Neuronavigation module update and improvement (#65)

Neuronavigation module updatings and improvements * Revert "Revert "ENH: Update neuronavigator modules"" This reverts commit 2ecc37998e18c762b82413314fcf75d1491ca1be. * ENH: Update corregistration comments. * ENH: Restructuring InVesalius Navigator spatial tracker communication. * ENH: Restructuring the spatial tracker communication. * ENH: Updating navigation tools. * Code refactoring for navigator development - Delete previous git mistakes while tracking files - Code fix to run invesalius navigator and start code refactoring * Update navigator GUI - Improvement on manipulation of markers creation and edition - Buttons and panels size adjustment * Improvement on trackers connection - MicronTracker supports dynamic reference * VTK6 adjustments - SetInputData -Using SetInputData instead SetInput * Update Create Markers and fix sphere creation - Improvement on manipulation of markers creation and edition - Using SetInputConnection(GetOutputPort()) instead SetInputData(GetOutput()) * GUI update and creation of fiducial markers * Fix Fiducial Markers * Update - Load Fiducial points using "Load Markers" * Fix Trackers (PLH) and Navigation * Update ComboBox and trackers connection * Full support for Analyze, NIfTI and PAR/REC images - Support for Analyze, NIfTI, Compressed NIfTI and PAR/REC images - Support for Analyze limited due to lack of orientation info - Image orientation standardized to RAS+ * ComboBox Update - Set "Select tracker" when the tracker is not connected * Fixed usp-navegador version - Changed GetValue to GetValue() - Changed SetInputData to SetInput - Changed SetInputConnection to SetInputData * Manually merged rmatsuda master_merge branch to usp-navegador - Improved navigation GUI - Improved navigation control of spatial trackers - Added management of makers creation - Added dialogs for better neuronavigation control * Added TMS trigger and enhanced tracker device control - Serial communication to detect TMS trigger - Added MicronTracker calibration and marker files - Enhanced tracker manipulation * Navigation cleaning and improvements in viewer volume - Cleaned unecessary navigation functions - Optimized volume camera and ball reference positions - Enhanced markers manipulation - Removed blank lines * Improved task_navigator GUI - Better code using GridBagSizer - Removed useless code * Improvement in coordinates handling for neuronavigation * Significant refactor of navigation pipeline - Improvement in navigation panel controls - Refactoring of volume and slice updates - Improvement in communication with tracking devices - Refactoring of entire navigation pipeline * Improved colour and size of navigation markers * Added trigger and volume camera controls - Reformulated markers creation - Created control of volume camera - Control for external trigger marker creation * Minor code adjustments * GUI improvements * Minor code optimization - Improved load markers

Neuronavigation module update and improvement (#65)
Neuronavigation module updatings and improvements * Revert "Revert "ENH: Update neuronavigator modules"" This reverts commit 2ecc37998e18c762b82413314fcf75d1491ca1be. * ENH: Update corregistration comments. * ENH: Restructuring InVesalius Navigator spatial tracker communication. * ENH: Restructuring the spatial tracker communication. * ENH: Updating navigation tools. * Code refactoring for navigator development - Delete previous git mistakes while tracking files - Code fix to run invesalius navigator and start code refactoring * Update navigator GUI - Improvement on manipulation of markers creation and edition - Buttons and panels size adjustment * Improvement on trackers connection - MicronTracker supports dynamic reference * VTK6 adjustments - SetInputData -Using SetInputData instead SetInput * Update Create Markers and fix sphere creation - Improvement on manipulation of markers creation and edition - Using SetInputConnection(GetOutputPort()) instead SetInputData(GetOutput()) * GUI update and creation of fiducial markers * Fix Fiducial Markers * Update - Load Fiducial points using "Load Markers" * Fix Trackers (PLH) and Navigation * Update ComboBox and trackers connection * Full support for Analyze, NIfTI and PAR/REC images - Support for Analyze, NIfTI, Compressed NIfTI and PAR/REC images - Support for Analyze limited due to lack of orientation info - Image orientation standardized to RAS+ * ComboBox Update - Set "Select tracker" when the tracker is not connected * Fixed usp-navegador version - Changed GetValue to GetValue() - Changed SetInputData to SetInput - Changed SetInputConnection to SetInputData * Manually merged rmatsuda master_merge branch to usp-navegador - Improved navigation GUI - Improved navigation control of spatial trackers - Added management of makers creation - Added dialogs for better neuronavigation control * Added TMS trigger and enhanced tracker device control - Serial communication to detect TMS trigger - Added MicronTracker calibration and marker files - Enhanced tracker manipulation * Navigation cleaning and improvements in viewer volume - Cleaned unecessary navigation functions - Optimized volume camera and ball reference positions - Enhanced markers manipulation - Removed blank lines * Improved task_navigator GUI - Better code using GridBagSizer - Removed useless code * Improvement in coordinates handling for neuronavigation * Significant refactor of navigation pipeline - Improvement in navigation panel controls - Refactoring of volume and slice updates - Improvement in communication with tracking devices - Refactoring of entire navigation pipeline * Improved colour and size of navigation markers * Added trigger and volume camera controls - Reformulated markers creation - Created control of volume camera - Control for external trigger marker creation * Minor code adjustments * GUI improvements * Minor code optimization - Improved load markers
Victor Hugo Souza · Thiago Franco de Moraes
1 parent 6a586fc7
Showing 39 changed files with 2773 additions and 825 deletions Show diff stats
.gitignore
invesalius/constants.py
invesalius/control.py
invesalius/data/bases.py
invesalius/data/co_registration.py
invesalius/data/coordinates.py
invesalius/data/coregistration.py
invesalius/data/imagedata_utils.py
invesalius/data/slice_.py
invesalius/data/styles.py
invesalius/data/trackers.py
invesalius/data/trigger.py
invesalius/data/viewer_slice.py
invesalius/data/viewer_volume.py
invesalius/gui/default_tasks.py
invesalius/gui/dialogs.py
invesalius/gui/frame.py
invesalius/gui/task_importer.py
invesalius/gui/task_navigator.py
invesalius/reader/analyze_reader.py
@@ -8,6 +8,7 @@ invesalius/*.swo
 invesalius/*.swp
 invesalius/data/*.log
 invesalius/data/*.pyc
+invesalius/data/*.pyd
 invesalius/gui/*.log
 invesalius/gui/*.pyc
 invesalius/gui/widgets/*.log
@@ -21,6 +22,7 @@ invesalius/reader/*.pyc
 tags
 *.c
+.idea
 build
 *.patch
 *.tgz
@@ -29,4 +31,4 @@ build
 *.cpp
 *.diff
 -*.directory
+*.directory
 \ No newline at end of file
@@ -487,8 +487,9 @@ VTK_WARNING = 0
 [ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,
 ID_PROJECT_CLOSE, ID_PROJECT_INFO, ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET,
-ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_ANALYZE_IMPORT, ID_PREFERENCES,
-ID_DICOM_NETWORK, ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED] = [wx.NewId() for number in range(15)]
+ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK,
+ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED, ID_ANALYZE_IMPORT, ID_NIFTI_IMPORT,
+ID_PARREC_IMPORT] = [wx.NewId() for number in range(17)]
 ID_EXIT = wx.ID_EXIT
 ID_ABOUT = wx.ID_ABOUT
@@ -637,3 +638,53 @@ BOOLEAN_UNION = 1
 BOOLEAN_DIFF = 2
 BOOLEAN_AND = 3
 BOOLEAN_XOR = 4
+
+#------------ Navigation defaults -------------------
+
+SELECT = 0
+MTC = 1
+FASTRAK = 2
+ISOTRAKII = 3
+PATRIOT = 4
+DEBUGTRACK = 5
+DISCTRACK = 6
+DEFAULT_TRACKER = SELECT
+
+TRACKER = [_("Select tracker:"), _("Claron MicronTracker"),
+           _("Polhemus FASTRAK"), _("Polhemus ISOTRAK II"),
+           _("Polhemus PATRIOT"), _("Debug tracker"),
+           _("Disconnect tracker")]
+
+STATIC_REF = 0
+DYNAMIC_REF = 1
+DEFAULT_REF_MODE = DYNAMIC_REF
+REF_MODE = [_("Static ref."), _("Dynamic ref.")]
+
+IR1 = wx.NewId()
+IR2 = wx.NewId()
+IR3 = wx.NewId()
+TR1 = wx.NewId()
+TR2 = wx.NewId()
+TR3 = wx.NewId()
+SET = wx.NewId()
+
+BTNS_IMG = {IR1: {0: _('LEI')},
+            IR2: {1: _('REI')},
+            IR3: {2: _('NAI')}}
+
+TIPS_IMG = [wx.ToolTip(_("Select left ear in image")),
+            wx.ToolTip(_("Select right ear in image")),
+            wx.ToolTip(_("Select nasion in image"))]
+
+BTNS_TRK = {TR1: {3: _('LET')},
+            TR2: {4: _('RET')},
+            TR3: {5: _('NAT')},
+            SET: {6: _('SET')}}
+
+TIPS_TRK = [wx.ToolTip(_("Select left ear with spatial tracker")),
+            wx.ToolTip(_("Select right ear with spatial tracker")),
+            wx.ToolTip(_("Select nasion with spatial tracker")),
+            wx.ToolTip(_("Show set coordinates in image"))]
+
+CAL_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'mtc_files', 'CalibrationFiles'))
+MAR_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'mtc_files', 'Markers'))
@@ -16,11 +16,9 @@
 #    PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
 #    detalhes.
 #--------------------------------------------------------------------------
-import math
 import os
 import plistlib
 import wx
-import numpy
 from wx.lib.pubsub import pub as Publisher
 import invesalius.constants as const
@@ -32,10 +30,10 @@ import invesalius.data.surface as srf
 import invesalius.data.volume as volume
 import invesalius.gui.dialogs as dialog
 import invesalius.project as prj
-import invesalius.reader.analyze_reader as analyze
 import invesalius.reader.dicom_grouper as dg
 import invesalius.reader.dicom_reader as dcm
 import invesalius.reader.bitmap_reader as bmp
+import invesalius.reader.others_reader as oth
 import invesalius.session as ses
@@ -65,6 +63,8 @@ class Controller():
         Publisher.subscribe(self.OnImportMedicalImages, 'Import directory')
         Publisher.subscribe(self.OnShowDialogImportDirectory,
                                  'Show import directory dialog')
+        Publisher.subscribe(self.OnShowDialogImportOtherFiles,
+                                 'Show import other files dialog')
         Publisher.subscribe(self.OnShowDialogOpenProject,
                                  'Show open project dialog')
@@ -77,7 +77,9 @@ class Controller():
         Publisher.subscribe(self.OnOpenDicomGroup,
                                  'Open DICOM group')
         Publisher.subscribe(self.OnOpenBitmapFiles,
-                                'Open bitmap files')
+                                 'Open bitmap files')
+        Publisher.subscribe(self.OnOpenOtherFiles,
+                                 'Open other files')
         Publisher.subscribe(self.Progress, "Update dicom load")
         Publisher.subscribe(self.Progress, "Update bitmap load")
         Publisher.subscribe(self.OnLoadImportPanel, "End dicom load")
@@ -88,7 +90,6 @@ class Controller():
         Publisher.subscribe(self.OnShowDialogCloseProject, 'Close Project')
         Publisher.subscribe(self.OnOpenProject, 'Open project')
         Publisher.subscribe(self.OnOpenRecentProject, 'Open recent project')
-        Publisher.subscribe(self.OnShowAnalyzeFile, 'Show analyze dialog')
         Publisher.subscribe(self.OnShowBitmapFile, 'Show bitmap dialog')
         Publisher.subscribe(self.ShowBooleanOpDialog, 'Show boolean dialog')
@@ -116,6 +117,10 @@ class Controller():
     def OnShowDialogImportDirectory(self, pubsub_evt):
         self.ShowDialogImportDirectory()
+    def OnShowDialogImportOtherFiles(self, pubsub_evt):
+        id_type = pubsub_evt.data
+        self.ShowDialogImportOtherFiles(id_type)
+
     def OnShowDialogOpenProject(self, pubsub_evt):
         self.ShowDialogOpenProject()
@@ -126,15 +131,6 @@ class Controller():
     def OnShowDialogCloseProject(self, pubsub_evt):
         self.ShowDialogCloseProject()
-    def OnShowAnalyzeFile(self, pubsub_evt):
-        dirpath = dialog.ShowOpenAnalyzeDialog()
-        imagedata = analyze.ReadAnalyze(dirpath)
-        if imagedata:
-            self.CreateAnalyzeProject(imagedata)
-            
-        self.LoadProject()
-        Publisher.sendMessage("Enable state project", True)
-
     def OnShowBitmapFile(self, pubsub_evt):
         self.ShowDialogImportBitmapFile()
 ###########################
@@ -163,7 +159,6 @@ class Controller():
             self.StartImportBitmapPanel(dirpath)
         #    Publisher.sendMessage("Load data to import panel", dirpath)
-
     def ShowDialogImportDirectory(self):
         # Offer to save current project if necessary
         session = ses.Session()
@@ -186,6 +181,40 @@ class Controller():
             self.StartImportPanel(dirpath)
             Publisher.sendMessage("Load data to import panel", dirpath)
+    def ShowDialogImportOtherFiles(self, id_type):
+        # Offer to save current project if necessary
+        session = ses.Session()
+        st = session.project_status
+        if (st == const.PROJ_NEW) or (st == const.PROJ_CHANGE):
+            filename = session.project_path[1]
+            answer = dialog.SaveChangesDialog2(filename)
+            if answer:
+                self.ShowDialogSaveProject()
+            self.CloseProject()
+            # Publisher.sendMessage("Enable state project", False)
+            Publisher.sendMessage('Set project name')
+            Publisher.sendMessage("Stop Config Recording")
+            Publisher.sendMessage("Set slice interaction style", const.STATE_DEFAULT)
+
+        # Warning for limited support to Analyze format
+        if id_type == const.ID_ANALYZE_IMPORT:
+            dialog.ImportAnalyzeWarning()
+
+        # Import project treating compressed nifti exception
+        suptype = ('hdr', 'nii', 'nii.gz', 'par')
+        filepath = dialog.ShowImportOtherFilesDialog(id_type)
+        name = filepath.rpartition('\\')[-1].split('.')
+
+        if name[-1] == 'gz':
+            name[1] = 'nii.gz'
+
+        filetype = name[1].lower()
+
+        if filetype in suptype:
+            Publisher.sendMessage("Open other files", filepath)
+        else:
+            dialog.ImportInvalidFiles()
+
     def ShowDialogOpenProject(self):
         # Offer to save current project if necessary
         session = ses.Session()
@@ -281,8 +310,6 @@ class Controller():
         else:
             dialog.InexistentPath(filepath)
-
-
     def OpenProject(self, filepath):
         Publisher.sendMessage('Begin busy cursor')
         path = os.path.abspath(filepath)
@@ -342,7 +369,7 @@ class Controller():
     def StartImportPanel(self, path):
-        # retrieve DICOM files splited into groups
+        # retrieve DICOM files split into groups
         reader = dcm.ProgressDicomReader()
         reader.SetWindowEvent(self.frame)
         reader.SetDirectoryPath(path)
@@ -410,21 +437,33 @@ class Controller():
         self.ImportMedicalImages(directory)
     def ImportMedicalImages(self, directory):
-        # OPTION 1: DICOM?
         patients_groups = dcm.GetDicomGroups(directory)
+        name = directory.rpartition('\\')[-1].split('.')
+        print "patients: ", patients_groups
+
         if len(patients_groups):
+            # OPTION 1: DICOM
             group = dcm.SelectLargerDicomGroup(patients_groups)
-            matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0,0],gui=True)
+            matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=True)
             self.CreateDicomProject(dicom, matrix, matrix_filename)
-        # OPTION 2: ANALYZE?
         else:
-            imagedata = analyze.ReadDirectory(directory)
-            if imagedata:
-                self.CreateAnalyzeProject(imagedata)
-            # OPTION 3: Nothing...
+            # OPTION 2: NIfTI, Analyze or PAR/REC
+            if name[-1] == 'gz':
+                name[1] = 'nii.gz'
+
+            suptype = ('hdr', 'nii', 'nii.gz', 'par')
+            filetype = name[1].lower()
+
+            if filetype in suptype:
+                group = oth.ReadOthers(directory)
             else:
                 utils.debug("No medical images found on given directory")
                 return
+
+            matrix, matrix_filename = self.OpenOtherFiles(group)
+            self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
+            # OPTION 4: Nothing...
+
         self.LoadProject()
         Publisher.sendMessage("Enable state project", True)
@@ -493,43 +532,6 @@ class Controller():
         Publisher.sendMessage('End busy cursor')
-    def CreateAnalyzeProject(self, imagedata):
-        header = imagedata.get_header()
-        proj = prj.Project()
-        proj.imagedata = None
-        proj.name = _("Untitled")
-        proj.SetAcquisitionModality("MRI")
-        #TODO: Verify if all Analyse are in AXIAL orientation
-
-        # To get  Z, X, Y (used by InVesaliu), not X, Y, Z
-        matrix, matrix_filename = image_utils.analyze2mmap(imagedata)
-        if header['orient'] == 0:
-            proj.original_orientation =  const.AXIAL
-        elif header['orient'] == 1:
-            proj.original_orientation = const.CORONAL
-        elif header['orient'] == 2:
-            proj.original_orientation = const.SAGITAL
-        else:
-            proj.original_orientation =  const.SAGITAL
-
-        proj.threshold_range = (int(header['glmin']),
-                                int(header['glmax']))
-        proj.window = proj.threshold_range[1] - proj.threshold_range[0]
-        proj.level =  (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
-        proj.spacing = header['pixdim'][1:4]
-        proj.matrix_shape = matrix.shape 
-
-        self.Slice = sl.Slice()
-        self.Slice.matrix = matrix
-        self.Slice.matrix_filename = matrix_filename
-
-        self.Slice.window_level = proj.level
-        self.Slice.window_width = proj.window
-        self.Slice.spacing = header.get_zooms()[:3]
-
-        Publisher.sendMessage('Update threshold limits list',
-                                   proj.threshold_range)
-
     def CreateDicomProject(self, dicom, matrix, matrix_filename):
         name_to_const = {"AXIAL":const.AXIAL,
                          "CORONAL":const.CORONAL,
@@ -604,6 +606,40 @@ class Controller():
         dirpath = session.CreateProject(filename)
+    def CreateOtherProject(self, name, matrix, matrix_filename):
+        name_to_const = {"AXIAL": const.AXIAL,
+                         "CORONAL": const.CORONAL,
+                         "SAGITTAL": const.SAGITAL}
+
+        proj = prj.Project()
+        proj.name = name
+        proj.modality = 'MRI'
+        proj.SetAcquisitionModality('MRI')
+        proj.matrix_shape = matrix.shape
+        proj.matrix_dtype = matrix.dtype.name
+        proj.matrix_filename = matrix_filename
+
+        # 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
+        orientation = 'CORONAL'
+
+        proj.original_orientation =\
+            name_to_const[orientation]
+
+        proj.window = self.Slice.window_width
+        proj.level = self.Slice.window_level
+        proj.threshold_range = int(matrix.min()), int(matrix.max())
+        proj.spacing = self.Slice.spacing
+
+        ######
+        session = ses.Session()
+        filename = proj.name + ".inv3"
+
+        filename = filename.replace("/", "")  # Fix problem case other/Skull_DICOM
+
+        dirpath = session.CreateProject(filename)
+
     def OnOpenBitmapFiles(self, pubsub_evt):
         rec_data = pubsub_evt.data
         bmp_data = bmp.BitmapData()
@@ -688,6 +724,26 @@ class Controller():
         self.LoadProject()
         Publisher.sendMessage("Enable state project", True)
+    def OnOpenOtherFiles(self, pubsub_evt):
+        filepath = pubsub_evt.data
+        name = filepath.rpartition('\\')[-1].split('.')
+
+        if name[-1] == 'gz':
+            name[1] = 'nii.gz'
+
+        suptype = ('hdr', 'nii', 'nii.gz', 'par')
+        filetype = name[1].lower()
+
+        if filetype in suptype:
+            group = oth.ReadOthers(filepath)
+        else:
+            dialog.ImportInvalidFiles()
+
+        matrix, matrix_filename = self.OpenOtherFiles(group)
+        self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
+        self.LoadProject()
+        Publisher.sendMessage("Enable state project", True)
+
     def OpenDicomGroup(self, dicom_group, interval, file_range, gui=True):
         # Retrieve general DICOM headers
         dicom = dicom_group.GetDicomSample()
@@ -773,6 +829,30 @@ class Controller():
         return self.matrix, self.filename, dicom
+    def OpenOtherFiles(self, group):
+        # Retreaving matrix from image data
+        self.matrix, scalar_range, self.filename = image_utils.img2memmap(group)
+
+        hdr = group.header
+        hdr.set_data_dtype('int16')
+        dims = hdr.get_zooms()
+        dimsf = tuple([float(s) for s in dims])
+
+        wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
+        ww = float((scalar_range[1] - scalar_range[0]))
+
+        self.Slice = sl.Slice()
+        self.Slice.matrix = self.matrix
+        self.Slice.matrix_filename = self.filename
+
+        self.Slice.spacing = dimsf
+        self.Slice.window_level = wl
+        self.Slice.window_width = ww
+
+        scalar_range = int(scalar_range[0]), int(scalar_range[1])
+        Publisher.sendMessage('Update threshold limits list', scalar_range)
+        return self.matrix, self.filename
+
     def LoadImagedataInfo(self):
         proj = prj.Project()
-from numpy import *
 from math import sqrt
+import numpy as np
-class Bases:
-    
-    def __init__(self, p1, p2, p3):
-                
-        self.p1 = array([p1[0], p1[1], p1[2]])
-        self.p2 = array([p2[0], p2[1], p2[2]])
-        self.p3 = array([p3[0], p3[1], p3[2]])
-        
-        print "p1: ", self.p1
-        print "p2: ", self.p2
-        print "p3: ", self.p3
-        self.sub1 = self.p2 - self.p1
-        self.sub2 = self.p3 - self.p1
-        
-    def Basecreation(self):
-        #g1
-        g1 = self.sub1
-        
-        #g2
-        lamb1 = g1[0]*self.sub2[0] + g1[1]*self.sub2[1] + g1[2]*self.sub2[2]
-        lamb2 = dot(g1, g1)
-        lamb = lamb1/lamb2
-        
-        #Ponto q    
-        q = self.p1 + lamb*self.sub1
-         
-        #g1 e g2 com origem em q   
-        g1 = self.p1 - q
-        g2 = self.p3 - q
-        
-        #testa se o g1 nao eh um vetor nulo
-        if g1.any() == False:
-            g1 = self.p2 - q
-            
-        #g3 - Produto vetorial NumPy
-        g3 = cross(g2, g1)
-        
-        #normalizacao dos vetores
-        g1 = g1/sqrt(lamb2)
-        g2 = g2/sqrt(dot(g2, g2))
-        g3 = g3/sqrt(dot(g3, g3))
-            
-        M = matrix([[g1[0],g1[1],g1[2]], [g2[0],g2[1],g2[2]], [g3[0],g3[1],g3[2]]])
-        q.shape = (3, 1)
-        q = matrix(q.copy())
-        print"M: ", M
-        print
-        print"q: ", q
-        print
-        Minv = M.I
-        
-        return M, q, Minv
-    
-def FlipX(point):
-        
-        point = matrix(point + (0,))
-               
-        #inverter o eixo z
-        ## possivel explicacaoo -- origem do eixo do imagedata esta no canto
-        ## superior esquerdo e origem da superfice eh no canto inferior esquerdo
-        ## ou a ordem de empilhamento das fatias
-        
-        point[0, 2] = -point[0, 2]
-        
-        #Flip em y
-        Mrot = 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]])
-        Mtrans = 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]])
-        Mtrans_return = matrix([[1.0, 0, 0, point[0, 0]],
+def angle_calculation(ap_axis, coil_axis):
+    """
+    Calculate angle between two given axis (in degrees)
+
+    :param ap_axis: anterior posterior axis represented
+    :param coil_axis: tms coil axis
+    :return: angle between the two given axes
+    """
+
+    ap_axis = np.array([ap_axis[0], ap_axis[1]])
+    coil_axis = np.array([float(coil_axis[0]), float(coil_axis[1])])
+    angle = np.rad2deg(np.arccos((np.dot(ap_axis, coil_axis))/(
+        np.linalg.norm(ap_axis)*np.linalg.norm(coil_axis))))
+
+    return float(angle)
+
+
+def base_creation(fiducials):
+    """
+    Calculate the origin and matrix for coordinate system
+    transformation.
