor.SetUserMatrix(m_img_vtk)
         # self.obj_axes.SetUserMatrix(m_rot_vtk)
+        self.x_actor.SetUserMatrix(m_img_vtk)
+        self.y_actor.SetUserMatrix(m_img_vtk)
+        self.z_actor.SetUserMatrix(m_img_vtk)
         self.Refresh()
@@ -1267,13 +1389,42 @@ class Viewer(wx.Panel):
         else:
             if self.obj_actor:
                 self.ren.RemoveActor(self.obj_actor)
+                self.ren.RemoveActor(self.x_actor)
+                self.ren.RemoveActor(self.y_actor)
+                self.ren.RemoveActor(self.z_actor)
+                self.ren.RemoveActor(self.mark_actor)
                 self.obj_actor = None
+                self.x_actor = None
+                self.y_actor = None
+                self.z_actor = None
+                self.mark_actor = None
         self.Refresh()
     def UpdateShowObjectState(self, state):
         self.obj_state = state
         if self.obj_actor and not self.obj_state:
             self.obj_actor.SetVisibility(self.obj_state)
+            self.x_actor.SetVisibility(self.obj_state)
+            self.y_actor.SetVisibility(self.obj_state)
+            self.z_actor.SetVisibility(self.obj_state)
+
+        self.Refresh()
+
+    def OnUpdateTracts(self, evt=None, flag=None, actor=None, root=None, affine_vtk=None, count=0):
+        mapper = vtk.vtkCompositePolyDataMapper2()
+        mapper.SetInputDataObject(root)
+
+        self.actor_tracts = vtk.vtkActor()
+        self.actor_tracts.SetMapper(mapper)
+        self.actor_tracts.SetUserMatrix(affine_vtk)
+
+        self.ren.AddActor(self.actor_tracts)
+        self.Refresh()
+
+    def OnRemoveTracts(self):
+        if self.actor_tracts:
+            self.ren.RemoveActor(self.actor_tracts)
+            self.actor_tracts = None
             self.Refresh()
     def __bind_events_wx(self):
@@ -1448,10 +1599,12 @@ class Viewer(wx.Panel):
     def SetVolumeCameraState(self, camera_state):
         self.camera_state = camera_state
-    def SetVolumeCamera(self, arg, position):
+    # def SetVolumeCamera(self, arg, position):
+    def SetVolumeCamera(self, cam_focus):
         if self.camera_state:
             # TODO: exclude dependency on initial focus
-            cam_focus = np.array(bases.flip_x(position[:3]))
+            # cam_focus = np.array(bases.flip_x(position[:3]))
+            # cam_focus = np.array(bases.flip_x(position))
             cam = self.ren.GetActiveCamera()
             if self.initial_focus is None:
@@ -1545,16 +1698,16 @@ class Viewer(wx.Panel):
     def OnShowRaycasting(self):
         if not self.raycasting_volume:
             self.raycasting_volume = True
-            self._to_show_ball += 1
-            self._check_and_set_ball_visibility()
+            # self._to_show_ball += 1
+            # self._check_and_set_ball_visibility()
             if self.on_wl:
                 self.text.Show()
     def OnHideRaycasting(self):
         self.raycasting_volume = False
         self.text.Hide()
-        self._to_show_ball -= 1
-        self._check_and_set_ball_visibility()
+        # self._to_show_ball -= 1
+        # self._check_and_set_ball_visibility()
     def OnSize(self, evt):
         self.UpdateRender()
@@ -1581,16 +1734,16 @@ class Viewer(wx.Panel):
         #self.ShowOrientationCube()
         self.interactor.Render()
-        self._to_show_ball += 1
-        self._check_and_set_ball_visibility()
+        # self._to_show_ball += 1
+        # self._check_and_set_ball_visibility()
     def RemoveActor(self, actor):
         utils.debug("RemoveActor")
         ren = self.ren
         ren.RemoveActor(actor)
         self.interactor.Render()
-        self._to_show_ball -= 1
-        self._check_and_set_ball_visibility()
+        # self._to_show_ball -= 1
+        # self._check_and_set_ball_visibility()
     def RemoveAllActor(self):
         utils.debug("RemoveAllActor")
@@ -1602,7 +1755,8 @@ class Viewer(wx.Panel):
     def LoadVolume(self, volume, colour, ww, wl):
         self.raycasting_volume = True
-        self._to_show_ball += 1
+        # self._to_show_ball += 1
+        # self._check_and_set_ball_visibility()
         self.light = self.ren.GetLights().GetNextItem()
@@ -1622,15 +1776,14 @@ class Viewer(wx.Panel):
             self.ren.ResetCamera()
             self.ren.ResetCameraClippingRange()
-        self._check_and_set_ball_visibility()
         self.UpdateRender()
     def UnloadVolume(self, volume):
         self.ren.RemoveVolume(volume)
         del volume
         self.raycasting_volume = False
-        self._to_show_ball -= 1
-        self._check_and_set_ball_visibility()
+        # self._to_show_ball -= 1
+        # self._check_and_set_ball_visibility()
     def OnSetViewAngle(self, view):
         self.SetViewAngle(view)
@@ -1777,16 +1930,17 @@ class Viewer(wx.Panel):
                 self.SetViewAngle(const.VOL_ISO)
                 self.repositioned_coronal_plan = 1
-    def _check_and_set_ball_visibility(self):
-        #TODO: When creating Raycasting volume and cross is pressed, it is not
-        # automatically creating the ball reference.
-        if self._mode_cross:
-            if self._to_show_ball > 0 and not self._ball_ref_visibility:
-                self.ActivateBallReference()
-                self.interactor.Render()
-            elif not self._to_show_ball and self._ball_ref_visibility:
-                self.RemoveBallReference()
-                self.interactor.Render()
+    # def _check_and_set_ball_visibility(self):
+    #     #TODO: When creating Raycasting volume and cross is pressed, it is not
+    #     # automatically creating the ball reference.
+    #     # print("mode_cross, show_ball, ball_vis ", self._mode_cross, self._to_show_ball, self._ball_ref_visibility)
+    #     if self._mode_cross:
+    #         if self._to_show_ball > 0 and not self._ball_ref_visibility:
+    #             self.ActivateBallReference()
+    #             self.interactor.Render()
+    #         elif not self._to_show_ball and self._ball_ref_visibility:
+    #             self.RemoveBallReference()
+    #             self.interactor.Render()
 class SlicePlane:
     def __init__(self):
@@ -287,3 +287,21 @@ class TextZero(object):
         #  font.SetWeight(wx.FONTWEIGHT_BOLD)
         font.SetSymbolicSize(self.symbolic_syze)
         canvas.draw_text(self.text, (x, y), font=font)
+
+
+def numpy_to_vtkMatrix4x4(affine):
+    """
+    Convert a numpy 4x4 array to a vtk 4x4 matrix
+    :param affine: 4x4 array
+    :return: vtkMatrix4x4 object representing the affine
+    """
+    # test for type and shape of affine matrix
+    # assert isinstance(affine, np.ndarray)
+    assert affine.shape == (4, 4)
+
+    affine_vtk = vtk.vtkMatrix4x4()
+    for row in range(0, 4):
+        for col in range(0, 4):
+            affine_vtk.SetElement(row, col, affine[row, col])
+
+    return affine_vtk
@@ -387,6 +387,15 @@ def ShowImportOtherFilesDialog(id_type):
     if id_type == const.ID_NIFTI_IMPORT:
         dlg.SetMessage(_("Import NIFTi 1 file"))
         dlg.SetWildcard(WILDCARD_NIFTI)
+    elif id_type == const.ID_TREKKER_MASK:
+        dlg.SetMessage(_("Import Trekker mask"))
+        dlg.SetWildcard(WILDCARD_NIFTI)
+    elif id_type == const.ID_TREKKER_IMG:
+        dlg.SetMessage(_("Import Trekker anatomical image"))
+        dlg.SetWildcard(WILDCARD_NIFTI)
+    elif id_type == const.ID_TREKKER_FOD:
+        dlg.SetMessage(_("Import Trekker FOD"))
+        dlg.SetWildcard(WILDCARD_NIFTI)
     elif id_type == const.ID_PARREC_IMPORT:
         dlg.SetMessage(_("Import PAR/REC file"))
         dlg.SetWildcard(WILDCARD_PARREC)
@@ -508,79 +517,11 @@ def ShowSaveAsProjectDialog(default_filename=None):
     return filename, wildcard == INV_COMPRESSED
-# Dialog for neuronavigation markers
-def ShowSaveMarkersDialog(default_filename=None):
-    current_dir = os.path.abspath(".")
-    dlg = wx.FileDialog(None,
-                        _("Save markers as..."),  # title
-                        "",  # last used directory
-                        default_filename,
-                        _("Markers files (*.mks)|*.mks"),
-                        wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
-    # dlg.SetFilterIndex(0) # default is VTI
-
-    filename = None
-    try:
-        if dlg.ShowModal() == wx.ID_OK:
-            filename = dlg.GetPath()
-            ok = 1
-        else:
-            ok = 0
-    except(wx._core.PyAssertionError):  # TODO: fix win64
-        filename = dlg.GetPath()
-        ok = 1
-
-    if (ok):
-        extension = "mks"
-        if sys.platform != 'win32':
-            if filename.split(".")[-1] != extension:
-                filename = filename + "." + extension
-
-    os.chdir(current_dir)
-    return filename
-
-def ShowSaveCoordsDialog(default_filename=None):
-    current_dir = os.path.abspath(".")
-    dlg = wx.FileDialog(None,
-                        _("Save coords as..."),  # title
-                        "",  # last used directory
-                        default_filename,
-                        _("Coordinates files (*.csv)|*.csv"),
-                        wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
-    # dlg.SetFilterIndex(0) # default is VTI
-
-    filename = None
-    try:
-        if dlg.ShowModal() == wx.ID_OK:
-            filename = dlg.GetPath()
-            ok = 1
-        else:
-            ok = 0
-    except(wx._core.PyAssertionError):  # TODO: fix win64
-        filename = dlg.GetPath()
-        ok = 1
+def ShowLoadSaveDialog(message=_(u"Load File"), current_dir=os.path.abspath("."), style=wx.FD_OPEN | wx.FD_CHANGE_DIR,
+                       wildcard=_("Registration files (*.obr)|*.obr"), default_filename="", save_ext=None):
-    if (ok):
-        extension = "csv"
-        if sys.platform != 'win32':
-            if filename.split(".")[-1] != extension:
-                filename = filename + "." + extension
-
-    os.chdir(current_dir)
-    return filename
-
-
-def ShowLoadMarkersDialog():
-    current_dir = os.path.abspath(".")
-
-    dlg = wx.FileDialog(None, message=_("Load markers"),
-                        defaultDir="",
-                        defaultFile="",
-                        wildcard=_("Markers files (*.mks)|*.mks"),
-                        style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
-
-    # inv3 filter is default
-    dlg.SetFilterIndex(0)
+    dlg = wx.FileDialog(None, message=message, defaultDir="", defaultFile=default_filename,
+                        wildcard=wildcard, style=style)
     # Show the dialog and retrieve the user response. If it is the OK response,
     # process the data.
@@ -589,73 +530,25 @@ def ShowLoadMarkersDialog():
         if dlg.ShowModal() == wx.ID_OK:
             # This returns a Python list of files that were selected.
             filepath = dlg.GetPath()
+            ok_press = 1
+        else:
+            ok_press = 0
     except(wx._core.PyAssertionError):  # FIX: win64
         filepath = dlg.GetPath()
+        ok_press = 1
-    # Destroy the dialog. Don't do this until you are done with it!
-    # BAD things can happen otherwise!
-    dlg.Destroy()
-    os.chdir(current_dir)
-    return filepath
-
-
-def ShowSaveRegistrationDialog(default_filename=None):
-    current_dir = os.path.abspath(".")
-    dlg = wx.FileDialog(None,
-                        _("Save object registration as..."),  # title
-                        "",  # last used directory
-                        default_filename,
-                        _("Registration files (*.obr)|*.obr"),
-                        wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
-    # dlg.SetFilterIndex(0) # default is VTI
-
-    filename = None
-    try:
-        if dlg.ShowModal() == wx.ID_OK:
-            filename = dlg.GetPath()
-            ok = 1
-        else:
-            ok = 0
-    except(wx._core.PyAssertionError):  # TODO: fix win64
-        filename = dlg.GetPath()
-        ok = 1
-
-    if (ok):
-        extension = "obr"
+    # fix the extension if set different than expected
+    if save_ext and ok_press:
+        extension = save_ext
         if sys.platform != 'win32':
-            if filename.split(".")[-1] != extension:
-                filename = filename + "." + extension
-
-    os.chdir(current_dir)
-    return filename
-
-
-def ShowLoadRegistrationDialog():
-    current_dir = os.path.abspath(".")
-
-    dlg = wx.FileDialog(None, message=_("Load object registration"),
-                        defaultDir="",
-                        defaultFile="",
-                        wildcard=_("Registration files (*.obr)|*.obr"),
-                        style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
-
-    # inv3 filter is default
-    dlg.SetFilterIndex(0)
-
-    # Show the dialog and retrieve the user response. If it is the OK response,
-    # process the data.
-    filepath = None
-    try:
-        if dlg.ShowModal() == wx.ID_OK:
-            # This returns a Python list of files that were selected.
-            filepath = dlg.GetPath()
-    except(wx._core.PyAssertionError):  # FIX: win64
-        filepath = dlg.GetPath()
+            if filepath.split(".")[-1] != extension:
+                filepath = filepath + "." + extension
     # Destroy the dialog. Don't do this until you are done with it!
     # BAD things can happen otherwise!
     dlg.Destroy()
     os.chdir(current_dir)
+
     return filepath
@@ -920,31 +813,9 @@ def SurfaceSelectionRequiredForDuplication():
 # Dialogs for neuronavigation mode
-def InvalidFiducials():
-    msg = _("Fiducials are invalid. Select all coordinates.")
-    if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                               wx.ICON_INFORMATION | wx.OK)
-    else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                               wx.ICON_INFORMATION | wx.OK)
-    dlg.ShowModal()
-    dlg.Destroy()
-
+# ----------------------------------
-def InvalidObjectRegistration():
-    msg = _("Perform coil registration before navigation.")
-    if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                               wx.ICON_INFORMATION | wx.OK)
-    else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                               wx.ICON_INFORMATION | wx.OK)
-    dlg.ShowModal()
-    dlg.Destroy()
-
-
-def NavigationTrackerWarning(trck_id, lib_mode):
+def ShowNavigationTrackerWarning(trck_id, lib_mode):
     """
     Spatial Tracker connection error
     """
@@ -976,85 +847,46 @@ def NavigationTrackerWarning(trck_id, lib_mode):
     dlg.Destroy()
-def InvalidMarkersFile():
-    msg = _("The TXT file is invalid.")
-    if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                               wx.ICON_INFORMATION | wx.OK)
-    else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                               wx.ICON_INFORMATION | wx.OK)
-    dlg.ShowModal()
-    dlg.Destroy()
-
-
-def NoMarkerSelected():
-    msg = _("No data selected")
+def ShowEnterMarkerID(default):
+    msg = _("Edit marker ID")
     if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                                wx.ICON_INFORMATION | wx.OK)
+        dlg = wx.TextEntryDialog(None, "", msg, defaultValue=default)
     else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                                wx.ICON_INFORMATION | wx.OK)
+        dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", value=default)
     dlg.ShowModal()
+    result = dlg.GetValue()
     dlg.Destroy()
+    return result
-def DeleteAllMarkers():
-    msg = _("Do you really want to delete all markers?")
