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	8	invesalius/*.swp
9	9	invesalius/data/*.log
10	10	invesalius/data/*.pyc
	11	+invesalius/data/*.pyd
11	12	invesalius/gui/*.log
12	13	invesalius/gui/*.pyc
13	14	invesalius/gui/widgets/*.log
...	...	@@ -21,6 +22,7 @@ invesalius/reader/*.pyc
21	22	tags
22	23	*.c
23	24
	25	+.idea
24	26	build
25	27	*.patch
26	28	*.tgz
...	...	@@ -29,4 +31,4 @@ build
29	31	*.cpp
30	32	*.diff
31	33
32	34	-*.directory
	35	+*.directory
33	36	\ No newline at end of file
...	...
...	...	@@ -487,8 +487,9 @@ VTK_WARNING = 0
487	487
488	488	[ID_DICOM_IMPORT, ID_PROJECT_OPEN, ID_PROJECT_SAVE_AS, ID_PROJECT_SAVE,
489	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	493	ID_EXIT = wx.ID_EXIT
493	494	ID_ABOUT = wx.ID_ABOUT
494	495
...	...	@@ -637,3 +638,53 @@ BOOLEAN_UNION = 1
637	638	BOOLEAN_DIFF = 2
638	639	BOOLEAN_AND = 3
639	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'))
...	...
...	...	@@ -16,11 +16,9 @@
16	16	# PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais
17	17	# detalhes.
18	18	#--------------------------------------------------------------------------
19		-import math
20	19	import os
21	20	import plistlib
22	21	import wx
23		-import numpy
24	22	from wx.lib.pubsub import pub as Publisher
25	23
26	24	import invesalius.constants as const
...	...	@@ -32,10 +30,10 @@ import invesalius.data.surface as srf
32	30	import invesalius.data.volume as volume
33	31	import invesalius.gui.dialogs as dialog
34	32	import invesalius.project as prj
35		-import invesalius.reader.analyze_reader as analyze
36	33	import invesalius.reader.dicom_grouper as dg
37	34	import invesalius.reader.dicom_reader as dcm
38	35	import invesalius.reader.bitmap_reader as bmp
	36	+import invesalius.reader.others_reader as oth
39	37	import invesalius.session as ses
40	38
41	39
...	...	@@ -65,6 +63,8 @@ class Controller():
65	63	Publisher.subscribe(self.OnImportMedicalImages, 'Import directory')
66	64	Publisher.subscribe(self.OnShowDialogImportDirectory,
67	65	'Show import directory dialog')
	66	+ Publisher.subscribe(self.OnShowDialogImportOtherFiles,
	67	+ 'Show import other files dialog')
68	68	Publisher.subscribe(self.OnShowDialogOpenProject,
69	69	'Show open project dialog')
70	70
...	...	@@ -77,7 +77,9 @@ class Controller():
77	77	Publisher.subscribe(self.OnOpenDicomGroup,
78	78	'Open DICOM group')
79	79	Publisher.subscribe(self.OnOpenBitmapFiles,
80		- 'Open bitmap files')
	80	+ 'Open bitmap files')
	81	+ Publisher.subscribe(self.OnOpenOtherFiles,
	82	+ 'Open other files')
81	83	Publisher.subscribe(self.Progress, "Update dicom load")
82	84	Publisher.subscribe(self.Progress, "Update bitmap load")
83	85	Publisher.subscribe(self.OnLoadImportPanel, "End dicom load")
...	...	@@ -88,7 +90,6 @@ class Controller():
88	90	Publisher.subscribe(self.OnShowDialogCloseProject, 'Close Project')
89	91	Publisher.subscribe(self.OnOpenProject, 'Open project')
90	92	Publisher.subscribe(self.OnOpenRecentProject, 'Open recent project')
91		- Publisher.subscribe(self.OnShowAnalyzeFile, 'Show analyze dialog')
92	93	Publisher.subscribe(self.OnShowBitmapFile, 'Show bitmap dialog')
93	94
94	95	Publisher.subscribe(self.ShowBooleanOpDialog, 'Show boolean dialog')
...	...	@@ -116,6 +117,10 @@ class Controller():
116	117	def OnShowDialogImportDirectory(self, pubsub_evt):
117	118	self.ShowDialogImportDirectory()
118	119
	120	+ def OnShowDialogImportOtherFiles(self, pubsub_evt):
	121	+ id_type = pubsub_evt.data
	122	+ self.ShowDialogImportOtherFiles(id_type)
	123	+
119	124	def OnShowDialogOpenProject(self, pubsub_evt):
120	125	self.ShowDialogOpenProject()
121	126
...	...	@@ -126,15 +131,6 @@ class Controller():