+    q: origin of coordinate system
+    g1, g2, g3: orthogonal vectors of coordinate system
+
+    :param fiducials: array of 3 rows (p1, p2, p3) and 3 columns (x, y, z) with fiducials coordinates
+    :return: matrix and origin for base transformation
+    """
+
+    p1 = fiducials[0, :]
+    p2 = fiducials[1, :]
+    p3 = fiducials[2, :]
+
+    sub1 = p2 - p1
+    sub2 = p3 - p1
+    lamb = (sub1[0]*sub2[0]+sub1[1]*sub2[1]+sub1[2]*sub2[2])/np.dot(sub1, sub1)
+
+    q = p1 + lamb*sub1
+    g1 = p1 - q
+    g2 = p3 - q
+
+    if not g1.any():
+        g1 = p2 - q
+
+    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))
+
+    m = np.matrix([[g1[0], g1[1], g1[2]],
+                   [g2[0], g2[1], g2[2]],
+                   [g3[0], g3[1], g3[2]]])
+
+    q.shape = (3, 1)
+    q = np.matrix(q.copy())
+    m_inv = m.I
+
+    # print"M: ", m
+    # print"q: ", q
+
+    return m, q, m_inv
+
+
+def calculate_fre(fiducials, minv, n, q1, q2):
+    """
+    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 q1: origin of first base
+    :param q2: origin of second base
+    :return: float number of fiducial registration error
+    """
+
+    img = np.zeros([3, 3])
+    dist = np.zeros([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 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*Mtrans*Mrot*Mtrans_return
-        x, y, z  = point_rot.tolist()[0][:3]
-        return x, y, z
+    point_rot = point*m_trans*m_rot*m_trans_return
+    x, y, z = point_rot.tolist()[0][:3]
+
+    return x, y, z
@@ -1,65 +0,0 @@
-import threading
-
-import serial
-import wx
-from wx.lib.pubsub import pub as Publisher
-
-from numpy import *
-from math import sqrt
-from time import sleep
-
-class Corregister(threading.Thread):
-    
-    def __init__(self, bases, flag):
-        threading.Thread.__init__(self)
-        self.Minv = bases[0]
-        self.N = bases[1]
-        self.q1 = bases[2]
-        self.q2 = bases[3]
-        self.flag = flag
-        self._pause_ = 0
-        self.start()
-        
-    def stop(self):
-        # Stop neuronavigation
-        self._pause_ = 1
-        
-    def Coordinates(self):        
-        #Get Polhemus points for neuronavigation       
-        ser = serial.Serial(0)
-        ser.write("Y")       
-        ser.write("P")
-        str = ser.readline()
-        ser.write("Y")
-        str = str.replace("\r\n","")
-        str = str.replace("-"," -")
-        aostr = [s for s in str.split()]
-        #aoflt -> 0:letter 1:x 2:y 3:z
-        aoflt = [float(aostr[1]), float(aostr[2]), float(aostr[3]),
-                  float(aostr[4]), float(aostr[5]), float(aostr[6])]      
-        ser.close()
-        
-        #Unit change: inches to millimeters
-        x = 25.4
-        y = 25.4
-        z = -25.4
-
-        coord = (aoflt[0]*x, aoflt[1]*y, aoflt[2]*z)
-        return coord
-       
-    def run(self):
-        while self.flag == True:
-            #Neuronavigation with Polhemus
-            trck = self.Coordinates()
-            tracker = matrix([[trck[0]], [trck[1]], [trck[2]]])            
-            img = self.q1 + (self.Minv*self.N)*(tracker - self.q2)
-            coord = [float(img[0]), float(img[1]), float(img[2])]
-            coord_cam = float(img[0]), float(img[1]), float(img[2])
-            Publisher.sendMessage('Set ball reference position based on bound', coord_cam)
-            Publisher.sendMessage('Set camera in volume', coord_cam)
-            wx.CallAfter(Publisher.sendMessage, 'Render volume viewer')
-            wx.CallAfter(Publisher.sendMessage, 'Co-registered Points', coord)
-            sleep(0.005)
-
-            if self._pause_:
-                return
@@ -0,0 +1,277 @@
+#--------------------------------------------------------------------------
+# 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.
+#--------------------------------------------------------------------------
+
+from math import sin, cos
+import numpy as np
+
+from random import uniform
+
+
+def GetCoordinates(trck_init, trck_id, ref_mode):
+
+    """
+    Read coordinates from spatial tracking devices using
+
+    :param trck_init: Initialization variable of tracking device and connection type. See tracker.py.
+    :param trck_id: ID of tracking device.
+    :param ref_mode: Single or dynamic reference mode of tracking.
+    :return: array of six coordinates (x, y, z, alpha, beta, gamma)
+    """
+
+    coord = None
+    if trck_id:
+        getcoord = {1: ClaronCoord,
+                    2: PolhemusCoord,
+                    3: PolhemusCoord,
+                    4: PolhemusCoord,
+                    5: DebugCoord}
+        coord = getcoord[trck_id](trck_init, trck_id, ref_mode)
+    else:
+        print "Select Tracker"
+
+    return coord
+
+
+def ClaronCoord(trck_init, trck_id, ref_mode):
+    trck = trck_init[0]
+    scale = 10. * np.array([1., 1.0, -1.0])
+    coord = None
+    k = 0
+    # TODO: try to replace while and use some Claron internal computation
+    if ref_mode:
+        while k < 20:
+            try:
+                trck.Run()
+                probe = np.array([trck.PositionTooltipX1 * scale[0], trck.PositionTooltipY1 * scale[1],
+                                  trck.PositionTooltipZ1 * scale[2], trck.AngleX1, trck.AngleY1, trck.AngleZ1])
+                reference = np.array([trck.PositionTooltipX2 * scale[0], trck.PositionTooltipY2 * scale[1],
+                                      trck.PositionTooltipZ2 * scale[2], trck.AngleX2, trck.AngleY2, trck.AngleZ2])
+                k = 30
+            except AttributeError:
+                k += 1
+                print "wait, collecting coordinates ..."
+        if k == 30:
+            coord = dynamic_reference(probe, reference)
+    else:
+        while k < 20:
+            try:
+                trck.Run()
+                coord = np.array([trck.PositionTooltipX1 * scale[0], trck.PositionTooltipY1 * scale[1],
+                                  trck.PositionTooltipZ1 * scale[2], trck.AngleX1, trck.AngleY1, trck.AngleZ1])
+                k = 30
+            except AttributeError:
+                k += 1
+                print "wait, collecting coordinates ..."
+
+    return coord
+
+
+def PolhemusCoord(trck, trck_id, ref_mode):
+    coord = None
+
+    if trck[1] == 'serial':
+        coord = PolhemusSerialCoord(trck[0], trck_id, ref_mode)
+
+    elif trck[1] == 'usb':
+        coord = PolhemusUSBCoord(trck[0], trck_id, ref_mode)
+
+    elif trck[1] == 'wrapper':
+        coord = PolhemusWrapperCoord(trck[0], trck_id, ref_mode)
+
+    return coord
+
+
+def PolhemusWrapperCoord(trck, trck_id, ref_mode):
+    if trck_id == 2:
+        scale = 10. * np.array([1., 1.0, -1.0])
+    else:
+        scale = 25.4 * np.array([1., 1.0, -1.0])
+    coord = None
+
+    if ref_mode:
+        trck.Run()
+        probe = np.array([float(trck.PositionTooltipX1) * scale[0], float(trck.PositionTooltipY1) * scale[1],
+                          float(trck.PositionTooltipZ1) * scale[2], float(trck.AngleX1), float(trck.AngleY1),
+                          float(trck.AngleZ1)])
+        reference = np.array([float(trck.PositionTooltipX2) * scale[0], float(trck.PositionTooltipY2) * scale[1],
+                          float(trck.PositionTooltipZ2) * scale[2], float(trck.AngleX2), float(trck.AngleY2),
+                          float(trck.AngleZ2)])
+
+        if probe.all() and reference.all():
+            coord = dynamic_reference(probe, reference)
+
+    else:
+        trck.Run()
+        coord = np.array([float(trck.PositionTooltipX1) * scale[0], float(trck.PositionTooltipY1) * scale[1],
+                          float(trck.PositionTooltipZ1) * scale[2], float(trck.AngleX1), float(trck.AngleY1),
+                          float(trck.AngleZ1)])
+
+    return coord
+
+
+def PolhemusUSBCoord(trck, trck_id, ref_mode):
+    endpoint = trck[0][(0, 0)][0]
+    # Tried to write some settings to Polhemus in trackers.py while initializing the device.
+    # TODO: Check if it's working properly.
+    trck.write(0x02, "P")
+    if trck_id == 2:
+        scale = 10. * np.array([1., 1.0, -1.0])
+    else:
+        scale = 25.4 * np.array([1., 1.0, -1.0])
+    coord = None
+
+    if ref_mode:
+
+        data = trck.read(endpoint.bEndpointAddress, 2 * endpoint.wMaxPacketSize)
+        data = str2float(data.tostring())
+
+        # six coordinates of first and second sensor: x, y, z and alfa, beta and gama
+        # jump one element for reference to avoid the sensor ID returned by Polhemus
+        probe = data[0] * scale[0], data[1] * scale[1], data[2] * scale[2], \
+                data[3], data[4], data[5], data[6]
+        reference = data[7] * scale[0], data[8] * scale[1], data[9] * scale[2], data[10], \
+                    data[11], data[12], data[13]
+
+        if probe.all() and reference.all():
+            coord = dynamic_reference(probe, reference)
+
+        return coord
+
+    else:
+        data = trck.read(endpoint.bEndpointAddress, endpoint.wMaxPacketSize)
+        coord = str2float(data.tostring())
+
+        coord = np.array((coord[0] * scale[0], coord[1] * scale[1], coord[2] * scale[2],
+                          coord[3], coord[4], coord[5]))
+
+        return coord
+
+
+def PolhemusSerialCoord(trck_init, trck_id, ref_mode):
+    # mudanca para fastrak - ref 1 tem somente x, y, z
+    # aoflt -> 0:letter 1:x 2:y 3:z
+    # this method is not optimized to work with all trackers, only with ISOTRAK
+    # serial connection is obsolete, remove in future
+    trck_init.write("P")
+    lines = trck_init.readlines()
+
+    coord = None
+
+    if lines[0][0] != '0':
+        print "The Polhemus is not connected!"
+    else:
+        for s in lines:
+            if s[1] == '1':
+                data = s
+            elif s[1] == '2':
+                data = s
+
+        # single ref mode
+        if not ref_mode:
+            data = data.replace('-', ' -')
+            data = [s for s in data.split()]
+            j = 0
+            while j == 0:
+                try:
+                    plh1 = [float(s) for s in data[1:len(data)]]
+                    j = 1
+                except ValueError:
+                    trck_init.write("P")
+                    data = trck_init.readline()
+                    data = data.replace('-', ' -')
+                    data = [s for s in data.split()]
+                    print "Trying to fix the error!!"
+
+            coord = data[0:6]
+    return coord
+
+
+def DebugCoord(trk_init, trck_id, ref_mode):
+    """
+    Method to simulate a tracking device for debug and error check. Generate a random
+    x, y, z, alfa, beta and gama coordinates in interval [1, 200[
+    :param trk_init: tracker initialization instance
+    :param ref_mode: flag for singular of dynamic reference
+    :param trck_id: id of tracking device
+    :return: six coordinates x, y, z, alfa, beta and gama
+    """
+
+    if ref_mode:
+        probe = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+                          uniform(1, 200), uniform(1, 200), uniform(1, 200)])
+        reference = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+                              uniform(1, 200), uniform(1, 200), uniform(1, 200)])
+
+        coord = dynamic_reference(probe, reference)
+
+    else:
+        coord = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+                          uniform(1, 200), uniform(1, 200), uniform(1, 200)])
+
+    return coord
+
+
+def dynamic_reference(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])
+
+    vet = probe[0:3] - reference[0:3]
+    vet = np.mat(vet.reshape(3, 1))
+
+    # Attitude Matrix given by Patriot Manual
+    Mrot = np.mat([[cos(a) * cos(b), sin(b) * sin(g) * cos(a) - cos(g) * sin(a),
+                       cos(a) * sin(b) * cos(g) + sin(a) * sin(g)],
+                      [cos(b) * sin(a), sin(b) * sin(g) * sin(a) + cos(g) * cos(a),
+                       cos(g) * sin(b) * sin(a) - sin(g) * cos(a)],
+                      [-sin(b), sin(g) * cos(b), cos(b) * cos(g)]])
+
+    coord_rot = Mrot.T * vet
+    coord_rot = np.squeeze(np.asarray(coord_rot))
+
+    return coord_rot[0], coord_rot[1], coord_rot[2], probe[3], probe[4], probe[5]
+
+
+def str2float(data):
+    """
+    Converts string detected wth Polhemus device to float array of coordinates. THis method applies
+    a correction for the minus sign in string that raises error while splitting the string into coordinates.
+    :param data: string of coordinates read with Polhemus
+    :return: six float coordinates x, y, z, alfa, beta and gama
+    """
+
+    count = 0
+    for i, j in enumerate(data):
+        if j == '-':
+            data = data[:i + count] + ' ' + data[i + count:]
+            count += 1
+
+    data = [s for s in data.split()]
+    data = [float(s) for s in data[1:len(data)]]
+
+    return data
@@ -0,0 +1,81 @@
+#--------------------------------------------------------------------------
+# 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.
+#--------------------------------------------------------------------------
+
+import threading
+from time import sleep
+
+from numpy import mat
+import wx
+from wx.lib.pubsub import pub as Publisher
+
+import invesalius.data.coordinates as dco
+
+# TODO: Optimize navigation thread. Remove the infinite loop and optimize sleep.
+
+
+class Coregistration(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 = dco.GetCoordinates(trck_init, trck_id, trck_mode)
+            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])
+
+            # 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', coord[0:3])
+            wx.CallAfter(Publisher.sendMessage, 'Set camera in volume', coord[0:3])
+
+            # 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
@@ -592,41 +592,55 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
     return matrix, scalar_range, temp_file
-def analyze2mmap(analyze):
-    data = analyze.get_data()
-    header = analyze.get_header()
+
+def img2memmap(group):
+    """
+    From a nibabel image data creates a memmap file in the temp folder and
+    returns it and its related filename.
+    """
+
     temp_file = tempfile.mktemp()
-    # Sagital
-    if header['orient'] == 2:
-        print "Orientation Sagital"
-        shape = tuple([data.shape[i] for i in (1, 2, 0)])
-        matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
-        for n, slice in enumerate(data):
-            matrix[:,:, n] = slice
-
-    # Coronal
-    elif header['orient'] == 1:
-        print "Orientation coronal"
-        shape = tuple([data.shape[i] for i in (1, 0, 2)])
-        matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
-        for n, slice in enumerate(data):
-            matrix[:,n,:] = slice
-
-    # AXIAL
-    elif header['orient'] == 0:
-        print "no orientation"
-        shape = tuple([data.shape[i] for i in (0, 1, 2)])
-        matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
-        for n, slice in enumerate(data):
-            matrix[n] = slice
+    data = group.get_data()
+    # Normalize image pixel values and convert to int16
+    data = imgnormalize(data)
-    else:
-        print "Orientation Sagital"
-        shape = tuple([data.shape[i] for i in (1, 2, 0)])
-        matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
-        for n, slice in enumerate(data):
-            matrix[:,:, n] = slice
+    # Convert RAS+ to default InVesalius orientation ZYX
+    data = numpy.swapaxes(data, 0, 2)
+    data = numpy.fliplr(data)
+    matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=data.shape)
+    matrix[:] = data[:]
     matrix.flush()
-    return matrix, temp_file
+
+    scalar_range = numpy.amin(matrix), numpy.amax(matrix)
+
+    return matrix, scalar_range, temp_file
+
+
+def imgnormalize(data, srange=(0, 255)):
+    """
+    Normalize image pixel intensity for int16 gray scale values.
+
+    :param data: image matrix
+    :param srange: range for normalization, default is 0 to 255
+    :return: normalized pixel intensity matrix
+    """
+
+    dataf = numpy.asarray(data)
+    rangef = numpy.asarray(srange)
+    faux = numpy.ravel(dataf).astype(float)
+    minimum = numpy.min(faux)
+    maximum = numpy.max(faux)
+    lower = rangef[0]
+    upper = rangef[1]
+
+    if minimum == maximum:
+        datan = numpy.ones(dataf.shape)*(upper + lower) / 2.
+    else:
+        datan = (faux-minimum)*(upper-lower) / (maximum-minimum) + lower
+
+    datan = numpy.reshape(datan, dataf.shape)
+    datan = datan.astype(numpy.int16)
+
+    return datan
 \ No newline at end of file
@@ -531,10 +531,12 @@ class Slice(object):
                 image = self.do_colour_image(ww_wl_image)
             if self.current_mask and self.current_mask.is_shown:
                 if self.buffer_slices[orientation].vtk_mask:
-                    print "Getting from buffer"
+                    # Prints that during navigation causes delay in update
+                    # print "Getting from buffer"
                     mask = self.buffer_slices[orientation].vtk_mask
                 else:
-                    print "Do not getting from buffer"
+                    # Prints that during navigation causes delay in update
+                    # print "Do not getting from buffer"
                     n_mask = self.get_mask_slice(orientation, slice_number)
                     mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
                     mask = self.do_colour_mask(mask, self.opacity)
@@ -230,10 +230,8 @@ class CrossInteractorStyle(DefaultInteractorStyle):
         coord = self.viewer.calcultate_scroll_position(px, py)
         Publisher.sendMessage('Update cross position', (wx, wy, wz))
         self.ScrollSlice(coord)
-        Publisher.sendMessage('Set ball reference position based on bound',
-                                   (wx, wy, wz))
+        Publisher.sendMessage('Set ball reference position', (wx, wy, wz))
         Publisher.sendMessage('Set camera in volume', (wx, wy, wz))
-        Publisher.sendMessage('Render volume viewer')
         iren.Render()
@@ -0,0 +1,222 @@
+#--------------------------------------------------------------------------
+# 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.
+#--------------------------------------------------------------------------
+
+# TODO: Disconnect tracker when a new one is connected
+# TODO: Test if there are too many prints when connection fails
+
+
+def TrackerConnection(tracker_id, action):
+    """
+    Initialize spatial trackers for coordinate detection during navigation.
+
+    :param tracker_id: ID of tracking device.
+    :param action: string with to decide whether connect or disconnect the selected device.
+    :return spatial tracker initialization instance or None if could not open device.
+    """
+
+    if action == 'connect':
+        trck_fcn = {1: ClaronTracker,
+                    2: PolhemusTracker,    # FASTRAK
+                    3: PolhemusTracker,    # ISOTRAK
+                    4: PolhemusTracker,    # PATRIOT
+                    5: DebugTracker}
+
+        trck_init = trck_fcn[tracker_id](tracker_id)
+
+    elif action == 'disconnect':
+        trck_init = DisconnectTracker(tracker_id)
+
+    return trck_init
+
+
+def DefaultTracker(tracker_id):
+    trck_init = None
+    try:
+        # import spatial tracker library
+        print 'Connect to default tracking device.'
+
+    except:
+        print 'Could not connect to default tracker.'
+
+    # return tracker initialization variable and type of connection
+    return trck_init, 'wrapper'
+
+
+def ClaronTracker(tracker_id):
+    import invesalius.constants as const
+
+    trck_init = None
+    try:
+        import pyclaron
+
+        lib_mode = 'wrapper'
+        trck_init = pyclaron.pyclaron()
+        trck_init.CalibrationDir = const.CAL_DIR
+        trck_init.MarkerDir = const.MAR_DIR
+        trck_init.NumberFramesProcessed = 10
+        trck_init.FramesExtrapolated = 0
+        trck_init.Initialize()
+
+        if trck_init.GetIdentifyingCamera():
+            trck_init.Run()
+            print "MicronTracker camera identified."
+        else:
+            trck_init = None
+
+    except ImportError:
+        lib_mode = 'error'
+        print 'The ClaronTracker library is not installed.'
+
+    return trck_init, lib_mode
+
+
+def PolhemusTracker(tracker_id):
+    trck_init = None
+    try:
+        trck_init = PlhWrapperConnection()
+        lib_mode = 'wrapper'
+        if not trck_init:
+            print 'Could not connect with Polhemus wrapper, trying USB connection...'
+            trck_init = PlhUSBConnection(tracker_id)
+            lib_mode = 'usb'
+            if not trck_init:
+                print 'Could not connect with Polhemus USB, trying serial connection...'
+                trck_init = PlhSerialConnection(tracker_id)
+                lib_mode = 'serial'
+    except:
+        lib_mode = 'error'
+        print 'Could not connect to Polhemus.'
+
+    return trck_init, lib_mode
+
+
+def DebugTracker(tracker_id):
+    trck_init = True
+    print 'Debug device started.'
+    return trck_init, 'debug'
+
+
+def PlhWrapperConnection():
+    trck_init = None
+    try:
+        import polhemus
+
+        trck_init = polhemus.polhemus()
+        trck_check = trck_init.Initialize()
+
+        if trck_check:
+            # First run is necessary to discard the first coord collection
+            trck_init.Run()
+    except:
+        print 'Could not connect to Polhemus via wrapper.'
+
+    return trck_init
+
+
+def PlhSerialConnection(tracker_id):
+    trck_init = None
+    try:
+        import serial
+
+        trck_init = serial.Serial(0, baudrate=115200, timeout=0.2)
+
+        if tracker_id == 2:
+            # Polhemus FASTRAK needs configurations first
+            trck_init.write(0x02, "u")
+            trck_init.write(0x02, "F")
+        elif tracker_id == 3:
+            # Polhemus ISOTRAK needs to set tracking point from
+            # center to tip.
+            trck_init.write("Y")
+
+        trck_init.write('P')
+        data = trck_init.readlines()
+
+        if not data:
+            trck_init = None
+
+    except:
+        print 'Could not connect to Polhemus serial.'
+
+    return trck_init
+
+
+def PlhUSBConnection(tracker_id):
+    trck_init = None
+    try:
+        import usb.core as uc
+        trck_init = uc.find(idVendor=0x0F44, idProduct=0x0003)
+        cfg = trck_init.get_active_configuration()
+        for i in cfg:
+            for x in i:
+                # TODO: try better code
+                x = x
+        trck_init.set_configuration()
+        endpoint = trck_init[0][(0, 0)][0]
+        if tracker_id == 2:
+            # Polhemus FASTRAK needs configurations first
+            # TODO: Check configurations to standardize initialization for all Polhemus devices
+            trck_init.write(0x02, "u")
+            trck_init.write(0x02, "F")
+        # First run to confirm that everything is working
+        trck_init.write(0x02, "P")
+        data = trck_init.read(endpoint.bEndpointAddress,
+                              endpoint.wMaxPacketSize)
+        if not data:
+            trck_init = None
+
+    except uc.USBError as err:
+        print 'Could not set configuration %s' % err
+    else:
+        print 'Could not connect to Polhemus USB.'
+
+    return trck_init
+
+
+def DisconnectTracker(tracker_id):
+    """
+    Disconnect current spatial tracker
+
+    :param tracker_id: ID of tracking device.
+    """
+    trck_init = None
+    # TODO: create individual functions to disconnect each other device, e.g. Polhemus.
+    if tracker_id == 1:
+        try:
+            import pyclaron
+            pyclaron.pyclaron().Close()
+            lib_mode = 'wrapper'
+        except ImportError:
+            lib_mode = 'error'
+            print 'The ClaronTracker library is not installed.'
+
+    elif tracker_id == 4:
+        try:
+            import polhemus
+            polhemus.polhemus().Close()
+            lib_mode = 'wrapper'
+        except ImportError:
+            lib_mode = 'error'
+            print 'The polhemus library is not installed.'
+
+    elif tracker_id == 5:
+        print 'Debug tracker disconnected.'
+        lib_mode = 'debug'
+
+    return trck_init, lib_mode
 \ No newline at end of file
@@ -0,0 +1,64 @@
+#--------------------------------------------------------------------------
+# 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.
+#--------------------------------------------------------------------------
+
+import threading
+from time import sleep
+
+import wx
+from wx.lib.pubsub import pub as Publisher
+
+
+class Trigger(threading.Thread):
+    """
+    Thread created to use external trigger to interact with software during neuronavigation
+    """
+
+    def __init__(self, nav_id):
+        threading.Thread.__init__(self)
+        self.trigger_init = None
+        try:
+            import serial
+
+            self.trigger_init = serial.Serial('COM1', baudrate=115200, timeout=0)
+            self.nav_id = nav_id
+            self._pause_ = False
+            self.start()
+
+        except ImportError:
+            print 'PySerial library not installed. Please install to use Trigger option.'
+
+        except serial.serialutil.SerialException:
+            print 'Connection with port COM1 failed.'