+def ShowConfirmationDialog(msg=_('Proceed?')):
+    # msg = _("Do you want to delete all markers?")
     if sys.platform == 'darwin':
         dlg = wx.MessageDialog(None, "", msg,
                                wx.OK | wx.CANCEL | wx.ICON_QUESTION)
     else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
+        dlg = wx.MessageDialog(None, msg, "InVesalius 3",
                                wx.OK | wx.CANCEL | wx.ICON_QUESTION)
     result = dlg.ShowModal()
     dlg.Destroy()
     return result
-def DeleteTarget():
-    msg = _("Target deleted")
-    if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                                wx.ICON_INFORMATION | wx.OK)
-    else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                                wx.ICON_INFORMATION | wx.OK)
-    dlg.ShowModal()
-    dlg.Destroy()
-def NewTarget():
-    msg = _("New target selected")
-    if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                                wx.ICON_INFORMATION | wx.OK)
-    else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                                wx.ICON_INFORMATION | wx.OK)
-    dlg.ShowModal()
-    dlg.Destroy()
+def ShowColorDialog(color_current):
+    cdata = wx.ColourData()
+    cdata.SetColour(wx.Colour(color_current))
+    dlg = wx.ColourDialog(None, data=cdata)
+    dlg.GetColourData().SetChooseFull(True)
-def InvalidTargetID():
-    msg = _("Sorry, you cannot use 'TARGET' ID")
-    if sys.platform == 'darwin':
-        dlg = wx.MessageDialog(None, "", msg,
-                                wx.ICON_INFORMATION | wx.OK)
+    if dlg.ShowModal() == wx.ID_OK:
+        color_new = dlg.GetColourData().GetColour().Get(includeAlpha=False)
     else:
-        dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
-                                wx.ICON_INFORMATION | wx.OK)
-    dlg.ShowModal()
-    dlg.Destroy()
+        color_new = None
-def EnterMarkerID(default):
-    msg = _("Edit marker ID")
-    if sys.platform == 'darwin':
-        dlg = wx.TextEntryDialog(None, "", msg, defaultValue=default)
-    else:
-        dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", value=default)
-    dlg.ShowModal()
-    result = dlg.GetValue()
     dlg.Destroy()
-    return result
+    return color_new
+
+# ----------------------------------
 class NewMask(wx.Dialog):
@@ -3569,7 +3401,10 @@ class ObjectCalibrationDialog(wx.Dialog):
             else:
                 coord = coord_raw[0, :]
         else:
-            NavigationTrackerWarning(0, 'choose')
+            ShowNavigationTrackerWarning(0, 'choose')
+
+        if btn_id == 3:
+            coord = np.zeros([6,])
         # Update text controls with tracker coordinates
         if coord is not None or np.sum(coord) != 0.0:
@@ -3582,7 +3417,7 @@ class ObjectCalibrationDialog(wx.Dialog):
                     self.ball_actors[btn_id].GetProperty().SetColor(0.0, 1.0, 0.0)
             self.Refresh()
         else:
-            NavigationTrackerWarning(0, 'choose')
+            ShowNavigationTrackerWarning(0, 'choose')
     def OnChoiceRefMode(self, evt):
         # When ref mode is changed the tracker coordinates are set to nan
@@ -1185,12 +1185,13 @@ class MenuBar(wx.MenuBar):
         else:
             self.FindItemById(const.ID_GOTO_COORD).Enable(False)
-    def OnEnableNavigation(self, status):
+    def OnEnableNavigation(self, nav_status, vis_status):
         """
         Disable mode menu when navigation is on.
-        :param status: Navigation status
+        :param nav_status: Navigation status
+        :param vis_status: Status of items visualization during navigation
         """
-        value = status
+        value = nav_status
         if value:
             self.FindItemById(const.ID_MODE_NAVIGATION).Enable(False)
         else:
@@ -18,10 +18,13 @@
 #--------------------------------------------------------------------------
 from functools import partial
+# import os
+import queue
 import sys
-import os
+import threading
 import numpy as np
+# import Trekker
 import wx
 try:
@@ -31,22 +34,23 @@ except ImportError:
     import wx.lib.hyperlink as hl
     import wx.lib.foldpanelbar as fpb
+import wx.lib.colourselect as csel
 import wx.lib.masked.numctrl
 from pubsub import pub as Publisher
-import wx.lib.colourselect as csel
-import wx.lib.platebtn as pbtn
-
-from math import cos, sin, pi
 from time import sleep
-import invesalius.data.transformations as tr
 import invesalius.constants as const
 import invesalius.data.bases as db
+# import invesalius.data.brainmesh_handler as brain
 import invesalius.data.coordinates as dco
 import invesalius.data.coregistration as dcr
+import invesalius.data.slice_ as sl
 import invesalius.data.trackers as dt
+import invesalius.data.tractography as dti
+import invesalius.data.transformations as tr
 import invesalius.data.trigger as trig
 import invesalius.data.record_coords as rec
+import invesalius.data.vtk_utils as vtk_utils
 import invesalius.gui.dialogs as dlg
 from invesalius import utils
@@ -136,7 +140,7 @@ class InnerFoldPanel(wx.Panel):
         # Study this.
         fold_panel = fpb.FoldPanelBar(self, -1, wx.DefaultPosition,
-                                          (10, 290), 0, fpb.FPB_SINGLE_FOLD)
+                                      (10, 310), 0, fpb.FPB_SINGLE_FOLD)
         # Fold panel style
         style = fpb.CaptionBarStyle()
         style.SetCaptionStyle(fpb.CAPTIONBAR_GRADIENT_V)
@@ -161,15 +165,23 @@ class InnerFoldPanel(wx.Panel):
                                       leftSpacing=0, rightSpacing=0)
         # Fold 3 - Markers panel
-        item = fold_panel.AddFoldPanel(_("Extra tools"), collapsed=True)
+        item = fold_panel.AddFoldPanel(_("Markers"), collapsed=True)
         mtw = MarkersPanel(item)
         fold_panel.ApplyCaptionStyle(item, style)
         fold_panel.AddFoldPanelWindow(item, mtw, spacing= 0,
                                       leftSpacing=0, rightSpacing=0)
-        # Fold 4 - DBS
+        # Fold 4 - Tractography panel
+        item = fold_panel.AddFoldPanel(_("Tractography"), collapsed=True)
+        otw = TractographyPanel(item)
+        fold_panel.ApplyCaptionStyle(item, style)
+        fold_panel.AddFoldPanelWindow(item, otw, spacing=0,
+                                      leftSpacing=0, rightSpacing=0)
+        item.Hide()
+
+        # Fold 5 - DBS
         self.dbs_item = fold_panel.AddFoldPanel(_("Deep Brain Stimulation"), collapsed=True)
         dtw = DbsPanel(self.dbs_item) #Atribuir nova var, criar panel
@@ -239,8 +251,8 @@ class InnerFoldPanel(wx.Panel):
     def OnHideDbs(self):
         self.dbs_item.Hide()
-    def OnCheckStatus(self, status):
-        if status:
+    def OnCheckStatus(self, nav_status, vis_status):
+        if nav_status:
             self.checktrigger.Enable(False)
             self.checkobj.Enable(False)
         else:
@@ -295,6 +307,23 @@ class NeuronavigationPanel(wx.Panel):
         self.obj_reg = None
         self.obj_reg_status = False
         self.track_obj = False
+        self.event = threading.Event()
+
+        self.coord_queue = QueueCustom(maxsize=1)
+        # self.visualization_queue = QueueCustom(maxsize=1)
+        self.trigger_queue = QueueCustom(maxsize=1)
+        self.coord_tracts_queue = QueueCustom(maxsize=1)
+        self.tracts_queue = QueueCustom(maxsize=1)
+
+        # Tractography parameters
+        self.trk_inp = None
+        self.trekker = None
+        self.n_threads = None
+        self.view_tracts = False
+        self.n_tracts = const.N_TRACTS
+        self.seed_offset = const.SEED_OFFSET
+        self.seed_radius = const.SEED_RADIUS
+        self.sleep_nav = const.SLEEP_NAVIGATION
         self.tracker_id = const.DEFAULT_TRACKER
         self.ref_mode_id = const.DEFAULT_REF_MODE
@@ -405,10 +434,17 @@ class NeuronavigationPanel(wx.Panel):
         Publisher.subscribe(self.LoadImageFiducials, 'Load image fiducials')
         Publisher.subscribe(self.UpdateTriggerState, 'Update trigger state')
         Publisher.subscribe(self.UpdateTrackObjectState, 'Update track object state')
-        Publisher.subscribe(self.UpdateImageCoordinates, 'Set ball reference position')
+        Publisher.subscribe(self.UpdateImageCoordinates, 'Update cross position')
         Publisher.subscribe(self.OnDisconnectTracker, 'Disconnect tracker')
         Publisher.subscribe(self.UpdateObjectRegistration, 'Update object registration')
         Publisher.subscribe(self.OnCloseProject, 'Close project data')
+        Publisher.subscribe(self.UpdateTrekkerObject, 'Update Trekker object')
+        Publisher.subscribe(self.UpdateNumTracts, 'Update number of tracts')
+        Publisher.subscribe(self.UpdateSeedOffset, 'Update seed offset')
+        Publisher.subscribe(self.UpdateSeedRadius, 'Update seed radius')
+        Publisher.subscribe(self.UpdateSleep, 'Update sleep')
+        Publisher.subscribe(self.UpdateNumberThreads, 'Update number of threads')
+        Publisher.subscribe(self.UpdateTractsVisualization, 'Update tracts visualization')
     def LoadImageFiducials(self, marker_id, coord):
         for n in const.BTNS_IMG_MKS:
@@ -420,7 +456,37 @@ class NeuronavigationPanel(wx.Panel):
                 for m in [0, 1, 2]:
                     self.numctrls_coord[btn_id][m].SetValue(coord[m])
-    def UpdateImageCoordinates(self, position):
+    def UpdateFRE(self, fre):
+        # TODO: Exhibit FRE in a warning dialog and only starts navigation after user clicks ok
+        self.txtctrl_fre.SetValue(str(round(fre, 2)))
+        if fre <= 3:
+            self.txtctrl_fre.SetBackgroundColour('GREEN')
+        else:
+            self.txtctrl_fre.SetBackgroundColour('RED')
+
+    def UpdateTrekkerObject(self, data):
+        # self.trk_inp = data
+        self.trekker = data
+
+    def UpdateNumTracts(self, data):
+        self.n_tracts = data
+
+    def UpdateSeedOffset(self, data):
+        self.seed_offset = data
+
+    def UpdateSeedRadius(self, data):
+        self.seed_radius = data
+
+    def UpdateSleep(self, data):
+        self.sleep_nav = data
+
+    def UpdateNumberThreads(self, data):
+        self.n_threads = data
+
+    def UpdateTractsVisualization(self, data):
+        self.view_tracts = data
+
+    def UpdateImageCoordinates(self, arg, position):
         # TODO: Change from world coordinates to matrix coordinates. They are better for multi software communication.
         self.current_coord = position
         for m in [0, 1, 2]:
@@ -473,7 +539,7 @@ class NeuronavigationPanel(wx.Panel):
                                       label=_("Tracker disconnected successfully"))
                 self.trk_init = dt.TrackerConnection(self.tracker_id, None, 'connect')
                 if not self.trk_init[0]:
-                    dlg.NavigationTrackerWarning(self.tracker_id, self.trk_init[1])
+                    dlg.ShowNavigationTrackerWarning(self.tracker_id, self.trk_init[1])
                     ctrl.SetSelection(0)
                     print("Tracker not connected!")
                 else:
@@ -488,7 +554,7 @@ class NeuronavigationPanel(wx.Panel):
                 self.trk_init = dt.TrackerConnection(self.tracker_id, trck, 'disconnect')
                 if not self.trk_init[0]:
                     if evt is not False:
-                        dlg.NavigationTrackerWarning(self.tracker_id, 'disconnect')
+                        dlg.ShowNavigationTrackerWarning(self.tracker_id, 'disconnect')
                     self.tracker_id = 0
                     ctrl.SetSelection(self.tracker_id)
                     Publisher.sendMessage('Update status text in GUI',
@@ -507,7 +573,7 @@ class NeuronavigationPanel(wx.Panel):
                 self.tracker_id = choice
                 self.trk_init = dt.TrackerConnection(self.tracker_id, None, 'connect')
                 if not self.trk_init[0]:
-                    dlg.NavigationTrackerWarning(self.tracker_id, self.trk_init[1])
+                    dlg.ShowNavigationTrackerWarning(self.tracker_id, self.trk_init[1])
                     self.tracker_id = 0
                     ctrl.SetSelection(self.tracker_id)
@@ -549,7 +615,18 @@ class NeuronavigationPanel(wx.Panel):
         coord = None
         if self.trk_init and self.tracker_id:
+            # if self.tracker_id == const.DEBUGTRACK:
+            #     if btn_id == 3:
+            #         coord1 = np.array([-120., 0., 0., 0., 0., 0.])
+            #     elif btn_id == 4:
+            #         coord1 = np.array([120., 0., 0., 0., 0., 0.])
+            #     elif btn_id == 5:
+            #         coord1 = np.array([0., 120., 0., 0., 0., 0.])
+            #     coord2 = np.zeros([3, 6])
+            #     coord_raw = np.vstack([coord1, coord2])
+            # else:
             coord_raw = dco.GetCoordinates(self.trk_init, self.tracker_id, self.ref_mode_id)
+
             if self.ref_mode_id:
                 coord = dco.dynamic_reference_m(coord_raw[0, :], coord_raw[1, :])
             else:
@@ -557,7 +634,7 @@ class NeuronavigationPanel(wx.Panel):
                 coord[2] = -coord[2]
         else:
-            dlg.NavigationTrackerWarning(0, 'choose')
+            dlg.ShowNavigationTrackerWarning(0, 'choose')
         # Update number controls with tracker coordinates
         if coord is not None:
@@ -569,112 +646,152 @@ class NeuronavigationPanel(wx.Panel):
         btn_nav = btn[0]
         choice_trck = btn[1]
         choice_ref = btn[2]
+        errors = False
+
+        # initialize jobs list
+        jobs_list = []
+        vis_components = [self.trigger_state, self.view_tracts]
+        vis_queues = [self.coord_queue, self.trigger_queue, self.tracts_queue]
         nav_id = btn_nav.GetValue()
-        if nav_id:
+        if not nav_id:
+            self.event.set()
+
+            # print("coord unfinished: {}, queue {}", self.coord_queue.unfinished_tasks, self.coord_queue.qsize())
+            # print("coord_tracts unfinished: {}, queue {}", self.coord_tracts_queue.unfinished_tasks, self.coord_tracts_queue.qsize())
+            # print("tracts unfinished: {}, queue {}", self.tracts_queue.unfinished_tasks, self.tracts_queue.qsize())
+            self.coord_queue.clear()
+            # self.visualization_queue.clear()
+            if self.trigger_state:
+                self.trigger_queue.clear()
+            if self.view_tracts:
+                self.coord_tracts_queue.clear()
+                self.tracts_queue.clear()
+
+            # print("coord after unfinished: {}, queue {}", self.coord_queue.unfinished_tasks, self.coord_queue.qsize())
+            # print("coord_tracts after unfinished: {}, queue {}", self.coord_tracts_queue.unfinished_tasks, self.coord_tracts_queue.qsize())
+            # print("tracts after unfinished: {}, queue {}", self.tracts_queue.unfinished_tasks, self.tracts_queue.qsize())
+            self.coord_queue.join()
+            # self.visualization_queue.join()
+            if self.trigger_state:
+                self.trigger_queue.join()
+            if self.view_tracts:
+                self.coord_tracts_queue.join()
+                self.tracts_queue.join()
+
+            # print("coord join unfinished: {}, queue {}", self.coord_queue.unfinished_tasks, self.coord_queue.qsize())
+            # print("vis join unfinished: {}, queue {}", self.visualization_queue.unfinished_tasks, self.visualization_queue.qsize())
+
+            tooltip = wx.ToolTip(_("Start neuronavigation"))
+            btn_nav.SetToolTip(tooltip)
+
+            # Enable all navigation buttons
+            choice_ref.Enable(True)
+            choice_trck.Enable(True)
+            for btn_c in self.btns_coord:
+                btn_c.Enable(True)
+
+            # if self.trigger_state:
+            #     self.trigger.stop()
+
+            Publisher.sendMessage("Navigation status", nav_status=False, vis_status=vis_components)
+
+        else:
+
             if np.isnan(self.fiducials).any():
-                dlg.InvalidFiducials()
+                wx.MessageBox(_("Invalid fiducials, select all coordinates."), _("InVesalius 3"))
                 btn_nav.SetValue(False)
-            elif not self.trk_init[0]:
-                dlg.NavigationTrackerWarning(0, 'choose')
+            elif not self.trk_init[0] or not self.tracker_id:
+                dlg.ShowNavigationTrackerWarning(0, 'choose')
+                errors = True
             else:
+                if self.event.is_set():
+                    self.event.clear()
+
+                # prepare GUI for navigation
+                Publisher.sendMessage("Navigation status", nav_status=True, vis_status=vis_components)
+                Publisher.sendMessage("Toggle Cross", id=const.SLICE_STATE_CROSS)
+                Publisher.sendMessage("Hide current mask")
                 tooltip = wx.ToolTip(_("Stop neuronavigation"))
                 btn_nav.SetToolTip(tooltip)
-                # Disable all navigation buttons
+                # disable all navigation buttons
                 choice_ref.Enable(False)
                 choice_trck.Enable(False)
                 for btn_c in self.btns_coord:
                     btn_c.Enable(False)
-                # fids_head_img = np.zeros([3, 3])
-                # for ic in range(0, 3):
-                #     fids_head_img[ic, :] = np.asarray(db.flip_x_m(self.fiducials[ic, :]))
-                #
-                # m_head_aux, q_head_aux, m_inv_head_aux = db.base_creation(fids_head_img)
-                # m_head = np.asmatrix(np.identity(4))
-                # m_head[:3, :3] = m_head_aux[:3, :3]
-
-                m, q1, minv = db.base_creation_old(self.fiducials[:3, :])
-                n, q2, ninv = db.base_creation_old(self.fiducials[3:, :])
-
+                # fiducials matrix
                 m_change = tr.affine_matrix_from_points(self.fiducials[3:, :].T, self.fiducials[:3, :].T,
                                                         shear=False, scale=False)
-
-                # coreg_data = [m_change, m_head]
-
+                # initialize spatial tracker parameters
                 tracker_mode = self.trk_init, self.tracker_id, self.ref_mode_id
-                # FIXME: FRE is taking long to calculate so it updates on GUI delayed to navigation - I think its fixed
-                # TODO: Exhibit FRE in a warning dialog and only starts navigation after user clicks ok
-                fre = db.calculate_fre(self.fiducials, minv, n, q1, q2)
-
-                self.txtctrl_fre.SetValue(str(round(fre, 2)))
-                if fre <= 3:
-                    self.txtctrl_fre.SetBackgroundColour('GREEN')
-                else:
-                    self.txtctrl_fre.SetBackgroundColour('RED')
-
-                if self.trigger_state:
-                    self.trigger = trig.Trigger(nav_id)
-                Publisher.sendMessage("Navigation status", status=True)
-                Publisher.sendMessage("Toggle Cross", id=const.SLICE_STATE_CROSS)
-                Publisher.sendMessage("Hide current mask")
+                # compute fiducial registration error (FRE)
+                # this is the old way to compute the fre, left here to recheck if new works fine.