126	131	def OnShowDialogCloseProject(self, pubsub_evt):
127	132	self.ShowDialogCloseProject()
128	133
129		- def OnShowAnalyzeFile(self, pubsub_evt):
130		- dirpath = dialog.ShowOpenAnalyzeDialog()
131		- imagedata = analyze.ReadAnalyze(dirpath)
132		- if imagedata:
133		- self.CreateAnalyzeProject(imagedata)
134		-
135		- self.LoadProject()
136		- Publisher.sendMessage("Enable state project", True)
137		-
138	134	def OnShowBitmapFile(self, pubsub_evt):
139	135	self.ShowDialogImportBitmapFile()
140	136	###########################
...	...	@@ -163,7 +159,6 @@ class Controller():
163	159	self.StartImportBitmapPanel(dirpath)
164	160	# Publisher.sendMessage("Load data to import panel", dirpath)
165	161
166		-
167	162	def ShowDialogImportDirectory(self):
168	163	# Offer to save current project if necessary
169	164	session = ses.Session()
...	...	@@ -186,6 +181,40 @@ class Controller():
186	181	self.StartImportPanel(dirpath)
187	182	Publisher.sendMessage("Load data to import panel", dirpath)
188	183
	184	+ def ShowDialogImportOtherFiles(self, id_type):
	185	+ # Offer to save current project if necessary
	186	+ session = ses.Session()
	187	+ st = session.project_status
	188	+ if (st == const.PROJ_NEW) or (st == const.PROJ_CHANGE):
	189	+ filename = session.project_path[1]
	190	+ answer = dialog.SaveChangesDialog2(filename)
	191	+ if answer:
	192	+ self.ShowDialogSaveProject()
	193	+ self.CloseProject()
	194	+ # Publisher.sendMessage("Enable state project", False)
	195	+ Publisher.sendMessage('Set project name')
	196	+ Publisher.sendMessage("Stop Config Recording")
	197	+ Publisher.sendMessage("Set slice interaction style", const.STATE_DEFAULT)
	198	+
	199	+ # Warning for limited support to Analyze format
	200	+ if id_type == const.ID_ANALYZE_IMPORT:
	201	+ dialog.ImportAnalyzeWarning()
	202	+
	203	+ # Import project treating compressed nifti exception
	204	+ suptype = ('hdr', 'nii', 'nii.gz', 'par')
	205	+ filepath = dialog.ShowImportOtherFilesDialog(id_type)
	206	+ name = filepath.rpartition('\\')[-1].split('.')
	207	+
	208	+ if name[-1] == 'gz':
	209	+ name[1] = 'nii.gz'
	210	+
	211	+ filetype = name[1].lower()
	212	+
	213	+ if filetype in suptype:
	214	+ Publisher.sendMessage("Open other files", filepath)
	215	+ else:
	216	+ dialog.ImportInvalidFiles()
	217	+
189	218	def ShowDialogOpenProject(self):
190	219	# Offer to save current project if necessary
191	220	session = ses.Session()
...	...	@@ -281,8 +310,6 @@ class Controller():
281	310	else:
282	311	dialog.InexistentPath(filepath)
283	312
284		-
285		-
286	313	def OpenProject(self, filepath):
287	314	Publisher.sendMessage('Begin busy cursor')
288	315	path = os.path.abspath(filepath)
...	...	@@ -342,7 +369,7 @@ class Controller():
342	369
343	370	def StartImportPanel(self, path):
344	371
345		- # retrieve DICOM files splited into groups
	372	+ # retrieve DICOM files split into groups
346	373	reader = dcm.ProgressDicomReader()
347	374	reader.SetWindowEvent(self.frame)
348	375	reader.SetDirectoryPath(path)
...	...	@@ -410,21 +437,33 @@ class Controller():
410	437	self.ImportMedicalImages(directory)
411	438
412	439	def ImportMedicalImages(self, directory):
413		- # OPTION 1: DICOM?
414	440	patients_groups = dcm.GetDicomGroups(directory)
	441	+ name = directory.rpartition('\\')[-1].split('.')
	442	+ print "patients: ", patients_groups
	443	+
415	444	if len(patients_groups):
	445	+ # OPTION 1: DICOM
416	446	group = dcm.SelectLargerDicomGroup(patients_groups)
417		- matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0,0],gui=True)
	447	+ matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=True)
418	448	self.CreateDicomProject(dicom, matrix, matrix_filename)
419		- # OPTION 2: ANALYZE?