+
+    def stop(self):
+        if self.trigger_init:
+            self.trigger_init.close()
+        self._pause_ = True
+
+    def run(self):
+        while self.nav_id:
+            lines = self.trigger_init.readlines()
+            # Following lines can simulate a trigger in 3 sec repetitions
+            # sleep(3)
+            # lines = True
+            if lines:
+                wx.CallAfter(Publisher.sendMessage, 'Create marker')
+            sleep(0.175)
+            if self._pause_:
+                return
@@ -911,17 +911,15 @@ class Viewer(wx.Panel):
         if self.slice_data.cursor:
             self.slice_data.cursor.SetColour(colour_vtk)
-    def Navigation(self, pubsub_evt):
+    def UpdateSlicesNavigation(self, pubsub_evt):
         # Get point from base change
-        x, y, z = pubsub_evt.data
-        coord_cross = x, y, z
-        position = self.slice_data.actor.GetInput().FindPoint(x, y, z)
-        coord_cross = self.slice_data.actor.GetInput().GetPoint(position)
-        coord = self.calcultate_scroll_position(position)
-        Publisher.sendMessage('Update cross position', coord_cross)
+        wx, wy, wz = pubsub_evt.data
+        px, py = self.get_slice_pixel_coord_by_world_pos(wx, wy, wz)
+        coord = self.calcultate_scroll_position(px, py)
+        self.cross.SetFocalPoint((wx, wy, wz))
         self.ScrollSlice(coord)
-        self.interactor.Render()
+        Publisher.sendMessage('Set ball reference position', (wx, wy, wz))
     def ScrollSlice(self, coord):
         if self.orientation == "AXIAL":
@@ -1165,8 +1163,8 @@ class Viewer(wx.Panel):
                                   self.orientation))
         Publisher.subscribe(self.__update_cross_position,
                                 'Update cross position')
-        Publisher.subscribe(self.Navigation,
-                                 'Co-registered Points')
+        Publisher.subscribe(self.UpdateSlicesNavigation,
+                            'Co-registered points')
         ###
         #  Publisher.subscribe(self.ChangeBrushColour,
                                  #  'Add mask')
@@ -22,7 +22,8 @@
 import sys
-import numpy
+import numpy as np
+from numpy.core.umath_tests import inner1d
 import wx
 import vtk
 from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor
@@ -45,10 +46,11 @@ class Viewer(wx.Panel):
         self.interaction_style = st.StyleStateManager()
-        self.ball_reference = None
-        self.initial_foco = None
+        self.initial_focus = None
-        style =  vtk.vtkInteractorStyleTrackballCamera()
+        self.staticballs = []
+
+        style = vtk.vtkInteractorStyleTrackballCamera()
         self.style = style
         interactor = wxVTKRenderWindowInteractor(self, -1, size = self.GetSize())
@@ -111,6 +113,9 @@ class Viewer(wx.Panel):
         self.repositioned_coronal_plan = 0
         self.added_actor = 0
+        self.camera_state = True
+
+        self.ball_actor = None
         self._mode_cross = False
         self._to_show_ball = 0
         self._ball_ref_visibility = False
@@ -153,6 +158,7 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.ResetCamClippingRange, 'Reset cam clipping range')
         Publisher.subscribe(self.SetVolumeCamera, 'Set camera in volume')
+        Publisher.subscribe(self.SetVolumeCameraState, 'Update volume camera state')
         Publisher.subscribe(self.OnEnableStyle, 'Enable style')
         Publisher.subscribe(self.OnDisableStyle, 'Disable style')
@@ -174,23 +180,24 @@ class Viewer(wx.Panel):
         Publisher.subscribe(self.OnStartSeed,'Create surface by seeding - start')
         Publisher.subscribe(self.OnEndSeed,'Create surface by seeding - end')
-        Publisher.subscribe(self.ActivateBallReference,
-                'Activate ball reference')
-        Publisher.subscribe(self.DeactivateBallReference,
-                'Deactivate ball reference')
-        Publisher.subscribe(self.SetBallReferencePosition,
-                'Set ball reference position')
-        Publisher.subscribe(self.SetBallReferencePositionBasedOnBound,
-                'Set ball reference position based on bound')
         Publisher.subscribe(self.SetStereoMode, 'Set stereo mode')
         Publisher.subscribe(self.Reposition3DPlane, 'Reposition 3D Plane')
         Publisher.subscribe(self.RemoveVolume, 'Remove Volume')
+        Publisher.subscribe(self.SetBallReferencePosition,
+                            'Set ball reference position')
         Publisher.subscribe(self._check_ball_reference, 'Enable style')
         Publisher.subscribe(self._uncheck_ball_reference, 'Disable style')
+        # Related to marker creation in navigation tools
+        Publisher.subscribe(self.AddMarker, 'Add marker')
+        Publisher.subscribe(self.HideAllMarkers, 'Hide all markers')
+        Publisher.subscribe(self.ShowAllMarkers, 'Show all markers')
+        Publisher.subscribe(self.RemoveAllMarkers, 'Remove all markers')
+        Publisher.subscribe(self.RemoveMarker, 'Remove marker')
+
     def SetStereoMode(self, pubsub_evt):
         mode = pubsub_evt.data
         ren_win = self.interactor.GetRenderWindow()
@@ -220,43 +227,6 @@ class Viewer(wx.Panel):
         self.interactor.Render()
-    def CreateBallReference(self):
-        MRAD = 3.0
-        proj = prj.Project()
-        s = proj.spacing
-        # The sphere's radius will be MRAD times bigger than the media of the
-        # spacing values.
-        r = (s[0] + s[1] + s[2]) / 3.0 * MRAD
-        self.ball_reference = vtk.vtkSphereSource()
-        self.ball_reference.SetRadius(r)
-
-        mapper = vtk.vtkPolyDataMapper()
-        mapper.SetInputConnection(self.ball_reference.GetOutputPort())
-
-        p = vtk.vtkProperty()
-        p.SetColor(1, 0, 0)
-
-        self.ball_actor = vtk.vtkActor()
-        self.ball_actor.SetMapper(mapper)
-        self.ball_actor.SetProperty(p)
-
-    def RemoveBallReference(self):
-        self._ball_ref_visibility = False
-        if self.ball_reference:
-            self.ren.RemoveActor(self.ball_actor)
-
-    def ActivateBallReference(self, pubsub_evt):
-        self._mode_cross = True
-        self._ball_ref_visibility = True
-        if self._to_show_ball:
-            if not self.ball_reference:
-                self.CreateBallReference()
-            self.ren.AddActor(self.ball_actor)
-
-    def DeactivateBallReference(self, pubsub_evt):
-        self._mode_cross = False
-        self.RemoveBallReference()
-
     def _check_ball_reference(self, pubsub_evt):
         st = pubsub_evt.data
         if st == const.SLICE_STATE_CROSS:
@@ -279,19 +249,6 @@ class Viewer(wx.Panel):
             self._to_show_ball -= 1
         self._check_and_set_ball_visibility()
-    def SetBallReferencePosition(self, pubsub_evt):
-        x, y, z = pubsub_evt.data
-        self.ball_reference.SetCenter(x, y, z)
-
-    def SetBallReferencePositionBasedOnBound(self, pubsub_evt):
-        if self._to_show_ball:
-            self.ActivateBallReference(None)
-            coord = pubsub_evt.data
-            x, y, z = bases.FlipX(coord)
-            self.ball_reference.SetCenter(x, y, z)
-        else:
-            self.DeactivateBallReference(None)
-
     def OnStartSeed(self, pubsub_evt):
         index = pubsub_evt.data
         self.seed_points = []
@@ -402,7 +359,6 @@ class Viewer(wx.Panel):
         actor.PickableOff()
         self.ren.AddActor(actor)
-
         self.points_reference.append(actor)
     def RemoveAllPointsReference(self):
@@ -418,6 +374,113 @@ class Viewer(wx.Panel):
         actor = self.points_reference.pop(point)
         self.ren.RemoveActor(actor)
+    def AddMarker(self, pubsub_evt):
+        """
+        Markers create by navigation tools and
+        rendered in volume viewer.
+        """
+        self.ball_id = pubsub_evt.data[0]
+        ballsize = pubsub_evt.data[1]
+        ballcolour = pubsub_evt.data[2]
+        coord = pubsub_evt.data[3]
+        x, y, z = bases.flip_x(coord)
+
+        ball_ref = vtk.vtkSphereSource()
+        ball_ref.SetRadius(ballsize)
+        ball_ref.SetCenter(x, y, z)
+
+        mapper = vtk.vtkPolyDataMapper()
+        mapper.SetInputConnection(ball_ref.GetOutputPort())
+
+        prop = vtk.vtkProperty()
+        prop.SetColor(ballcolour)
+
+        #adding a new actor for the present ball
+        self.staticballs.append(vtk.vtkActor())
+
+        self.staticballs[self.ball_id].SetMapper(mapper)
+        self.staticballs[self.ball_id].SetProperty(prop)
+
+        self.ren.AddActor(self.staticballs[self.ball_id])
+        self.ball_id = self.ball_id + 1
+        self.UpdateRender()
+
+    def HideAllMarkers(self, pubsub_evt):
+        ballid = pubsub_evt.data
+        for i in range(0, ballid):
+            self.staticballs[i].SetVisibility(0)
+        self.UpdateRender()
+
+    def ShowAllMarkers(self, pubsub_evt):
+        ballid = pubsub_evt.data
+        for i in range(0, ballid):
+            self.staticballs[i].SetVisibility(1)
+        self.UpdateRender()
+
+    def RemoveAllMarkers(self, pubsub_evt):
+        ballid = pubsub_evt.data
+        for i in range(0, ballid):
+            self.ren.RemoveActor(self.staticballs[i])
+        self.staticballs = []
+        self.UpdateRender()
+
+    def RemoveMarker(self, pubsub_evt):
+        index = pubsub_evt.data
+        self.ren.RemoveActor(self.staticballs[index])
+        del self.staticballs[index]
+        self.ball_id = self.ball_id - 1
+        self.UpdateRender()
+
+    def CreateBallReference(self):
+        """
+        Red sphere on volume visualization to reference center of
+        cross in slice planes.
+        The sphere's radius will be scale times bigger than the average of
+        image spacing values.
+        """
+        scale = 3.0
+        proj = prj.Project()
+        s = proj.spacing
+        r = (s[0] + s[1] + s[2]) / 3.0 * scale
+
+        ball_source = vtk.vtkSphereSource()
+        ball_source.SetRadius(r)
+
+        mapper = vtk.vtkPolyDataMapper()
+        mapper.SetInputConnection(ball_source.GetOutputPort())
+
+        self.ball_actor = vtk.vtkActor()
+        self.ball_actor.SetMapper(mapper)
+        self.ball_actor.GetProperty().SetColor(1, 0, 0)
+
+        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 SetBallReferencePosition(self, pubsub_evt):
+        if self._to_show_ball:
+            if not self.ball_actor:
+                self.ActivateBallReference()
+
+            coord = pubsub_evt.data
+            x, y, z = bases.flip_x(coord)
+            self.ball_actor.SetPosition(x, y, z)
+
+        else:
+            self.RemoveBallReference()
+
     def __bind_events_wx(self):
         #self.Bind(wx.EVT_SIZE, self.OnSize)
         pass
@@ -580,30 +643,38 @@ class Viewer(wx.Panel):
         self.ren.ResetCamera()
         self.ren.ResetCameraClippingRange()
+    def SetVolumeCameraState(self, pubsub_evt):
+        self.camera_state = pubsub_evt.data
+
     def SetVolumeCamera(self, pubsub_evt):
-        
-        coord_camera = pubsub_evt.data
-        coord_camera = numpy.array(bases.FlipX(coord_camera))
-        
-        cam = self.ren.GetActiveCamera()
-        
-        if self.initial_foco is None:
-            self.initial_foco = numpy.array(cam.GetFocalPoint())
-        
-        cam_initialposition = numpy.array(cam.GetPosition())
-        cam_initialfoco = numpy.array(cam.GetFocalPoint())
-        
-        cam_sub = cam_initialposition - cam_initialfoco
-        cam_sub_norm = numpy.linalg.norm(cam_sub)
-        vet1 = cam_sub/cam_sub_norm
-        
-        cam_sub_novo = coord_camera - self.initial_foco
-        cam_sub_novo_norm = numpy.linalg.norm(cam_sub_novo)
-        vet2 = cam_sub_novo/cam_sub_novo_norm
-        vet2 = vet2*cam_sub_norm + coord_camera
-        
-        cam.SetFocalPoint(coord_camera)
-        cam.SetPosition(vet2)
+        if self.camera_state:
+            #TODO: exclude dependency on initial focus
+            cam_focus = np.array(bases.flip_x(pubsub_evt.data))
+            cam = self.ren.GetActiveCamera()
+
+            if self.initial_focus is None:
+                self.initial_focus = np.array(cam.GetFocalPoint())
+
+            cam_pos0 = np.array(cam.GetPosition())
+            cam_focus0 = np.array(cam.GetFocalPoint())
+
+            v0 = cam_pos0 - cam_focus0
+            v0n = np.sqrt(inner1d(v0, v0))
+
+            v1 = (cam_focus - self.initial_focus)
+            v1n = np.sqrt(inner1d(v1, v1))
+            if not v1n:
+                v1n = 1.0
+            cam_pos = (v1/v1n)*v0n + cam_focus
+
+            cam.SetFocalPoint(cam_focus)
+            cam.SetPosition(cam_pos)
+
+        # It works without doing the reset. Check with trackers if there is any difference.
+        # Need to be outside condition for sphere marker position update
+        # self.ren.ResetCameraClippingRange()
+        # self.ren.ResetCamera()
+        self.interactor.Render()
     def OnExportSurface(self, pubsub_evt):
         filename, filetype = pubsub_evt.data
@@ -706,19 +777,18 @@ class Viewer(wx.Panel):
         self.interactor.Render()
         self._to_show_ball -= 1
         self._check_and_set_ball_visibility()
-        
+
     def RemoveAllActor(self, pubsub_evt):
         utils.debug("RemoveAllActor")
         self.ren.RemoveAllProps()
         Publisher.sendMessage('Render volume viewer')
-        
     def LoadSlicePlane(self, pubsub_evt):
         self.slice_plane = SlicePlane()
     def LoadVolume(self, pubsub_evt):
         self.raycasting_volume = True
-        #self._to_show_ball += 1
+        self._to_show_ball += 1
         volume = pubsub_evt.data[0]
         colour = pubsub_evt.data[1]
@@ -895,14 +965,16 @@ class Viewer(wx.Panel):
                 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(None)
+                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):
@@ -250,7 +250,8 @@ class UpperTaskPanel(wx.Panel):
             tasks = [(_("Load data"), importer.TaskPanel),
                      (_("Select region of interest"), slice_.TaskPanel),
                      (_("Configure 3D surface"), surface.TaskPanel),
-                     (_("Utilize navigation system"), navigator.TaskPanel)]
+                     (_("Export data"), exporter.TaskPanel),
+                     (_("Navigation system"), navigator.TaskPanel)]
         for i in xrange(len(tasks)):
             (name, panel) = tasks[i]
@@ -22,8 +22,11 @@ import os
 import random
 import sys
+import vtk
 import wx
 import wx.combo
+
+from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor
 from wx.lib import masked
 from wx.lib.agw import floatspin
 from wx.lib.wordwrap import wordwrap
@@ -206,48 +209,27 @@ class ProgressDialog(object):
         self.dlg.Destroy()
-
-#---------
-WILDCARD_OPEN = "InVesalius 3 project (*.inv3)|*.inv3|"\
+# ---------
+WILDCARD_OPEN = "InVesalius 3 project (*.inv3)|*.inv3|" \
                 "All files (*.*)|*.*"
-WILDCARD_ANALYZE = "Analyze (*.hdr)|*.hdr|"\
-                "All files (*.*)|*.*"
+WILDCARD_ANALYZE = "Analyze 7.5 (*.hdr)|*.hdr|" \
+                   "All files (*.*)|*.*"
-def ShowOpenProjectDialog():
-    # Default system path
-    current_dir = os.path.abspath(".")
-    dlg = wx.FileDialog(None, message=_("Open InVesalius 3 project..."),
-                        defaultDir="",
-                        defaultFile="", wildcard=WILDCARD_OPEN,
-                        style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
+WILDCARD_NIFTI = "NIfTI 1 (*.nii)|*.nii|" \
+                 "Compressed NIfTI (*.nii.gz)|*.nii.gz|" \
+                 "All files (*.*)|*.*"
-    # inv3 filter is default
-    dlg.SetFilterIndex(0)
+WILDCARD_PARREC = "PAR/REC (*.par)|*.par|" \
+                  "All files (*.*)|*.*"
-    # 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()
-    # 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 ShowOpenAnalyzeDialog():
+def ShowOpenProjectDialog():
     # Default system path
     current_dir = os.path.abspath(".")
-    dlg = wx.FileDialog(None, message=_("Open Analyze file"),
+    dlg = wx.FileDialog(None, message=_("Open InVesalius 3 project..."),
                         defaultDir="",
-                        defaultFile="", wildcard=WILDCARD_ANALYZE,
+                        defaultFile="", wildcard=WILDCARD_OPEN,
                         style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
     # inv3 filter is default
@@ -260,7 +242,7 @@ def ShowOpenAnalyzeDialog():
         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
+    except(wx._core.PyAssertionError):  # FIX: win64
         filepath = dlg.GetPath()
     # Destroy the dialog. Don't do this until you are done with it!
@@ -353,6 +335,47 @@ def ShowImportBitmapDirDialog():
     return path
+def ShowImportOtherFilesDialog(id_type):
+    # Default system path
+    current_dir = os.path.abspath(".")
+    dlg = wx.FileDialog(None, message=_("Import Analyze 7.5 file"),
+                        defaultDir="",
+                        defaultFile="", wildcard=WILDCARD_ANALYZE,
+                        style=wx.FD_OPEN | wx.FD_CHANGE_DIR)
+
+    if id_type == const.ID_NIFTI_IMPORT:
+        dlg.SetMessage(_("Import NIFTi 1 file"))
+        dlg.SetWildcard(WILDCARD_NIFTI)
+    elif id_type == const.ID_PARREC_IMPORT:
+        dlg.SetMessage(_("Import PAR/REC file"))
+        dlg.SetWildcard(WILDCARD_PARREC)
+
+    # inv3 filter is default
+    dlg.SetFilterIndex(0)
+
+    # Show the dialog and retrieve the user response. If it is the OK response,
+    # process the data.
+    filename = None
+    try:
+        if dlg.ShowModal() == wx.ID_OK:
+            # GetPath returns in unicode, if a path has non-ascii characters a
+            # UnicodeEncodeError is raised. To avoid this, path is encoded in utf-8
+            if sys.platform == "win32":
+                filename = dlg.GetPath()
+            else:
+                filename = dlg.GetPath().encode('utf-8')
+
+    except(wx._core.PyAssertionError):  # TODO: error win64
+        if (dlg.GetPath()):
+            filename = dlg.GetPath()
+
+    # 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 filename
+
+
 def ShowSaveAsProjectDialog(default_filename=None):
     current_dir = os.path.abspath(".")
     dlg = wx.FileDialog(None,
@@ -380,10 +403,70 @@ def ShowSaveAsProjectDialog(default_filename=None):
             if filename.split(".")[-1] != extension:
                 filename = filename + "." + extension
+    os.chdir(current_dir)
+    return filename
+
+
+# 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 (*.txt)|*.txt"),
+                        wx.SAVE | wx.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 = "txt"
+        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="",
+                        style=wx.OPEN|wx.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()
+
+    # 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
+
+
 class MessageDialog(wx.Dialog):
     def __init__(self, message):
         pre = wx.PreDialog()
@@ -509,6 +592,7 @@ def ImportEmptyDirectory(dirpath):
     dlg.ShowModal()
     dlg.Destroy()
+
 def ImportInvalidFiles(ftype="DICOM"):
     if ftype == "Bitmap":
         msg =  _("There are no Bitmap, JPEG, PNG or TIFF files in the selected folder.")
@@ -524,6 +608,20 @@ def ImportInvalidFiles(ftype=&quot;DICOM&quot;):
     dlg.ShowModal()
     dlg.Destroy()
+
+def ImportAnalyzeWarning():
+    msg1 = _("Warning! InVesalius has limited support to Analyze format.\n")
+    msg2 = _("Slices may be wrongly oriented and functions may not work properly.")
+    if sys.platform == 'darwin':
+        dlg = wx.MessageDialog(None, "", msg1 + msg2,
+                                wx.ICON_INFORMATION | wx.OK)
+    else:
+        dlg = wx.MessageDialog(None, msg1 + msg2, "InVesalius 3",
+                                wx.ICON_INFORMATION | wx.OK)
+    dlg.ShowModal()
+    dlg.Destroy()
+
+
 def InexistentMask():
     msg = _("A mask is needed to create a surface.")
     if sys.platform == 'darwin':
@@ -593,6 +691,86 @@ def SurfaceSelectionRequiredForDuplication():
     dlg.ShowModal()
     dlg.Destroy()
+
+# Dialogs for neuronavigation mode
+def InvalidFiducials():
+    msg = _("Fiducials are invalid. Select six 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 NavigationTrackerWarning(trck_id, lib_mode):
+    """
+    Spatial Tracker connection error
+    """
+    trck = {1: 'Claron MicronTracker',
+            2: 'Polhemus FASTRAK',
+            3: 'Polhemus ISOTRAK',
+            4: 'Polhemus PATRIOT',
+            5: 'Debug tracker device'}
+
+    if lib_mode == 'choose':
+        msg = _('No tracking device selected')
+    elif lib_mode == 'error':
+        msg = trck[trck_id] + _(' is not installed.')
+    elif lib_mode == 'disconnect':
+        msg = trck[trck_id] + _(' disconnected.')
+    else:
+        msg = trck[trck_id] + _(' is not connected.')
+
+    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 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")
+    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 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", defaultValue=default)
+    dlg.ShowModal()
+    result = dlg.GetValue()
+    dlg.Destroy()
+    return result
+
+
 class NewMask(wx.Dialog):
     def __init__(self,
                  parent=None,
@@ -828,6 +1006,8 @@ def ShowAboutDialog(parent):
     info.Developers = ["Paulo Henrique Junqueira Amorim",
                        "Thiago Franco de Moraes",
                        "Jorge Vicente Lopes da Silva",
+                       "Victor Hugo de Oliveira e Souza (navigator)",
+                       "Renan Hiroshi Matsuda (navigator)"
                        "Tatiana Al-Chueyr (former)",
                        "Guilherme Cesar Soares Ruppert (former)",
                        "Fabio de Souza Azevedo (former)",
@@ -396,7 +396,11 @@ class Frame(wx.Frame):
         elif id == const.ID_PROJECT_OPEN:
             self.ShowOpenProject()
         elif id == const.ID_ANALYZE_IMPORT:
-            self.ShowAnalyzeImporter()
+            self.ShowImportOtherFiles(id)
+        elif id == const.ID_NIFTI_IMPORT:
+            self.ShowImportOtherFiles(id)
+        elif id == const.ID_PARREC_IMPORT:
+            self.ShowImportOtherFiles(id)
         elif id == const.ID_TIFF_JPG_PNG:
             self.ShowBitmapImporter()
         elif id == const.ID_PROJECT_SAVE:
@@ -538,6 +542,12 @@ class Frame(wx.Frame):
         Show import DICOM panel. as dicom        """
         Publisher.sendMessage('Show import directory dialog')
+    def ShowImportOtherFiles(self, id_file):
+        """
+        Show import Analyze, NiFTI1 or PAR/REC dialog.
+        """
+        Publisher.sendMessage('Show import other files dialog', id_file)
+
     def ShowRetrieveDicomPanel(self):
         Publisher.sendMessage('Show retrieve dicom panel')
@@ -553,12 +563,6 @@ class Frame(wx.Frame):
         """
         Publisher.sendMessage('Show save dialog', True)
-    def ShowAnalyzeImporter(self):
-        """
-        Show save as dialog.
-        """
-        Publisher.sendMessage('Show analyze dialog', True)
-
     def ShowBitmapImporter(self):
         """
         Tiff, BMP, JPEG and PNG
@@ -672,7 +676,9 @@ class MenuBar(wx.MenuBar):
         #Import Others Files
         others_file_menu = wx.Menu()
-        others_file_menu.Append(const.ID_ANALYZE_IMPORT, "Analyze")
+        others_file_menu.Append(const.ID_ANALYZE_IMPORT, _("Analyze 7.5"))
+        others_file_menu.Append(const.ID_NIFTI_IMPORT, _("NIfTI 1"))
+        others_file_menu.Append(const.ID_PARREC_IMPORT, _("PAR/REC"))
         others_file_menu.Append(const.ID_TIFF_JPG_PNG, u"TIFF,BMP,JPG or PNG (\xb5CT)")
         # FILE
@@ -64,8 +64,8 @@ class InnerTaskPanel(wx.Panel):
         self.float_hyper_list = []
         # Fixed hyperlink items
-        tooltip = wx.ToolTip(_("Select DICOM files to be reconstructed"))
-        link_import_local = hl.HyperLinkCtrl(self, -1, _("Import DICOM images..."))
+        tooltip = wx.ToolTip(_("Select DICOM, Analyze, NIfTI or REC/PAR files to be reconstructed"))
+        link_import_local = hl.HyperLinkCtrl(self, -1, _("Import medical images..."))
         link_import_local.SetUnderlines(False, False, False)
         link_import_local.SetBold(True)
         link_import_local.SetColours("BLACK", "BLACK", "BLACK")
@@ -17,433 +17,727 @@
 #    detalhes.
 #--------------------------------------------------------------------------
-import os
+from functools import partial
 import sys
-import serial
+import numpy as np
 import wx
 import wx.lib.hyperlink as hl
 import wx.lib.masked.numctrl
-import wx.lib.platebtn as pbtn
 from wx.lib.pubsub import pub as Publisher
+import invesalius.constants as const
 import invesalius.data.bases as db
-import invesalius.data.co_registration as dcr
-import invesalius.project as project
-IR1 = wx.NewId()
-IR2 = wx.NewId()
-IR3 = wx.NewId()
-PR1 = wx.NewId()
-PR2 = wx.NewId()
-PR3 = wx.NewId()
-Neuronavigate = wx.NewId()
-Corregistration = wx.NewId()
-GetPoint = wx.NewId()
+import invesalius.data.coordinates as dco
+import invesalius.data.coregistration as dcr
+import invesalius.data.trackers as dt
+import invesalius.data.trigger as trig
+import invesalius.gui.dialogs as dlg
+import invesalius.gui.widgets.foldpanelbar as fpb
+import invesalius.gui.widgets.colourselect as csel
+
 class TaskPanel(wx.Panel):
-    """
-    This panel works as a "frame", drawing a white margin arround 
-    the panel that really matters (InnerTaskPanel).