+                # fre = db.calculate_fre(self.fiducials, minv, n, q1, q2)
+                fre = db.calculate_fre_m(self.fiducials)
+                self.UpdateFRE(fre)
                 if self.track_obj:
-                    if self.obj_reg_status:
+                    # if object tracking is selected
+                    if not self.obj_reg_status:
+                        # check if object registration was performed
+                        wx.MessageBox(_("Perform coil registration before navigation."), _("InVesalius 3"))
+                        errors = True
+                    else:
+                        # if object registration was correctly performed continue with navigation
                         # obj_reg[0] is object 3x3 fiducial matrix and obj_reg[1] is 3x3 orientation matrix
                         obj_fiducials, obj_orients, obj_ref_mode, obj_name = self.obj_reg
-                        if self.trk_init and self.tracker_id:
-
-                            coreg_data = [m_change, obj_ref_mode]
-
-                            if self.ref_mode_id:
-                                coord_raw = dco.GetCoordinates(self.trk_init, self.tracker_id, self.ref_mode_id)
-                                obj_data = db.object_registration(obj_fiducials, obj_orients, coord_raw, m_change)
-                                coreg_data.extend(obj_data)
-
-                                self.correg = dcr.CoregistrationObjectDynamic(coreg_data, nav_id, tracker_mode)
-                            else:
-                                coord_raw = np.array([None])
-                                obj_data = db.object_registration(obj_fiducials, obj_orients, coord_raw, m_change)
-                                coreg_data.extend(obj_data)
-
-                                self.correg = dcr.CoregistrationObjectStatic(coreg_data, nav_id, tracker_mode)
+                        coreg_data = [m_change, obj_ref_mode]
+                        if self.ref_mode_id:
+                            coord_raw = dco.GetCoordinates(self.trk_init, self.tracker_id, self.ref_mode_id)
                         else:
-                            dlg.NavigationTrackerWarning(0, 'choose')
-
-                    else:
-                        dlg.InvalidObjectRegistration()
-
-                else:
-                    coreg_data = [m_change, 0]
-                    if self.ref_mode_id:
-                        # self.correg = dcr.CoregistrationDynamic_old(bases_coreg, nav_id, tracker_mode)
-                        self.correg = dcr.CoregistrationDynamic(coreg_data, nav_id, tracker_mode)
-                    else:
-                        self.correg = dcr.CoregistrationStatic(coreg_data, nav_id, tracker_mode)
+                            coord_raw = np.array([None])
-        else:
-            tooltip = wx.ToolTip(_("Start neuronavigation"))
-            btn_nav.SetToolTip(tooltip)
-
-            # Enable all navigation buttons
-            choice_ref.Enable(True)
-            choice_trck.Enable(True)
-            for btn_c in self.btns_coord:
-                btn_c.Enable(True)
-
-            if self.trigger_state:
-                self.trigger.stop()
+                        obj_data = db.object_registration(obj_fiducials, obj_orients, coord_raw, m_change)
+                        coreg_data.extend(obj_data)
-            self.correg.stop()
+                        jobs_list.append(dcr.CoordinateCorregistrate(self.ref_mode_id, tracker_mode, coreg_data, self.coord_queue,
+                                                                     self.view_tracts, self.coord_tracts_queue,
+                                                                     self.event, self.sleep_nav))
-            Publisher.sendMessage("Navigation status", status=False)
+                else:
+                    coreg_data = (m_change, 0)
+                    jobs_list.append(dcr.CoordinateCorregistrateNoObject(self.ref_mode_id, tracker_mode, coreg_data,
+                                                                         self.coord_queue,
+                                                                         self.view_tracts, self.coord_tracts_queue,
+                                                                         self.event, self.sleep_nav))
+
+                if not errors:
+                    #TODO: Test the trigger thread
+                    if self.trigger_state:
+                        # self.trigger = trig.Trigger(nav_id)
+                        jobs_list.append(trig.TriggerNew(self.trigger_queue, self.event, self.sleep_nav))
+
+                    if self.view_tracts:
+                        # initialize Trekker parameters
+                        slic = sl.Slice()
+                        affine = slic.affine
+                        affine_vtk = vtk_utils.numpy_to_vtkMatrix4x4(affine)
+                        Publisher.sendMessage("Update marker offset state", create=True)
+                        self.trk_inp = self.trekker, affine, self.seed_offset, self.n_tracts, self.seed_radius, self.n_threads
+                        # print("Appending the tract computation thread!")
+                        jobs_list.append(dti.ComputeTractsThread(self.trk_inp, affine_vtk,
+                                                                 self.coord_tracts_queue, self.tracts_queue,
+                                                                 self.event, self.sleep_nav))
+
+                    jobs_list.append(UpdateNavigationScene(vis_queues, vis_components,
+                                                           self.event, self.sleep_nav))
+
+                    for jobs in jobs_list:
+                        # jobs.daemon = True
+                        jobs.start()
+                        # del jobs
     def ResetImageFiducials(self):
         for m in range(0, 3):
@@ -699,6 +816,8 @@ class NeuronavigationPanel(wx.Panel):
         Publisher.sendMessage('Update object registration')
         Publisher.sendMessage('Update track object state', flag=False, obj_name=False)
         Publisher.sendMessage('Delete all markers')
+        Publisher.sendMessage("Update marker offset state", create=False)
+        Publisher.sendMessage("Remove tracts")
         # TODO: Reset camera initial focus
         Publisher.sendMessage('Reset cam clipping range')
@@ -830,8 +949,7 @@ class ObjectRegistrationPanel(wx.Panel):
     def UpdateTrackerInit(self, nav_prop):
         self.nav_prop = nav_prop
-    def UpdateNavigationStatus(self, status):
-        nav_status = status
+    def UpdateNavigationStatus(self, nav_status, vis_status):
         if nav_status:
             self.checkrecordcoords.Enable(1)
             self.checktrack.Enable(0)
@@ -898,37 +1016,50 @@ class ObjectRegistrationPanel(wx.Panel):
                 pass
         else:
-            dlg.NavigationTrackerWarning(0, 'choose')
+            dlg.ShowNavigationTrackerWarning(0, 'choose')
     def OnLinkLoad(self, event=None):
-        filename = dlg.ShowLoadRegistrationDialog()
+        filename = dlg.ShowLoadSaveDialog(message=_(u"Load object registration"),
+                                          wildcard=_("Registration files (*.obr)|*.obr"))
+        # data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\pilot_20200131'
+        # coil_path = 'magstim_coil_dell_laptop.obr'
+        # filename = os.path.join(data_dir, coil_path)
-        if filename:
-            data = np.loadtxt(filename, delimiter='\t')
-            self.obj_fiducials = data[:, :3]
-            self.obj_orients = data[:, 3:]
-
-            text_file = open(filename, "r")
-            header = text_file.readline().split('\t')
-            text_file.close()
-
-            self.obj_name = header[1]
-            self.obj_ref_mode = int(header[-1])
-
-            self.checktrack.Enable(1)
-            Publisher.sendMessage('Update object registration',
-                                  data=(self.obj_fiducials, self.obj_orients, self.obj_ref_mode, self.obj_name))
-            Publisher.sendMessage('Update status text in GUI', label=_("Ready"))
-            self.checktrack.SetValue(True)
-            Publisher.sendMessage('Update track object state', flag=True, obj_name=self.obj_name)
-            Publisher.sendMessage('Change camera checkbox', status=False)
-            wx.MessageBox(_("Object file successfully loaded"), _("Load"))
+        try:
+            if filename:
+                #TODO: Improve method to read the file, using "with" similar to OnLoadParameters
+                data = np.loadtxt(filename, delimiter='\t')
+                self.obj_fiducials = data[:, :3]
+                self.obj_orients = data[:, 3:]
+
+                text_file = open(filename, "r")
+                header = text_file.readline().split('\t')
+                text_file.close()
+
+                self.obj_name = header[1]
+                self.obj_ref_mode = int(header[-1])
+
+                self.checktrack.Enable(1)
+                self.checktrack.SetValue(True)
+                Publisher.sendMessage('Update object registration',
+                                      data=(self.obj_fiducials, self.obj_orients, self.obj_ref_mode, self.obj_name))
+                Publisher.sendMessage('Update status text in GUI',
+                                      label=_("Object file successfully loaded"))
+                Publisher.sendMessage('Update track object state', flag=True, obj_name=self.obj_name)
+                Publisher.sendMessage('Change camera checkbox', status=False)
+                # wx.MessageBox(_("Object file successfully loaded"), _("Load"))
+        except:
+            wx.MessageBox(_("Object registration file incompatible."), _("InVesalius 3"))
+            Publisher.sendMessage('Update status text in GUI', label="")
     def ShowSaveObjectDialog(self, evt):
         if np.isnan(self.obj_fiducials).any() or np.isnan(self.obj_orients).any():
             wx.MessageBox(_("Digitize all object fiducials before saving"), _("Save error"))
         else:
-            filename = dlg.ShowSaveRegistrationDialog("object_registration.obr")
+            filename = dlg.ShowLoadSaveDialog(message=_(u"Save object registration as..."),
+                                              wildcard=_("Registration files (*.obr)|*.obr"),
+                                              style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
+                                              default_filename="object_registration.obr", save_ext="obr")
             if filename:
                 hdr = 'Object' + "\t" + utils.decode(self.obj_name, const.FS_ENCODE) + "\t" + 'Reference' + "\t" + str('%d' % self.obj_ref_mode)
                 data = np.hstack([self.obj_fiducials, self.obj_orients])
@@ -969,8 +1100,8 @@ class MarkersPanel(wx.Panel):
         self.tgt_flag = self.tgt_index = None
         self.nav_status = False
-        self.marker_colour = (1.0, 1.0, 0.)
-        self.marker_size = 3
+        self.marker_colour = const.MARKER_COLOUR
+        self.marker_size = const.MARKER_SIZE
         # Change marker size
         spin_size = wx.SpinCtrl(self, -1, "", size=wx.Size(40, 23))
@@ -1045,7 +1176,8 @@ class MarkersPanel(wx.Panel):
         self.Update()
     def __bind_events(self):
-        Publisher.subscribe(self.UpdateCurrentCoord, 'Co-registered points')
+        # Publisher.subscribe(self.UpdateCurrentCoord, 'Co-registered points')
+        Publisher.subscribe(self.UpdateCurrentCoord, 'Update cross position')
         Publisher.subscribe(self.OnDeleteSingleMarker, 'Delete fiducial marker')
         Publisher.subscribe(self.OnDeleteAllMarkers, 'Delete all markers')
         Publisher.subscribe(self.OnCreateMarker, 'Create marker')
@@ -1055,8 +1187,8 @@ class MarkersPanel(wx.Panel):
         self.current_coord = position[:]
         #self.current_angle = pubsub_evt.data[1][3:]
-    def UpdateNavigationStatus(self, status):
-        if not status:
+    def UpdateNavigationStatus(self, nav_status, vis_status):
+        if not nav_status:
             sleep(0.5)
             #self.current_coord[3:] = 0, 0, 0
             self.nav_status = False
@@ -1073,6 +1205,9 @@ class MarkersPanel(wx.Panel):
         menu_id.AppendSeparator()
         target_menu = menu_id.Append(1, _('Set as target'))
         menu_id.Bind(wx.EVT_MENU, self.OnMenuSetTarget, target_menu)
+        # TODO: Create the remove target option so the user can disable the target without removing the marker
+        # target_menu_rem = menu_id.Append(3, _('Remove target'))
+        # menu_id.Bind(wx.EVT_MENU, self.OnMenuRemoveTarget, target_menu_rem)
         target_menu.Enable(True)
         self.PopupMenu(menu_id)
@@ -1089,10 +1224,10 @@ class MarkersPanel(wx.Panel):
         if evt == 'TARGET':
             id_label = evt
         else:
-            id_label = dlg.EnterMarkerID(self.lc.GetItemText(list_index, 4))
+            id_label = dlg.ShowEnterMarkerID(self.lc.GetItemText(list_index, 4))
             if id_label == 'TARGET':
                 id_label = ''
-                dlg.InvalidTargetID()
+                wx.MessageBox(_("Invalid TARGET ID."), _("InVesalius 3"))
         self.lc.SetItem(list_index, 4, id_label)
         # Add the new ID to exported list
         if len(self.list_coord[list_index]) > 8:
@@ -1122,34 +1257,29 @@ class MarkersPanel(wx.Panel):
         Publisher.sendMessage('Disable or enable coil tracker', status=True)
         self.OnMenuEditMarkerId('TARGET')
         self.tgt_flag = True
-        dlg.NewTarget()
+        wx.MessageBox(_("New target selected."), _("InVesalius 3"))
     def OnMenuSetColor(self, evt):
         index = self.lc.GetFocusedItem()
-        cdata = wx.ColourData()
-        cdata.SetColour(wx.Colour(self.list_coord[index][6]*255,self.list_coord[index][7]*255,self.list_coord[index][8]*255))
-        dlg = wx.ColourDialog(self, data=cdata)
-        dlg.GetColourData().SetChooseFull(True)
-        if dlg.ShowModal() == wx.ID_OK:
-            self.r, self.g, self.b = dlg.GetColourData().GetColour().Get(includeAlpha=False)
-            r = float(self.r) / 255.0
-            g = float(self.g) / 255.0
-            b = float(self.b) / 255.0
-        dlg.Destroy()
-        color = [r,g,b]
-
-        Publisher.sendMessage('Set new color', index=index, color=color)
-
-        self.list_coord[index][6] = r
-        self.list_coord[index][7] = g
-        self.list_coord[index][8] = b
+
+        color_current = [self.list_coord[index][n] * 255 for n in range(6, 9)]
+
+        color_new = dlg.ShowColorDialog(color_current=color_current)
+
+        if color_new:
+            assert len(color_new) == 3
+            for n, col in enumerate(color_new):
+                self.list_coord[index][n+6] = col/255.0
+
+            Publisher.sendMessage('Set new color', index=index, color=color_new)
     def OnDeleteAllMarkers(self, evt=None):
         if self.list_coord:
             if evt is None:
                 result = wx.ID_OK
             else:
-                result = dlg.DeleteAllMarkers()
+                # result = dlg.DeleteAllMarkers()
+                result = dlg.ShowConfirmationDialog(msg=_("Remove all markers? Cannot be undone."))
             if result == wx.ID_OK:
                 self.list_coord = []
@@ -1162,7 +1292,7 @@ class MarkersPanel(wx.Panel):
                     self.tgt_flag = self.tgt_index = None
                     Publisher.sendMessage('Disable or enable coil tracker', status=False)
                     if not hasattr(evt, 'data'):
-                        dlg.DeleteTarget()
+                        wx.MessageBox(_("Target deleted."), _("InVesalius 3"))
     def OnDeleteSingleMarker(self, evt=None, marker_id=None):
         # OnDeleteSingleMarker is used for both pubsub and button click events
@@ -1183,14 +1313,16 @@ class MarkersPanel(wx.Panel):
             else:
                 index = None
+        #TODO: There are bugs when no marker is selected, test and improve
         if index:
             if self.tgt_flag and self.tgt_index == index[0]:
                 self.tgt_flag = self.tgt_index = None
                 Publisher.sendMessage('Disable or enable coil tracker', status=False)
-                dlg.DeleteTarget()
+                wx.MessageBox(_("No data selected."), _("InVesalius 3"))
+
             self.DeleteMarker(index)
         else:
-            dlg.NoMarkerSelected()
+            wx.MessageBox(_("Target deleted."), _("InVesalius 3"))
     def DeleteMarker(self, index):
         for i in reversed(index):
@@ -1213,12 +1345,16 @@ class MarkersPanel(wx.Panel):
             self.CreateMarker(self.current_coord, self.marker_colour, self.marker_size)
     def OnLoadMarkers(self, evt):
-        filepath = dlg.ShowLoadMarkersDialog()
+        filename = dlg.ShowLoadSaveDialog(message=_(u"Load markers"),
+                                          wildcard=_("Markers files (*.mks)|*.mks"))
+        # data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\pilot_20200131'
+        # marker_path = 'markers.mks'
+        # filename = os.path.join(data_dir, marker_path)
-        if filepath:
+        if filename:
             try:
                 count_line = self.lc.GetItemCount()
-                content = [s.rstrip() for s in open(filepath)]
+                content = [s.rstrip() for s in open(filename)]
                 for data in content:
                     target = None
                     line = [s for s in data.split()]
@@ -1254,7 +1390,7 @@ class MarkersPanel(wx.Panel):
                         self.CreateMarker(coord, colour, size, line[7])
                     count_line += 1
             except:
-                dlg.InvalidMarkersFile()
+                wx.MessageBox(_("Invalid markers file."), _("InVesalius 3"))
     def OnMarkersVisibility(self, evt, ctrl):
@@ -1266,7 +1402,11 @@ class MarkersPanel(wx.Panel):
             ctrl.SetLabel('Hide')
     def OnSaveMarkers(self, evt):
-        filename = dlg.ShowSaveMarkersDialog("markers.mks")
+        filename = dlg.ShowLoadSaveDialog(message=_(u"Save markers as..."),
+                                          wildcard=_("Marker files (*.mks)|*.mks"),
+                                          style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
+                                          default_filename="markers.mks", save_ext="mks")
+
         if filename:
             if self.list_coord:
                 text_file = open(filename, "w")
@@ -1339,3 +1479,459 @@ class DbsPanel(wx.Panel):
         except AttributeError:
             default_colour = wx.SystemSettings_GetColour(wx.SYS_COLOUR_MENUBAR)
+
+class TractographyPanel(wx.Panel):
+
+    def __init__(self, parent):
+        wx.Panel.__init__(self, parent)
+        try:
+            default_colour = wx.SystemSettings.GetColour(wx.SYS_COLOUR_MENUBAR)
+        except AttributeError:
+            default_colour = wx.SystemSettings_GetColour(wx.SYS_COLOUR_MENUBAR)
+        self.SetBackgroundColour(default_colour)
+
+        self.affine = None
+        self.affine_vtk = None
+        self.trekker = None
+        self.n_tracts = const.N_TRACTS
+        self.peel_depth = const.PEEL_DEPTH
+        self.view_tracts = False
+        self.seed_offset = const.SEED_OFFSET
+        self.seed_radius = const.SEED_RADIUS
+        self.sleep_nav = const.SLEEP_NAVIGATION
+        self.brain_opacity = const.BRAIN_OPACITY
+        self.brain_peel = None
+        self.brain_actor = None
+        self.n_peels = const.MAX_PEEL_DEPTH
+        self.p_old = np.array([[0., 0., 0.]])