420	449	else:
421		- imagedata = analyze.ReadDirectory(directory)
422		- if imagedata:
423		- self.CreateAnalyzeProject(imagedata)
424		- # OPTION 3: Nothing...
	450	+ # OPTION 2: NIfTI, Analyze or PAR/REC
	451	+ if name[-1] == 'gz':
	452	+ name[1] = 'nii.gz'
	453	+
	454	+ suptype = ('hdr', 'nii', 'nii.gz', 'par')
	455	+ filetype = name[1].lower()
	456	+
	457	+ if filetype in suptype:
	458	+ group = oth.ReadOthers(directory)
425	459	else:
426	460	utils.debug("No medical images found on given directory")
427	461	return
	462	+
	463	+ matrix, matrix_filename = self.OpenOtherFiles(group)
	464	+ self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
	465	+ # OPTION 4: Nothing...
	466	+
428	467	self.LoadProject()
429	468	Publisher.sendMessage("Enable state project", True)
430	469
...	...	@@ -493,43 +532,6 @@ class Controller():
493	532
494	533	Publisher.sendMessage('End busy cursor')
495	534
496		- def CreateAnalyzeProject(self, imagedata):
497		- header = imagedata.get_header()
498		- proj = prj.Project()
499		- proj.imagedata = None
500		- proj.name = _("Untitled")
501		- proj.SetAcquisitionModality("MRI")
502		- #TODO: Verify if all Analyse are in AXIAL orientation
503		-
504		- # To get Z, X, Y (used by InVesaliu), not X, Y, Z
505		- matrix, matrix_filename = image_utils.analyze2mmap(imagedata)
506		- if header['orient'] == 0:
507		- proj.original_orientation = const.AXIAL
508		- elif header['orient'] == 1:
509		- proj.original_orientation = const.CORONAL
510		- elif header['orient'] == 2:
511		- proj.original_orientation = const.SAGITAL
512		- else:
513		- proj.original_orientation = const.SAGITAL
514		-
515		- proj.threshold_range = (int(header['glmin']),
516		- int(header['glmax']))
517		- proj.window = proj.threshold_range[1] - proj.threshold_range[0]
518		- proj.level = (0.5 * (proj.threshold_range[1] + proj.threshold_range[0]))
519		- proj.spacing = header['pixdim'][1:4]
520		- proj.matrix_shape = matrix.shape
521		-
522		- self.Slice = sl.Slice()
523		- self.Slice.matrix = matrix
524		- self.Slice.matrix_filename = matrix_filename
525		-
526		- self.Slice.window_level = proj.level
527		- self.Slice.window_width = proj.window
528		- self.Slice.spacing = header.get_zooms()[:3]
529		-
530		- Publisher.sendMessage('Update threshold limits list',
531		- proj.threshold_range)
532		-
533	535	def CreateDicomProject(self, dicom, matrix, matrix_filename):
534	536	name_to_const = {"AXIAL":const.AXIAL,
535	537	"CORONAL":const.CORONAL,
...	...	@@ -604,6 +606,40 @@ class Controller():
604	606
605	607	dirpath = session.CreateProject(filename)
606	608
	609	+ def CreateOtherProject(self, name, matrix, matrix_filename):
	610	+ name_to_const = {"AXIAL": const.AXIAL,
	611	+ "CORONAL": const.CORONAL,
	612	+ "SAGITTAL": const.SAGITAL}
	613	+
	614	+ proj = prj.Project()
	615	+ proj.name = name
	616	+ proj.modality = 'MRI'
	617	+ proj.SetAcquisitionModality('MRI')
	618	+ proj.matrix_shape = matrix.shape
	619	+ proj.matrix_dtype = matrix.dtype.name
	620	+ proj.matrix_filename = matrix_filename
	621	+
	622	+ # Orientation must be CORONAL in order to as_closes_canonical and
	623	+ # swap axis in img2memmap to work in a standardized way.
	624	+ # TODO: Create standard import image for all acquisition orientations
	625	+ orientation = 'CORONAL'
	626	+
	627	+ proj.original_orientation =\
	628	+ name_to_const[orientation]
	629	+
	630	+ proj.window = self.Slice.window_width
	631	+ proj.level = self.Slice.window_level
	632	+ proj.threshold_range = int(matrix.min()), int(matrix.max())
	633	+ proj.spacing = self.Slice.spacing
	634	+
	635	+ ######
	636	+ session = ses.Session()
	637	+ filename = proj.name + ".inv3"
	638	+
	639	+ filename = filename.replace("/", "") # Fix problem case other/Skull_DICOM
	640	+
	641	+ dirpath = session.CreateProject(filename)
	642	+
607	643	def OnOpenBitmapFiles(self, pubsub_evt):
608	644	rec_data = pubsub_evt.data
609	645	bmp_data = bmp.BitmapData()
...	...	@@ -688,6 +724,26 @@ class Controller():
688	724	self.LoadProject()
689	725	Publisher.sendMessage("Enable state project", True)
690	726
	727	+ def OnOpenOtherFiles(self, pubsub_evt):
	728	+ filepath = pubsub_evt.data
	729	+ name = filepath.rpartition('\\')[-1].split('.')