-    """
     def __init__(self, parent):
-        # note: don't change this class!!!
         wx.Panel.__init__(self, parent)
         inner_panel = InnerTaskPanel(self)
         sizer = wx.BoxSizer(wx.HORIZONTAL)
-        sizer.Add(inner_panel, 1, wx.EXPAND | wx.GROW | wx.BOTTOM | wx.RIGHT |
-                  wx.LEFT, 8)
+        sizer.Add(inner_panel, 1, wx.EXPAND|wx.GROW|wx.BOTTOM|wx.RIGHT |
+                  wx.LEFT, 7)
         sizer.Fit(self)
         self.SetSizer(sizer)
         self.Update()
         self.SetAutoLayout(1)
+
 class InnerTaskPanel(wx.Panel):
+    def __init__(self, parent):
+        wx.Panel.__init__(self, parent)
+        default_colour = self.GetBackgroundColour()
+        background_colour = wx.Colour(255,255,255)
+        self.SetBackgroundColour(background_colour)
+
+        txt_nav = wx.StaticText(self, -1, _('Select fiducials and navigate'),
+                                size=wx.Size(90, 20))
+        txt_nav.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
+
+        # Create horizontal sizer to represent lines in the panel
+        txt_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        txt_sizer.Add(txt_nav, 1, wx.EXPAND|wx.GROW, 5)
+
+        # Fold panel which contains navigation configurations
+        fold_panel = FoldPanel(self)
+        fold_panel.SetBackgroundColour(default_colour)
+
+
+        # Add line sizer into main sizer
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+        main_sizer.Add(txt_sizer, 0, wx.GROW|wx.EXPAND|wx.LEFT|wx.RIGHT, 5)
+        main_sizer.Add(fold_panel, 1, wx.GROW|wx.EXPAND|wx.LEFT|wx.RIGHT, 5)
+        main_sizer.AddSpacer(5)
+        main_sizer.Fit(self)
+
+        self.SetSizerAndFit(main_sizer)
+        self.Update()
+        self.SetAutoLayout(1)
+        self.sizer = main_sizer
+
+
+class FoldPanel(wx.Panel):
     def __init__(self, parent):
-        wx.Panel.__init__(self, parent, size=wx.Size(320,300))
-        self.SetBackgroundColour(wx.Colour(221, 221, 221, 255))
+        wx.Panel.__init__(self, parent)
+
+        inner_panel = InnerFoldPanel(self)
+
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        sizer.Add(inner_panel, 0, wx.EXPAND|wx.GROW)
+        sizer.Fit(self)
+
+        self.SetSizerAndFit(sizer)
+        self.Update()
         self.SetAutoLayout(1)
-        self.__bind_events()
-        self.aux_img_ref1 = 0
-        self.aux_img_ref2 = 0
-        self.aux_img_ref3 = 0
-        self.flagpoint = 0
-        self.aux_plh_ref1 = 1
-        self.aux_plh_ref2 = 1
-        self.aux_plh_ref3 = 1
-        self.a = 0, 0, 0
-        self.coord1a = (0, 0, 0)
-        self.coord2a = (0, 0, 0)
-        self.coord3a = (0, 0, 0)
-        self.coord1b = (0, 0, 0)
-        self.coord2b = (0, 0, 0)
-        self.coord3b = (0, 0, 0)
-        self.correg = None
-                
-        self.button_img_ref1 = wx.ToggleButton(self, IR1, label = 'TEI', size = wx.Size(30,23))
-        self.button_img_ref1.Bind(wx.EVT_TOGGLEBUTTON, self.Img_Ref_ToggleButton1)
-        
-        self.button_img_ref2 = wx.ToggleButton(self, IR2, label = 'TDI', size = wx.Size(30,23))
-        self.button_img_ref2.Bind(wx.EVT_TOGGLEBUTTON, self.Img_Ref_ToggleButton2)
-        
-        self.button_img_ref3 = wx.ToggleButton(self, IR3, label = 'FNI', size = wx.Size(30,23))
-        self.button_img_ref3.Bind(wx.EVT_TOGGLEBUTTON, self.Img_Ref_ToggleButton3)
-
-        self.button_plh_ref1 = wx.Button(self, PR1, label = 'TEP', size = wx.Size(30,23))
-        self.button_plh_ref2 = wx.Button(self, PR2, label = 'TDP', size = wx.Size(30,23))
-        self.button_plh_ref3 = wx.Button(self, PR3, label = 'FNP', size = wx.Size(30,23))
-        self.button_crg = wx.Button(self, Corregistration, label = 'Corregistrate')
-        self.button_getpoint = wx.Button(self, GetPoint, label = 'GP', size = wx.Size(23,23))
-        self.Bind(wx.EVT_BUTTON, self.Buttons)
-                       
-        self.button_neuronavigate = wx.ToggleButton(self, Neuronavigate, "Neuronavigate")
-        self.button_neuronavigate.Bind(wx.EVT_TOGGLEBUTTON, self.Neuronavigate_ToggleButton)
-        
-        self.numCtrl1a = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1a', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2a = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2a', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3a = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3a', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl1b = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1b', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2b = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2b', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3b = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3b', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl1c = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1c', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2c = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2c', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3c = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3c', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl1d = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1d', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2d = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2d', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3d = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3d', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl1e = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1e', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2e = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2e', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3e = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3e', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl1f = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1f', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2f = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2f', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3f = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3f', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl1g = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl1g', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl2g = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl2g', parent=self, integerWidth = 4, fractionWidth = 1)
-        self.numCtrl3g = wx.lib.masked.numctrl.NumCtrl(
-            name='numCtrl3g', parent=self, integerWidth = 4, fractionWidth = 1)
-
-        RefImg_sizer1 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        RefImg_sizer1.AddMany([ (self.button_img_ref1),
-                                (self.numCtrl1a),
-                                (self.numCtrl2a),
-                                (self.numCtrl3a)])
-        
-        RefImg_sizer2 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        RefImg_sizer2.AddMany([ (self.button_img_ref2),
-                                (self.numCtrl1b),
-                                (self.numCtrl2b),
-                                (self.numCtrl3b)])
-        
-        RefImg_sizer3 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        RefImg_sizer3.AddMany([ (self.button_img_ref3),
-                                (self.numCtrl1c),
-                                (self.numCtrl2c),
-                                (self.numCtrl3c)])
-        
-        RefPlh_sizer1 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        RefPlh_sizer1.AddMany([ (self.button_plh_ref1, 0, wx.GROW|wx.EXPAND),
-                                (self.numCtrl1d, wx.RIGHT),
-                                (self.numCtrl2d),
-                                (self.numCtrl3d, wx.LEFT)])
-        
-        RefPlh_sizer2 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        RefPlh_sizer2.AddMany([ (self.button_plh_ref2, 0, wx.GROW|wx.EXPAND),
-                                (self.numCtrl1e, 0, wx.RIGHT),
-                                (self.numCtrl2e),
-                                (self.numCtrl3e, 0, wx.LEFT)])
-        
-        RefPlh_sizer3 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        RefPlh_sizer3.AddMany([ (self.button_plh_ref3, 0, wx.GROW|wx.EXPAND),
-                                (self.numCtrl1f, wx.RIGHT),
-                                (self.numCtrl2f),
-                                (self.numCtrl3f, wx.LEFT)])
-        
-        Buttons_sizer4 = wx.FlexGridSizer(rows=1, cols=3, hgap=5, vgap=5)
-        Buttons_sizer4.AddMany([ (self.button_crg, wx.RIGHT),
-                                (self.button_neuronavigate, wx.LEFT)])
-        
-        GetPoint_sizer5 = wx.FlexGridSizer(rows=1, cols=4, hgap=5, vgap=5)
-        GetPoint_sizer5.AddMany([ (self.button_getpoint, 0, wx.GROW|wx.EXPAND),
-                                (self.numCtrl1g, wx.RIGHT),
-                                (self.numCtrl2g),
-                                (self.numCtrl3g, wx.LEFT)])
-        
-        text = wx.StaticText(self, -1, 'Neuronavigator')
+class InnerFoldPanel(wx.Panel):
+    def __init__(self, parent):
+        wx.Panel.__init__(self, parent)
+        default_colour = wx.SystemSettings_GetColour(wx.SYS_COLOUR_MENUBAR)
+        self.SetBackgroundColour(default_colour)
+
+        # Fold panel and its style settings
+        # FIXME: If we dont insert a value in size or if we set wx.DefaultSize,
+        # the fold_panel doesnt show. This means that, for some reason, Sizer
+        # is not working properly in this panel. It might be on some child or
+        # parent panel. Perhaps we need to insert the item into the sizer also...
+        # Study this.
+
+        fold_panel = fpb.FoldPanelBar(self, -1, wx.DefaultPosition,
+                                      (10, 293), 0, fpb.FPB_SINGLE_FOLD)
+
+        # Fold panel style
+        style = fpb.CaptionBarStyle()
+        style.SetCaptionStyle(fpb.CAPTIONBAR_GRADIENT_V)
+        style.SetFirstColour(default_colour)
+        style.SetSecondColour(default_colour)
+
+        # Fold 1 - Navigation panel
+        item = fold_panel.AddFoldPanel(_("Neuronavigation"), collapsed=True)
+        ntw = NeuronavigationPanel(item)
+
+        fold_panel.ApplyCaptionStyle(item, style)
+        fold_panel.AddFoldPanelWindow(item, ntw, Spacing= 0,
+                                      leftSpacing=0, rightSpacing=0)
+        fold_panel.Expand(fold_panel.GetFoldPanel(0))
+
+        # Fold 2 - Markers panel
+        item = fold_panel.AddFoldPanel(_("Extra tools"), collapsed=True)
+        mtw = MarkersPanel(item)
+
+        fold_panel.ApplyCaptionStyle(item, style)
+        fold_panel.AddFoldPanelWindow(item, mtw, Spacing= 0,
+                                      leftSpacing=0, rightSpacing=0)
+
-        Ref_sizer = wx.FlexGridSizer(rows=9, cols=1, hgap=5, vgap=5)
-        Ref_sizer.AddGrowableCol(0, 1)
-        Ref_sizer.AddGrowableRow(0, 1)
-        Ref_sizer.AddGrowableRow(1, 1)
-        Ref_sizer.AddGrowableRow(2, 1)
-        Ref_sizer.AddGrowableRow(3, 1)
-        Ref_sizer.AddGrowableRow(4, 1)
-        Ref_sizer.AddGrowableRow(5, 1)
-        Ref_sizer.AddGrowableRow(6, 1)
-        Ref_sizer.AddGrowableRow(7, 1)
-        Ref_sizer.AddGrowableRow(8, 1)
-        Ref_sizer.SetFlexibleDirection(wx.BOTH)
-        Ref_sizer.AddMany([ (text, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (RefImg_sizer1, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (RefImg_sizer2, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (RefImg_sizer3, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (RefPlh_sizer1, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (RefPlh_sizer2, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (RefPlh_sizer3, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (Buttons_sizer4, 0, wx.ALIGN_CENTER_HORIZONTAL),
-                            (GetPoint_sizer5, 0, wx.ALIGN_CENTER_HORIZONTAL)])
+        # Check box for camera update in volume rendering during navigation
+        tooltip = wx.ToolTip(_("Update camera in volume"))
+        checkcamera = wx.CheckBox(self, -1, _('Volume camera'))
+        checkcamera.SetToolTip(tooltip)
+        checkcamera.SetValue(True)
+        checkcamera.Bind(wx.EVT_CHECKBOX, partial(self.UpdateVolumeCamera, ctrl=checkcamera))
+
+        # Check box for camera update in volume rendering during navigation
+        tooltip = wx.ToolTip(_("Enable external trigger for creating markers"))
+        checktrigger = wx.CheckBox(self, -1, _('External trigger'))
+        checktrigger.SetToolTip(tooltip)
+        checktrigger.SetValue(False)
+        checktrigger.Bind(wx.EVT_CHECKBOX, partial(self.UpdateExternalTrigger, ctrl=checktrigger))
+
+        if sys.platform != 'win32':
+            checkcamera.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
+            checktrigger.SetWindowVariant(wx.WINDOW_VARIANT_SMALL)
+
+        line_sizer = wx.BoxSizer(wx.HORIZONTAL)
+        line_sizer.Add(checkcamera, 0, wx.ALIGN_LEFT | wx.RIGHT | wx.LEFT, 5)
+        line_sizer.Add(checktrigger, 1,wx.ALIGN_RIGHT | wx.RIGHT | wx.LEFT, 5)
+        line_sizer.Fit(self)
+
+        # Panel sizer to expand fold panel
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        sizer.Add(fold_panel, 0, wx.GROW|wx.EXPAND)
+        sizer.Add(line_sizer, 1, wx.GROW | wx.EXPAND)
+        sizer.Fit(self)
+
+        self.SetSizer(sizer)
+        self.Update()
+        self.SetAutoLayout(1)
+    def UpdateExternalTrigger(self, evt, ctrl):
+        Publisher.sendMessage('Update trigger state', ctrl.GetValue())
+
+    def UpdateVolumeCamera(self, evt, ctrl):
+        Publisher.sendMessage('Update volume camera state', ctrl.GetValue())
+
+
+
+
+class NeuronavigationPanel(wx.Panel):
+    def __init__(self, parent):
+        wx.Panel.__init__(self, parent)
+        default_colour = wx.SystemSettings_GetColour(wx.SYS_COLOUR_MENUBAR)
+        self.SetBackgroundColour(default_colour)
+
+        self.SetAutoLayout(1)
+
+        self.__bind_events()
+
+        # Initialize global variables
+        self.fiducials = np.full([6, 3], np.nan)
+        self.correg = None
+        self.current_coord = 0, 0, 0
+        self.trk_init = None
+        self.trigger = None
+        self.trigger_state = False
+
+        self.tracker_id = const.DEFAULT_TRACKER
+        self.ref_mode_id = const.DEFAULT_REF_MODE
+
+        # Initialize list of buttons and numctrls for wx objects
+        self.btns_coord = [None] * 7
+        self.numctrls_coord = [list(), list(), list(), list(), list(), list(), list()]
+
+        # ComboBox for spatial tracker device selection
+        tooltip = wx.ToolTip(_("Choose the tracking device"))
+        choice_trck = wx.ComboBox(self, -1, "",
+                                  choices=const.TRACKER, style=wx.CB_DROPDOWN|wx.CB_READONLY)
+        choice_trck.SetToolTip(tooltip)
+        choice_trck.SetSelection(const.DEFAULT_TRACKER)
+        choice_trck.Bind(wx.EVT_COMBOBOX, partial(self.OnChoiceTracker, ctrl=choice_trck))
+
+        # ComboBox for tracker reference mode
+        tooltip = wx.ToolTip(_("Choose the navigation reference mode"))
+        choice_ref = wx.ComboBox(self, -1, "",
+                                 choices=const.REF_MODE, style=wx.CB_DROPDOWN|wx.CB_READONLY)
+        choice_ref.SetSelection(const.DEFAULT_REF_MODE)
+        choice_ref.SetToolTip(tooltip)
+        choice_ref.Bind(wx.EVT_COMBOBOX, partial(self.OnChoiceRefMode, ctrl=choice_trck))
+
+        # Toggle buttons for image fiducials
+        btns_img = const.BTNS_IMG
+        tips_img = const.TIPS_IMG
+
+        for k in btns_img:
+            n = btns_img[k].keys()[0]
+            lab = btns_img[k].values()[0]
+            self.btns_coord[n] = wx.ToggleButton(self, k, label=lab, size=wx.Size(30, 23))
+            self.btns_coord[n].SetToolTip(tips_img[n])
+            self.btns_coord[n].Bind(wx.EVT_TOGGLEBUTTON, self.OnImageFiducials)
+
+        # Push buttons for tracker fiducials
+        btns_trk = const.BTNS_TRK
+        tips_trk = const.TIPS_TRK
+
+        for k in btns_trk:
+            n = btns_trk[k].keys()[0]
+            lab = btns_trk[k].values()[0]
+            self.btns_coord[n] = wx.Button(self, k, label=lab, size=wx.Size(30, 23))
+            self.btns_coord[n].SetToolTip(tips_trk[n-3])
+            # Excepetion for event of button that set image coordinates
+            if n == 6:
+                self.btns_coord[n].Bind(wx.EVT_BUTTON, self.OnSetImageCoordinates)
+            else:
+                self.btns_coord[n].Bind(wx.EVT_BUTTON, self.OnTrackerFiducials)
+
+        # TODO: Find a better allignment between FRE, text and navigate button
+        txt_fre = wx.StaticText(self, -1, _('FRE:'))
+
+        # Fiducial registration error text box
+        tooltip = wx.ToolTip(_("Fiducial registration error"))
+        txtctrl_fre = wx.TextCtrl(self, value="", size=wx.Size(60, -1), style=wx.TE_CENTRE)
+        txtctrl_fre.SetFont(wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD))
+        txtctrl_fre.SetBackgroundColour('WHITE')
+        txtctrl_fre.SetEditable(0)
+        txtctrl_fre.SetToolTip(tooltip)
+
+        # Toggle button for neuronavigation
+        tooltip = wx.ToolTip(_("Start navigation"))
+        btn_nav = wx.ToggleButton(self, -1, _("Navigate"), size=wx.Size(80, -1))
+        btn_nav.SetToolTip(tooltip)
+        btn_nav.Bind(wx.EVT_TOGGLEBUTTON, partial(self.OnNavigate, btn=(btn_nav, choice_trck, choice_ref, txtctrl_fre)))
+
+        # Image and tracker coordinates number controls
+        for m in range(0, 7):
+            for n in range(0, 3):
+                self.numctrls_coord[m].append(
+                    wx.lib.masked.numctrl.NumCtrl(parent=self, integerWidth=4, fractionWidth=1))
+
+        # Sizers to group all GUI objects
+        choice_sizer = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
+        choice_sizer.AddMany([(choice_trck, wx.LEFT),
+                              (choice_ref, wx.RIGHT)])
+
+        coord_sizer = wx.GridBagSizer(hgap=5, vgap=5)
+
+        for m in range(0, 7):
+            coord_sizer.Add(self.btns_coord[m], pos=wx.GBPosition(m, 0))
+            for n in range(0, 3):
+                coord_sizer.Add(self.numctrls_coord[m][n], pos=wx.GBPosition(m, n+1))
+                if m in range(1, 6):
+                    self.numctrls_coord[m][n].SetEditable(False)
+
+        nav_sizer = wx.FlexGridSizer(rows=1, cols=3, hgap=5, vgap=5)
+        nav_sizer.AddMany([(txt_fre, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
+                           (txtctrl_fre, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL),
+                           (btn_nav, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)])
+
+        group_sizer = wx.FlexGridSizer(rows=9, cols=1, hgap=5, vgap=5)
+        group_sizer.AddGrowableCol(0, 1)
+        group_sizer.AddGrowableRow(0, 1)
+        group_sizer.AddGrowableRow(1, 1)
+        group_sizer.AddGrowableRow(2, 1)
+        group_sizer.SetFlexibleDirection(wx.BOTH)
+        group_sizer.AddMany([(choice_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL),
+                             (coord_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL),
+                             (nav_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL)])
+
         main_sizer = wx.BoxSizer(wx.HORIZONTAL)
-        main_sizer.Add(Ref_sizer, 1, wx.ALIGN_CENTER_HORIZONTAL, 10)
+        main_sizer.Add(group_sizer, 1, wx.ALIGN_CENTER_HORIZONTAL, 10)
         self.sizer = main_sizer
         self.SetSizer(main_sizer)
         self.Fit()
-        tooltip = wx.ToolTip("Pick the coordinates x, y, z in the image")
-        self.button_img_ref1.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Pick the coordinates x, y, z in the image")
-        self.button_img_ref2.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Pick the coordinates x, y, z in the image")
-        self.button_img_ref3.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Pick the coordinates x, y, z in the space")
-        self.button_plh_ref1.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Pick the coordinates x, y, z in the space")
-        self.button_plh_ref2.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Pick the coordinates x, y, z in the space")
-        self.button_plh_ref3.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1a.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1b.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1c.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1d.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1e.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1f.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("X Coordinate")
-        self.numCtrl1g.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2a.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2b.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2c.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2d.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2e.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2f.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Y Coordinate")
-        self.numCtrl2g.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3a.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3b.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3c.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3d.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3e.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3f.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Z Coordinate")
-        self.numCtrl3g.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Corregistration of the real position with the image position")
-        self.button_crg.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Neuronavigation")
-        self.button_neuronavigate.SetToolTip(tooltip)
-        tooltip = wx.ToolTip("Get Cross Center Coordinates")
-        self.button_getpoint.SetToolTip(tooltip)
-        
     def __bind_events(self):
-        Publisher.subscribe(self.__update_points_img, 'Update cross position')
-        Publisher.subscribe(self.__update_points_plh, 'Update plh position')
-         
-    def __update_points_img(self, pubsub_evt):
-        x, y, z = pubsub_evt.data[1]
-        self.a = x, y, z
-        if self.aux_img_ref1 == 0: 
-            self.numCtrl1a.SetValue(x)
-            self.numCtrl2a.SetValue(y)
-            self.numCtrl3a.SetValue(z)
-        if self.aux_img_ref2 == 0:   
-            self.numCtrl1b.SetValue(x)
-            self.numCtrl2b.SetValue(y)
-            self.numCtrl3b.SetValue(z)
-        if self.aux_img_ref3 == 0:
-            self.numCtrl1c.SetValue(x)
-            self.numCtrl2c.SetValue(y)
-            self.numCtrl3c.SetValue(z)
+        Publisher.subscribe(self.LoadImageFiducials, 'Load image fiducials')
+        Publisher.subscribe(self.UpdateTriggerState, 'Update trigger state')
+        Publisher.subscribe(self.UpdateImageCoordinates, 'Set ball reference position')
+
+    def LoadImageFiducials(self, pubsub_evt):
+        marker_id = pubsub_evt.data[0]
+        coord = pubsub_evt.data[1]
+        for n in const.BTNS_IMG:
+            btn_id = const.BTNS_IMG[n].keys()[0]
+            fid_id = const.BTNS_IMG[n].values()[0]
+            if marker_id == fid_id and not self.btns_coord[btn_id].GetValue():
+                self.btns_coord[btn_id].SetValue(True)
+                self.fiducials[btn_id, :] = coord[0:3]
+                for m in [0, 1, 2]:
+                    self.numctrls_coord[btn_id][m].SetValue(coord[m])
+
+    def UpdateImageCoordinates(self, pubsub_evt):
+        # TODO: Change from world coordinates to matrix coordinates. They are better for multi software communication.
+        self.current_coord = pubsub_evt.data
+        for m in [0, 1, 2, 6]:
+            if m == 6 and self.btns_coord[m].IsEnabled():
+                for n in [0, 1, 2]:
+                    self.numctrls_coord[m][n].SetValue(self.current_coord[n])
+            elif m != 6 and not self.btns_coord[m].GetValue():
+                # btn_state = self.btns_coord[m].GetValue()
+                # if not btn_state:
+                for n in [0, 1, 2]:
+                    self.numctrls_coord[m][n].SetValue(self.current_coord[n])
+
+    def UpdateTriggerState (self, pubsub_evt):
+        self.trigger_state = pubsub_evt.data
+
+    def OnChoiceTracker(self, evt, ctrl):
+        if evt:
+            choice = evt.GetSelection()
+        else:
+            choice = self.tracker_id
+
+        if self.trk_init:
+            trck = self.trk_init[0]
+        else:
+            trck = None
+
+        # Conditions check if click was on current selection and if any other tracker
+        # has been initialized before
+        if trck and choice != 6:
+            self.ResetTrackerFiducials()
+            self.trk_init = dt.TrackerConnection(self.tracker_id, 'disconnect')
+            self.tracker_id = choice
+            if not self.trk_init[0]:
+                self.trk_init = dt.TrackerConnection(self.tracker_id, 'connect')
+                if not self.trk_init[0]:
+                    dlg.NavigationTrackerWarning(self.tracker_id, self.trk_init[1])
+                    ctrl.SetSelection(0)
+                    print "Tracker not connected!"
+                else:
+                    ctrl.SetSelection(self.tracker_id)
+                    print "Tracker connected!"
+        elif choice == 6:
+            if trck:
+                self.trk_init = dt.TrackerConnection(self.tracker_id, 'disconnect')
+                if not self.trk_init[0]:
+                    dlg.NavigationTrackerWarning(self.tracker_id, 'disconnect')
+                    self.tracker_id = 0
+                    ctrl.SetSelection(self.tracker_id)
+                    print "Tracker disconnected!"
+                else:
+                    print "Tracker still connected!"
+            else:
+                ctrl.SetSelection(self.tracker_id)
+
+        else:
+            # If trk_init is None try to connect. If doesn't succeed show dialog.