+        self.tracts_run = None
+        self.trekker_cfg = const.TREKKER_CONFIG
+        self.nav_status = False
+
+        self.SetAutoLayout(1)
+        self.__bind_events()
+
+        # Button for creating new coil
+        tooltip = wx.ToolTip(_("Load brain visualization"))
+        btn_mask = wx.Button(self, -1, _("Load brain"), size=wx.Size(65, 23))
+        btn_mask.SetToolTip(tooltip)
+        btn_mask.Enable(1)
+        btn_mask.Bind(wx.EVT_BUTTON, self.OnLinkBrain)
+        # self.btn_new = btn_new
+
+        # Button for import config coil file
+        tooltip = wx.ToolTip(_("Load FOD"))
+        btn_load = wx.Button(self, -1, _("Load FOD"), size=wx.Size(65, 23))
+        btn_load.SetToolTip(tooltip)
+        btn_load.Enable(1)
+        btn_load.Bind(wx.EVT_BUTTON, self.OnLinkFOD)
+        # self.btn_load = btn_load
+
+        # Save button for object registration
+        tooltip = wx.ToolTip(_(u"Load Trekker configuration parameters"))
+        btn_load_cfg = wx.Button(self, -1, _(u"Configure"), size=wx.Size(65, 23))
+        btn_load_cfg.SetToolTip(tooltip)
+        btn_load_cfg.Enable(1)
+        btn_load_cfg.Bind(wx.EVT_BUTTON, self.OnLoadParameters)
+        # self.btn_load_cfg = btn_load_cfg
+
+        # Create a horizontal sizer to represent button save
+        line_btns = wx.BoxSizer(wx.HORIZONTAL)
+        line_btns.Add(btn_load, 1, wx.LEFT | wx.TOP | wx.RIGHT, 4)
+        line_btns.Add(btn_load_cfg, 1, wx.LEFT | wx.TOP | wx.RIGHT, 4)
+        line_btns.Add(btn_mask, 1, wx.LEFT | wx.TOP | wx.RIGHT, 4)
+
+        # Change peeling depth
+        text_peel_depth = wx.StaticText(self, -1, _("Peeling depth (mm):"))
+        spin_peel_depth = wx.SpinCtrl(self, -1, "", size=wx.Size(50, 23))
+        spin_peel_depth.Enable(1)
+        spin_peel_depth.SetRange(0, const.MAX_PEEL_DEPTH)
+        spin_peel_depth.SetValue(const.PEEL_DEPTH)
+        spin_peel_depth.Bind(wx.EVT_TEXT, partial(self.OnSelectPeelingDepth, ctrl=spin_peel_depth))
+        spin_peel_depth.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectPeelingDepth, ctrl=spin_peel_depth))
+
+        # Change number of tracts
+        text_ntracts = wx.StaticText(self, -1, _("Number tracts:"))
+        spin_ntracts = wx.SpinCtrl(self, -1, "", size=wx.Size(50, 23))
+        spin_ntracts.Enable(1)
+        spin_ntracts.SetRange(1, 2000)
+        spin_ntracts.SetValue(const.N_TRACTS)
+        spin_ntracts.Bind(wx.EVT_TEXT, partial(self.OnSelectNumTracts, ctrl=spin_ntracts))
+        spin_ntracts.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectNumTracts, ctrl=spin_ntracts))
+
+        # Change seed offset for computing tracts
+        text_offset = wx.StaticText(self, -1, _("Seed offset (mm):"))
+        spin_offset = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23), inc = 0.1)
+        spin_offset.Enable(1)
+        spin_offset.SetRange(0, 100.0)
+        spin_offset.SetValue(self.seed_offset)
+        spin_offset.Bind(wx.EVT_TEXT, partial(self.OnSelectOffset, ctrl=spin_offset))
+        spin_offset.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectOffset, ctrl=spin_offset))
+        # self.spin_offset = spin_offset
+
+        # Change seed radius for computing tracts
+        text_radius = wx.StaticText(self, -1, _("Seed radius (mm):"))
+        spin_radius = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23), inc=0.1)
+        spin_radius.Enable(1)
+        spin_radius.SetRange(0, 100.0)
+        spin_radius.SetValue(self.seed_radius)
+        spin_radius.Bind(wx.EVT_TEXT, partial(self.OnSelectRadius, ctrl=spin_radius))
+        spin_radius.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectRadius, ctrl=spin_radius))
+        # self.spin_radius = spin_radius
+
+        # Change sleep pause between navigation loops
+        text_sleep = wx.StaticText(self, -1, _("Sleep (s):"))
+        spin_sleep = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23), inc=0.01)
+        spin_sleep.Enable(1)
+        spin_sleep.SetRange(0.01, 10.0)
+        spin_sleep.SetValue(self.sleep_nav)
+        spin_sleep.Bind(wx.EVT_TEXT, partial(self.OnSelectSleep, ctrl=spin_sleep))
+        spin_sleep.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectSleep, ctrl=spin_sleep))
+
+        # Change opacity of brain mask visualization
+        text_opacity = wx.StaticText(self, -1, _("Brain opacity:"))
+        spin_opacity = wx.SpinCtrlDouble(self, -1, "", size=wx.Size(50, 23), inc=0.1)
+        spin_opacity.Enable(0)
+        spin_opacity.SetRange(0, 1.0)
+        spin_opacity.SetValue(self.brain_opacity)
+        spin_opacity.Bind(wx.EVT_TEXT, partial(self.OnSelectOpacity, ctrl=spin_opacity))
+        spin_opacity.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectOpacity, ctrl=spin_opacity))
+        self.spin_opacity = spin_opacity
+
+        # Create a horizontal sizer to threshold configs
+        border = 1
+        line_peel_depth = wx.BoxSizer(wx.HORIZONTAL)
+        line_peel_depth.AddMany([(text_peel_depth, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, border),
+                                 (spin_peel_depth, 0, wx.ALL | wx.EXPAND | wx.GROW, border)])
+
+        line_ntracts = wx.BoxSizer(wx.HORIZONTAL)
+        line_ntracts.AddMany([(text_ntracts, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, border),
+                              (spin_ntracts, 0, wx.ALL | wx.EXPAND | wx.GROW, border)])
+
+        line_offset = wx.BoxSizer(wx.HORIZONTAL)
+        line_offset.AddMany([(text_offset, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, border),
+                             (spin_offset, 0, wx.ALL | wx.EXPAND | wx.GROW, border)])
+
+        line_radius = wx.BoxSizer(wx.HORIZONTAL)
+        line_radius.AddMany([(text_radius, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, border),
+                             (spin_radius, 0, wx.ALL | wx.EXPAND | wx.GROW, border)])
+
+        line_sleep = wx.BoxSizer(wx.HORIZONTAL)
+        line_sleep.AddMany([(text_sleep, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, border),
+                            (spin_sleep, 0, wx.ALL | wx.EXPAND | wx.GROW, border)])
+
+        line_opacity = wx.BoxSizer(wx.HORIZONTAL)
+        line_opacity.AddMany([(text_opacity, 1, wx.EXPAND | wx.GROW | wx.TOP | wx.RIGHT | wx.LEFT, border),
+                            (spin_opacity, 0, wx.ALL | wx.EXPAND | wx.GROW, border)])
+
+        # Check box to enable tract visualization
+        checktracts = wx.CheckBox(self, -1, _('Enable tracts'))
+        checktracts.SetValue(False)
+        checktracts.Enable(0)
+        checktracts.Bind(wx.EVT_CHECKBOX, partial(self.OnEnableTracts, ctrl=checktracts))
+        self.checktracts = checktracts
+
+        # Check box to enable surface peeling
+        checkpeeling = wx.CheckBox(self, -1, _('Peel surface'))
+        checkpeeling.SetValue(False)
+        checkpeeling.Enable(0)
+        checkpeeling.Bind(wx.EVT_CHECKBOX, partial(self.OnShowPeeling, ctrl=checkpeeling))
+        self.checkpeeling = checkpeeling
+
+        border_last = 1
+        line_checks = wx.BoxSizer(wx.HORIZONTAL)
+        line_checks.Add(checktracts, 0, wx.ALIGN_LEFT | wx.RIGHT | wx.LEFT, border_last)
+        line_checks.Add(checkpeeling, 0, wx.ALIGN_RIGHT | wx.RIGHT | wx.LEFT, border_last)
+
+        # Add line sizers into main sizer
+        border = 1
+        border_last = 10
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.Add(line_btns, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, border_last)
+        main_sizer.Add(line_peel_depth, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, border)
+        main_sizer.Add(line_ntracts, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, border)
+        main_sizer.Add(line_offset, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, border)
+        main_sizer.Add(line_radius, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, border)
+        main_sizer.Add(line_sleep, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, border)
+        main_sizer.Add(line_opacity, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP, border)
+        main_sizer.Add(line_checks, 0, wx.GROW | wx.EXPAND | wx.LEFT | wx.RIGHT | wx.TOP | wx.BOTTOM, border_last)
+        main_sizer.Fit(self)
+
+        self.SetSizer(main_sizer)
+        self.Update()
+
+    def __bind_events(self):
+        Publisher.subscribe(self.OnCloseProject, 'Close project data')
+        Publisher.subscribe(self.OnUpdateTracts, 'Update cross position')
+        Publisher.subscribe(self.UpdateNavigationStatus, 'Navigation status')
+
+    def OnSelectPeelingDepth(self, evt, ctrl):
+        self.peel_depth = ctrl.GetValue()
+        if self.checkpeeling.GetValue():
+            actor = self.brain_peel.get_actor(self.peel_depth)
+            Publisher.sendMessage('Update peel', flag=True, actor=actor)
+
+    def OnSelectNumTracts(self, evt, ctrl):
+        self.n_tracts = ctrl.GetValue()
+        # self.tract.n_tracts = ctrl.GetValue()
+        Publisher.sendMessage('Update number of tracts', data=self.n_tracts)
+
+    def OnSelectOffset(self, evt, ctrl):
+        self.seed_offset = ctrl.GetValue()
+        # self.tract.seed_offset = ctrl.GetValue()
+        Publisher.sendMessage('Update seed offset', data=self.seed_offset)
+
+    def OnSelectRadius(self, evt, ctrl):
+        self.seed_radius = ctrl.GetValue()
+        # self.tract.seed_offset = ctrl.GetValue()
+        Publisher.sendMessage('Update seed radius', data=self.seed_radius)
+
+    def OnSelectSleep(self, evt, ctrl):
+        self.sleep_nav = ctrl.GetValue()
+        # self.tract.seed_offset = ctrl.GetValue()
+        Publisher.sendMessage('Update sleep', data=self.sleep_nav)
+
+    def OnSelectOpacity(self, evt, ctrl):
+        self.brain_actor.GetProperty().SetOpacity(ctrl.GetValue())
+        Publisher.sendMessage('Update peel', flag=True, actor=self.brain_actor)
+
+    def OnShowPeeling(self, evt, ctrl):
+        # self.view_peeling = ctrl.GetValue()
+        if ctrl.GetValue():
+            actor = self.brain_peel.get_actor(self.peel_depth)
+        else:
+            actor = None
+        Publisher.sendMessage('Update peel', flag=ctrl.GetValue(), actor=actor)
+
+    def OnEnableTracts(self, evt, ctrl):
+        self.view_tracts = ctrl.GetValue()
+        Publisher.sendMessage('Update tracts visualization', data=self.view_tracts)
+        if not self.view_tracts:
+            Publisher.sendMessage('Remove tracts')
+            Publisher.sendMessage("Update marker offset state", create=False)
+
+    def UpdateNavigationStatus(self, nav_status, vis_status):
+        self.nav_status = nav_status
+
+    def OnLinkBrain(self, event=None):
+        Publisher.sendMessage('Update status text in GUI', label=_("Busy"))
+        Publisher.sendMessage('Begin busy cursor')
+        mask_path = dlg.ShowImportOtherFilesDialog(const.ID_TREKKER_MASK)
+        img_path = dlg.ShowImportOtherFilesDialog(const.ID_TREKKER_IMG)
+        # data_dir = os.environ.get('OneDriveConsumer') + '\\data\\dti'
+        # mask_file = 'sub-P0_dwi_mask.nii'
+        # mask_path = os.path.join(data_dir, mask_file)
+        # img_file = 'sub-P0_T1w_biascorrected.nii'
+        # img_path = os.path.join(data_dir, img_file)
+
+        if not self.affine_vtk:
+            slic = sl.Slice()
+            self.affine = slic.affine
+            self.affine_vtk = vtk_utils.numpy_to_vtkMatrix4x4(self.affine)
+
+        try:
+            self.brain_peel = brain.Brain(img_path, mask_path, self.n_peels, self.affine_vtk)
+            self.brain_actor = self.brain_peel.get_actor(self.peel_depth)
+            self.brain_actor.GetProperty().SetOpacity(self.brain_opacity)
+            Publisher.sendMessage('Update peel', flag=True, actor=self.brain_actor)
+            self.checkpeeling.Enable(1)
+            self.checkpeeling.SetValue(True)
+            self.spin_opacity.Enable(1)
+            Publisher.sendMessage('Update status text in GUI', label=_("Brain model loaded"))
+        except:
+            wx.MessageBox(_("Unable to load brain mask."), _("InVesalius 3"))
+
+        Publisher.sendMessage('End busy cursor')
+
+    def OnLinkFOD(self, event=None):
+        Publisher.sendMessage('Update status text in GUI', label=_("Busy"))
+        Publisher.sendMessage('Begin busy cursor')
+        filename = dlg.ShowImportOtherFilesDialog(const.ID_TREKKER_FOD)
+        # Juuso
+        # data_dir = os.environ.get('OneDriveConsumer') + '\\data\\dti'
+        # FOD_path = 'sub-P0_dwi_FOD.nii'
+        # Baran
+        # data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\pilot_20200131'
+        # FOD_path = 'Baran_FOD.nii'
+        # filename = os.path.join(data_dir, FOD_path)
+
+        if not self.affine_vtk:
+            slic = sl.Slice()
+            self.affine = slic.affine
+            self.affine_vtk = vtk_utils.numpy_to_vtkMatrix4x4(self.affine)
+
+        # try:
+
+        self.trekker = Trekker.initialize(filename.encode('utf-8'))
+        self.trekker, n_threads = dti.set_trekker_parameters(self.trekker, self.trekker_cfg)
+
+        self.checktracts.Enable(1)
+        self.checktracts.SetValue(True)
+        self.view_tracts = True
+        Publisher.sendMessage('Update Trekker object', data=self.trekker)
+        Publisher.sendMessage('Update number of threads', data=n_threads)
+        Publisher.sendMessage('Update tracts visualization', data=1)
+        Publisher.sendMessage('Update status text in GUI', label=_("Trekker initialized"))
+        # except:
+        #     wx.MessageBox(_("Unable to initialize Trekker, check FOD and config files."), _("InVesalius 3"))
+
+        Publisher.sendMessage('End busy cursor')
+
+    def OnLoadParameters(self, event=None):
+        import json
+        filename = dlg.ShowLoadSaveDialog(message=_(u"Load Trekker configuration"),
+                                          wildcard=_("JSON file (*.json)|*.json"))
+        try:
+            # Check if filename exists, read the JSON file and check if all parameters match
+            # with the required list defined in the constants module
+            # if a parameter is missing, raise an error
+            if filename:
+                with open(filename) as json_file:
+                    self.trekker_cfg = json.load(json_file)
+                assert all(name in self.trekker_cfg for name in const.TREKKER_CONFIG)
+                if self.trekker:
+                    self.trekker, n_threads = dti.set_trekker_parameters(self.trekker, self.trekker_cfg)
+                    Publisher.sendMessage('Update Trekker object', data=self.trekker)
+                    Publisher.sendMessage('Update number of threads', data=n_threads)
+
+                Publisher.sendMessage('Update status text in GUI', label=_("Trekker config loaded"))
+
+        except (AssertionError, json.decoder.JSONDecodeError):
+            # Inform user that file is not compatible
+            self.trekker_cfg = const.TREKKER_CONFIG
+            wx.MessageBox(_("File incompatible, using default configuration."), _("InVesalius 3"))
+            Publisher.sendMessage('Update status text in GUI', label="")
+
+    def OnUpdateTracts(self, arg, position):
+        """
+        Minimal working version of tract computation. Updates when cross sends Pubsub message to update.
