app.py

-#!/usr/bin/python
+#!/usr/bin/env python3
 #--------------------------------------------------------------------------
 # Software:     InVesalius - Software de Reconstrucao 3D de Imagens Medicas
 # Copyright:    (C) 2001  Centro de Pesquisas Renato Archer
@@ -65,21 +65,9 @@ import invesalius.i18n as i18n
 import invesalius.session as ses
 import invesalius.utils as utils
 
-FS_ENCODE = sys.getfilesystemencoding()
+from invesalius import inv_paths
 
-if sys.platform == 'win32':
-    from invesalius.expanduser import expand_user
-    try:
-        USER_DIR = expand_user()
-    except:
-        USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
-else:
-    USER_DIR = utils.decode(os.path.expanduser('~'),FS_ENCODE)
-
-USER_INV_DIR = os.path.join(USER_DIR, u'.invesalius')
-USER_PRESET_DIR = os.path.join(USER_INV_DIR, u'presets')
-USER_RAYCASTING_PRESETS_DIRECTORY = os.path.join(USER_PRESET_DIR, u'raycasting')
-USER_LOG_DIR = os.path.join(USER_INV_DIR, u'logs')
+FS_ENCODE = sys.getfilesystemencoding()
 
 # ------------------------------------------------------------------
 
@@ -147,9 +135,8 @@ class Inv3SplashScreen(SplashScreen):
             create_session = True
 
         install_lang = 0
-        # Check if there is a language set (if session file exists
-        if session.ReadLanguage():
-            lang = session.GetLanguage()
+        lang = session.GetLanguage()
+        if lang:
             if (lang != "False"):
                 _ = i18n.InstallLanguage(lang)
                 install_lang = 1
@@ -179,7 +166,9 @@ class Inv3SplashScreen(SplashScreen):
                     invdir = os.path.join(homedir, ".invesalius")
                     shutil.rmtree(invdir)
                     sys.exit()
-                    
+
+            dialog.Destroy()
+
         # Session file should be created... So we set the recent
         # choosen language
         if (create_session):
@@ -187,18 +176,20 @@ class Inv3SplashScreen(SplashScreen):
             session.SetLanguage(lang)
             session.WriteSessionFile()
 
-        session.SaveConfigFileBackup()
+        #  session.SaveConfigFileBackup()
 
            
         # Only after language was defined, splash screen will be
         # shown
         if lang:
-            #  print "LANG", lang, _, wx.Locale(), wx.GetLocale()
-            import locale
-            try:
-                locale.setlocale(locale.LC_ALL, '')
-            except locale.Error:
-                pass
+            
+            #import locale
+            #try:
+            #    locale.setlocale(locale.LC_ALL, '')
+            #except locale.Error:
+            #    pass
+            
+            
             # For pt_BR, splash_pt.png should be used
             if (lang.startswith('pt')):
                 icon_file = "splash_pt.png"
@@ -244,9 +235,9 @@ class Inv3SplashScreen(SplashScreen):
         self.main = Frame(None)
         self.control = Controller(self.main)
         
-        self.fc = wx.FutureCall(1, self.ShowMain)
+        self.fc = wx.CallLater(200, self.ShowMain)
         options, args = parse_comand_line()
-        wx.FutureCall(1, use_cmd_optargs, options, args)
+        wx.CallLater(1, use_cmd_optargs, options, args)
 
         # Check for updates
         from threading import Thread
@@ -333,6 +324,13 @@ def parse_comand_line():
     parser.add_option("-a", "--export-to-all",
                       help="Export to STL for all mask presets.")
 
+    parser.add_option("--export-project",
+                      help="Export slices and mask to HDF5 or Nifti file.")
+
+    parser.add_option("--no-masks", action="store_false",
+                      dest="save_masks", default=True,
+                      help="Make InVesalius not export mask when exporting project.")
+
     options, args = parser.parse_args()
     return options, args
 
@@ -426,6 +424,17 @@ def check_for_export(options, suffix='', remove_surfaces=False):
         finally:
             exit(0)
 