+            if choice:
+                self.tracker_id = choice
+                self.trk_init = dt.TrackerConnection(self.tracker_id, 'connect')
+                if not self.trk_init[0]:
+                    dlg.NavigationTrackerWarning(self.tracker_id, self.trk_init[1])
+                    self.tracker_id = 0
+                    ctrl.SetSelection(self.tracker_id)
+
+    def OnChoiceRefMode(self, evt, ctrl):
+        # When ref mode is changed the tracker coords are set to zero
+        self.ref_mode_id = evt.GetSelection()
+        self.ResetTrackerFiducials()
+        # Some trackers do not accept restarting within this time window
+        # TODO: Improve the restarting of trackers after changing reference mode
+        # self.OnChoiceTracker(None, ctrl)
+        print "Reference mode changed!"
+
+    def OnSetImageCoordinates(self, evt):
+        # FIXME: Cross does not update in last clicked slice, only on the other two
+        btn_id = const.BTNS_TRK[evt.GetId()].keys()[0]
+
+        wx, wy, wz = self.numctrls_coord[btn_id][0].GetValue(), \
+                     self.numctrls_coord[btn_id][1].GetValue(), \
+                     self.numctrls_coord[btn_id][2].GetValue()
+
+        Publisher.sendMessage('Set ball reference position', (wx, wy, wz))
+        Publisher.sendMessage('Set camera in volume', (wx, wy, wz))
+        Publisher.sendMessage('Co-registered points', (wx, wy, wz))
+        Publisher.sendMessage('Update cross position', (wx, wy, wz))
+
+    def OnImageFiducials(self, evt):
+        btn_id = const.BTNS_IMG[evt.GetId()].keys()[0]
+        marker_id = const.BTNS_IMG[evt.GetId()].values()[0]
+
+        if self.btns_coord[btn_id].GetValue():
+            coord = self.numctrls_coord[btn_id][0].GetValue(),\
+                    self.numctrls_coord[btn_id][1].GetValue(),\
+                    self.numctrls_coord[btn_id][2].GetValue()
+
+            self.fiducials[btn_id, :] = coord[0:3]
+            Publisher.sendMessage('Create marker', (coord, marker_id))
+        else:
+            for n in [0, 1, 2]:
+                self.numctrls_coord[btn_id][n].SetValue(self.current_coord[n])
+
+            self.fiducials[btn_id, :] = np.nan
+            Publisher.sendMessage('Delete fiducial marker', marker_id)
+
+    def OnTrackerFiducials(self, evt):
+        btn_id = const.BTNS_TRK[evt.GetId()].keys()[0]
+        coord = None
+
+        if self.trk_init and self.tracker_id:
+            coord = dco.GetCoordinates(self.trk_init, self.tracker_id, self.ref_mode_id)
+        else:
+            dlg.NavigationTrackerWarning(0, 'choose')
+
+        # Update number controls with tracker coordinates
+        if coord is not None:
+            self.fiducials[btn_id, :] = coord[0:3]
+            for n in [0, 1, 2]:
+                self.numctrls_coord[btn_id][n].SetValue(float(coord[n]))
+
+    def OnNavigate(self, evt, btn):
+        btn_nav = btn[0]
+        choice_trck = btn[1]
+        choice_ref = btn[2]
+        txtctrl_fre = btn[3]
+
+        nav_id = btn_nav.GetValue()
+        if nav_id:
+            if np.isnan(self.fiducials).any():
+                dlg.InvalidFiducials()
+                btn_nav.SetValue(False)
+
+            else:
+                tooltip = wx.ToolTip(_("Stop neuronavigation"))
+                btn_nav.SetToolTip(tooltip)
+
+                # Disable all navigation buttons
+                choice_ref.Enable(False)
+                choice_trck.Enable(False)
+                for btn_c in self.btns_coord:
+                    btn_c.Enable(False)
+
+                m, q1, minv = db.base_creation(self.fiducials[0:3, :])
+                n, q2, ninv = db.base_creation(self.fiducials[3::, :])
+
+                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)
+
+                txtctrl_fre.SetValue(str(round(fre, 2)))
+                if fre <= 3:
+                    txtctrl_fre.SetBackgroundColour('GREEN')
+                else:
+                    txtctrl_fre.SetBackgroundColour('RED')
+
+                if self.trigger_state:
+                    self.trigger = trig.Trigger(nav_id)
+
+                self.correg = dcr.Coregistration((minv, n, q1, q2), nav_id, tracker_mode)
+
+        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()
-        
-    def __update_points_plh(self, pubsub_evt):
-        coord = pubsub_evt.data   
-        if self.aux_plh_ref1 == 0:    
-            self.numCtrl1d.SetValue(coord[0])
-            self.numCtrl2d.SetValue(coord[1])
-            self.numCtrl3d.SetValue(coord[2])
-            self.aux_plh_ref1 = 1
-        if self.aux_plh_ref2 == 0:    
-            self.numCtrl1e.SetValue(coord[0])
-            self.numCtrl2e.SetValue(coord[1])
-            self.numCtrl3e.SetValue(coord[2])
-            self.aux_plh_ref2 = 1
-        if self.aux_plh_ref3 == 0:
-            self.numCtrl1f.SetValue(coord[0])
-            self.numCtrl2f.SetValue(coord[1])
-            self.numCtrl3f.SetValue(coord[2])
-            self.aux_plh_ref3 = 1
-           
-    def Buttons(self, evt):
-        id = evt.GetId()
-        x, y, z = self.a
-        if id == PR1:
-            self.aux_plh_ref1 = 0
-            self.coord1b = self.Coordinates()
-            coord = self.coord1b
-        elif id == PR2:
-            self.aux_plh_ref2 = 0
-            self.coord2b = self.Coordinates()
-            coord = self.coord2b
-        elif id == PR3:
-            self.aux_plh_ref3 = 0
-            self.coord3b = self.Coordinates()
-            coord = self.coord3b
-        elif id == GetPoint:
-            x, y, z = self.a
-            self.numCtrl1g.SetValue(x)
-            self.numCtrl2g.SetValue(y)
-            self.numCtrl3g.SetValue(z)
-            info = self.a, self.flagpoint
-            self.SaveCoordinates(info)
-            self.flagpoint = 1 
-        elif id == Corregistration and self.aux_img_ref1 == 1 and self.aux_img_ref2 == 1 and self.aux_img_ref3 == 1:
-            print "Coordenadas Imagem: ", self.coord1a, self.coord2a, self.coord3a
-            print "Coordenadas Polhemus: ", self.coord1b, self.coord2b, self.coord3b
-            
-            self.M, self.q1, self.Minv = db.Bases(self.coord1a, self.coord2a, self.coord3a).Basecreation()
-            self.N, self.q2, self.Ninv = db.Bases(self.coord1b, self.coord2b, self.coord3b).Basecreation()
-                
-        if self.aux_plh_ref1 == 0 or self.aux_plh_ref2 == 0 or self.aux_plh_ref3 == 0:
-            Publisher.sendMessage('Update plh position', coord)         
-   
-    def Coordinates(self):
-        #Get Polhemus points for base creation       
-        ser = serial.Serial(0)
-        ser.write("Y")       
-        ser.write("P")
-        str = ser.readline()
-        ser.write("Y")
-        str = str.replace("\r\n","")
-        str = str.replace("-"," -")
-        aostr = [s for s in str.split()]
-        #aoflt -> 0:letter 1:x 2:y 3:z
-        aoflt = [float(aostr[1]), float(aostr[2]), float(aostr[3]),
-                  float(aostr[4]), float(aostr[5]), float(aostr[6])]      
-        ser.close()
-        #Unit change: inches to millimeters
-        x = 25.4
-        y = 25.4
-        z = -25.4
-
-        coord = (aoflt[0]*x, aoflt[1]*y, aoflt[2]*z)
-        return coord
-    
-    def Img_Ref_ToggleButton1(self, evt):
-        id = evt.GetId()
-        flag1 = self.button_img_ref1.GetValue()
-        x, y, z = self.a
-        if flag1 == True:
-            self.coord1a = x, y, z
-            self.aux_img_ref1 = 1
-        elif flag1 == False:
-            self.aux_img_ref1 = 0
-            self.coord1a = (0, 0, 0)
-            self.numCtrl1a.SetValue(x)
-            self.numCtrl2a.SetValue(y)
-            self.numCtrl3a.SetValue(z)
-            
-    def Img_Ref_ToggleButton2(self, evt):
-        id = evt.GetId()
-        flag2 = self.button_img_ref2.GetValue()
-        x, y, z = self.a
-        if flag2 == True:
-            self.coord2a = x, y, z
-            self.aux_img_ref2 = 1
-        elif flag2 == False:
-            self.aux_img_ref2 = 0
-            self.coord2a = (0, 0, 0)
-            self.numCtrl1b.SetValue(x)
-            self.numCtrl2b.SetValue(y)
-            self.numCtrl3b.SetValue(z)
-            
-    def Img_Ref_ToggleButton3(self, evt):
-        id = evt.GetId()
-        flag3 = self.button_img_ref3.GetValue()
-        x, y, z = self.a
-        if flag3 == True:
-            self.coord3a = x, y, z
-            self.aux_img_ref3 = 1
-        elif flag3 == False:
-            self.aux_img_ref3 = 0
-            self.coord3a = (0, 0, 0)
-            self.numCtrl1c.SetValue(x)
-            self.numCtrl2c.SetValue(y)
-            self.numCtrl3c.SetValue(z)
-      
-    def Neuronavigate_ToggleButton(self, evt):
-        id = evt.GetId()
-        flag4 = self.button_neuronavigate.GetValue()
-        bases = self.Minv, self.N, self.q1, self.q2
-        if flag4 == True:
-            self.correg = dcr.Corregister(bases, flag4)
-        elif flag4 == False:
             self.correg.stop()
+
+    def ResetTrackerFiducials(self):
+        for m in range(3, 6):
+            for n in range(0, 3):
+                self.numctrls_coord[m][n].SetValue(0.0)
+
+
+class MarkersPanel(wx.Panel):
+    def __init__(self, parent):
+        wx.Panel.__init__(self, parent)
+        default_colour = wx.SystemSettings_GetColour(wx.SYS_COLOUR_MENUBAR)
+        self.SetBackgroundColour(default_colour)
+
+        self.SetAutoLayout(1)
+
+        self.__bind_events()
+
+        self.current_coord = 0, 0, 0
+        self.list_coord = []
+        self.marker_ind = 0
+
+        self.marker_colour = (0.0, 0.0, 1.)
+        self.marker_size = 4
+
+        # Change marker size
+        spin_size = wx.SpinCtrl(self, -1, "", size=wx.Size(40, 23))
+        spin_size.SetRange(1, 99)
+        spin_size.SetValue(self.marker_size)
+        spin_size.Bind(wx.EVT_TEXT, partial(self.OnSelectSize, ctrl=spin_size))
+        spin_size.Bind(wx.EVT_SPINCTRL, partial(self.OnSelectSize, ctrl=spin_size))
+
+        # Marker colour select
+        select_colour = csel.ColourSelect(self, -1, colour=[255*s for s in self.marker_colour], size=wx.Size(20, 23))
+        select_colour.Bind(csel.EVT_COLOURSELECT, partial(self.OnSelectColour, ctrl=select_colour))
+
+        btn_create = wx.Button(self, -1, label=_('Create marker'), size=wx.Size(135, 23))
+        btn_create.Bind(wx.EVT_BUTTON, self.OnCreateMarker)
+
+        sizer_create = wx.FlexGridSizer(rows=1, cols=3, hgap=5, vgap=5)
+        sizer_create.AddMany([(spin_size, 1),
+                              (select_colour, 0),
+                              (btn_create, 0)])
+
+        # Buttons to save and load markers and to change its visibility as well
+        btn_save = wx.Button(self, -1, label=_('Save'), size=wx.Size(65, 23))
+        btn_save.Bind(wx.EVT_BUTTON, self.OnSaveMarkers)
+
+        btn_load = wx.Button(self, -1, label=_('Load'), size=wx.Size(65, 23))
+        btn_load.Bind(wx.EVT_BUTTON, self.OnLoadMarkers)
+
+        btn_visibility = wx.ToggleButton(self, -1, _("Hide"), size=wx.Size(65, 23))
+        btn_visibility.Bind(wx.EVT_TOGGLEBUTTON, partial(self.OnMarkersVisibility, ctrl=btn_visibility))
+
+        sizer_btns = wx.FlexGridSizer(rows=1, cols=3, hgap=5, vgap=5)
+        sizer_btns.AddMany([(btn_save, 1, wx.RIGHT),
+                            (btn_load, 0, wx.LEFT | wx.RIGHT),
+                            (btn_visibility, 0, wx.LEFT)])
+
+        # Buttons to delete or remove markers
+        btn_delete_single = wx.Button(self, -1, label=_('Remove'), size=wx.Size(65, 23))
+        btn_delete_single.Bind(wx.EVT_BUTTON, self.OnDeleteSingleMarker)
+
+        btn_delete_all = wx.Button(self, -1, label=_('Delete all markers'), size=wx.Size(135, 23))
+        btn_delete_all.Bind(wx.EVT_BUTTON, self.OnDeleteAllMarkers)
+
+        sizer_delete = wx.FlexGridSizer(rows=1, cols=2, hgap=5, vgap=5)
+        sizer_delete.AddMany([(btn_delete_single, 1, wx.RIGHT),
+                              (btn_delete_all, 0, wx.LEFT)])
+
+        # List of markers
+        self.lc = wx.ListCtrl(self, -1, style=wx.LC_REPORT, size=wx.Size(0,120))
+        self.lc.InsertColumn(0, '#')
+        self.lc.InsertColumn(1, 'X')
+        self.lc.InsertColumn(2, 'Y')
+        self.lc.InsertColumn(3, 'Z')
+        self.lc.InsertColumn(4, 'ID')
+        self.lc.SetColumnWidth(0, 28)
+        self.lc.SetColumnWidth(1, 50)
+        self.lc.SetColumnWidth(2, 50)
+        self.lc.SetColumnWidth(3, 50)
+        self.lc.SetColumnWidth(4, 50)
+        self.lc.Bind(wx.EVT_LIST_ITEM_RIGHT_CLICK, self.OnListEditMarkerId)
+
+        # Add all lines into main sizer
+        group_sizer = wx.BoxSizer(wx.VERTICAL)
+        group_sizer.Add(sizer_create, 0, wx.TOP | wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
+        group_sizer.Add(sizer_btns, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
+        group_sizer.Add(sizer_delete, 0, wx.BOTTOM | wx.ALIGN_CENTER_HORIZONTAL, 5)
+        group_sizer.Add(self.lc, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_HORIZONTAL, 5)
+        group_sizer.Fit(self)
+
+        self.SetSizer(group_sizer)
+        self.Update()
+
+    def __bind_events(self):
+        Publisher.subscribe(self.UpdateCurrentCoord, 'Set ball reference position')
+        Publisher.subscribe(self.OnDeleteSingleMarker, 'Delete fiducial marker')
+        Publisher.subscribe(self.OnCreateMarker, 'Create marker')
+
+    def UpdateCurrentCoord(self, pubsub_evt):
+        self.current_coord = pubsub_evt.data
+
+    def OnListEditMarkerId(self, evt):
+        menu_id = wx.Menu()
+        menu_id.Append(-1, _('Edit ID'))
+        menu_id.Bind(wx.EVT_MENU, self.OnMenuEditMarkerId)
+        self.PopupMenu(menu_id)
+        menu_id.Destroy()
+
+    def OnMenuEditMarkerId(self, evt):
+        id_label = dlg.EnterMarkerID(self.lc.GetItemText(self.lc.GetFocusedItem(), 4))
+        list_index = self.lc.GetFocusedItem()
+        self.lc.SetStringItem(list_index, 4, id_label)
+        # Add the new ID to exported list
+        self.list_coord[list_index][7] = str(id_label)
+
+    def OnDeleteAllMarkers(self, pubsub_evt):
+        self.list_coord = []
+        self.marker_ind = 0
+        Publisher.sendMessage('Remove all markers', self.lc.GetItemCount())
+        self.lc.DeleteAllItems()
+
+    def OnDeleteSingleMarker(self, evt):
+        # OnDeleteSingleMarker is used for both pubsub and button click events
+        # Pubsub is used for fiducial handle and button click for all others
+
+        if hasattr(evt, 'data'):
+            marker_id = evt.data
+            if self.lc.GetItemCount():
+                for id_n in range(self.lc.GetItemCount()):
+                    item = self.lc.GetItem(id_n, 4)
+                    if item.GetText() == marker_id:
+                        if marker_id == "LEI" or marker_id == "REI" or marker_id == "NAI":
+                            self.lc.Focus(item.GetId())
+                            break
+        else:
+            if self.lc.GetFocusedItem() is not -1 and self.lc.GetItemCount():
+                index = self.lc.GetFocusedItem()
+                del self.list_coord[index]
+                self.lc.DeleteItem(index)
+                for n in range(0, self.lc.GetItemCount()):
+                    self.lc.SetStringItem(n, 0, str(n+1))
+                self.marker_ind -= 1
+                Publisher.sendMessage('Remove marker', index)
+            elif not self.lc.GetItemCount():
+                pass
+            else:
+                dlg.NoMarkerSelected()
+
+    def OnCreateMarker(self, evt):
+        # OnCreateMarker is used for both pubsub and button click events
+        # Pubsub is used for markers created with fiducial buttons, trigger and create marker button
+        if hasattr(evt, 'data'):
+            if evt.data:
+                self.CreateMarker(evt.data[0], (0.0, 1.0, 0.0), self.marker_size, evt.data[1])
+            else:
+                self.CreateMarker(self.current_coord, self.marker_colour, self.marker_size)
+        else:
+            self.CreateMarker(self.current_coord, self.marker_colour, self.marker_size)
+
+    def OnLoadMarkers(self, evt):
+        filepath = dlg.ShowLoadMarkersDialog()
+
+        if filepath:
+            try:
+                content = [s.rstrip() for s in open(filepath)]
+                for data in content:
+                    line = [s for s in data.split()]
+                    coord = float(line[0]), float(line[1]), float(line[2])
+                    colour = float(line[3]), float(line[4]), float(line[5])
+                    size = float(line[6])
+
+                    if len(line) == 8:
+                        if line[7] == "LEI" or line[7] == "REI" or line[7] == "NAI":
+                            Publisher.sendMessage('Load image fiducials', (line[7], coord))
+                    else:
+                        line.append("")
+                    self.CreateMarker(coord, colour, size, line[7])
+            except:
+                dlg.InvalidMarkersFile()
+
+    def OnMarkersVisibility(self, evt, ctrl):
+
+        if ctrl.GetValue():
+            Publisher.sendMessage('Hide all markers',  self.lc.GetItemCount())
+            ctrl.SetLabel('Show')
+        else:
+            Publisher.sendMessage('Show all markers',  self.lc.GetItemCount())
+            ctrl.SetLabel('Hide')
+            
+    def OnSaveMarkers(self, evt):
+        filename = dlg.ShowSaveMarkersDialog("markers.txt")
+        if filename:
+            if self.list_coord:
+                text_file = open(filename, "w")
+                list_slice1 = self.list_coord[0]
+                coord = str('%.3f' %self.list_coord[0][0]) + "\t" + str('%.3f' %self.list_coord[0][1]) + "\t" + str('%.3f' %self.list_coord[0][2])
+                properties = str('%.3f' %list_slice1[3]) + "\t" + str('%.3f' %list_slice1[4]) + "\t" + str('%.3f' %list_slice1[5]) + "\t" + str('%.1f' %list_slice1[6]) + "\t" + list_slice1[7]
+                line = coord + "\t" + properties + "\n"
+                list_slice = self.list_coord[1:]
+
+                for value in list_slice:
+                    coord = str('%.3f' %value[0]) + "\t" + str('%.3f' %value[1]) + "\t" + str('%.3f' %value[2])
+                    properties = str('%.3f' %value[3]) + "\t" + str('%.3f' %value[4]) + "\t" + str('%.3f' %value[5]) + "\t" + str('%.1f' %value[6]) + "\t" + value[7]
+                    line = line + coord + "\t" + properties + "\n"
+
+                text_file.writelines(line)
+                text_file.close()
-    def SaveCoordinates(self, info):
-        #Create a file and write the points given by getpoint's button 
-        x, y, z = info[0]
-        flag = info[1]
-
-        if flag == 0:
-            text_file = open("points.txt", "w")
-            line = str('%.2f' %x) + "\t" + str('%.2f' %y) + "\t" + str('%.2f' %z) + "\n"
-            text_file.writelines(line)
-            text_file.close()
+    def OnSelectColour(self, evt, ctrl):
+        self.marker_colour = [colour/255.0 for colour in ctrl.GetValue()]
+
+    def OnSelectSize(self, evt, ctrl):
+        self.marker_size = ctrl.GetValue()
+
+    def CreateMarker(self, coord, colour, size, marker_id=""):
+        # TODO: Use matrix coordinates and not world coordinates as current method.
+        # This makes easier for inter-software comprehension.
+
+        Publisher.sendMessage('Add marker', (self.marker_ind, size, colour,  coord))
+
+        self.marker_ind += 1
+
+        # List of lists with coordinates and properties of a marker
+        line = [coord[0], coord[1], coord[2], colour[0], colour[1], colour[2], self.marker_size, marker_id]
+
+        # Adding current line to a list of all markers already created
+        if not self.list_coord:
+            self.list_coord = [line]
         else:
-            text_file = open("points.txt", "r")
-            filedata = text_file.read()
-            line = filedata + str('%.2f' %x) + "\t" + str('%.2f' %y) + "\t" + str('%.2f' %z) + "\n"
-            text_file = open("points.txt", "w")
-            text_file.write(line)
-            text_file.close()
-        
+            self.list_coord.append(line)
+
+        # Add item to list control in panel
+        num_items = self.lc.GetItemCount()
+        self.lc.InsertStringItem(num_items, str(num_items + 1))
+        self.lc.SetStringItem(num_items, 1, str(round(coord[0], 2)))
+        self.lc.SetStringItem(num_items, 2, str(round(coord[1], 2)))
+        self.lc.SetStringItem(num_items, 3, str(round(coord[2], 2)))
+        self.lc.SetStringItem(num_items, 4, str(marker_id))
+        self.lc.EnsureVisible(num_items)
@@ -1,43 +0,0 @@
-#--------------------------------------------------------------------------
-# 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.
-#--------------------------------------------------------------------------
-
-import os
-import multiprocessing
-import tempfile
-
-import vtk
-
-from nibabel import AnalyzeImage, squeeze_image
-
-def ReadAnalyze(filename):
-    anlz = squeeze_image(AnalyzeImage.from_filename(filename))
-    return anlz
-
-def ReadDirectory(dir_):
-    """ 
-    Looking for analyze files in the given directory
-    """
-    imagedata = None
-    for root, sub_folders, files in os.walk(dir_):
-        for file in files:
-            if file.split(".")[-1] == "hdr":
-                filename = os.path.join(root,file)
-                imagedata = ReadAnalyze(filename)
-                return imagedata
-    return imagedata
@@ -0,0 +1,51 @@
+#--------------------------------------------------------------------------
+# 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.
+#--------------------------------------------------------------------------
+
+import os
+
+import vtk
+import nibabel as nib
+
+import invesalius.constants as const
+
+
+def ReadOthers(dir_):
+    """
+    Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
+    remove singleton image dimensions and convert image orientation to
+    RAS+ canonical coordinate system. Analyze header does not support
+    affine transformation matrix, though cannot be converted automatically
+    to canonical orientation.