+        Position refers to the coordinates in InVesalius 2D space. To represent the same coordinates in the 3D space,
+        flip_x the coordinates and multiply the z coordinate by -1. This is all done in the flix_x function.
+
+        :param arg: event for pubsub
+        :param position: list or array with the x, y, and z coordinates in InVesalius space
+        """
+        # Minimal working version of tract computation
+        # It updates when cross updates
+        # pass
+        if self.view_tracts and not self.nav_status:
+            # print("Running during navigation")
+            coord_flip = db.flip_x_m(position[:3])[:3, 0]
+            dti.compute_tracts(self.trekker, coord_flip, self.affine, self.affine_vtk,
+                               self.n_tracts)
+
+    def OnCloseProject(self):
+        self.checktracts.SetValue(False)
+        self.checktracts.Enable(0)
+        self.checkpeeling.SetValue(False)
+        self.checkpeeling.Enable(0)
+
+        self.spin_opacity.SetValue(const.BRAIN_OPACITY)
+        self.spin_opacity.Enable(0)
+        Publisher.sendMessage('Update peel', flag=False, actor=self.brain_actor)
+
+        self.peel_depth = const.PEEL_DEPTH
+        self.n_tracts = const.N_TRACTS
+
+        Publisher.sendMessage('Remove tracts')
+
+
+class QueueCustom(queue.Queue):
+    """
+    A custom queue subclass that provides a :meth:`clear` method.
+    https://stackoverflow.com/questions/6517953/clear-all-items-from-the-queue
+    Modified to a LIFO Queue type (Last-in-first-out). Seems to make sense for the navigation
+    threads, as the last added coordinate should be the first to be processed.
+    In the first tests in a short run, seems to increase the coord queue size considerably,
+    possibly limiting the queue size is good.
+    """
+
+    def clear(self):
+        """
+        Clears all items from the queue.
+        """
+
+        with self.mutex:
+            unfinished = self.unfinished_tasks - len(self.queue)
+            if unfinished <= 0:
+                if unfinished < 0:
+                    raise ValueError('task_done() called too many times')
+                self.all_tasks_done.notify_all()
+            self.unfinished_tasks = unfinished
+            self.queue.clear()
+            self.not_full.notify_all()
+
+
+class UpdateNavigationScene(threading.Thread):
+
+    def __init__(self, vis_queues, vis_components, event, sle):
+        """Class (threading) to update the navigation scene with all graphical elements.
+
+        Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
+
+        :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
+        :type affine_vtk: vtkMatrix4x4
+        :param visualization_queue: Queue instance that manage coordinates to be visualized
+        :type visualization_queue: queue.Queue
+        :param event: Threading event to coordinate when tasks as done and allow UI release
+        :type event: threading.Event
+        :param sle: Sleep pause in seconds
+        :type sle: float
+        """
+
+        threading.Thread.__init__(self, name='UpdateScene')
+        self.trigger_state, self.view_tracts = vis_components
+        self.coord_queue, self.trigger_queue, self.tracts_queue = vis_queues
+        self.sle = sle
+        self.event = event
+
+    def run(self):
+        # count = 0
+        while not self.event.is_set():
+            got_coords = False
+            try:
+                coord, m_img, view_obj = self.coord_queue.get_nowait()
+                got_coords = True
+
+                # print('UpdateScene: get {}'.format(count))
+
+                # use of CallAfter is mandatory otherwise crashes the wx interface
+                if self.view_tracts:
+                    bundle, affine_vtk, coord_offset = self.tracts_queue.get_nowait()
+                    wx.CallAfter(Publisher.sendMessage, 'Remove tracts')
+                    wx.CallAfter(Publisher.sendMessage, 'Update tracts', flag=True, root=bundle,
+                                 affine_vtk=affine_vtk)
+                    wx.CallAfter(Publisher.sendMessage, 'Update marker offset', coord_offset=coord_offset)
+                    self.tracts_queue.task_done()
+
+                if self.trigger_state:
+                    trigger_on = self.trigger_queue.get_nowait()
+                    if trigger_on:
+                        wx.CallAfter(Publisher.sendMessage, 'Create marker')
+                    self.trigger_queue.task_done()
+
+                # TODO: If using the view_tracts substitute the raw coord from the offset coordinate, so the user
+                # see the red cross in the position of the offset marker
+                wx.CallAfter(Publisher.sendMessage, 'Update cross position', arg=m_img, position=coord)
+
+                if view_obj:
+                    wx.CallAfter(Publisher.sendMessage, 'Update object matrix', m_img=m_img, coord=coord)
+
+                self.coord_queue.task_done()
+                # print('UpdateScene: done {}'.format(count))
+                # count += 1
+
+                sleep(self.sle)
+            except queue.Empty:
+                if got_coords:
+                    self.coord_queue.task_done()
+
+
+class InputAttributes(object):
+    # taken from https://stackoverflow.com/questions/2466191/set-attributes-from-dictionary-in-python
+    def __init__(self, *initial_data, **kwargs):
+        for dictionary in initial_data:
+            for key in dictionary:
+                setattr(self, key, dictionary[key])
+        for key in kwargs:
+            setattr(self, key, kwargs[key])
@@ -313,8 +313,9 @@ class Project(metaclass=Singleton):
         self.spacing = project["spacing"]
         if project.get("affine", ""):
             self.affine = project["affine"]
+            # self.affine = project.get("affine")
             Publisher.sendMessage('Update affine matrix',
-                                  affine=self.affine, status=True)
+                                  affine=np.asarray(self.affine).reshape(4, 4), status=True)
         self.compress = project.get("compress", True)
	@@ -37,6 +37,8 @@ from invesalius.data import vtk_utils as vtk_utils		@@ -37,6 +37,8 @@ from invesalius.data import vtk_utils as vtk_utils
37	import invesalius.reader.bitmap_reader as bitmap_reader	37	import invesalius.reader.bitmap_reader as bitmap_reader
38	import invesalius.utils as utils	38	import invesalius.utils as utils
39	import invesalius.data.converters as converters	39	import invesalius.data.converters as converters
		40	+import invesalius.data.slice_ as sl
		41	+import invesalius.data.transformations as tr
40		42
41	from invesalius import inv_paths	43	from invesalius import inv_paths
42		44
	@@ -516,3 +518,67 @@ def image_normalize(image, min_=0.0, max_=1.0, output_dtype=np.int16):		@@ -516,3 +518,67 @@ def image_normalize(image, min_=0.0, max_=1.0, output_dtype=np.int16):
516	imin, imax = image.min(), image.max()	518	imin, imax = image.min(), image.max()
517	output[:] = (image - imin) * ((max_ - min_) / (imax - imin)) + min_	519	output[:] = (image - imin) * ((max_ - min_) / (imax - imin)) + min_
518	return output	520	return output
		521	+
		522	+
		523	+def world2invspace(affine=None):
		524	+ """
		525	+ Normalize image pixel intensity for int16 gray scale values.
		526	+
		527	+ :param repos: list of translation and rotation [trans_x, trans_y, trans_z, rot_x, rot_y, rot_z] to reposition the
		528	+ vtk object prior to applying the affine matrix transformation. Note: rotation given in degrees
		529	+ :param user_matrix: affine matrix from image header, prefered QForm matrix
		530	+ :return: vtk transform filter for repositioning the polydata and affine matrix to be used as SetUserMatrix in actor
		531	+ """
		532	+
		533	+ # remove scaling factor for non-unitary voxel dimensions
		534	+ scale, shear, angs, trans, persp = tr.decompose_matrix(affine)
		535	+ affine_noscale = tr.compose_matrix(scale=None, shear=shear, angles=angs, translate=trans, perspective=persp)
		536	+ # repos_img = [0.] * 6
		537	+ # repos_img[1] = -float(shape[1])
		538	+ #
		539	+ # repos_mat = np.identity(4)
		540	+ # # translation
		541	+ # repos_mat[:3, -1] = repos_img[:3]
		542	+ # # rotation (in principle for invesalius space no rotation is needed)
		543	+ # repos_mat[:3, :3] = tr.euler_matrix(*np.deg2rad(repos_img[3:]), axes='sxyz')[:3, :3]
		544	+
		545	+ # if repos:
		546	+ # transx, transy, transz, rotx, roty, rotz = repos
		547	+ # # create a transform that rotates the stl source
		548	+ # transform = vtk.vtkTransform()
		549	+ # transform.PostMultiply()
		550	+ # transform.RotateX(rotx)
		551	+ # transform.RotateY(roty)
		552	+ # transform.RotateZ(rotz)
		553	+ # transform.Translate(transx, transy, transz)
		554	+ #
		555	+ # transform_filt = vtk.vtkTransformPolyDataFilter()
		556	+ # transform_filt.SetTransform(transform)
		557	+ # transform_filt.Update()
		558	+
		559	+ # assuming vtk default transformation order is PreMultiply, the user matrix is set so:
		560	+ # 1. Replace the object -> 2. Transform the object to desired position/orientation
		561	+ # PreMultiplty: M = M*A where M is current transformation and A is applied transformation
		562	+ # user_matrix = np.linalg.inv(user_matrix) @ repos_mat
		563	+
		564	+ return np.linalg.inv(affine_noscale)
		565	+
		566	+
		567	+def convert_world_to_voxel(xyz, affine):
		568	+ """
		569	+ Convert a coordinate from the world space ((x, y, z); scanner space; millimeters) to the
		570	+ voxel space ((i, j, k)). This is achieved by multiplying a coordinate by the inverse
		571	+ of the affine transformation.
		572	+ More information: https://nipy.org/nibabel/coordinate_systems.html
		573	+ :param xyz: a list or array of 3 coordinates (x, y, z) in the world coordinates
		574	+ :param affine: a 4x4 array containing the image affine transformation in homogeneous coordinates
		575	+ :return: a 1x3 array with the point coordinates in image space (i, j, k)
		576	+ """
		577	+
		578	+ # print("xyz: ", xyz, "\naffine", affine)
		579	+ # convert xyz coordinate to 1x4 homogeneous coordinates array
		580	+ xyz_homo = np.hstack((xyz, 1.)).reshape([4, 1])
		581	+ ijk_homo = np.linalg.inv(affine) @ xyz_homo
		582	+ ijk = ijk_homo.T[np.newaxis, 0, :3]
		583	+
		584	+ return ijk
	@@ -82,6 +82,9 @@ class Slice(metaclass=utils.Singleton):		@@ -82,6 +82,9 @@ class Slice(metaclass=utils.Singleton):
82	self.blend_filter = None	82	self.blend_filter = None
83	self.histogram = None	83	self.histogram = None
84	self._matrix = None	84	self._matrix = None
		85	+ self._affine = np.identity(4)
		86	+ self._n_tracts = 0
		87	+ self._tracker = None
85	self.aux_matrices = {}	88	self.aux_matrices = {}
86	self.aux_matrices_colours = {}	89	self.aux_matrices_colours = {}
87	self.state = const.STATE_DEFAULT	90	self.state = const.STATE_DEFAULT
	@@ -144,6 +147,30 @@ class Slice(metaclass=utils.Singleton):		@@ -144,6 +147,30 @@ class Slice(metaclass=utils.Singleton):
144	(s * d / 2.0) for (d, s) in zip(self.matrix.shape[::-1], self.spacing)	147	(s * d / 2.0) for (d, s) in zip(self.matrix.shape[::-1], self.spacing)
145	]	148	]
146		149
		150	+ @property
		151	+ def affine(self):
		152	+ return self._affine
		153	+
		154	+ @affine.setter
		155	+ def affine(self, value):
		156	+ self._affine = value
		157	+
		158	+ @property
		159	+ def n_tracts(self):
		160	+ return self._n_tracts
		161	+
		162	+ @n_tracts.setter
		163	+ def n_tracts(self, value):
		164	+ self._n_tracts = value
		165	+
		166	+ @property
		167	+ def tracker(self):
		168	+ return self._tracker
		169	+
		170	+ @tracker.setter
		171	+ def tracker(self, value):
		172	+ self._tracker = value
		173	+
147	def __bind_events(self):	174	def __bind_events(self):
148	# General slice control	175	# General slice control
149	Publisher.subscribe(self.CreateSurfaceFromIndex, "Create surface from index")	176	Publisher.subscribe(self.CreateSurfaceFromIndex, "Create surface from index")
	@@ -47,6 +47,14 @@ from invesalius.data.measures import (CircleDensityMeasure, MeasureData,		@@ -47,6 +47,14 @@ from invesalius.data.measures import (CircleDensityMeasure, MeasureData,
47		47
48	from invesalius_cy import floodfill	48	from invesalius_cy import floodfill
49		49
		50	+# For tracts
		51	+import invesalius.data.tractography as dtr
		52	+# import invesalius.project as prj
		53	+import invesalius.data.slice_ as sl
		54	+import invesalius.data.bases as bases
		55	+# from time import sleep
		56	+# ---
		57	+
50	ORIENTATIONS = {	58	ORIENTATIONS = {
51	"AXIAL": const.AXIAL,	59	"AXIAL": const.AXIAL,
52	"CORONAL": const.CORONAL,	60	"CORONAL": const.CORONAL,
	@@ -465,6 +473,18 @@ class CrossInteractorStyle(DefaultInteractorStyle):		@@ -465,6 +473,18 @@ class CrossInteractorStyle(DefaultInteractorStyle):
465	self.slice_actor = viewer.slice_data.actor	473	self.slice_actor = viewer.slice_data.actor
466	self.slice_data = viewer.slice_data	474	self.slice_data = viewer.slice_data
467		475
		476	+ # tracts
		477	+ # self.seed = [0., 0., 0.]
		478	+ # slic = sl.Slice()
		479	+ # self.affine = slic.affine
		480	+ # self.tracker = slic.tracker
		481	+ #
		482	+ # self.affine_vtk = vtk.vtkMatrix4x4()
		483	+ # for row in range(0, 4):
		484	+ # for col in range(0, 4):
		485	+ # self.affine_vtk.SetElement(row, col, self.affine[row, col])
		486	+ # ---
		487	+
468	self.picker = vtk.vtkWorldPointPicker()	488	self.picker = vtk.vtkWorldPointPicker()
469		489
470	self.AddObserver("MouseMoveEvent", self.OnCrossMove)	490	self.AddObserver("MouseMoveEvent", self.OnCrossMove)
	@@ -478,6 +498,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):		@@ -478,6 +498,7 @@ class CrossInteractorStyle(DefaultInteractorStyle):
478		498
479	def CleanUp(self):	499	def CleanUp(self):
480	self.viewer._set_cross_visibility(0)	500	self.viewer._set_cross_visibility(0)
		501	+ Publisher.sendMessage('Remove tracts')
481	Publisher.sendMessage('Toggle toolbar item',	502	Publisher.sendMessage('Toggle toolbar item',
482	_id=self.state_code, value=False)	503	_id=self.state_code, value=False)
483		504
	@@ -497,12 +518,20 @@ class CrossInteractorStyle(DefaultInteractorStyle):		@@ -497,12 +518,20 @@ class CrossInteractorStyle(DefaultInteractorStyle):
497	wx, wy, wz = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)	518	wx, wy, wz = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)
498	px, py = self.viewer.get_slice_pixel_coord_by_world_pos(wx, wy, wz)	519	px, py = self.viewer.get_slice_pixel_coord_by_world_pos(wx, wy, wz)
499	coord = self.viewer.calcultate_scroll_position(px, py)	520	coord = self.viewer.calcultate_scroll_position(px, py)
500	- Publisher.sendMessage('Update cross position', position=(wx, wy, wz))	521	+
		522	+ # Tracts
		523	+ # pos_world_aux = np.ones([4, 1])
		524	+ # pos_world_aux[:3, -1] = bases.flip_x((wx, wy, wz))[:3]
		525	+ # pos_world = np.linalg.inv(self.affine) @ pos_world_aux
		526	+ # seed_aux = pos_world.reshape([1, 4])[0, :3]
		527	+ # self.seed = seed_aux[np.newaxis, :]
		528	+ # print("Check the seed: ", self.seed)
		529	+ #
		530	+
		531	+ Publisher.sendMessage('Update cross position', arg=None, position=(wx, wy, wz, 0., 0., 0.))