+    if options.export_project:
+        from invesalius.project import Project
+        prj = Project()
+        export_filename = options.export_project
+        if suffix:
+            export_filename, ext = os.path.splitext(export_filename)
+            export_filename = u'{}-{}{}'.format(export_filename, suffix, ext)
+
+        prj.export_project(export_filename, save_masks=options.save_masks)
+        print("Saved {}".format(export_filename))
+
 
 def export(path_, threshold_range, remove_surface=False):
     import invesalius.constants as const
@@ -489,17 +498,14 @@ if __name__ == '__main__':
 
         os.chdir(path)
 
-    # Create raycasting presets' folder, if it doens't exist
-    if not os.path.isdir(USER_RAYCASTING_PRESETS_DIRECTORY):
-        os.makedirs(USER_RAYCASTING_PRESETS_DIRECTORY)
-
-    # Create logs' folder, if it doesn't exist
-    if not os.path.isdir(USER_LOG_DIR):
-        os.makedirs(USER_LOG_DIR)
+    if not inv_paths.USER_INV_DIR.exists():
+        inv_paths.create_conf_folders()
+        if inv_paths.OLD_USER_INV_DIR.exists():
+            inv_paths.copy_old_files()
 
     if hasattr(sys,"frozen") and sys.frozen == "windows_exe":
         # Set system standard error output to file
-        path = os.path.join(USER_LOG_DIR, u"stderr.log")
+        path = inv_paths.USER_LOG_DIR.join("stderr.log")
         sys.stderr = open(path, "w")
 
     # Add current directory to PYTHONPATH, so other classes can

debian/changelog

+invesalius (3.1.99993-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Thiago Franco de Moraes <tfmoraes@cti.gov.br>  Tue, 21 May 2019 11:30:01 -0300
+
 invesalius (3.1.99992-3) unstable; urgency=medium
 
   * Force Python3 >= 3.7 (its also python3-dev rather than python3-all-dev)

debian/control

@@ -30,6 +30,7 @@ Depends: ${python3:Depends},
          python3-nibabel,
          python3-serial,
          python3-psutil,
+         python3-h5py,
          invesalius-bin
 Description: 3D medical imaging reconstruction software
  InVesalius generates 3D medical imaging reconstructions based on a sequence of

debian/patches/10_import_cython_modules.patch

 Author: Thiago Franco Moraes
-Last-Update: 2016-10-06 14:28:25 +0000
+Last-Update: 2019-05-21 11:28:25 -0300
 Description: Import cython modules
 
+diff --git a/invesalius/data/mask.py b/invesalius/data/mask.py
+index 2bae7b49..40df971d 100644
 --- a/invesalius/data/mask.py
 +++ b/invesalius/data/mask.py
-@@ -30,7 +30,7 @@
+@@ -30,7 +30,7 @@ import invesalius.constants as const
  import invesalius.data.imagedata_utils as iu
  import invesalius.session as ses
  
@@ -13,45 +15,54 @@ Description: Import cython modules
  
  from wx.lib.pubsub import pub as Publisher
  from scipy import ndimage
+diff --git a/invesalius/data/slice_.py b/invesalius/data/slice_.py
+index 44976042..f6ce9e41 100644
 --- a/invesalius/data/slice_.py
 +++ b/invesalius/data/slice_.py
-@@ -31,9 +31,9 @@
+@@ -35,10 +35,10 @@ import invesalius.session as ses
  import invesalius.utils as utils
  from invesalius.data.mask import Mask
  from invesalius.project import Project
 -from invesalius.data import mips
 +from invesalius_cy import mips
  
--from invesalius.data import transforms
-+from invesalius_cy import transforms
- import invesalius.data.transformations as transformations
+ from invesalius.data import transforms
+-import invesalius.data.transformations as transformations
++import invesalius_cy as transformations
  OTHER=0
  PLIST=1
+ WIDGET=2
+diff --git a/invesalius/data/styles.py b/invesalius/data/styles.py
+index 5f302d4d..3bd712a4 100644
 --- a/invesalius/data/styles.py
 +++ b/invesalius/data/styles.py
-@@ -45,7 +45,7 @@
+@@ -47,7 +47,7 @@ from skimage.morphology import watershed
  import invesalius.gui.dialogs as dialogs
- from invesalius.data.measures import MeasureData
+ from invesalius.data.measures import MeasureData, CircleDensityMeasure, PolygonDensityMeasure
  