+
+    :param dir_: file path
+    :return: imagedata object
+    """
+
+    if not const.VTK_WARNING:
+        log_path = os.path.join(const.LOG_FOLDER, 'vtkoutput.txt')
+        fow = vtk.vtkFileOutputWindow()
+        fow.SetFileName(log_path)
+        ow = vtk.vtkOutputWindow()
+        ow.SetInstance(fow)
+
+    imagedata = nib.squeeze_image(nib.load(dir_))
+    imagedata = nib.as_closest_canonical(imagedata)
+    imagedata.update_header()
+
+    return imagedata
 \ No newline at end of file
@@ -0,0 +1 @@
+This folder contains all the calibration files for the installed MicronTrackers
 \ No newline at end of file
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=1Probe
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-61.602408326043872
+EndPos(0,1)=4.2184025144074082e-016
+EndPos(0,2)=-4.556586682229099e-016
+EndPos(1,0)=61.602408326043872
+EndPos(1,1)=-9.6115500328270063e-017
+EndPos(1,2)=-1.1391466705572748e-016
+
+[Facet1V2]
+EndPos(0,0)=-61.59657019736504
+EndPos(0,1)=11.949604571287503
+EndPos(0,2)=1.1391466705572748e-016
+EndPos(1,0)=-61.602408326043872
+EndPos(1,1)=4.2184025144074082e-016
+EndPos(1,2)=-4.556586682229099e-016
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=145.66478105979206
+R0,0=-8.4560706371216821e-002
+R1,0=-0.52109081782374
+R2,0=0.84930197604725266
+S1=-13.147426563284974
+R0,1=4.5008904130328986e-002
+R1,1=-0.85348236485506712
+R2,1=-0.5191743940434248
+S2=9.0630880541399712
+R0,2=0.99540126857813949
+R1,2=-5.6756022725552024e-003
+R2,2=9.5624798310161907e-002
@@ -0,0 +1,38 @@
+
+[Marker]
+FacetsCount=1
+Name=1b
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-13.977391161539257
+EndPos(0,1)=1.2440742880315269e-015
+EndPos(0,2)=-9.6300745155986073e-015
+EndPos(1,0)=13.977391161539257
+EndPos(1,1)=1.2515682934477468e-015
+EndPos(1,2)=-9.6789243286821155e-015
+
+[Facet1V2]
+EndPos(0,0)=13.977391161539257
+EndPos(0,1)=1.2515682934477468e-015
+EndPos(0,2)=-9.6789243286821155e-015
+EndPos(1,0)=14.019670530273789
+EndPos(1,1)=15.245637552880362
+EndPos(1,2)=-9.7055696812731187e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=2Coil
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-8.9266116684264851
+EndPos(0,1)=-7.9898502660127542e-016
+EndPos(0,2)=1.0214990704373533e-015
+EndPos(1,0)=8.9266116684264833
+EndPos(1,1)=-6.360897244681129e-016
+EndPos(1,2)=2.6438799470143262e-015
+
+[Facet1V2]
+EndPos(0,0)=8.9266116684264833
+EndPos(0,1)=-6.360897244681129e-016
+EndPos(0,2)=2.6438799470143262e-015
+EndPos(1,0)=9.0134937152069554
+EndPos(1,1)=-12.059011297429047
+EndPos(1,2)=3.6653790174516793e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.20000000000000079
+R0,0=0.96592582628906842
+R1,0=-1.457167719820518e-016
+R2,0=-0.25881904510252007
+S1=-14.79999999999999
+R0,1=7.9979483404574392e-002
+R1,1=0.95105651629515409
+R2,1=0.29848749562898386
+S2=99.400000000000091
+R0,2=0.24615153938604106
+R1,2=-0.30901699437494573
+R2,2=0.91865005134999966
@@ -0,0 +1,38 @@
+
+[Marker]
+FacetsCount=1
+Name=2b
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-13.9690559296461
+EndPos(0,1)=-9.08090028293946e-017
+EndPos(0,2)=3.7518297647387081e-015
+EndPos(1,0)=13.969055929646105
+EndPos(1,1)=-1.1456717217429434e-016
+EndPos(1,2)=3.7783785761971358e-015
+
+[Facet1V2]
+EndPos(0,0)=-13.924452046559736
+EndPos(0,1)=-15.196209648340083
+EndPos(0,2)=3.7349350665378906e-015
+EndPos(1,0)=-13.9690559296461
+EndPos(1,1)=-9.08090028293946e-017
+EndPos(1,2)=3.7518297647387081e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=3Coil
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-8.9434442564413246
+EndPos(0,1)=-6.1153268241647966e-016
+EndPos(0,2)=3.4944724709513123e-016
+EndPos(1,0)=8.9434442564413299
+EndPos(1,1)=-8.8089826871897666e-016
+EndPos(1,2)=-4.6592966279350834e-016
+
+[Facet1V2]
+EndPos(0,0)=-8.9439343674574907
+EndPos(0,1)=11.937904678416533
+EndPos(0,2)=-5.2417087064269685e-016
+EndPos(1,0)=-8.9434442564413246
+EndPos(1,1)=-6.1153268241647966e-016
+EndPos(1,2)=3.4944724709513123e-016
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.80000000000000182
+R0,0=0.9563047559630351
+R1,0=1.8041124150158794e-016
+R2,0=-0.29237170472273794
+S1=47.299999999999962
+R0,1=9.0347825433700193e-002
+R1,1=0.95105651629515331
+R2,1=0.29551442139416562
+S2=42.399999999999991
+R0,2=0.27806201495688238
+R1,2=-0.30901699437494834
+R2,2=0.90949986972269081
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=4Coil
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-8.9585812958876883
+EndPos(0,1)=-4.8569430893988515e-016
+EndPos(0,2)=2.3154142102162125e-015
+EndPos(1,0)=8.95858129588769
+EndPos(1,1)=-1.2210192124187057e-016
+EndPos(1,2)=4.6308284204324244e-016
+
+[Facet1V2]
+EndPos(0,0)=8.95858129588769
+EndPos(0,1)=-1.2210192124187057e-016
+EndPos(0,2)=4.6308284204324244e-016
+EndPos(1,0)=8.8914854228233384
+EndPos(1,1)=11.981845264775341
+EndPos(1,2)=3.4731213153243185e-016
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=-0.40000000000000141
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=10.700000000000001
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=110.09999999999999
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,38 @@
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=5Ref
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-8.9120676333490003
+EndPos(0,1)=2.3980817331903383e-016
+EndPos(0,2)=-1.2505552149377763e-015
+EndPos(1,0)=8.9120676333490003
+EndPos(1,1)=2.6645352591003756e-017
+EndPos(1,2)=0.
+
+[Facet1V2]
+EndPos(0,0)=-8.9951734202602971
+EndPos(0,1)=-12.045839883319603
+EndPos(0,2)=-4.5474735088646413e-016
+EndPos(1,0)=-8.9120676333490003
+EndPos(1,1)=2.3980817331903383e-016
+EndPos(1,2)=-1.2505552149377763e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,37 @@
+[Marker]
+FacetsCount=1
+Name=COOLCARD
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-31.763129600371474
+EndPos(0,1)=-6.4066430885648868e-016
+EndPos(0,2)=1.9712913472123418e-015
+EndPos(1,0)=31.763129600371467
+EndPos(1,1)=-6.4440270518456277e-016
+EndPos(1,2)=1.9656972001890368e-015
+
+[Facet1V2]
+EndPos(0,0)=-31.746690593113094
+EndPos(0,1)=25.423398067377672
+EndPos(0,2)=1.9712913472123418e-015
+EndPos(1,0)=-31.763129600371474
+EndPos(1,1)=-6.4066430885648868e-016
+EndPos(1,2)=1.9712913472123418e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=Pointer Template
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-8.9079792482800304
+EndPos(0,1)=4.7658354227811601e-016
+EndPos(0,2)=-3.8126683382249281e-015
+EndPos(1,0)=8.9079792482800322
+EndPos(1,1)=-3.754900636130611e-016
+EndPos(1,2)=4.6214161675453676e-016
+
+[Facet1V2]
+EndPos(0,0)=8.9079792482800322
+EndPos(0,1)=-3.754900636130611e-016
+EndPos(0,2)=4.6214161675453676e-016
+EndPos(1,0)=8.97037014055695
+EndPos(1,1)=-11.854493390526288
+EndPos(1,2)=-5.1990931884885378e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=Ref
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-8.9120676333490003
+EndPos(0,1)=2.3980817331903383e-016
+EndPos(0,2)=-1.2505552149377763e-015
+EndPos(1,0)=8.9120676333490003
+EndPos(1,1)=2.6645352591003756e-017
+EndPos(1,2)=0.
+
+[Facet1V2]
+EndPos(0,0)=-8.9951734202602971
+EndPos(0,1)=-12.045839883319603
+EndPos(0,2)=-4.5474735088646413e-016
+EndPos(1,0)=-8.9120676333490003
+EndPos(1,1)=2.3980817331903383e-016
+EndPos(1,2)=-1.2505552149377763e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,37 @@
+[Marker]
+FacetsCount=1
+Name=TTblock
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-44.89806848621749
+EndPos(0,1)=1.5829351718288365e-017
+EndPos(0,2)=-2.4650420593630429e-015
+EndPos(1,0)=44.898068486217483
+EndPos(1,1)=8.5012292344588403e-016
+EndPos(1,2)=-2.4138677168217271e-015
+
+[Facet1V2]
+EndPos(0,0)=-0.25683199956524938
+EndPos(0,1)=42.807497943328485
+EndPos(0,2)=-8.1564930877711453e-003
+EndPos(1,0)=0.23846937714486499
+EndPos(1,1)=-42.932871913619174
+EndPos(1,2)=-8.1564930877712043e-003
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,37 @@
+[Marker]
+FacetsCount=1
+Name=a
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-32.971498168704073
+EndPos(0,1)=2.5755541490385065e-016
+EndPos(0,2)=1.6979881553090628e-016
+EndPos(1,0)=32.971498168704088
+EndPos(1,1)=3.2816886463184776e-016
+EndPos(1,2)=4.4082384801292978e-017
+
+[Facet1V2]
+EndPos(0,0)=-32.975185360462866
+EndPos(0,1)=46.723702252369826
+EndPos(0,2)=-8.9797450521152372e-018
+EndPos(1,0)=-32.971498168704073
+EndPos(1,1)=2.5755541490385065e-016
+EndPos(1,2)=1.6979881553090628e-016
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,38 @@
+
+[Marker]
+FacetsCount=1
+Name=coil
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-70.299927206216339
+EndPos(0,1)=1.1368683772161603e-016
+EndPos(0,2)=1.3642420526593924e-015
+EndPos(1,0)=70.299927206216339
+EndPos(1,1)=-1.1368683772161603e-016
+EndPos(1,2)=6.8212102632969619e-016
+
+[Facet1V2]
+EndPos(0,0)=-69.651993385067129
+EndPos(0,1)=-65.744122964094188
+EndPos(0,2)=3.410605131648481e-016
+EndPos(1,0)=-70.299927206216339
+EndPos(1,1)=1.1368683772161603e-016
+EndPos(1,2)=1.3642420526593924e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
@@ -0,0 +1,39 @@
+
+[Marker]
+FacetsCount=1
+SliderControlledXpointsCount=0
+Name=probe
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-61.602408326043872
+EndPos(0,1)=4.2184025144074082e-016
+EndPos(0,2)=-4.556586682229099e-016
+EndPos(1,0)=61.602408326043872
+EndPos(1,1)=-9.6115500328270063e-017
+EndPos(1,2)=-1.1391466705572748e-016
+
+[Facet1V2]
+EndPos(0,0)=-61.59657019736504
+EndPos(0,1)=11.949604571287503
+EndPos(0,2)=1.1391466705572748e-016
+EndPos(1,0)=-61.602408326043872
+EndPos(1,1)=4.2184025144074082e-016
+EndPos(1,2)=-4.556586682229099e-016
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=145.66478105979206
+R0,0=-8.4560706371216821e-002
+R1,0=-0.52109081782374
+R2,0=0.84930197604725266
+S1=-13.147426563284974
+R0,1=4.5008904130328986e-002
+R1,1=-0.85348236485506712
+R2,1=-0.5191743940434248
+S2=9.0630880541399712
+R0,2=0.99540126857813949
+R1,2=-5.6756022725552024e-003
+R2,2=9.5624798310161907e-002
@@ -0,0 +1,38 @@
+
+[Marker]
+FacetsCount=1
+Name=sptr
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-52.19791804784397
+EndPos(0,1)=1.2304185897405721e-016
+EndPos(0,2)=6.9721287355505385e-016
+EndPos(1,0)=52.19791804784397
+EndPos(1,1)=-7.4104692177650016e-017
+EndPos(1,2)=5.9481366254593747e-016
+
+[Facet1V2]
+EndPos(0,0)=-52.224959539439432
+EndPos(0,1)=11.532261461857525
+EndPos(0,2)=6.9918899867979109e-016
+EndPos(1,0)=-52.19791804784397
+EndPos(1,1)=1.2304185897405721e-016
+EndPos(1,2)=6.9721287355505385e-016
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=132.5915439593966
+R0,0=-3.3573683844187456e-002
+R1,0=-0.99175827123861893
+R2,0=0.12364602372465228
+S1=-3.8041069565099583
+R0,1=-3.9209531312008813e-002
+R1,1=-0.12231349340138305
+R2,1=-0.9917167045009595
+S2=-0.29142356239092942
+R0,2=0.99866682152128394
+R1,2=-3.8143685738751404e-002
+R2,2=-3.4779862432738673e-002
@@ -0,0 +1,38 @@
+
+[Marker]
+FacetsCount=1
+Name=try4
+
+[Facet1]
+VectorsCount=2
+
+[Facet1V1]
+EndPos(0,0)=-57.030279071976651
+EndPos(0,1)=-1.7053025658242405e-016
+EndPos(0,2)=-3.1832314562052489e-015
+EndPos(1,0)=57.030279071976658
+EndPos(1,1)=1.7053025658242405e-016
+EndPos(1,2)=-1.8189894035458565e-015
+
+[Facet1V2]
+EndPos(0,0)=-56.190229598357341
+EndPos(0,1)=93.77396683857414
+EndPos(0,2)=0.
+EndPos(1,0)=-57.030279071976651
+EndPos(1,1)=-1.7053025658242405e-016
+EndPos(1,2)=-3.1832314562052489e-015
+
+[Tooltip2MarkerXf]
+Scale=1.
+S0=0.
+R0,0=1.
+R1,0=0.
+R2,0=0.
+S1=0.
+R0,1=0.
+R1,1=1.
+R2,1=0.
+S2=0.
+R0,2=0.
+R1,2=0.
+R2,2=1.
	@@ -8,6 +8,7 @@ invesalius/*.swo		@@ -8,6 +8,7 @@ invesalius/*.swo
8	invesalius/*.swp	8	invesalius/*.swp
9	invesalius/data/*.log	9	invesalius/data/*.log
10	invesalius/data/*.pyc	10	invesalius/data/*.pyc
		11	+invesalius/data/*.pyd
11	invesalius/gui/*.log	12	invesalius/gui/*.log
12	invesalius/gui/*.pyc	13	invesalius/gui/*.pyc
13	invesalius/gui/widgets/*.log	14	invesalius/gui/widgets/*.log
	@@ -21,6 +22,7 @@ invesalius/reader/*.pyc		@@ -21,6 +22,7 @@ invesalius/reader/*.pyc
21	tags	22	tags
22	*.c	23	*.c
23		24
		25	+.idea
24	build	26	build
25	*.patch	27	*.patch
26	*.tgz	28	*.tgz
	@@ -29,4 +31,4 @@ build		@@ -29,4 +31,4 @@ build
29	*.cpp	31	*.cpp
30	*.diff	32	*.diff
31		33
32	-*.directory	34	-*.directory
		35	+*.directory
33	\ No newline at end of file	36	\ No newline at end of file
	@@ -487,8 +487,9 @@ VTK_WARNING = 0		@@ -487,8 +487,9 @@ VTK_WARNING = 0
487		487
488	[ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,	488	[ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,
489	ID_PROJECT_CLOSE, ID_PROJECT_INFO, ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET,	489	ID_PROJECT_CLOSE, ID_PROJECT_INFO, ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET,
490	-ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_ANALYZE_IMPORT, ID_PREFERENCES,
491	-ID_DICOM_NETWORK, ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED] = [wx.NewId() for number in range(15)]	490	+ID_PRINT_SCREENSHOT, ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK,
		491	+ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED, ID_ANALYZE_IMPORT, ID_NIFTI_IMPORT,
		492	+ID_PARREC_IMPORT] = [wx.NewId() for number in range(17)]
492	ID_EXIT = wx.ID_EXIT	493	ID_EXIT = wx.ID_EXIT
493	ID_ABOUT = wx.ID_ABOUT	494	ID_ABOUT = wx.ID_ABOUT
494		495
	@@ -637,3 +638,53 @@ BOOLEAN_UNION = 1		@@ -637,3 +638,53 @@ BOOLEAN_UNION = 1
637	BOOLEAN_DIFF = 2	638	BOOLEAN_DIFF = 2
638	BOOLEAN_AND = 3	639	BOOLEAN_AND = 3
639	BOOLEAN_XOR = 4	640	BOOLEAN_XOR = 4
		641	+
		642	+#------------ Navigation defaults -------------------
		643	+
		644	+SELECT = 0
		645	+MTC = 1
		646	+FASTRAK = 2
		647	+ISOTRAKII = 3
		648	+PATRIOT = 4
		649	+DEBUGTRACK = 5
		650	+DISCTRACK = 6
		651	+DEFAULT_TRACKER = SELECT
		652	+
		653	+TRACKER = [_("Select tracker:"), _("Claron MicronTracker"),
		654	+ _("Polhemus FASTRAK"), _("Polhemus ISOTRAK II"),
		655	+ _("Polhemus PATRIOT"), _("Debug tracker"),
		656	+ _("Disconnect tracker")]
		657	+
		658	+STATIC_REF = 0
		659	+DYNAMIC_REF = 1
		660	+DEFAULT_REF_MODE = DYNAMIC_REF
		661	+REF_MODE = [_("Static ref."), _("Dynamic ref.")]
		662	+
		663	+IR1 = wx.NewId()
		664	+IR2 = wx.NewId()
		665	+IR3 = wx.NewId()
		666	+TR1 = wx.NewId()
		667	+TR2 = wx.NewId()
		668	+TR3 = wx.NewId()
		669	+SET = wx.NewId()
		670	+
		671	+BTNS_IMG = {IR1: {0: _('LEI')},
		672	+ IR2: {1: _('REI')},
		673	+ IR3: {2: _('NAI')}}
		674	+
		675	+TIPS_IMG = [wx.ToolTip(_("Select left ear in image")),
		676	+ wx.ToolTip(_("Select right ear in image")),
		677	+ wx.ToolTip(_("Select nasion in image"))]
		678	+
		679	+BTNS_TRK = {TR1: {3: _('LET')},
		680	+ TR2: {4: _('RET')},
		681	+ TR3: {5: _('NAT')},
		682	+ SET: {6: _('SET')}}
		683	+
		684	+TIPS_TRK = [wx.ToolTip(_("Select left ear with spatial tracker")),
		685	+ wx.ToolTip(_("Select right ear with spatial tracker")),
		686	+ wx.ToolTip(_("Select nasion with spatial tracker")),
		687	+ wx.ToolTip(_("Show set coordinates in image"))]
		688	+
		689	+CAL_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'mtc_files', 'CalibrationFiles'))
		690	+MAR_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'mtc_files', 'Markers'))
1	-from numpy import *
2	from math import sqrt	1	from math import sqrt
		2	+import numpy as np
3		3
4	-class Bases:
5	-
6	- def __init__(self, p1, p2, p3):
7	-
8	- self.p1 = array([p1[0], p1[1], p1[2]])
9	- self.p2 = array([p2[0], p2[1], p2[2]])
10	- self.p3 = array([p3[0], p3[1], p3[2]])
11	-
12	- print "p1: ", self.p1
13	- print "p2: ", self.p2
14	- print "p3: ", self.p3
15		4
16	- self.sub1 = self.p2 - self.p1
17	- self.sub2 = self.p3 - self.p1
18	-
19	- def Basecreation(self):
20	- #g1
21	- g1 = self.sub1
22	-
23	- #g2
24	- lamb1 = g1[0]self.sub2[0] + g1[1]self.sub2[1] + g1[2]*self.sub2[2]
25	- lamb2 = dot(g1, g1)
26	- lamb = lamb1/lamb2
27	-
28	- #Ponto q
29	- q = self.p1 + lamb*self.sub1
30	-
31	- #g1 e g2 com origem em q
32	- g1 = self.p1 - q
33	- g2 = self.p3 - q
34	-
35	- #testa se o g1 nao eh um vetor nulo
36	- if g1.any() == False:
37	- g1 = self.p2 - q
38	-
39	- #g3 - Produto vetorial NumPy
40	- g3 = cross(g2, g1)
41	-
42	- #normalizacao dos vetores
43	- g1 = g1/sqrt(lamb2)
44	- g2 = g2/sqrt(dot(g2, g2))
45	- g3 = g3/sqrt(dot(g3, g3))
46	-
47	- M = matrix([[g1[0],g1[1],g1[2]], [g2[0],g2[1],g2[2]], [g3[0],g3[1],g3[2]]])
48	- q.shape = (3, 1)
49	- q = matrix(q.copy())
50	- print"M: ", M
51	- print
52	- print"q: ", q
53	- print
54	- Minv = M.I
55	-
56	- return M, q, Minv
57	-
58	-def FlipX(point):
59	-
60	- point = matrix(point + (0,))
61	-
62	- #inverter o eixo z
63	- ## possivel explicacaoo -- origem do eixo do imagedata esta no canto
64	- ## superior esquerdo e origem da superfice eh no canto inferior esquerdo
65	- ## ou a ordem de empilhamento das fatias
66	-
67	- point[0, 2] = -point[0, 2]
68	-
69	- #Flip em y
70	- Mrot = matrix([[1.0, 0.0, 0.0, 0.0],
71	- [0.0, -1.0, 0.0, 0.0],
72	- [0.0, 0.0, -1.0, 0.0],
73	- [0.0, 0.0, 0.0, 1.0]])
74	- Mtrans = matrix([[1.0, 0, 0, -point[0, 0]],
75	- [0.0, 1.0, 0, -point[0, 1]],
76	- [0.0, 0.0, 1.0, -point[0, 2]],
77	- [0.0, 0.0, 0.0, 1.0]])
78	- Mtrans_return = matrix([[1.0, 0, 0, point[0, 0]],	5	+def angle_calculation(ap_axis, coil_axis):
		6	+ """
		7	+ Calculate angle between two given axis (in degrees)
		8	+
		9	+ :param ap_axis: anterior posterior axis represented
		10	+ :param coil_axis: tms coil axis
		11	+ :return: angle between the two given axes
		12	+ """
		13	+
		14	+ ap_axis = np.array([ap_axis[0], ap_axis[1]])
		15	+ coil_axis = np.array([float(coil_axis[0]), float(coil_axis[1])])
		16	+ angle = np.rad2deg(np.arccos((np.dot(ap_axis, coil_axis))/(
		17	+ np.linalg.norm(ap_axis)*np.linalg.norm(coil_axis))))
		18	+
		19	+ return float(angle)
		20	+
		21	+
		22	+def base_creation(fiducials):
		23	+ """
		24	+ Calculate the origin and matrix for coordinate system
		25	+ transformation.
		26	+ q: origin of coordinate system
		27	+ g1, g2, g3: orthogonal vectors of coordinate system
		28	+
		29	+ :param fiducials: array of 3 rows (p1, p2, p3) and 3 columns (x, y, z) with fiducials coordinates
		30	+ :return: matrix and origin for base transformation
		31	+ """
		32	+
		33	+ p1 = fiducials[0, :]
		34	+ p2 = fiducials[1, :]
		35	+ p3 = fiducials[2, :]
		36	+
		37	+ sub1 = p2 - p1
		38	+ sub2 = p3 - p1
		39	+ lamb = (sub1[0]sub2[0]+sub1[1]sub2[1]+sub1[2]*sub2[2])/np.dot(sub1, sub1)
		40	+
		41	+ q = p1 + lamb*sub1
		42	+ g1 = p1 - q
		43	+ g2 = p3 - q
		44	+
		45	+ if not g1.any():
		46	+ g1 = p2 - q
		47	+
		48	+ g3 = np.cross(g2, g1)
		49	+
		50	+ g1 = g1/sqrt(np.dot(g1, g1))
		51	+ g2 = g2/sqrt(np.dot(g2, g2))
		52	+ g3 = g3/sqrt(np.dot(g3, g3))
		53	+
		54	+ m = np.matrix([[g1[0], g1[1], g1[2]],
		55	+ [g2[0], g2[1], g2[2]],
		56	+ [g3[0], g3[1], g3[2]]])
		57	+
		58	+ q.shape = (3, 1)
		59	+ q = np.matrix(q.copy())
		60	+ m_inv = m.I
		61	+
		62	+ # print"M: ", m
		63	+ # print"q: ", q
		64	+
		65	+ return m, q, m_inv
		66	+
		67	+
		68	+def calculate_fre(fiducials, minv, n, q1, q2):
		69	+ """
		70	+ Calculate the Fiducial Registration Error for neuronavigation.