501	self.ScrollSlice(coord)	532	self.ScrollSlice(coord)
502	- Publisher.sendMessage('Set ball reference position', position=(wx, wy, wz))
503	- Publisher.sendMessage('Co-registered points', arg=None, position=(wx, wy, wz, 0., 0., 0.))
504		533
505	- iren.Render()	534	+ # iren.Render()
506		535
507	def ScrollSlice(self, coord):	536	def ScrollSlice(self, coord):
508	if self.orientation == "AXIAL":	537	if self.orientation == "AXIAL":
	@@ -522,6 +551,92 @@ class CrossInteractorStyle(DefaultInteractorStyle):		@@ -522,6 +551,92 @@ class CrossInteractorStyle(DefaultInteractorStyle):
522	index=coord[0])	551	index=coord[0])
523		552
524		553
		554	+class TractsInteractorStyle(CrossInteractorStyle):
		555	+ """
		556	+ Interactor style responsible for tracts visualization.
		557	+ """
		558	+ def __init__(self, viewer):
		559	+ CrossInteractorStyle.__init__(self, viewer)
		560	+
		561	+ # self.state_code = const.SLICE_STATE_TRACTS
		562	+
		563	+ self.viewer = viewer
		564	+ # print("Im fucking brilliant!")
		565	+ self.tracts = None
		566	+
		567	+ # data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
		568	+ # FOD_path = b"sub-P0_dwi_FOD.nii"
		569	+ # full_path = os.path.join(data_dir, FOD_path)
		570	+ # self.tracker = Trekker.tracker(full_path)
		571	+ # self.orientation = viewer.orientation
		572	+ # self.slice_actor = viewer.slice_data.actor
		573	+ # self.slice_data = viewer.slice_data
		574	+
		575	+ # self.picker = vtk.vtkWorldPointPicker()
		576	+
		577	+ self.AddObserver("MouseMoveEvent", self.OnTractsMove)
		578	+ self.AddObserver("LeftButtonPressEvent", self.OnTractsMouseClick)
		579	+ self.AddObserver("LeftButtonReleaseEvent", self.OnTractsReleaseLeftButton)
		580	+
		581	+ # def SetUp(self):
		582	+ # self.viewer._set_cross_visibility(1)
		583	+ # Publisher.sendMessage('Toggle toolbar item',
		584	+ # _id=self.state_code, value=True)
		585	+
		586	+ # def CleanUp(self):
		587	+ # self.viewer._set_cross_visibility(0)
		588	+ # Publisher.sendMessage('Toggle toolbar item',
		589	+ # _id=self.state_code, value=False)
		590	+
		591	+ def OnTractsMove(self, obj, evt):
		592	+ # The user moved the mouse with left button pressed
		593	+ if self.left_pressed:
		594	+ # print("OnTractsMove interactor style")
		595	+ # iren = obj.GetInteractor()
		596	+ self.ChangeTracts(True)
		597	+
		598	+ def OnTractsMouseClick(self, obj, evt):
		599	+ # print("Single mouse click")
		600	+ # self.tracts = dtr.compute_tracts(self.tracker, self.seed, self.left_pressed)
		601	+ self.ChangeTracts(True)
		602	+
		603	+ def OnTractsReleaseLeftButton(self, obj, evt):
		604	+ # time.sleep(3.)
		605	+ self.tracts.stop()
		606	+ # self.ChangeCrossPosition(iren)
		607	+
		608	+ def ChangeTracts(self, pressed):
		609	+ # print("Trying to compute tracts")
		610	+ self.tracts = dtr.compute_tracts(self.tracker, self.seed, self.affine_vtk, pressed)
		611	+ # mouse_x, mouse_y = iren.GetEventPosition()
		612	+ # wx, wy, wz = self.viewer.get_coordinate_cursor(mouse_x, mouse_y, self.picker)
		613	+ # px, py = self.viewer.get_slice_pixel_coord_by_world_pos(wx, wy, wz)
		614	+ # coord = self.viewer.calcultate_scroll_position(px, py)
		615	+ # Publisher.sendMessage('Update cross position', position=(wx, wy, wz))
		616	+ # # self.ScrollSlice(coord)
		617	+ # Publisher.sendMessage('Set ball reference position', position=(wx, wy, wz))
		618	+ # Publisher.sendMessage('Co-registered points', arg=None, position=(wx, wy, wz, 0., 0., 0.))
		619	+
		620	+ # iren.Render()
		621	+
		622	+ # def ScrollSlice(self, coord):
		623	+ # if self.orientation == "AXIAL":
		624	+ # Publisher.sendMessage(('Set scroll position', 'SAGITAL'),
		625	+ # index=coord[0])
		626	+ # Publisher.sendMessage(('Set scroll position', 'CORONAL'),
		627	+ # index=coord[1])
		628	+ # elif self.orientation == "SAGITAL":
		629	+ # Publisher.sendMessage(('Set scroll position', 'AXIAL'),
		630	+ # index=coord[2])
		631	+ # Publisher.sendMessage(('Set scroll position', 'CORONAL'),
		632	+ # index=coord[1])
		633	+ # elif self.orientation == "CORONAL":
		634	+ # Publisher.sendMessage(('Set scroll position', 'AXIAL'),
		635	+ # index=coord[2])
		636	+ # Publisher.sendMessage(('Set scroll position', 'SAGITAL'),
		637	+ # index=coord[0])
		638	+
		639	+
525	class WWWLInteractorStyle(DefaultInteractorStyle):	640	class WWWLInteractorStyle(DefaultInteractorStyle):
526	"""	641	"""
527	Interactor style responsible for Window Level & Width functionality.	642	Interactor style responsible for Window Level & Width functionality.
	@@ -2784,6 +2899,7 @@ class Styles:		@@ -2784,6 +2899,7 @@ class Styles:
2784	const.SLICE_STATE_SELECT_MASK_PARTS: SelectMaskPartsInteractorStyle,	2899	const.SLICE_STATE_SELECT_MASK_PARTS: SelectMaskPartsInteractorStyle,
2785	const.SLICE_STATE_FFILL_SEGMENTATION: FloodFillSegmentInteractorStyle,	2900	const.SLICE_STATE_FFILL_SEGMENTATION: FloodFillSegmentInteractorStyle,
2786	const.SLICE_STATE_CROP_MASK: CropMaskInteractorStyle,	2901	const.SLICE_STATE_CROP_MASK: CropMaskInteractorStyle,
		2902	+ const.SLICE_STATE_TRACTS: TractsInteractorStyle,
2787	}	2903	}
2788		2904
2789	@classmethod	2905	@classmethod
@@ -0,0 +1,471 @@		@@ -0,0 +1,471 @@
	1	+# -- coding: utf-8 --
	2	+
	3	+#--------------------------------------------------------------------------
	4	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
	5	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
	6	+# Homepage: http://www.softwarepublico.gov.br
	7	+# Contact: invesalius@cti.gov.br
	8	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
	9	+#--------------------------------------------------------------------------
	10	+# Este programa e software livre; voce pode redistribui-lo e/ou
	11	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
	12	+# publicada pela Free Software Foundation; de acordo com a versao 2
	13	+# da Licenca.
	14	+#
	15	+# Este programa eh distribuido na expectativa de ser util, mas SEM
	16	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
	17	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
	18	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
	19	+# detalhes.
	20	+#--------------------------------------------------------------------------
	21	+
	22	+# Author: Victor Hugo Souza (victorhos-at-hotmail.com)
	23	+# Contributions: Dogu Baran Aydogan
	24	+# Initial date: 8 May 2020
	25	+
	26	+import threading
	27	+import time
	28	+
	29	+import numpy as np
	30	+import queue
	31	+from pubsub import pub as Publisher
	32	+import vtk
	33	+
	34	+import invesalius.constants as const
	35	+import invesalius.data.imagedata_utils as img_utils
	36	+
	37	+# Nice print for arrays
	38	+# np.set_printoptions(precision=2)
	39	+# np.set_printoptions(suppress=True)
	40	+
	41	+
	42	+def compute_directions(trk_n):
	43	+ """Compute direction of a single tract in each point and return as an RGB color
	44	+
	45	+ :param trk_n: nx3 array of doubles (x, y, z) point coordinates composing the tract
	46	+ :type trk_n: numpy.ndarray
	47	+ :return: nx3 array of int (x, y, z) RGB colors in the range 0 - 255
	48	+ :rtype: numpy.ndarray
	49	+ """
	50	+
	51	+ # trk_d = np.diff(trk_n, axis=0, append=2*trk_n[np.newaxis, -1, :])
	52	+ trk_d = np.diff(trk_n, axis=0, append=trk_n[np.newaxis, -2, :])
	53	+ trk_d[-1, :] *= -1
	54	+ # check that linalg norm makes second norm
	55	+ # https://stackoverflow.com/questions/21030391/how-to-normalize-an-array-in-numpy
	56	+ direction = 255 * np.absolute((trk_d / np.linalg.norm(trk_d, axis=1)[:, None]))
	57	+ return direction.astype(int)
	58	+
	59	+
	60	+def compute_tubes(trk, direction):
	61	+ """Compute and assign colors to a vtkTube for visualization of a single tract
	62	+
	63	+ :param trk: nx3 array of doubles (x, y, z) point coordinates composing the tract
	64	+ :type trk: numpy.ndarray
	65	+ :param direction: nx3 array of int (x, y, z) RGB colors in the range 0 - 255
	66	+ :type direction: numpy.ndarray
	67	+ :return: a vtkTubeFilter instance
	68	+ :rtype: vtkTubeFilter
	69	+ """
	70	+
	71	+ numb_points = trk.shape[0]
	72	+ points = vtk.vtkPoints()
	73	+ lines = vtk.vtkCellArray()
	74	+
	75	+ colors = vtk.vtkUnsignedCharArray()
	76	+ colors.SetNumberOfComponents(3)
	77	+
	78	+ k = 0
	79	+ lines.InsertNextCell(numb_points)
	80	+ for j in range(numb_points):
	81	+ points.InsertNextPoint(trk[j, :])
	82	+ colors.InsertNextTuple(direction[j, :])
	83	+ lines.InsertCellPoint(k)
	84	+ k += 1
	85	+
	86	+ trk_data = vtk.vtkPolyData()
	87	+ trk_data.SetPoints(points)
	88	+ trk_data.SetLines(lines)
	89	+ trk_data.GetPointData().SetScalars(colors)
	90	+
	91	+ # make it a tube
	92	+ trk_tube = vtk.vtkTubeFilter()
	93	+ trk_tube.SetRadius(0.5)
	94	+ trk_tube.SetNumberOfSides(4)
	95	+ trk_tube.SetInputData(trk_data)
	96	+ trk_tube.Update()
	97	+
	98	+ return trk_tube
	99	+
	100	+
	101	+def combine_tracts_root(out_list, root, n_block):
	102	+ """Adds a set of tracts to given position in a given vtkMultiBlockDataSet
	103	+
	104	+ :param out_list: List of vtkTubeFilters representing the tracts
	105	+ :type out_list: list
	106	+ :param root: A collection of tracts as a vtkMultiBlockDataSet
	107	+ :type root: vtkMultiBlockDataSet
	108	+ :param n_block: The location in the given vtkMultiBlockDataSet to insert the new tracts
	109	+ :type n_block: int
	110	+ :return: The updated collection of tracts as a vtkMultiBlockDataSet
	111	+ :rtype: vtkMultiBlockDataSet
	112	+ """
	113	+
	114	+ # create tracts only when at least one was computed
	115	+ # print("Len outlist in root: ", len(out_list))
	116	+ if not out_list.count(None) == len(out_list):
	117	+ for n, tube in enumerate(out_list):
	118	+ root.SetBlock(n_block + n, tube.GetOutput())
	119	+
	120	+ return root
	121	+
	122	+
	123	+def combine_tracts_branch(out_list):
	124	+ """Combines a set of tracts in vtkMultiBlockDataSet
	125	+
	126	+ :param out_list: List of vtkTubeFilters representing the tracts
	127	+ :type out_list: list
	128	+ :return: A collection of tracts as a vtkMultiBlockDataSet
	129	+ :rtype: vtkMultiBlockDataSet
	130	+ """
	131	+
	132	+ branch = vtk.vtkMultiBlockDataSet()
	133	+ # create tracts only when at least one was computed
	134	+ # print("Len outlist in root: ", len(out_list))
	135	+ if not out_list.count(None) == len(out_list):
	136	+ for n, tube in enumerate(out_list):
	137	+ branch.SetBlock(n, tube.GetOutput())
	138	+
	139	+ return branch
	140	+
	141	+
	142	+def tracts_computation(trk_list, root, n_tracts):
	143	+ """Convert the list of all computed tracts given by Trekker run and returns a vtkMultiBlockDataSet
	144	+
	145	+ :param trk_list: List of lists containing the computed tracts and corresponding coordinates
	146	+ :type trk_list: list
	147	+ :param root: A collection of tracts as a vtkMultiBlockDataSet
	148	+ :type root: vtkMultiBlockDataSet
	149	+ :param n_tracts:
	150	+ :type n_tracts: int
	151	+ :return: The updated collection of tracts as a vtkMultiBlockDataSet
	152	+ :rtype: vtkMultiBlockDataSet
	153	+ """
	154	+
	155	+ # Transform tracts to array
	156	+ trk_arr = [np.asarray(trk_n).T if trk_n else None for trk_n in trk_list]
	157	+
	158	+ # Compute the directions
	159	+ trk_dir = [compute_directions(trk_n) for trk_n in trk_arr]
	160	+
	161	+ # Compute the vtk tubes
	162	+ out_list = [compute_tubes(trk_arr_n, trk_dir_n) for trk_arr_n, trk_dir_n in zip(trk_arr, trk_dir)]
	163	+
	164	+ root = combine_tracts_root(out_list, root, n_tracts)
	165	+
	166	+ return root
	167	+
	168	+
	169	+def compute_tracts(trekker, position, affine, affine_vtk, n_tracts):
	170	+ """ Compute tractograms using the Trekker library.
	171	+
	172	+ :param trekker: Trekker library instance
	173	+ :type trekker: Trekker.T
	174	+ :param position: 3 double coordinates (x, y, z) in list or array
	175	+ :type position: list
	176	+ :param affine: 4 x 4 numpy double array
	177	+ :type affine: numpy.ndarray
	178	+ :param affine_vtk: vtkMatrix4x4 isntance with affine transformation matrix
	179	+ :type affine_vtk: vtkMatrix4x4
	180	+ :param n_tracts: number of tracts to compute
	181	+ :type n_tracts: int
	182	+ """
	183	+
	184	+ # during neuronavigation, root needs to be initialized outside the while loop so the new tracts
	185	+ # can be appended to the root block set
	186	+ root = vtk.vtkMultiBlockDataSet()
	187	+ # Juuso's
	188	+ # seed = np.array([[-8.49, -8.39, 2.5]])
	189	+ # Baran M1
	190	+ # seed = np.array([[27.53, -77.37, 46.42]])
	191	+ seed_trk = img_utils.convert_world_to_voxel(position, affine)
	192	+ # print("seed example: {}".format(seed_trk))
	193	+ trekker.seed_coordinates(np.repeat(seed_trk, n_tracts, axis=0))
	194	+ # print("trk list len: ", len(trekker.run()))
	195	+ trk_list = trekker.run()
	196	+ if trk_list:
	197	+ root = tracts_computation(trk_list, root, 0)
	198	+ Publisher.sendMessage('Remove tracts')
	199	+ Publisher.sendMessage('Update tracts', flag=True, root=root, affine_vtk=affine_vtk)
	200	+ else:
	201	+ Publisher.sendMessage('Remove tracts')
	202	+
	203	+
	204	+def tracts_computation_branch(trk_list):
	205	+ """Convert the list of all computed tracts given by Trekker run and returns a vtkMultiBlockDataSet
	206	+
	207	+ :param trk_list: List of lists containing the computed tracts and corresponding coordinates
	208	+ :type trk_list: list
	209	+ :return: The collection of tracts as a vtkMultiBlockDataSet
	210	+ :rtype: vtkMultiBlockDataSet
	211	+ """
	212	+ # Transform tracts to array
	213	+ trk_arr = [np.asarray(trk_n).T if trk_n else None for trk_n in trk_list]
	214	+ # Compute the directions
	215	+ trk_dir = [compute_directions(trk_n) for trk_n in trk_arr]
	216	+ # Compute the vtk tubes
	217	+ tube_list = [compute_tubes(trk_arr_n, trk_dir_n) for trk_arr_n, trk_dir_n in zip(trk_arr, trk_dir)]
	218	+ branch = combine_tracts_branch(tube_list)
	219	+
	220	+ return branch
	221	+
	222	+
	223	+class ComputeTractsThread(threading.Thread):
	224	+
	225	+ def __init__(self, inp, affine_vtk, coord_tracts_queue, tracts_queue, event, sle):
	226	+ """Class (threading) to compute real time tractography data for visualization.
	227	+
	228	+ Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
	229	+ For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one
	230	+ vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as
	231	+ bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.
	232	+ Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.