	730	+
	731	+ if name[-1] == 'gz':
	732	+ name[1] = 'nii.gz'
	733	+
	734	+ suptype = ('hdr', 'nii', 'nii.gz', 'par')
	735	+ filetype = name[1].lower()
	736	+
	737	+ if filetype in suptype:
	738	+ group = oth.ReadOthers(filepath)
	739	+ else:
	740	+ dialog.ImportInvalidFiles()
	741	+
	742	+ matrix, matrix_filename = self.OpenOtherFiles(group)
	743	+ self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
	744	+ self.LoadProject()
	745	+ Publisher.sendMessage("Enable state project", True)
	746	+
691	747	def OpenDicomGroup(self, dicom_group, interval, file_range, gui=True):
692	748	# Retrieve general DICOM headers
693	749	dicom = dicom_group.GetDicomSample()
...	...	@@ -773,6 +829,30 @@ class Controller():
773	829
774	830	return self.matrix, self.filename, dicom
775	831
	832	+ def OpenOtherFiles(self, group):
	833	+ # Retreaving matrix from image data
	834	+ self.matrix, scalar_range, self.filename = image_utils.img2memmap(group)
	835	+
	836	+ hdr = group.header
	837	+ hdr.set_data_dtype('int16')
	838	+ dims = hdr.get_zooms()
	839	+ dimsf = tuple([float(s) for s in dims])
	840	+
	841	+ wl = float((scalar_range[0] + scalar_range[1]) * 0.5)
	842	+ ww = float((scalar_range[1] - scalar_range[0]))
	843	+
	844	+ self.Slice = sl.Slice()
	845	+ self.Slice.matrix = self.matrix
	846	+ self.Slice.matrix_filename = self.filename
	847	+
	848	+ self.Slice.spacing = dimsf
	849	+ self.Slice.window_level = wl
	850	+ self.Slice.window_width = ww
	851	+
	852	+ scalar_range = int(scalar_range[0]), int(scalar_range[1])
	853	+ Publisher.sendMessage('Update threshold limits list', scalar_range)
	854	+ return self.matrix, self.filename
	855	+
776	856	def LoadImagedataInfo(self):
777	857	proj = prj.Project()
778	858
...	...
1		-from numpy import *
2	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	128	[0.0, 1.0, 0, point[0, 1]],
80	129	[0.0, 0.0, 1.0, point[0, 2]],
81	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		-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 @@
	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 @@
	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	592
593	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	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	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	647	\ No newline at end of file
...	...
...	...	@@ -531,10 +531,12 @@ class Slice(object):
531	531	image = self.do_colour_image(ww_wl_image)
532	532	if self.current_mask and self.current_mask.is_shown:
533	533	if self.buffer_slices[orientation].vtk_mask:
534		- print "Getting from buffer"
	534	+ # Prints that during navigation causes delay in update
	535	+ # print "Getting from buffer"
535	536	mask = self.buffer_slices[orientation].vtk_mask
536	537	else:
537		- print "Do not getting from buffer"
	538	+ # Prints that during navigation causes delay in update
	539	+ # print "Do not getting from buffer"
538	540	n_mask = self.get_mask_slice(orientation, slice_number)
539	541	mask = converters.to_vtk(n_mask, self.spacing, slice_number, orientation)
540	542	mask = self.do_colour_mask(mask, self.opacity)
...	...
...	...	@@ -230,10 +230,8 @@ class CrossInteractorStyle(DefaultInteractorStyle):
230	230	coord = self.viewer.calcultate_scroll_position(px, py)
231	231	Publisher.sendMessage('Update cross position', (wx, wy, wz))
232	232	self.ScrollSlice(coord)
233		- Publisher.sendMessage('Set ball reference position based on bound',
234		- (wx, wy, wz))
	233	+ Publisher.sendMessage('Set ball reference position', (wx, wy, wz))
235	234	Publisher.sendMessage('Set camera in volume', (wx, wy, wz))
236		- Publisher.sendMessage('Render volume viewer')
237	235
238	236	iren.Render()
239	237
...	...