		71	+
		72	+ :param fiducials: array of 6 rows (image and tracker fiducials) and 3 columns (x, y, z) with coordinates
		73	+ :param minv: inverse matrix given by base creation
		74	+ :param n: base change matrix given by base creation
		75	+ :param q1: origin of first base
		76	+ :param q2: origin of second base
		77	+ :return: float number of fiducial registration error
		78	+ """
		79	+
		80	+ img = np.zeros([3, 3])
		81	+ dist = np.zeros([3, 1])
		82	+
		83	+ p1 = np.mat(fiducials[3, :]).reshape(3, 1)
		84	+ p2 = np.mat(fiducials[4, :]).reshape(3, 1)
		85	+ p3 = np.mat(fiducials[5, :]).reshape(3, 1)
		86	+
		87	+ img[0, :] = np.asarray((q1 + (minv * n) * (p1 - q2)).reshape(1, 3))
		88	+ img[1, :] = np.asarray((q1 + (minv * n) * (p2 - q2)).reshape(1, 3))
		89	+ img[2, :] = np.asarray((q1 + (minv * n) * (p3 - q2)).reshape(1, 3))
		90	+
		91	+ dist[0] = np.sqrt(np.sum(np.power((img[0, :] - fiducials[0, :]), 2)))
		92	+ dist[1] = np.sqrt(np.sum(np.power((img[1, :] - fiducials[1, :]), 2)))
		93	+ dist[2] = np.sqrt(np.sum(np.power((img[2, :] - fiducials[2, :]), 2)))
		94	+
		95	+ return float(np.sqrt(np.sum(dist ** 2) / 3))
		96	+
		97	+
		98	+def flip_x(point):
		99	+ """
		100	+ Flip coordinates of a vector according to X axis
		101	+ Coronal Images do not require this transformation - 1 tested
		102	+ and for this case, at navigation, the z axis is inverted
		103	+
		104	+ It's necessary to multiply the z coordinate by (-1). Possibly
		105	+ because the origin of coordinate system of imagedata is
		106	+ located in superior left corner and the origin of VTK scene coordinate
		107	+ system (polygonal surface) is in the interior left corner. Second
		108	+ possibility is the order of slice stacking
		109	+
		110	+ :param point: list of coordinates x, y and z
		111	+ :return: flipped coordinates
		112	+ """
		113	+
		114	+ # TODO: check if the Flip function is related to the X or Y axis
		115	+
		116	+ point = np.matrix(point + (0,))
		117	+ point[0, 2] = -point[0, 2]
		118	+
		119	+ m_rot = np.matrix([[1.0, 0.0, 0.0, 0.0],
		120	+ [0.0, -1.0, 0.0, 0.0],
		121	+ [0.0, 0.0, -1.0, 0.0],
		122	+ [0.0, 0.0, 0.0, 1.0]])
		123	+ m_trans = np.matrix([[1.0, 0, 0, -point[0, 0]],
		124	+ [0.0, 1.0, 0, -point[0, 1]],
		125	+ [0.0, 0.0, 1.0, -point[0, 2]],
		126	+ [0.0, 0.0, 0.0, 1.0]])
		127	+ m_trans_return = np.matrix([[1.0, 0, 0, point[0, 0]],
79	[0.0, 1.0, 0, point[0, 1]],	128	[0.0, 1.0, 0, point[0, 1]],
80	[0.0, 0.0, 1.0, point[0, 2]],	129	[0.0, 0.0, 1.0, point[0, 2]],
81	[0.0, 0.0, 0.0, 1.0]])	130	[0.0, 0.0, 0.0, 1.0]])
82		131
83	- point_rot = pointMtransMrot*Mtrans_return
84	- x, y, z = point_rot.tolist()[0][:3]
85	- return x, y, z	132	+ point_rot = pointm_transm_rot*m_trans_return
		133	+ x, y, z = point_rot.tolist()[0][:3]
		134	+
		135	+ return x, y, z
	@@ -1,65 +0,0 @@	@@ -1,65 +0,0 @@
1	-import threading
2	-
3	-import serial
4	-import wx
5	-from wx.lib.pubsub import pub as Publisher
6	-
7	-from numpy import *
8	-from math import sqrt
9	-from time import sleep
10	-
11	-class Corregister(threading.Thread):
12	-
13	- def __init__(self, bases, flag):
14	- threading.Thread.__init__(self)
15	- self.Minv = bases[0]
16	- self.N = bases[1]
17	- self.q1 = bases[2]
18	- self.q2 = bases[3]
19	- self.flag = flag
20	- self._pause_ = 0
21	- self.start()
22	-
23	- def stop(self):
24	- # Stop neuronavigation
25	- self._pause_ = 1
26	-
27	- def Coordinates(self):
28	- #Get Polhemus points for neuronavigation
29	- ser = serial.Serial(0)
30	- ser.write("Y")
31	- ser.write("P")
32	- str = ser.readline()
33	- ser.write("Y")
34	- str = str.replace("\r\n","")
35	- str = str.replace("-"," -")
36	- aostr = [s for s in str.split()]
37	- #aoflt -> 0:letter 1:x 2:y 3:z
38	- aoflt = [float(aostr[1]), float(aostr[2]), float(aostr[3]),
39	- float(aostr[4]), float(aostr[5]), float(aostr[6])]
40	- ser.close()
41	-
42	- #Unit change: inches to millimeters
43	- x = 25.4
44	- y = 25.4
45	- z = -25.4
46	-
47	- coord = (aoflt[0]x, aoflt[1]y, aoflt[2]*z)
48	- return coord
49	-
50	- def run(self):
51	- while self.flag == True:
52	- #Neuronavigation with Polhemus
53	- trck = self.Coordinates()
54	- tracker = matrix([[trck[0]], [trck[1]], [trck[2]]])
55	- img = self.q1 + (self.Minvself.N)(tracker - self.q2)
56	- coord = [float(img[0]), float(img[1]), float(img[2])]
57	- coord_cam = float(img[0]), float(img[1]), float(img[2])
58	- Publisher.sendMessage('Set ball reference position based on bound', coord_cam)
59	- Publisher.sendMessage('Set camera in volume', coord_cam)
60	- wx.CallAfter(Publisher.sendMessage, 'Render volume viewer')
61	- wx.CallAfter(Publisher.sendMessage, 'Co-registered Points', coord)
62	- sleep(0.005)
63	-
64	- if self._pause_:
65	- return
@@ -0,0 +1,277 @@		@@ -0,0 +1,277 @@
	1	+#--------------------------------------------------------------------------
	2	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
	3	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
	4	+# Homepage: http://www.softwarepublico.gov.br
	5	+# Contact: invesalius@cti.gov.br
	6	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
	7	+#--------------------------------------------------------------------------
	8	+# Este programa e software livre; voce pode redistribui-lo e/ou
	9	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
	10	+# publicada pela Free Software Foundation; de acordo com a versao 2
	11	+# da Licenca.
	12	+#
	13	+# Este programa eh distribuido na expectativa de ser util, mas SEM
	14	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
	15	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
	16	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
	17	+# detalhes.
	18	+#--------------------------------------------------------------------------
	19	+
	20	+from math import sin, cos
	21	+import numpy as np
	22	+
	23	+from random import uniform
	24	+
	25	+
	26	+def GetCoordinates(trck_init, trck_id, ref_mode):
	27	+
	28	+ """
	29	+ Read coordinates from spatial tracking devices using
	30	+
	31	+ :param trck_init: Initialization variable of tracking device and connection type. See tracker.py.
	32	+ :param trck_id: ID of tracking device.
	33	+ :param ref_mode: Single or dynamic reference mode of tracking.
	34	+ :return: array of six coordinates (x, y, z, alpha, beta, gamma)
	35	+ """
	36	+
	37	+ coord = None
	38	+ if trck_id:
	39	+ getcoord = {1: ClaronCoord,
	40	+ 2: PolhemusCoord,
	41	+ 3: PolhemusCoord,
	42	+ 4: PolhemusCoord,
	43	+ 5: DebugCoord}
	44	+ coord = getcoord[trck_id](trck_init, trck_id, ref_mode)
	45	+ else:
	46	+ print "Select Tracker"
	47	+
	48	+ return coord
	49	+
	50	+
	51	+def ClaronCoord(trck_init, trck_id, ref_mode):
	52	+ trck = trck_init[0]
	53	+ scale = 10. * np.array([1., 1.0, -1.0])
	54	+ coord = None
	55	+ k = 0
	56	+ # TODO: try to replace while and use some Claron internal computation
	57	+ if ref_mode:
	58	+ while k < 20:
	59	+ try:
	60	+ trck.Run()
	61	+ probe = np.array([trck.PositionTooltipX1 * scale[0], trck.PositionTooltipY1 * scale[1],
	62	+ trck.PositionTooltipZ1 * scale[2], trck.AngleX1, trck.AngleY1, trck.AngleZ1])
	63	+ reference = np.array([trck.PositionTooltipX2 * scale[0], trck.PositionTooltipY2 * scale[1],
	64	+ trck.PositionTooltipZ2 * scale[2], trck.AngleX2, trck.AngleY2, trck.AngleZ2])
	65	+ k = 30
	66	+ except AttributeError:
	67	+ k += 1
	68	+ print "wait, collecting coordinates ..."
	69	+ if k == 30:
	70	+ coord = dynamic_reference(probe, reference)
	71	+ else:
	72	+ while k < 20:
	73	+ try:
	74	+ trck.Run()
	75	+ coord = np.array([trck.PositionTooltipX1 * scale[0], trck.PositionTooltipY1 * scale[1],
	76	+ trck.PositionTooltipZ1 * scale[2], trck.AngleX1, trck.AngleY1, trck.AngleZ1])
	77	+ k = 30
	78	+ except AttributeError:
	79	+ k += 1
	80	+ print "wait, collecting coordinates ..."
	81	+
	82	+ return coord
	83	+
	84	+
	85	+def PolhemusCoord(trck, trck_id, ref_mode):
	86	+ coord = None
	87	+
	88	+ if trck[1] == 'serial':
	89	+ coord = PolhemusSerialCoord(trck[0], trck_id, ref_mode)
	90	+
	91	+ elif trck[1] == 'usb':
	92	+ coord = PolhemusUSBCoord(trck[0], trck_id, ref_mode)
	93	+
	94	+ elif trck[1] == 'wrapper':
	95	+ coord = PolhemusWrapperCoord(trck[0], trck_id, ref_mode)
	96	+
	97	+ return coord
	98	+
	99	+
	100	+def PolhemusWrapperCoord(trck, trck_id, ref_mode):
	101	+ if trck_id == 2:
	102	+ scale = 10. * np.array([1., 1.0, -1.0])
	103	+ else:
	104	+ scale = 25.4 * np.array([1., 1.0, -1.0])
	105	+ coord = None
	106	+
	107	+ if ref_mode:
	108	+ trck.Run()
	109	+ probe = np.array([float(trck.PositionTooltipX1) * scale[0], float(trck.PositionTooltipY1) * scale[1],
	110	+ float(trck.PositionTooltipZ1) * scale[2], float(trck.AngleX1), float(trck.AngleY1),
	111	+ float(trck.AngleZ1)])
	112	+ reference = np.array([float(trck.PositionTooltipX2) * scale[0], float(trck.PositionTooltipY2) * scale[1],
	113	+ float(trck.PositionTooltipZ2) * scale[2], float(trck.AngleX2), float(trck.AngleY2),
	114	+ float(trck.AngleZ2)])
	115	+
	116	+ if probe.all() and reference.all():
	117	+ coord = dynamic_reference(probe, reference)
	118	+
	119	+ else:
	120	+ trck.Run()
	121	+ coord = np.array([float(trck.PositionTooltipX1) * scale[0], float(trck.PositionTooltipY1) * scale[1],
	122	+ float(trck.PositionTooltipZ1) * scale[2], float(trck.AngleX1), float(trck.AngleY1),
	123	+ float(trck.AngleZ1)])
	124	+
	125	+ return coord
	126	+
	127	+
	128	+def PolhemusUSBCoord(trck, trck_id, ref_mode):
	129	+ endpoint = trck[0][(0, 0)][0]
	130	+ # Tried to write some settings to Polhemus in trackers.py while initializing the device.
	131	+ # TODO: Check if it's working properly.
	132	+ trck.write(0x02, "P")
	133	+ if trck_id == 2:
	134	+ scale = 10. * np.array([1., 1.0, -1.0])
	135	+ else:
	136	+ scale = 25.4 * np.array([1., 1.0, -1.0])
	137	+ coord = None
	138	+
	139	+ if ref_mode:
	140	+
	141	+ data = trck.read(endpoint.bEndpointAddress, 2 * endpoint.wMaxPacketSize)
	142	+ data = str2float(data.tostring())
	143	+
	144	+ # six coordinates of first and second sensor: x, y, z and alfa, beta and gama
	145	+ # jump one element for reference to avoid the sensor ID returned by Polhemus
	146	+ probe = data[0] * scale[0], data[1] * scale[1], data[2] * scale[2], \
	147	+ data[3], data[4], data[5], data[6]
	148	+ reference = data[7] * scale[0], data[8] * scale[1], data[9] * scale[2], data[10], \
	149	+ data[11], data[12], data[13]
	150	+
	151	+ if probe.all() and reference.all():
	152	+ coord = dynamic_reference(probe, reference)
	153	+
	154	+ return coord
	155	+
	156	+ else:
	157	+ data = trck.read(endpoint.bEndpointAddress, endpoint.wMaxPacketSize)
	158	+ coord = str2float(data.tostring())
	159	+
	160	+ coord = np.array((coord[0] * scale[0], coord[1] * scale[1], coord[2] * scale[2],
	161	+ coord[3], coord[4], coord[5]))
	162	+
	163	+ return coord
	164	+
	165	+
	166	+def PolhemusSerialCoord(trck_init, trck_id, ref_mode):
	167	+ # mudanca para fastrak - ref 1 tem somente x, y, z
	168	+ # aoflt -> 0:letter 1:x 2:y 3:z
	169	+ # this method is not optimized to work with all trackers, only with ISOTRAK
	170	+ # serial connection is obsolete, remove in future
	171	+ trck_init.write("P")
	172	+ lines = trck_init.readlines()
	173	+
	174	+ coord = None
	175	+
	176	+ if lines[0][0] != '0':
	177	+ print "The Polhemus is not connected!"
	178	+ else:
	179	+ for s in lines:
	180	+ if s[1] == '1':
	181	+ data = s
	182	+ elif s[1] == '2':
	183	+ data = s
	184	+
	185	+ # single ref mode
	186	+ if not ref_mode:
	187	+ data = data.replace('-', ' -')
	188	+ data = [s for s in data.split()]
	189	+ j = 0
	190	+ while j == 0:
	191	+ try:
	192	+ plh1 = [float(s) for s in data[1:len(data)]]
	193	+ j = 1
	194	+ except ValueError:
	195	+ trck_init.write("P")
	196	+ data = trck_init.readline()
	197	+ data = data.replace('-', ' -')
	198	+ data = [s for s in data.split()]
	199	+ print "Trying to fix the error!!"
	200	+
	201	+ coord = data[0:6]
	202	+ return coord
	203	+
	204	+
	205	+def DebugCoord(trk_init, trck_id, ref_mode):
	206	+ """
	207	+ Method to simulate a tracking device for debug and error check. Generate a random
	208	+ x, y, z, alfa, beta and gama coordinates in interval [1, 200[
	209	+ :param trk_init: tracker initialization instance
	210	+ :param ref_mode: flag for singular of dynamic reference
	211	+ :param trck_id: id of tracking device
	212	+ :return: six coordinates x, y, z, alfa, beta and gama
	213	+ """
	214	+
	215	+ if ref_mode:
	216	+ probe = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
	217	+ uniform(1, 200), uniform(1, 200), uniform(1, 200)])
	218	+ reference = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
	219	+ uniform(1, 200), uniform(1, 200), uniform(1, 200)])
	220	+
	221	+ coord = dynamic_reference(probe, reference)
	222	+
	223	+ else:
	224	+ coord = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
	225	+ uniform(1, 200), uniform(1, 200), uniform(1, 200)])
	226	+
	227	+ return coord
	228	+
	229	+
	230	+def dynamic_reference(probe, reference):
	231	+ """
	232	+ Apply dynamic reference correction to probe coordinates. Uses the alpha, beta and gama
	233	+ rotation angles of reference to rotate the probe coordinate and returns the x, y, z
	234	+ difference between probe and reference. Angles sequences and equation was extracted from
	235	+ Polhemus manual and Attitude matrix in Wikipedia.
	236	+ General equation is:
	237	+ coord = Mrot * (probe - reference)
	238	+ :param probe: sensor one defined as probe
	239	+ :param reference: sensor two defined as reference
	240	+ :return: rotated and translated coordinates
	241	+ """
	242	+ a, b, g = np.radians(reference[3:6])
	243	+
	244	+ vet = probe[0:3] - reference[0:3]
	245	+ vet = np.mat(vet.reshape(3, 1))
	246	+
	247	+ # Attitude Matrix given by Patriot Manual
	248	+ Mrot = np.mat([[cos(a) * cos(b), sin(b) * sin(g) * cos(a) - cos(g) * sin(a),
	249	+ cos(a) * sin(b) * cos(g) + sin(a) * sin(g)],
	250	+ [cos(b) * sin(a), sin(b) * sin(g) * sin(a) + cos(g) * cos(a),
	251	+ cos(g) * sin(b) * sin(a) - sin(g) * cos(a)],
	252	+ [-sin(b), sin(g) * cos(b), cos(b) * cos(g)]])
	253	+
	254	+ coord_rot = Mrot.T * vet
	255	+ coord_rot = np.squeeze(np.asarray(coord_rot))
	256	+
	257	+ return coord_rot[0], coord_rot[1], coord_rot[2], probe[3], probe[4], probe[5]
	258	+
	259	+
	260	+def str2float(data):
	261	+ """
	262	+ Converts string detected wth Polhemus device to float array of coordinates. THis method applies
	263	+ a correction for the minus sign in string that raises error while splitting the string into coordinates.
	264	+ :param data: string of coordinates read with Polhemus
	265	+ :return: six float coordinates x, y, z, alfa, beta and gama
	266	+ """
	267	+
	268	+ count = 0
	269	+ for i, j in enumerate(data):
	270	+ if j == '-':
	271	+ data = data[:i + count] + ' ' + data[i + count:]
	272	+ count += 1
	273	+
	274	+ data = [s for s in data.split()]
	275	+ data = [float(s) for s in data[1:len(data)]]
	276	+
	277	+ return data
@@ -0,0 +1,81 @@		@@ -0,0 +1,81 @@
	1	+#--------------------------------------------------------------------------
	2	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
	3	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
	4	+# Homepage: http://www.softwarepublico.gov.br
	5	+# Contact: invesalius@cti.gov.br
	6	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
	7	+#--------------------------------------------------------------------------
	8	+# Este programa e software livre; voce pode redistribui-lo e/ou
	9	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
	10	+# publicada pela Free Software Foundation; de acordo com a versao 2
	11	+# da Licenca.
	12	+#
	13	+# Este programa eh distribuido na expectativa de ser util, mas SEM
	14	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
	15	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
	16	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
	17	+# detalhes.
	18	+#--------------------------------------------------------------------------
	19	+
	20	+import threading
	21	+from time import sleep
	22	+
	23	+from numpy import mat
	24	+import wx
	25	+from wx.lib.pubsub import pub as Publisher
	26	+
	27	+import invesalius.data.coordinates as dco
	28	+
	29	+# TODO: Optimize navigation thread. Remove the infinite loop and optimize sleep.
	30	+
	31	+
	32	+class Coregistration(threading.Thread):
	33	+ """
	34	+ Thread to update the coordinates with the fiducial points
	35	+ co-registration method while the Navigation Button is pressed.
	36	+ Sleep function in run method is used to avoid blocking GUI and
	37	+ for better real-time navigation
	38	+ """
	39	+
	40	+ def __init__(self, bases, nav_id, trck_info):
	41	+ threading.Thread.__init__(self)
	42	+ self.bases = bases
	43	+ self.nav_id = nav_id
	44	+ self.trck_info = trck_info
	45	+ self._pause_ = False
	46	+ self.start()
	47	+
	48	+ def stop(self):
	49	+ self._pause_ = True
	50	+
	51	+ def run(self):
	52	+ m_inv = self.bases[0]
	53	+ n = self.bases[1]
	54	+ q1 = self.bases[2]
	55	+ q2 = self.bases[3]
	56	+ trck_init = self.trck_info[0]
	57	+ trck_id = self.trck_info[1]
	58	+ trck_mode = self.trck_info[2]
	59	+
	60	+ while self.nav_id:
	61	+ trck_coord = dco.GetCoordinates(trck_init, trck_id, trck_mode)
	62	+ trck_xyz = mat([[trck_coord[0]], [trck_coord[1]], [trck_coord[2]]])
	63	+
	64	+ img = q1 + (m_invn)(trck_xyz - q2)
	65	+
	66	+ coord = (float(img[0]), float(img[1]), float(img[2]), trck_coord[3],
	67	+ trck_coord[4], trck_coord[5])
	68	+
	69	+ # Tried several combinations and different locations to send the messages,
	70	+ # however only this one does not block the GUI during navigation.
	71	+ wx.CallAfter(Publisher.sendMessage, 'Co-registered points', coord[0:3])
	72	+ wx.CallAfter(Publisher.sendMessage, 'Set camera in volume', coord[0:3])
	73	+
	74	+ # TODO: Optimize the value of sleep for each tracking device.
	75	+ # Debug tracker is not working with 0.175 so changed to 0.2
	76	+ # However, 0.2 is too low update frequency ~5 Hz. Need optimization URGENTLY.
	77	+ sleep(.3)
	78	+ # sleep(0.175)
	79	+
	80	+ if self._pause_:
	81	+ return
	@@ -592,41 +592,55 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):		@@ -592,41 +592,55 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
592		592
593	return matrix, scalar_range, temp_file	593	return matrix, scalar_range, temp_file
594		594
595	-def analyze2mmap(analyze):
596	- data = analyze.get_data()
597	- header = analyze.get_header()	595	+
		596	+def img2memmap(group):
		597	+ """
		598	+ From a nibabel image data creates a memmap file in the temp folder and
		599	+ returns it and its related filename.
		600	+ """
		601	+
598	temp_file = tempfile.mktemp()	602	temp_file = tempfile.mktemp()
599		603
600	- # Sagital
601	- if header['orient'] == 2:
602	- print "Orientation Sagital"
603	- shape = tuple([data.shape[i] for i in (1, 2, 0)])
604	- matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
605	- for n, slice in enumerate(data):
606	- matrix[:,:, n] = slice
607	-
608	- # Coronal
609	- elif header['orient'] == 1:
610	- print "Orientation coronal"
611	- shape = tuple([data.shape[i] for i in (1, 0, 2)])
612	- matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
613	- for n, slice in enumerate(data):
614	- matrix[:,n,:] = slice
615	-
616	- # AXIAL
617	- elif header['orient'] == 0:
618	- print "no orientation"
619	- shape = tuple([data.shape[i] for i in (0, 1, 2)])
620	- matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
621	- for n, slice in enumerate(data):
622	- matrix[n] = slice	604	+ data = group.get_data()
		605	+ # Normalize image pixel values and convert to int16
		606	+ data = imgnormalize(data)
623		607
624	- else:
625	- print "Orientation Sagital"
626	- shape = tuple([data.shape[i] for i in (1, 2, 0)])
627	- matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=shape)
628	- for n, slice in enumerate(data):
629	- matrix[:,:, n] = slice	608	+ # Convert RAS+ to default InVesalius orientation ZYX
		609	+ data = numpy.swapaxes(data, 0, 2)
		610	+ data = numpy.fliplr(data)
630		611
		612	+ matrix = numpy.memmap(temp_file, mode='w+', dtype=data.dtype, shape=data.shape)
		613	+ matrix[:] = data[:]
631	matrix.flush()	614	matrix.flush()
632	- return matrix, temp_file	615	+
		616	+ scalar_range = numpy.amin(matrix), numpy.amax(matrix)
		617	+
		618	+ return matrix, scalar_range, temp_file
		619	+
		620	+
		621	+def imgnormalize(data, srange=(0, 255)):
		622	+ """
		623	+ Normalize image pixel intensity for int16 gray scale values.
		624	+
		625	+ :param data: image matrix
		626	+ :param srange: range for normalization, default is 0 to 255
		627	+ :return: normalized pixel intensity matrix
		628	+ """
		629	+
		630	+ dataf = numpy.asarray(data)
		631	+ rangef = numpy.asarray(srange)
		632	+ faux = numpy.ravel(dataf).astype(float)
		633	+ minimum = numpy.min(faux)
		634	+ maximum = numpy.max(faux)
		635	+ lower = rangef[0]
		636	+ upper = rangef[1]
		637	+
		638	+ if minimum == maximum:
		639	+ datan = numpy.ones(dataf.shape)*(upper + lower) / 2.
		640	+ else:
		641	+ datan = (faux-minimum)*(upper-lower) / (maximum-minimum) + lower
		642	+
		643	+ datan = numpy.reshape(datan, dataf.shape)
		644	+ datan = datan.astype(numpy.int16)
		645	+
		646	+ return datan
633	\ No newline at end of file	647	\ No newline at end of file
	@@ -0,0 +1,222 @@		@@ -0,0 +1,222 @@
		1	+#--------------------------------------------------------------------------
		2	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
		3	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
		4	+# Homepage: http://www.softwarepublico.gov.br
		5	+# Contact: invesalius@cti.gov.br
		6	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
		7	+#--------------------------------------------------------------------------
		8	+# Este programa e software livre; voce pode redistribui-lo e/ou
		9	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
		10	+# publicada pela Free Software Foundation; de acordo com a versao 2
		11	+# da Licenca.
		12	+#
		13	+# Este programa eh distribuido na expectativa de ser util, mas SEM
		14	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
		15	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
		16	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
		17	+# detalhes.
		18	+#--------------------------------------------------------------------------
		19	+
		20	+# TODO: Disconnect tracker when a new one is connected
		21	+# TODO: Test if there are too many prints when connection fails
		22	+
		23	+
		24	+def TrackerConnection(tracker_id, action):
		25	+ """
		26	+ Initialize spatial trackers for coordinate detection during navigation.
		27	+
		28	+ :param tracker_id: ID of tracking device.
		29	+ :param action: string with to decide whether connect or disconnect the selected device.
		30	+ :return spatial tracker initialization instance or None if could not open device.
		31	+ """
		32	+
		33	+ if action == 'connect':
		34	+ trck_fcn = {1: ClaronTracker,
		35	+ 2: PolhemusTracker, # FASTRAK
		36	+ 3: PolhemusTracker, # ISOTRAK
		37	+ 4: PolhemusTracker, # PATRIOT
		38	+ 5: DebugTracker}
		39	+
		40	+ trck_init = trck_fcn[tracker_id](tracker_id)
		41	+
		42	+ elif action == 'disconnect':
		43	+ trck_init = DisconnectTracker(tracker_id)
		44	+
		45	+ return trck_init
		46	+
		47	+
		48	+def DefaultTracker(tracker_id):
		49	+ trck_init = None
		50	+ try:
		51	+ # import spatial tracker library
		52	+ print 'Connect to default tracking device.'