	233	+
	234	+ Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
	235	+
	236	+ :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
	237	+ :type inp: list
	238	+ :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
	239	+ :type affine_vtk: vtkMatrix4x4
	240	+ :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered
	241	+ :type coord_queue: queue.Queue
	242	+ :param visualization_queue: Queue instance that manage coordinates to be visualized
	243	+ :type visualization_queue: queue.Queue
	244	+ :param event: Threading event to coordinate when tasks as done and allow UI release
	245	+ :type event: threading.Event
	246	+ :param sle: Sleep pause in seconds
	247	+ :type sle: float
	248	+ """
	249	+
	250	+ threading.Thread.__init__(self, name='ComputeTractsThread')
	251	+ self.inp = inp
	252	+ self.affine_vtk = affine_vtk
	253	+ # self.coord_queue = coord_queue
	254	+ self.coord_tracts_queue = coord_tracts_queue
	255	+ self.tracts_queue = tracts_queue
	256	+ # self.visualization_queue = visualization_queue
	257	+ self.event = event
	258	+ self.sle = sle
	259	+
	260	+ def run(self):
	261	+
	262	+ trekker, affine, offset, n_tracts_total, seed_radius, n_threads = self.inp
	263	+ # n_threads = n_tracts_total
	264	+ p_old = np.array([[0., 0., 0.]])
	265	+ n_tracts = 0
	266	+
	267	+ # Compute the tracts
	268	+ # print('ComputeTractsThread: event {}'.format(self.event.is_set()))
	269	+ while not self.event.is_set():
	270	+ try:
	271	+ # print("Computing tracts")
	272	+ # get from the queue the coordinates, coregistration transformation matrix, and flipped matrix
	273	+ m_img_flip = self.coord_tracts_queue.get_nowait()
	274	+ # coord, m_img, m_img_flip = self.coord_queue.get_nowait()
	275	+ # print('ComputeTractsThread: get {}'.format(count))
	276	+
	277	+ # 20200402: in this new refactored version the m_img comes different than the position
	278	+ # the new version m_img is already flixped in y, which means that Y is negative
	279	+ # if only the Y is negative maybe no need for the flip_x funtcion at all in the navigation
	280	+ # but check all coord_queue before why now the m_img comes different than position
	281	+ # 20200403: indeed flip_x is just a -1 multiplication to the Y coordinate, remove function flip_x
	282	+ # m_img_flip = m_img.copy()
	283	+ # m_img_flip[1, -1] = -m_img_flip[1, -1]
	284	+
	285	+ # translate the coordinate along the normal vector of the object/coil
	286	+ coord_offset = m_img_flip[:3, -1] - offset * m_img_flip[:3, 2]
	287	+ # coord_offset = np.array([[27.53, -77.37, 46.42]])
	288	+ dist = abs(np.linalg.norm(p_old - np.asarray(coord_offset)))
	289	+ p_old = coord_offset.copy()
	290	+
	291	+ # print("p_new_shape", coord_offset.shape)
	292	+ # print("m_img_flip_shape", m_img_flip.shape)
	293	+ seed_trk = img_utils.convert_world_to_voxel(coord_offset, affine)
	294	+ # Juuso's
	295	+ # seed_trk = np.array([[-8.49, -8.39, 2.5]])
	296	+ # Baran M1
	297	+ # seed_trk = np.array([[27.53, -77.37, 46.42]])
	298	+ # print("Seed: {}".format(seed))
	299	+
	300	+ # set the seeds for trekker, one seed is repeated n_threads times
	301	+ # trekker has internal multiprocessing approach done in C. Here the number of available threads is give,
	302	+ # but in case a large number of tracts is requested, it will compute all in parallel automatically
	303	+ # for a more fluent navigation, better to compute the maximum number the computer handles
	304	+ trekker.seed_coordinates(np.repeat(seed_trk, n_threads, axis=0))
	305	+
	306	+ # run the trekker, this is the slowest line of code, be careful to just use once!
	307	+ trk_list = trekker.run()
	308	+
	309	+ if trk_list:
	310	+ # print("dist: {}".format(dist))
	311	+ if dist >= seed_radius:
	312	+ # when moving the coil further than the seed_radius restart the bundle computation
	313	+ bundle = vtk.vtkMultiBlockDataSet()
	314	+ n_branches = 0
	315	+ branch = tracts_computation_branch(trk_list)
	316	+ bundle.SetBlock(n_branches, branch)
	317	+ n_branches += 1
	318	+ n_tracts = branch.GetNumberOfBlocks()
	319	+
	320	+ # TODO: maybe keep computing even if reaches the maximum
	321	+ elif dist < seed_radius and n_tracts < n_tracts_total:
	322	+ # compute tracts blocks and add to bungle until reaches the maximum number of tracts
	323	+ branch = tracts_computation_branch(trk_list)
	324	+ if bundle:
	325	+ bundle.SetBlock(n_branches, branch)
	326	+ n_tracts += branch.GetNumberOfBlocks()
	327	+ n_branches += 1
	328	+
	329	+ else:
	330	+ bundle = None
	331	+
	332	+ # rethink if this should be inside the if condition, it may lock the thread if no tracts are found
	333	+ # use no wait to ensure maximum speed and avoid visualizing old tracts in the queue, this might
	334	+ # be more evident in slow computer or for heavier tract computations, it is better slow update
	335	+ # than visualizing old data
	336	+ # self.visualization_queue.put_nowait([coord, m_img, bundle])
	337	+ self.tracts_queue.put_nowait((bundle, self.affine_vtk, coord_offset))
	338	+ # print('ComputeTractsThread: put {}'.format(count))
	339	+
	340	+ self.coord_tracts_queue.task_done()
	341	+ # self.coord_queue.task_done()
	342	+ # print('ComputeTractsThread: done {}'.format(count))
	343	+
	344	+ # sleep required to prevent user interface from being unresponsive
	345	+ time.sleep(self.sle)
	346	+ # if no coordinates pass
	347	+ except queue.Empty:
	348	+ # print("Empty queue in tractography")
	349	+ pass
	350	+ # if queue is full mark as done (may not be needed in this new "nowait" method)
	351	+ except queue.Full:
	352	+ # self.coord_queue.task_done()
	353	+ self.coord_tracts_queue.task_done()
	354	+
	355	+
	356	+class ComputeTractsThreadSingleBlock(threading.Thread):
	357	+
	358	+ def __init__(self, inp, affine_vtk, coord_queue, visualization_queue, event, sle):
	359	+ """Class (threading) to compute real time tractography data for visualization in a single loop.
	360	+
	361	+ Different than ComputeTractsThread because it does not keep adding tracts to the bundle until maximum,
	362	+ is reached. It actually compute all requested tracts at once. (Might be deleted in the future)!
	363	+ Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
	364	+ For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one
	365	+ vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as
	366	+ bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.
	367	+ Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.
	368	+
	369	+ Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
	370	+
	371	+ :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
	372	+ :type inp: list
	373	+ :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
	374	+ :type affine_vtk: vtkMatrix4x4
	375	+ :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered
	376	+ :type coord_queue: queue.Queue
	377	+ :param visualization_queue: Queue instance that manage coordinates to be visualized
	378	+ :type visualization_queue: queue.Queue
	379	+ :param event: Threading event to coordinate when tasks as done and allow UI release
	380	+ :type event: threading.Event
	381	+ :param sle: Sleep pause in seconds
	382	+ :type sle: float
	383	+ """
	384	+
	385	+ threading.Thread.__init__(self, name='ComputeTractsThread')
	386	+ self.inp = inp
	387	+ self.affine_vtk = affine_vtk
	388	+ self.coord_queue = coord_queue
	389	+ self.visualization_queue = visualization_queue
	390	+ self.event = event
	391	+ self.sle = sle
	392	+
	393	+ def run(self):
	394	+
	395	+ trekker, affine, offset, n_tracts_total, seed_radius, n_threads = self.inp
	396	+ # as a single block, computes all the maximum number of tracts at once, not optimal for navigation
	397	+ n_threads = n_tracts_total
	398	+ p_old = np.array([[0., 0., 0.]])
	399	+ root = vtk.vtkMultiBlockDataSet()
	400	+
	401	+ # Compute the tracts
	402	+ # print('ComputeTractsThread: event {}'.format(self.event.is_set()))
	403	+ while not self.event.is_set():
	404	+ try:
	405	+ coord, m_img, m_img_flip = self.coord_queue.get_nowait()
	406	+
	407	+ # translate the coordinate along the normal vector of the object/coil
	408	+ coord_offset = m_img_flip[:3, -1] - offset * m_img_flip[:3, 2]
	409	+ # coord_offset = np.array([[27.53, -77.37, 46.42]])
	410	+ dist = abs(np.linalg.norm(p_old - np.asarray(coord_offset)))
	411	+ p_old = coord_offset.copy()
	412	+ seed_trk = img_utils.convert_world_to_voxel(coord_offset, affine)
	413	+ # Juuso's
	414	+ # seed_trk = np.array([[-8.49, -8.39, 2.5]])
	415	+ # Baran M1
	416	+ # seed_trk = np.array([[27.53, -77.37, 46.42]])
	417	+ # print("Seed: {}".format(seed))
	418	+
	419	+ # set the seeds for trekker, one seed is repeated n_threads times
	420	+ # trekker has internal multiprocessing approach done in C. Here the number of available threads is give,
	421	+ # but in case a large number of tracts is requested, it will compute all in parallel automatically
	422	+ # for a more fluent navigation, better to compute the maximum number the computer handles
	423	+ trekker.seed_coordinates(np.repeat(seed_trk, n_threads, axis=0))
	424	+ # run the trekker, this is the slowest line of code, be careful to just use once!
	425	+ trk_list = trekker.run()
	426	+
	427	+ if trk_list:
	428	+ # if the seed is outside the defined radius, restart the bundle computation
	429	+ if dist >= seed_radius:
	430	+ root = tracts_computation(trk_list, root, 0)
	431	+ self.visualization_queue.put_nowait((coord, m_img, root))
	432	+
	433	+ self.coord_queue.task_done()
	434	+ time.sleep(self.sle)
	435	+ except queue.Empty:
	436	+ pass
	437	+ except queue.Full:
	438	+ self.coord_queue.task_done()
	439	+
	440	+
	441	+def set_trekker_parameters(trekker, params):
	442	+ """Set all user-defined parameters for tractography computation using the Trekker library
	443	+
	444	+ :param trekker: Trekker instance
	445	+ :type trekker: Trekker.T
	446	+ :param params: Dictionary containing the parameters values to set in Trekker. Initial values are in constants.py
	447	+ :type params: dict
	448	+ :return: List containing the Trekker instance and number of threads for parallel processing in the computer
	449	+ :rtype: list
	450	+ """
	451	+ trekker.seed_maxTrials(params['seed_max'])
	452	+ # trekker.stepSize(params['step_size'])
	453	+ trekker.minFODamp(params['min_fod'])
	454	+ # trekker.probeQuality(params['probe_quality'])
	455	+ # trekker.maxEstInterval(params['max_interval'])
	456	+ # trekker.minRadiusOfCurvature(params['min_radius_curv'])
	457	+ # trekker.probeLength(params['probe_length'])
	458	+ trekker.writeInterval(params['write_interval'])
	459	+ trekker.maxLength(params['max_lenth'])
	460	+ trekker.minLength(params['min_lenth'])
	461	+ trekker.maxSamplingPerStep(params['max_sampling_step'])
	462	+
	463	+ # check number if number of cores is valid in configuration file,
	464	+ # otherwise use the maximum number of threads which is usually 2*N_CPUS
	465	+ n_threads = 2 * const.N_CPU
	466	+ if isinstance((params['numb_threads']), int) and params['numb_threads'] <= 2*const.N_CPU:
	467	+ n_threads = params['numb_threads']
	468	+
	469	+ trekker.numberOfThreads(n_threads)
	470	+ # print("Trekker config updated: n_threads, {}; seed_max, {}".format(n_threads, params['seed_max']))
	471	+ return trekker, n_threads
	@@ -39,7 +39,7 @@ class Trigger(threading.Thread):		@@ -39,7 +39,7 @@ class Trigger(threading.Thread):
39	try:	39	try:
40	import serial	40	import serial
41		41
42	- self.trigger_init = serial.Serial('COM1', baudrate=9600, timeout=0)	42	+ self.trigger_init = serial.Serial('COM5', baudrate=115200, timeout=0)
43	self.COM = True	43	self.COM = True
44		44
45	except:	45	except:
	@@ -82,3 +82,91 @@ class Trigger(threading.Thread):		@@ -82,3 +82,91 @@ class Trigger(threading.Thread):
82	if self.trigger_init:	82	if self.trigger_init:
83	self.trigger_init.close()	83	self.trigger_init.close()
84	return	84	return
		85	+
		86	+
		87	+class TriggerNew(threading.Thread):
		88	+
		89	+ def __init__(self, trigger_queue, event, sle):
		90	+ """Class (threading) to compute real time tractography data for visualization in a single loop.
		91	+
		92	+ Different than ComputeTractsThread because it does not keep adding tracts to the bundle until maximum,
		93	+ is reached. It actually compute all requested tracts at once. (Might be deleted in the future)!
		94	+ Tracts are computed using the Trekker library by Baran Aydogan (https://dmritrekker.github.io/)
		95	+ For VTK visualization, each tract (fiber) is a constructed as a tube and many tubes combined in one
		96	+ vtkMultiBlockDataSet named as a branch. Several branches are combined in another vtkMultiBlockDataSet named as
		97	+ bundle, to obtain fast computation and visualization. The bundle dataset is mapped to a single vtkActor.
		98	+ Mapper and Actor are computer in the data/viewer_volume.py module for easier handling in the invesalius 3D scene.
		99	+
		100	+ Sleep function in run method is used to avoid blocking GUI and more fluent, real-time navigation
		101	+
		102	+ :param inp: List of inputs: trekker instance, affine numpy array, seed_offset, seed_radius, n_threads
		103	+ :type inp: list
		104	+ :param affine_vtk: Affine matrix in vtkMatrix4x4 instance to update objects position in 3D scene
		105	+ :type affine_vtk: vtkMatrix4x4
		106	+ :param coord_queue: Queue instance that manage coordinates read from tracking device and coregistered
		107	+ :type coord_queue: queue.Queue
		108	+ :param visualization_queue: Queue instance that manage coordinates to be visualized
		109	+ :type visualization_queue: queue.Queue
		110	+ :param event: Threading event to coordinate when tasks as done and allow UI release
		111	+ :type event: threading.Event
		112	+ :param sle: Sleep pause in seconds
		113	+ :type sle: float
		114	+ """
		115	+
		116	+ threading.Thread.__init__(self, name='Trigger')
		117	+
		118	+ self.trigger_init = None
		119	+ self.stylusplh = False
		120	+ # self.COM = False
		121	+ self.__bind_events()
		122	+ try:
		123	+ import serial
		124	+
		125	+ self.trigger_init = serial.Serial('COM5', baudrate=115200, timeout=0)
		126	+ # self.COM = True
		127	+
		128	+ except:
		129	+ #wx.MessageBox(_('Connection with port COM1 failed'), _('Communication error'), wx.OK \| wx.ICON_ERROR)
		130	+ print("Trigger init error: Connection with port COM failed")
		131	+ # self.COM = False
		132	+ pass
		133	+
		134	+ # self.coord_queue = coord_queue
		135	+ self.trigger_queue = trigger_queue
		136	+ self.event = event
		137	+ self.sle = sle
		138	+
		139	+ def run(self):
		140	+
		141	+ while not self.event.is_set():
		142	+ trigger_on = False
		143	+ try:
		144	+ self.trigger_init.write(b'0')
		145	+ sleep(0.3)
		146	+ lines = self.trigger_init.readlines()
		147	+ # Following lines can simulate a trigger in 3 sec repetitions
		148	+ # sleep(3)
		149	+ # lines = True
		150	+ if lines:
		151	+ trigger_on = True
		152	+ # wx.CallAfter(Publisher.sendMessage, 'Create marker')
		153	+
		154	+ if self.stylusplh:
		155	+ trigger_on = True
		156	+ # wx.CallAfter(Publisher.sendMessage, 'Create marker')
		157	+ self.stylusplh = False
		158	+
		159	+ self.trigger_queue.put_nowait(trigger_on)
		160	+ sleep(self.sle)
		161	+
		162	+ except:
		163	+ print("Trigger not read, error")
		164	+ pass
		165	+
		166	+ # except queue.Empty:
		167	+ # pass
		168	+ # except queue.Full:
		169	+ # self.coord_queue.task_done()
		170	+ else:
		171	+ if self.trigger_init:
		172	+ self.trigger_init.close()
	@@ -287,3 +287,21 @@ class TextZero(object):		@@ -287,3 +287,21 @@ class TextZero(object):
287	# font.SetWeight(wx.FONTWEIGHT_BOLD)	287	# font.SetWeight(wx.FONTWEIGHT_BOLD)
288	font.SetSymbolicSize(self.symbolic_syze)	288	font.SetSymbolicSize(self.symbolic_syze)
289	canvas.draw_text(self.text, (x, y), font=font)	289	canvas.draw_text(self.text, (x, y), font=font)
		290	+
		291	+
		292	+def numpy_to_vtkMatrix4x4(affine):
		293	+ """
		294	+ Convert a numpy 4x4 array to a vtk 4x4 matrix
		295	+ :param affine: 4x4 array
		296	+ :return: vtkMatrix4x4 object representing the affine
		297	+ """
		298	+ # test for type and shape of affine matrix
		299	+ # assert isinstance(affine, np.ndarray)
		300	+ assert affine.shape == (4, 4)
		301	+
		302	+ affine_vtk = vtk.vtkMatrix4x4()
		303	+ for row in range(0, 4):
		304	+ for col in range(0, 4):
		305	+ affine_vtk.SetElement(row, col, affine[row, col])
		306	+
		307	+ return affine_vtk
	@@ -387,6 +387,15 @@ def ShowImportOtherFilesDialog(id_type):		@@ -387,6 +387,15 @@ def ShowImportOtherFilesDialog(id_type):
387	if id_type == const.ID_NIFTI_IMPORT:	387	if id_type == const.ID_NIFTI_IMPORT:
388	dlg.SetMessage(_("Import NIFTi 1 file"))	388	dlg.SetMessage(_("Import NIFTi 1 file"))
389	dlg.SetWildcard(WILDCARD_NIFTI)	389	dlg.SetWildcard(WILDCARD_NIFTI)
		390	+ elif id_type == const.ID_TREKKER_MASK:
		391	+ dlg.SetMessage(_("Import Trekker mask"))
		392	+ dlg.SetWildcard(WILDCARD_NIFTI)
		393	+ elif id_type == const.ID_TREKKER_IMG:
		394	+ dlg.SetMessage(_("Import Trekker anatomical image"))
		395	+ dlg.SetWildcard(WILDCARD_NIFTI)
		396	+ elif id_type == const.ID_TREKKER_FOD:
		397	+ dlg.SetMessage(_("Import Trekker FOD"))
		398	+ dlg.SetWildcard(WILDCARD_NIFTI)
390	elif id_type == const.ID_PARREC_IMPORT:	399	elif id_type == const.ID_PARREC_IMPORT:
391	dlg.SetMessage(_("Import PAR/REC file"))	400	dlg.SetMessage(_("Import PAR/REC file"))
392	dlg.SetWildcard(WILDCARD_PARREC)	401	dlg.SetWildcard(WILDCARD_PARREC)
	@@ -508,79 +517,11 @@ def ShowSaveAsProjectDialog(default_filename=None):		@@ -508,79 +517,11 @@ def ShowSaveAsProjectDialog(default_filename=None):
508	return filename, wildcard == INV_COMPRESSED	517	return filename, wildcard == INV_COMPRESSED
509		518
510		519
511	-# Dialog for neuronavigation markers
512	-def ShowSaveMarkersDialog(default_filename=None):
513	- current_dir = os.path.abspath(".")
514	- dlg = wx.FileDialog(None,
515	- _("Save markers as..."), # title
516	- "", # last used directory
517	- default_filename,
518	- _("Markers files (.mks)\|.mks"),
519	- wx.FD_SAVE \| wx.FD_OVERWRITE_PROMPT)
520	- # dlg.SetFilterIndex(0) # default is VTI
521	-
522	- filename = None
523	- try:
524	- if dlg.ShowModal() == wx.ID_OK:
525	- filename = dlg.GetPath()
526	- ok = 1
527	- else:
528	- ok = 0
529	- except(wx._core.PyAssertionError): # TODO: fix win64
530	- filename = dlg.GetPath()
531	- ok = 1
532	-
533	- if (ok):
534	- extension = "mks"
535	- if sys.platform != 'win32':
536	- if filename.split(".")[-1] != extension:
537	- filename = filename + "." + extension
538	-
539	- os.chdir(current_dir)
540	- return filename
541	-
542	-def ShowSaveCoordsDialog(default_filename=None):
543	- current_dir = os.path.abspath(".")
544	- dlg = wx.FileDialog(None,
545	- _("Save coords as..."), # title
546	- "", # last used directory
547	- default_filename,
548	- _("Coordinates files (.csv)\|.csv"),
549	- wx.FD_SAVE \| wx.FD_OVERWRITE_PROMPT)
550	- # dlg.SetFilterIndex(0) # default is VTI
551	-
552	- filename = None
553	- try:
554	- if dlg.ShowModal() == wx.ID_OK:
555	- filename = dlg.GetPath()
556	- ok = 1
557	- else:
558	- ok = 0
559	- except(wx._core.PyAssertionError): # TODO: fix win64
560	- filename = dlg.GetPath()
561	- ok = 1	520	+def ShowLoadSaveDialog(message=_(u"Load File"), current_dir=os.path.abspath("."), style=wx.FD_OPEN \| wx.FD_CHANGE_DIR,
		521	+ wildcard=_("Registration files (.obr)\|.obr"), default_filename="", save_ext=None):
562		522
563	- if (ok):
564	- extension = "csv"
565	- if sys.platform != 'win32':
566	- if filename.split(".")[-1] != extension:
567	- filename = filename + "." + extension
568	-
569	- os.chdir(current_dir)
570	- return filename
571	-
572	-
573	-def ShowLoadMarkersDialog():
574	- current_dir = os.path.abspath(".")
575	-
576	- dlg = wx.FileDialog(None, message=_("Load markers"),
577	- defaultDir="",
578	- defaultFile="",
579	- wildcard=_("Markers files (.mks)\|.mks"),
580	- style=wx.FD_OPEN\|wx.FD_CHANGE_DIR)
581	-
582	- # inv3 filter is default
583	- dlg.SetFilterIndex(0)	523	+ dlg = wx.FileDialog(None, message=message, defaultDir="", defaultFile=default_filename,
		524	+ wildcard=wildcard, style=style)
584		525
585	# Show the dialog and retrieve the user response. If it is the OK response,	526	# Show the dialog and retrieve the user response. If it is the OK response,
586	# process the data.	527	# process the data.
	@@ -589,73 +530,25 @@ def ShowLoadMarkersDialog():		@@ -589,73 +530,25 @@ def ShowLoadMarkersDialog():
589	if dlg.ShowModal() == wx.ID_OK:	530	if dlg.ShowModal() == wx.ID_OK:
590	# This returns a Python list of files that were selected.	531	# This returns a Python list of files that were selected.
591	filepath = dlg.GetPath()	532	filepath = dlg.GetPath()
		533	+ ok_press = 1
		534	+ else:
		535	+ ok_press = 0
592	except(wx._core.PyAssertionError): # FIX: win64	536	except(wx._core.PyAssertionError): # FIX: win64
593	filepath = dlg.GetPath()	537	filepath = dlg.GetPath()
		538	+ ok_press = 1
594		539
595	- # Destroy the dialog. Don't do this until you are done with it!
596	- # BAD things can happen otherwise!
597	- dlg.Destroy()
598	- os.chdir(current_dir)
599	- return filepath
600	-
601	-
602	-def ShowSaveRegistrationDialog(default_filename=None):
603	- current_dir = os.path.abspath(".")
604	- dlg = wx.FileDialog(None,
605	- _("Save object registration as..."), # title
606	- "", # last used directory
607	- default_filename,
608	- _("Registration files (.obr)\|.obr"),
609	- wx.FD_SAVE \| wx.FD_OVERWRITE_PROMPT)
610	- # dlg.SetFilterIndex(0) # default is VTI
611	-
612	- filename = None
613	- try:
614	- if dlg.ShowModal() == wx.ID_OK:
615	- filename = dlg.GetPath()
616	- ok = 1
617	- else:
618	- ok = 0
619	- except(wx._core.PyAssertionError): # TODO: fix win64
620	- filename = dlg.GetPath()
621	- ok = 1
622	-
623	- if (ok):
624	- extension = "obr"	540	+ # fix the extension if set different than expected
		541	+ if save_ext and ok_press:
		542	+ extension = save_ext
625	if sys.platform != 'win32':	543	if sys.platform != 'win32':
626	- if filename.split(".")[-1] != extension:
627	- filename = filename + "." + extension
628	-
629	- os.chdir(current_dir)
630	- return filename
631	-
632	-
633	-def ShowLoadRegistrationDialog():
634	- current_dir = os.path.abspath(".")
635	-
636	- dlg = wx.FileDialog(None, message=_("Load object registration"),
637	- defaultDir="",
638	- defaultFile="",
639	- wildcard=_("Registration files (.obr)\|.obr"),
640	- style=wx.FD_OPEN\|wx.FD_CHANGE_DIR)
641	-
642	- # inv3 filter is default
643	- dlg.SetFilterIndex(0)
644	-
645	- # Show the dialog and retrieve the user response. If it is the OK response,
646	- # process the data.
647	- filepath = None
648	- try:
649	- if dlg.ShowModal() == wx.ID_OK:
650	- # This returns a Python list of files that were selected.
651	- filepath = dlg.GetPath()
652	- except(wx._core.PyAssertionError): # FIX: win64
653	- filepath = dlg.GetPath()	544	+ if filepath.split(".")[-1] != extension:
		545	+ filepath = filepath + "." + extension
654		546
655	# Destroy the dialog. Don't do this until you are done with it!	547	# Destroy the dialog. Don't do this until you are done with it!
656	# BAD things can happen otherwise!	548	# BAD things can happen otherwise!
657	dlg.Destroy()	549	dlg.Destroy()
658	os.chdir(current_dir)	550	os.chdir(current_dir)
		551	+
659	return filepath	552	return filepath
660		553
661		554
	@@ -920,31 +813,9 @@ def SurfaceSelectionRequiredForDuplication():		@@ -920,31 +813,9 @@ def SurfaceSelectionRequiredForDuplication():
920		813
921		814
922	# Dialogs for neuronavigation mode	815	# Dialogs for neuronavigation mode
923	-def InvalidFiducials():
924	- msg = _("Fiducials are invalid. Select all coordinates.")
925	- if sys.platform == 'darwin':
926	- dlg = wx.MessageDialog(None, "", msg,
927	- wx.ICON_INFORMATION \| wx.OK)
928	- else:
929	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
930	- wx.ICON_INFORMATION \| wx.OK)
931	- dlg.ShowModal()
932	- dlg.Destroy()
933	-	816	+# ----------------------------------
934		817
935	-def InvalidObjectRegistration():
936	- msg = _("Perform coil registration before navigation.")
937	- if sys.platform == 'darwin':
938	- dlg = wx.MessageDialog(None, "", msg,
939	- wx.ICON_INFORMATION \| wx.OK)
940	- else:
941	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
942	- wx.ICON_INFORMATION \| wx.OK)
943	- dlg.ShowModal()
944	- dlg.Destroy()
945	-
946	-
947	-def NavigationTrackerWarning(trck_id, lib_mode):	818	+def ShowNavigationTrackerWarning(trck_id, lib_mode):
948	"""	819	"""
949	Spatial Tracker connection error	820	Spatial Tracker connection error
950	"""	821	"""
	@@ -976,85 +847,46 @@ def NavigationTrackerWarning(trck_id, lib_mode):		@@ -976,85 +847,46 @@ def NavigationTrackerWarning(trck_id, lib_mode):
976	dlg.Destroy()	847	dlg.Destroy()
977		848
978		849
979	-def InvalidMarkersFile():
980	- msg = _("The TXT file is invalid.")
981	- if sys.platform == 'darwin':
982	- dlg = wx.MessageDialog(None, "", msg,
983	- wx.ICON_INFORMATION \| wx.OK)
984	- else:
985	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
986	- wx.ICON_INFORMATION \| wx.OK)
987	- dlg.ShowModal()
988	- dlg.Destroy()
989	-
990	-
991	-def NoMarkerSelected():
992	- msg = _("No data selected")	850	+def ShowEnterMarkerID(default):
		851	+ msg = _("Edit marker ID")
993	if sys.platform == 'darwin':	852	if sys.platform == 'darwin':
994	- dlg = wx.MessageDialog(None, "", msg,
995	- wx.ICON_INFORMATION \| wx.OK)	853	+ dlg = wx.TextEntryDialog(None, "", msg, defaultValue=default)
996	else:	854	else:
997	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
998	- wx.ICON_INFORMATION \| wx.OK)	855	+ dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", value=default)
999	dlg.ShowModal()	856	dlg.ShowModal()
		857	+ result = dlg.GetValue()
1000	dlg.Destroy()	858	dlg.Destroy()
		859	+ return result
1001		860
1002		861
1003	-def DeleteAllMarkers():
1004	- msg = _("Do you really want to delete all markers?")	862	+def ShowConfirmationDialog(msg=_('Proceed?')):
		863	+ # msg = _("Do you want to delete all markers?")
1005	if sys.platform == 'darwin':	864	if sys.platform == 'darwin':
1006	dlg = wx.MessageDialog(None, "", msg,	865	dlg = wx.MessageDialog(None, "", msg,
1007	wx.OK \| wx.CANCEL \| wx.ICON_QUESTION)	866	wx.OK \| wx.CANCEL \| wx.ICON_QUESTION)
1008	else:	867	else:
1009	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",	868	+ dlg = wx.MessageDialog(None, msg, "InVesalius 3",
1010	wx.OK \| wx.CANCEL \| wx.ICON_QUESTION)	869	wx.OK \| wx.CANCEL \| wx.ICON_QUESTION)
1011	result = dlg.ShowModal()	870	result = dlg.ShowModal()
1012	dlg.Destroy()	871	dlg.Destroy()
1013	return result	872	return result
1014		873
1015	-def DeleteTarget():
1016	- msg = _("Target deleted")
1017	- if sys.platform == 'darwin':
1018	- dlg = wx.MessageDialog(None, "", msg,
1019	- wx.ICON_INFORMATION \| wx.OK)
1020	- else:
1021	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
1022	- wx.ICON_INFORMATION \| wx.OK)
1023	- dlg.ShowModal()
1024	- dlg.Destroy()
1025		874
1026	-def NewTarget():
1027	- msg = _("New target selected")
1028	- if sys.platform == 'darwin':
1029	- dlg = wx.MessageDialog(None, "", msg,
1030	- wx.ICON_INFORMATION \| wx.OK)
1031	- else:
1032	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
1033	- wx.ICON_INFORMATION \| wx.OK)
1034	- dlg.ShowModal()
1035	- dlg.Destroy()	875	+def ShowColorDialog(color_current):
		876	+ cdata = wx.ColourData()
		877	+ cdata.SetColour(wx.Colour(color_current))
		878	+ dlg = wx.ColourDialog(None, data=cdata)
		879	+ dlg.GetColourData().SetChooseFull(True)
1036		880
1037	-def InvalidTargetID():
1038	- msg = _("Sorry, you cannot use 'TARGET' ID")
1039	- if sys.platform == 'darwin':
1040	- dlg = wx.MessageDialog(None, "", msg,
1041	- wx.ICON_INFORMATION \| wx.OK)	881	+ if dlg.ShowModal() == wx.ID_OK:
		882	+ color_new = dlg.GetColourData().GetColour().Get(includeAlpha=False)
1042	else:	883	else:
1043	- dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
1044	- wx.ICON_INFORMATION \| wx.OK)
1045	- dlg.ShowModal()
1046	- dlg.Destroy()	884	+ color_new = None
1047		885
1048	-def EnterMarkerID(default):
1049	- msg = _("Edit marker ID")
1050	- if sys.platform == 'darwin':
1051	- dlg = wx.TextEntryDialog(None, "", msg, defaultValue=default)
1052	- else:
1053	- dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", value=default)
1054	- dlg.ShowModal()
1055	- result = dlg.GetValue()
1056	dlg.Destroy()	886	dlg.Destroy()
1057	- return result	887	+ return color_new
		888	+
		889	+# ----------------------------------
1058		890
1059		891
1060	class NewMask(wx.Dialog):	892	class NewMask(wx.Dialog):
	@@ -3569,7 +3401,10 @@ class ObjectCalibrationDialog(wx.Dialog):		@@ -3569,7 +3401,10 @@ class ObjectCalibrationDialog(wx.Dialog):
3569	else:	3401	else:
3570	coord = coord_raw[0, :]	3402	coord = coord_raw[0, :]
3571	else:	3403	else:
3572	- NavigationTrackerWarning(0, 'choose')	3404	+ ShowNavigationTrackerWarning(0, 'choose')
		3405	+
		3406	+ if btn_id == 3:
		3407	+ coord = np.zeros([6,])
3573		3408
3574	# Update text controls with tracker coordinates	3409	# Update text controls with tracker coordinates
3575	if coord is not None or np.sum(coord) != 0.0:	3410	if coord is not None or np.sum(coord) != 0.0:
	@@ -3582,7 +3417,7 @@ class ObjectCalibrationDialog(wx.Dialog):		@@ -3582,7 +3417,7 @@ class ObjectCalibrationDialog(wx.Dialog):
3582	self.ball_actors[btn_id].GetProperty().SetColor(0.0, 1.0, 0.0)	3417	self.ball_actors[btn_id].GetProperty().SetColor(0.0, 1.0, 0.0)
3583	self.Refresh()	3418	self.Refresh()
3584	else:	3419	else:
3585	- NavigationTrackerWarning(0, 'choose')	3420	+ ShowNavigationTrackerWarning(0, 'choose')
3586		3421
3587	def OnChoiceRefMode(self, evt):	3422	def OnChoiceRefMode(self, evt):
3588	# When ref mode is changed the tracker coordinates are set to nan	3423	# When ref mode is changed the tracker coordinates are set to nan