		53	+
		54	+ except:
		55	+ print 'Could not connect to default tracker.'
		56	+
		57	+ # return tracker initialization variable and type of connection
		58	+ return trck_init, 'wrapper'
		59	+
		60	+
		61	+def ClaronTracker(tracker_id):
		62	+ import invesalius.constants as const
		63	+
		64	+ trck_init = None
		65	+ try:
		66	+ import pyclaron
		67	+
		68	+ lib_mode = 'wrapper'
		69	+ trck_init = pyclaron.pyclaron()
		70	+ trck_init.CalibrationDir = const.CAL_DIR
		71	+ trck_init.MarkerDir = const.MAR_DIR
		72	+ trck_init.NumberFramesProcessed = 10
		73	+ trck_init.FramesExtrapolated = 0
		74	+ trck_init.Initialize()
		75	+
		76	+ if trck_init.GetIdentifyingCamera():
		77	+ trck_init.Run()
		78	+ print "MicronTracker camera identified."
		79	+ else:
		80	+ trck_init = None
		81	+
		82	+ except ImportError:
		83	+ lib_mode = 'error'
		84	+ print 'The ClaronTracker library is not installed.'
		85	+
		86	+ return trck_init, lib_mode
		87	+
		88	+
		89	+def PolhemusTracker(tracker_id):
		90	+ trck_init = None
		91	+ try:
		92	+ trck_init = PlhWrapperConnection()
		93	+ lib_mode = 'wrapper'
		94	+ if not trck_init:
		95	+ print 'Could not connect with Polhemus wrapper, trying USB connection...'
		96	+ trck_init = PlhUSBConnection(tracker_id)
		97	+ lib_mode = 'usb'
		98	+ if not trck_init:
		99	+ print 'Could not connect with Polhemus USB, trying serial connection...'
		100	+ trck_init = PlhSerialConnection(tracker_id)
		101	+ lib_mode = 'serial'
		102	+ except:
		103	+ lib_mode = 'error'
		104	+ print 'Could not connect to Polhemus.'
		105	+
		106	+ return trck_init, lib_mode
		107	+
		108	+
		109	+def DebugTracker(tracker_id):
		110	+ trck_init = True
		111	+ print 'Debug device started.'
		112	+ return trck_init, 'debug'
		113	+
		114	+
		115	+def PlhWrapperConnection():
		116	+ trck_init = None
		117	+ try:
		118	+ import polhemus
		119	+
		120	+ trck_init = polhemus.polhemus()
		121	+ trck_check = trck_init.Initialize()
		122	+
		123	+ if trck_check:
		124	+ # First run is necessary to discard the first coord collection
		125	+ trck_init.Run()
		126	+ except:
		127	+ print 'Could not connect to Polhemus via wrapper.'
		128	+
		129	+ return trck_init
		130	+
		131	+
		132	+def PlhSerialConnection(tracker_id):
		133	+ trck_init = None
		134	+ try:
		135	+ import serial
		136	+
		137	+ trck_init = serial.Serial(0, baudrate=115200, timeout=0.2)
		138	+
		139	+ if tracker_id == 2:
		140	+ # Polhemus FASTRAK needs configurations first
		141	+ trck_init.write(0x02, "u")
		142	+ trck_init.write(0x02, "F")
		143	+ elif tracker_id == 3:
		144	+ # Polhemus ISOTRAK needs to set tracking point from
		145	+ # center to tip.
		146	+ trck_init.write("Y")
		147	+
		148	+ trck_init.write('P')
		149	+ data = trck_init.readlines()
		150	+
		151	+ if not data:
		152	+ trck_init = None
		153	+
		154	+ except:
		155	+ print 'Could not connect to Polhemus serial.'
		156	+
		157	+ return trck_init
		158	+
		159	+
		160	+def PlhUSBConnection(tracker_id):
		161	+ trck_init = None
		162	+ try:
		163	+ import usb.core as uc
		164	+ trck_init = uc.find(idVendor=0x0F44, idProduct=0x0003)
		165	+ cfg = trck_init.get_active_configuration()
		166	+ for i in cfg:
		167	+ for x in i:
		168	+ # TODO: try better code
		169	+ x = x
		170	+ trck_init.set_configuration()
		171	+ endpoint = trck_init[0][(0, 0)][0]
		172	+ if tracker_id == 2:
		173	+ # Polhemus FASTRAK needs configurations first
		174	+ # TODO: Check configurations to standardize initialization for all Polhemus devices
		175	+ trck_init.write(0x02, "u")
		176	+ trck_init.write(0x02, "F")
		177	+ # First run to confirm that everything is working
		178	+ trck_init.write(0x02, "P")
		179	+ data = trck_init.read(endpoint.bEndpointAddress,
		180	+ endpoint.wMaxPacketSize)
		181	+ if not data:
		182	+ trck_init = None
		183	+
		184	+ except uc.USBError as err:
		185	+ print 'Could not set configuration %s' % err
		186	+ else:
		187	+ print 'Could not connect to Polhemus USB.'
		188	+
		189	+ return trck_init
		190	+
		191	+
		192	+def DisconnectTracker(tracker_id):
		193	+ """
		194	+ Disconnect current spatial tracker
		195	+
		196	+ :param tracker_id: ID of tracking device.
		197	+ """
		198	+ trck_init = None
		199	+ # TODO: create individual functions to disconnect each other device, e.g. Polhemus.
		200	+ if tracker_id == 1:
		201	+ try:
		202	+ import pyclaron
		203	+ pyclaron.pyclaron().Close()
		204	+ lib_mode = 'wrapper'
		205	+ except ImportError:
		206	+ lib_mode = 'error'
		207	+ print 'The ClaronTracker library is not installed.'
		208	+
		209	+ elif tracker_id == 4:
		210	+ try:
		211	+ import polhemus
		212	+ polhemus.polhemus().Close()
		213	+ lib_mode = 'wrapper'
		214	+ except ImportError:
		215	+ lib_mode = 'error'
		216	+ print 'The polhemus library is not installed.'
		217	+
		218	+ elif tracker_id == 5:
		219	+ print 'Debug tracker disconnected.'
		220	+ lib_mode = 'debug'
		221	+
		222	+ return trck_init, lib_mode
0	\ No newline at end of file	223	\ No newline at end of file
@@ -0,0 +1,64 @@		@@ -0,0 +1,64 @@
	1	+#--------------------------------------------------------------------------
	2	+# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
	3	+# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
	4	+# Homepage: http://www.softwarepublico.gov.br
	5	+# Contact: invesalius@cti.gov.br
	6	+# License: GNU - GPL 2 (LICENSE.txt/LICENCA.txt)
	7	+#--------------------------------------------------------------------------
	8	+# Este programa e software livre; voce pode redistribui-lo e/ou
	9	+# modifica-lo sob os termos da Licenca Publica Geral GNU, conforme
	10	+# publicada pela Free Software Foundation; de acordo com a versao 2
	11	+# da Licenca.
	12	+#
	13	+# Este programa eh distribuido na expectativa de ser util, mas SEM
	14	+# QUALQUER GARANTIA; sem mesmo a garantia implicita de
	15	+# COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM
	16	+# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
	17	+# detalhes.
	18	+#--------------------------------------------------------------------------
	19	+
	20	+import threading
	21	+from time import sleep
	22	+
	23	+import wx
	24	+from wx.lib.pubsub import pub as Publisher
	25	+
	26	+
	27	+class Trigger(threading.Thread):
	28	+ """
	29	+ Thread created to use external trigger to interact with software during neuronavigation
	30	+ """
	31	+
	32	+ def __init__(self, nav_id):
	33	+ threading.Thread.__init__(self)
	34	+ self.trigger_init = None
	35	+ try:
	36	+ import serial
	37	+
	38	+ self.trigger_init = serial.Serial('COM1', baudrate=115200, timeout=0)
	39	+ self.nav_id = nav_id
	40	+ self._pause_ = False
	41	+ self.start()
	42	+
	43	+ except ImportError:
	44	+ print 'PySerial library not installed. Please install to use Trigger option.'
	45	+
	46	+ except serial.serialutil.SerialException:
	47	+ print 'Connection with port COM1 failed.'
	48	+
	49	+ def stop(self):
	50	+ if self.trigger_init:
	51	+ self.trigger_init.close()
	52	+ self._pause_ = True
	53	+
	54	+ def run(self):
	55	+ while self.nav_id:
	56	+ lines = self.trigger_init.readlines()
	57	+ # Following lines can simulate a trigger in 3 sec repetitions
	58	+ # sleep(3)
	59	+ # lines = True
	60	+ if lines:
	61	+ wx.CallAfter(Publisher.sendMessage, 'Create marker')
	62	+ sleep(0.175)
	63	+ if self._pause_:
	64	+ return
	@@ -22,8 +22,11 @@ import os		@@ -22,8 +22,11 @@ import os
22	import random	22	import random
23	import sys	23	import sys
24		24
		25	+import vtk
25	import wx	26	import wx
26	import wx.combo	27	import wx.combo
		28	+
		29	+from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor
27	from wx.lib import masked	30	from wx.lib import masked
28	from wx.lib.agw import floatspin	31	from wx.lib.agw import floatspin
29	from wx.lib.wordwrap import wordwrap	32	from wx.lib.wordwrap import wordwrap
	@@ -206,48 +209,27 @@ class ProgressDialog(object):		@@ -206,48 +209,27 @@ class ProgressDialog(object):
206	self.dlg.Destroy()	209	self.dlg.Destroy()
207		210
208		211
209	-
210	-#---------
211	-WILDCARD_OPEN = "InVesalius 3 project (.inv3)\|.inv3\|"\	212	+# ---------
		213	+WILDCARD_OPEN = "InVesalius 3 project (.inv3)\|.inv3\|" \
212	"All files (.)\|."	214	"All files (.)\|."
213		215
214	-WILDCARD_ANALYZE = "Analyze (.hdr)\|.hdr\|"\
215	- "All files (.)\|."	216	+WILDCARD_ANALYZE = "Analyze 7.5 (.hdr)\|.hdr\|" \
		217	+ "All files (.)\|."
216		218
217	-def ShowOpenProjectDialog():
218	- # Default system path
219	- current_dir = os.path.abspath(".")
220	- dlg = wx.FileDialog(None, message=_("Open InVesalius 3 project..."),
221	- defaultDir="",
222	- defaultFile="", wildcard=WILDCARD_OPEN,
223	- style=wx.FD_OPEN\|wx.FD_CHANGE_DIR)	219	+WILDCARD_NIFTI = "NIfTI 1 (.nii)\|.nii\|" \
		220	+ "Compressed NIfTI (.nii.gz)\|.nii.gz\|" \
		221	+ "All files (.)\|."
224		222
225	- # inv3 filter is default
226	- dlg.SetFilterIndex(0)	223	+WILDCARD_PARREC = "PAR/REC (.par)\|.par\|" \
		224	+ "All files (.)\|."
227		225
228	- # Show the dialog and retrieve the user response. If it is the OK response,
229	- # process the data.
230	- filepath = None
231	- try:
232	- if dlg.ShowModal() == wx.ID_OK:
233	- # This returns a Python list of files that were selected.
234	- filepath = dlg.GetPath()
235	- except(wx._core.PyAssertionError): #FIX: win64
236	- filepath = dlg.GetPath()
237		226
238	- # Destroy the dialog. Don't do this until you are done with it!
239	- # BAD things can happen otherwise!
240	- dlg.Destroy()
241	- os.chdir(current_dir)
242	- return filepath
243	-
244	-
245	-def ShowOpenAnalyzeDialog():	227	+def ShowOpenProjectDialog():
246	# Default system path	228	# Default system path
247	current_dir = os.path.abspath(".")	229	current_dir = os.path.abspath(".")
248	- dlg = wx.FileDialog(None, message=_("Open Analyze file"),	230	+ dlg = wx.FileDialog(None, message=_("Open InVesalius 3 project..."),
249	defaultDir="",	231	defaultDir="",
250	- defaultFile="", wildcard=WILDCARD_ANALYZE,	232	+ defaultFile="", wildcard=WILDCARD_OPEN,
251	style=wx.FD_OPEN\|wx.FD_CHANGE_DIR)	233	style=wx.FD_OPEN\|wx.FD_CHANGE_DIR)
252		234
253	# inv3 filter is default	235	# inv3 filter is default
	@@ -260,7 +242,7 @@ def ShowOpenAnalyzeDialog():		@@ -260,7 +242,7 @@ def ShowOpenAnalyzeDialog():
260	if dlg.ShowModal() == wx.ID_OK:	242	if dlg.ShowModal() == wx.ID_OK:
261	# This returns a Python list of files that were selected.	243	# This returns a Python list of files that were selected.
262	filepath = dlg.GetPath()	244	filepath = dlg.GetPath()
263	- except(wx._core.PyAssertionError): #FIX: win64	245	+ except(wx._core.PyAssertionError): # FIX: win64
264	filepath = dlg.GetPath()	246	filepath = dlg.GetPath()
265		247
266	# Destroy the dialog. Don't do this until you are done with it!	248	# Destroy the dialog. Don't do this until you are done with it!
	@@ -353,6 +335,47 @@ def ShowImportBitmapDirDialog():		@@ -353,6 +335,47 @@ def ShowImportBitmapDirDialog():
353	return path	335	return path
354		336
355		337
		338	+def ShowImportOtherFilesDialog(id_type):
		339	+ # Default system path
		340	+ current_dir = os.path.abspath(".")
		341	+ dlg = wx.FileDialog(None, message=_("Import Analyze 7.5 file"),
		342	+ defaultDir="",
		343	+ defaultFile="", wildcard=WILDCARD_ANALYZE,
		344	+ style=wx.FD_OPEN \| wx.FD_CHANGE_DIR)
		345	+
		346	+ if id_type == const.ID_NIFTI_IMPORT:
		347	+ dlg.SetMessage(_("Import NIFTi 1 file"))
		348	+ dlg.SetWildcard(WILDCARD_NIFTI)
		349	+ elif id_type == const.ID_PARREC_IMPORT:
		350	+ dlg.SetMessage(_("Import PAR/REC file"))
		351	+ dlg.SetWildcard(WILDCARD_PARREC)
		352	+
		353	+ # inv3 filter is default
		354	+ dlg.SetFilterIndex(0)
		355	+
		356	+ # Show the dialog and retrieve the user response. If it is the OK response,
		357	+ # process the data.
		358	+ filename = None
		359	+ try:
		360	+ if dlg.ShowModal() == wx.ID_OK:
		361	+ # GetPath returns in unicode, if a path has non-ascii characters a
		362	+ # UnicodeEncodeError is raised. To avoid this, path is encoded in utf-8
		363	+ if sys.platform == "win32":
		364	+ filename = dlg.GetPath()
		365	+ else:
		366	+ filename = dlg.GetPath().encode('utf-8')
		367	+
		368	+ except(wx._core.PyAssertionError): # TODO: error win64
		369	+ if (dlg.GetPath()):
		370	+ filename = dlg.GetPath()
		371	+
		372	+ # Destroy the dialog. Don't do this until you are done with it!
		373	+ # BAD things can happen otherwise!
		374	+ dlg.Destroy()
		375	+ os.chdir(current_dir)
		376	+ return filename
		377	+
		378	+
356	def ShowSaveAsProjectDialog(default_filename=None):	379	def ShowSaveAsProjectDialog(default_filename=None):
357	current_dir = os.path.abspath(".")	380	current_dir = os.path.abspath(".")
358	dlg = wx.FileDialog(None,	381	dlg = wx.FileDialog(None,
	@@ -380,10 +403,70 @@ def ShowSaveAsProjectDialog(default_filename=None):		@@ -380,10 +403,70 @@ def ShowSaveAsProjectDialog(default_filename=None):
380	if filename.split(".")[-1] != extension:	403	if filename.split(".")[-1] != extension:
381	filename = filename + "." + extension	404	filename = filename + "." + extension
382		405
		406	+ os.chdir(current_dir)
		407	+ return filename
		408	+
		409	+
		410	+# Dialog for neuronavigation markers
		411	+def ShowSaveMarkersDialog(default_filename=None):
		412	+ current_dir = os.path.abspath(".")
		413	+ dlg = wx.FileDialog(None,
		414	+ _("Save markers as..."), # title
		415	+ "", # last used directory
		416	+ default_filename,
		417	+ _("Markers (.txt)\|.txt"),
		418	+ wx.SAVE \| wx.OVERWRITE_PROMPT)
		419	+ # dlg.SetFilterIndex(0) # default is VTI
		420	+
		421	+ filename = None
		422	+ try:
		423	+ if dlg.ShowModal() == wx.ID_OK:
		424	+ filename = dlg.GetPath()
		425	+ ok = 1
		426	+ else:
		427	+ ok = 0
		428	+ except(wx._core.PyAssertionError): # TODO: fix win64
		429	+ filename = dlg.GetPath()
		430	+ ok = 1
		431	+
		432	+ if (ok):
		433	+ extension = "txt"
		434	+ if sys.platform != 'win32':
		435	+ if filename.split(".")[-1] != extension:
		436	+ filename = filename + "." + extension
383		437
384	os.chdir(current_dir)	438	os.chdir(current_dir)
385	return filename	439	return filename
386		440
		441	+
		442	+def ShowLoadMarkersDialog():
		443	+ current_dir = os.path.abspath(".")
		444	+
		445	+ dlg = wx.FileDialog(None, message=_("Load markers"),
		446	+ defaultDir="",
		447	+ defaultFile="",
		448	+ style=wx.OPEN\|wx.CHANGE_DIR)
		449	+
		450	+ # inv3 filter is default
		451	+ dlg.SetFilterIndex(0)
		452	+
		453	+ # Show the dialog and retrieve the user response. If it is the OK response,
		454	+ # process the data.
		455	+ filepath = None
		456	+ try:
		457	+ if dlg.ShowModal() == wx.ID_OK:
		458	+ # This returns a Python list of files that were selected.
		459	+ filepath = dlg.GetPath()
		460	+ except(wx._core.PyAssertionError): # FIX: win64
		461	+ filepath = dlg.GetPath()
		462	+
		463	+ # Destroy the dialog. Don't do this until you are done with it!
		464	+ # BAD things can happen otherwise!
		465	+ dlg.Destroy()
		466	+ os.chdir(current_dir)
		467	+ return filepath
		468	+
		469	+
387	class MessageDialog(wx.Dialog):	470	class MessageDialog(wx.Dialog):
388	def __init__(self, message):	471	def __init__(self, message):
389	pre = wx.PreDialog()	472	pre = wx.PreDialog()
	@@ -509,6 +592,7 @@ def ImportEmptyDirectory(dirpath):		@@ -509,6 +592,7 @@ def ImportEmptyDirectory(dirpath):
509	dlg.ShowModal()	592	dlg.ShowModal()
510	dlg.Destroy()	593	dlg.Destroy()
511		594
		595	+
512	def ImportInvalidFiles(ftype="DICOM"):	596	def ImportInvalidFiles(ftype="DICOM"):
513	if ftype == "Bitmap":	597	if ftype == "Bitmap":
514	msg = _("There are no Bitmap, JPEG, PNG or TIFF files in the selected folder.")	598	msg = _("There are no Bitmap, JPEG, PNG or TIFF files in the selected folder.")
	@@ -524,6 +608,20 @@ def ImportInvalidFiles(ftype="DICOM"):		@@ -524,6 +608,20 @@ def ImportInvalidFiles(ftype="DICOM"):
524	dlg.ShowModal()	608	dlg.ShowModal()
525	dlg.Destroy()	609	dlg.Destroy()
526		610
		611	+
		612	+def ImportAnalyzeWarning():
		613	+ msg1 = _("Warning! InVesalius has limited support to Analyze format.\n")
		614	+ msg2 = _("Slices may be wrongly oriented and functions may not work properly.")
		615	+ if sys.platform == 'darwin':
		616	+ dlg = wx.MessageDialog(None, "", msg1 + msg2,
		617	+ wx.ICON_INFORMATION \| wx.OK)
		618	+ else:
		619	+ dlg = wx.MessageDialog(None, msg1 + msg2, "InVesalius 3",
		620	+ wx.ICON_INFORMATION \| wx.OK)
		621	+ dlg.ShowModal()
		622	+ dlg.Destroy()
		623	+
		624	+
527	def InexistentMask():	625	def InexistentMask():
528	msg = _("A mask is needed to create a surface.")	626	msg = _("A mask is needed to create a surface.")
529	if sys.platform == 'darwin':	627	if sys.platform == 'darwin':
	@@ -593,6 +691,86 @@ def SurfaceSelectionRequiredForDuplication():		@@ -593,6 +691,86 @@ def SurfaceSelectionRequiredForDuplication():
593	dlg.ShowModal()	691	dlg.ShowModal()
594	dlg.Destroy()	692	dlg.Destroy()
595		693
		694	+
		695	+# Dialogs for neuronavigation mode
		696	+def InvalidFiducials():
		697	+ msg = _("Fiducials are invalid. Select six coordinates.")
		698	+ if sys.platform == 'darwin':
		699	+ dlg = wx.MessageDialog(None, "", msg,
		700	+ wx.ICON_INFORMATION \| wx.OK)
		701	+ else:
		702	+ dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
		703	+ wx.ICON_INFORMATION \| wx.OK)
		704	+ dlg.ShowModal()
		705	+ dlg.Destroy()
		706	+
		707	+
		708	+def NavigationTrackerWarning(trck_id, lib_mode):
		709	+ """
		710	+ Spatial Tracker connection error
		711	+ """
		712	+ trck = {1: 'Claron MicronTracker',
		713	+ 2: 'Polhemus FASTRAK',
		714	+ 3: 'Polhemus ISOTRAK',
		715	+ 4: 'Polhemus PATRIOT',
		716	+ 5: 'Debug tracker device'}
		717	+
		718	+ if lib_mode == 'choose':
		719	+ msg = _('No tracking device selected')
		720	+ elif lib_mode == 'error':
		721	+ msg = trck[trck_id] + _(' is not installed.')
		722	+ elif lib_mode == 'disconnect':
		723	+ msg = trck[trck_id] + _(' disconnected.')
		724	+ else:
		725	+ msg = trck[trck_id] + _(' is not connected.')
		726	+
		727	+ if sys.platform == 'darwin':
		728	+ dlg = wx.MessageDialog(None, "", msg,
		729	+ wx.ICON_INFORMATION \| wx.OK)
		730	+ else:
		731	+ dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
		732	+ wx.ICON_INFORMATION \| wx.OK)
		733	+
		734	+ dlg.ShowModal()
		735	+ dlg.Destroy()
		736	+
		737	+
		738	+def InvalidMarkersFile():
		739	+ msg = _("The TXT file is invalid.")
		740	+ if sys.platform == 'darwin':
		741	+ dlg = wx.MessageDialog(None, "", msg,
		742	+ wx.ICON_INFORMATION \| wx.OK)
		743	+ else:
		744	+ dlg = wx.MessageDialog(None, msg, "InVesalius 3 - Neuronavigator",
		745	+ wx.ICON_INFORMATION \| wx.OK)
		746	+ dlg.ShowModal()
		747	+ dlg.Destroy()
		748	+
		749	+
		750	+def NoMarkerSelected():
		751	+ msg = _("No data selected")
		752	+ if sys.platform == 'darwin':
		753	+ dlg = wx.MessageDialog(None, "", msg,
		754	+ wx.ICON_INFORMATION \| wx.OK)
		755	+ else:
		756	+ dlg = wx.MessageDialog(None,msg, "InVesalius 3 - Neuronavigator",
		757	+ wx.ICON_INFORMATION \| wx.OK)
		758	+ dlg.ShowModal()
		759	+ dlg.Destroy()
		760	+
		761	+
		762	+def EnterMarkerID(default):
		763	+ msg = _("Edit marker ID")
		764	+ if sys.platform == 'darwin':
		765	+ dlg = wx.TextEntryDialog(None, "", msg, defaultValue=default)
		766	+ else:
		767	+ dlg = wx.TextEntryDialog(None, msg, "InVesalius 3", defaultValue=default)
		768	+ dlg.ShowModal()
		769	+ result = dlg.GetValue()
		770	+ dlg.Destroy()
		771	+ return result
		772	+
		773	+
596	class NewMask(wx.Dialog):	774	class NewMask(wx.Dialog):
597	def __init__(self,	775	def __init__(self,
598	parent=None,	776	parent=None,
	@@ -828,6 +1006,8 @@ def ShowAboutDialog(parent):		@@ -828,6 +1006,8 @@ def ShowAboutDialog(parent):
828	info.Developers = ["Paulo Henrique Junqueira Amorim",	1006	info.Developers = ["Paulo Henrique Junqueira Amorim",
829	"Thiago Franco de Moraes",	1007	"Thiago Franco de Moraes",
830	"Jorge Vicente Lopes da Silva",	1008	"Jorge Vicente Lopes da Silva",
		1009	+ "Victor Hugo de Oliveira e Souza (navigator)",
		1010	+ "Renan Hiroshi Matsuda (navigator)"
831	"Tatiana Al-Chueyr (former)",	1011	"Tatiana Al-Chueyr (former)",
832	"Guilherme Cesar Soares Ruppert (former)",	1012	"Guilherme Cesar Soares Ruppert (former)",
833	"Fabio de Souza Azevedo (former)",	1013	"Fabio de Souza Azevedo (former)",