 -from . import floodfill
 +from invesalius_cy import floodfill
  
  import invesalius.data.watershed_process as watershed_process
  import invesalius.utils as utils
+diff --git a/invesalius/data/surface.py b/invesalius/data/surface.py
+index 4a7179b6..fb13078c 100644
 --- a/invesalius/data/surface.py
 +++ b/invesalius/data/surface.py
-@@ -48,7 +48,7 @@
- import invesalius.utils as utl
- import invesalius.data.vtk_utils as vu
+@@ -60,7 +60,7 @@ import invesalius.data.vtk_utils as vu
+ 
+ from invesalius.gui import dialogs
  
 -from invesalius.data import cy_mesh
 +from invesalius_cy import cy_mesh
  # TODO: Verificar ReleaseDataFlagOn and SetSource 
  
- class Surface():
+ 
+diff --git a/setup.py b/setup.py
+index b4962e1d..c8c61ad8 100644
 --- a/setup.py
 +++ b/setup.py
-@@ -11,26 +11,26 @@
+@@ -11,26 +11,26 @@ import numpy
  if sys.platform.startswith('linux'):
      setup(
          cmdclass = {'build_ext': build_ext},

debian/patches/series

-10_sample_path.patch
 10_import_cython_modules.patch
-10_remove_python2_shebang.patch
-10_remove_py2_prints.patch

debian/rules

@@ -39,6 +39,7 @@ override_dh_clean:
 
 create-launcher:
 	echo '#!/bin/sh' > invesalius3
+	echo 'export INV_SAMPLE_DIR="/usr/share/doc/invesalius-examples/examples/"' >> invesalius3
 	echo 'export PYTHONPATH=$$PYTHONPATH:"/usr/lib/invesalius"' >> invesalius3
 	echo 'export INVESALIUS_LIBRARY_PATH="/usr/share/invesalius/"' >> invesalius3
 	echo 'cd $$INVESALIUS_LIBRARY_PATH' >> invesalius3

invesalius/constants.py

@@ -24,6 +24,7 @@ import wx
 import itertools
 
 from invesalius import utils
+from invesalius import inv_paths
 
 #from invesalius.project import Project
 INVESALIUS_VERSION = "3.1.1"
@@ -98,9 +99,15 @@ SAGITAL = 3
 VOLUME = 4
 SURFACE = 5
 
+AXIAL_STR="AXIAL"
+CORONAL_STR="CORONAL"
+SAGITAL_STR="SAGITAL"
+
 # Measure type
 LINEAR = 6
 ANGULAR = 7
+DENSITY_ELLIPSE = 8
+DENSITY_POLYGON = 9
 
 # Colour representing each orientation
 ORIENTATION_COLOUR = {'AXIAL': (1,0,0), # Red
@@ -329,59 +336,13 @@ REDUCE_IMAGEDATA_QUALITY = 0
 # PATHS
 FS_ENCODE = sys.getfilesystemencoding()
 
-if sys.platform == 'win32':
-    from invesalius.expanduser import expand_user
-    try:
-        USER_DIR = expand_user()
-    except:
-        USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
-else:
-    USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
-
-USER_INV_DIR = os.path.join(USER_DIR, u'.invesalius')
-USER_PRESET_DIR = os.path.join(USER_INV_DIR, u'presets')
-USER_LOG_DIR = os.path.join(USER_INV_DIR, u'logs')
-
-FILE_PATH = utils.decode(os.path.split(__file__)[0], FS_ENCODE)
-
-if hasattr(sys,"frozen") and (sys.frozen == "windows_exe"\
-                            or sys.frozen == "console_exe"):
-    abs_path = os.path.abspath(FILE_PATH, u'..', u'..', u'..')
-    ICON_DIR = os.path.join(abs_path, u"icons")
-    SAMPLE_DIR = os.path.join(FILE_PATH, u'samples')
-    DOC_DIR = os.path.join(FILE_PATH, u'docs')
-    folder=RAYCASTING_PRESETS_DIRECTORY= os.path.join(abs_path, u"presets", u"raycasting")
-    RAYCASTING_PRESETS_COLOR_DIRECTORY = os.path.join(abs_path, u"presets", u"raycasting", u"color_list")
-
-else:
-    ICON_DIR = os.path.abspath(os.path.join(FILE_PATH, u'..', u'icons'))
-    SAMPLE_DIR = os.path.abspath(os.path.join(FILE_PATH, u'..', u'samples'))
-    DOC_DIR = os.path.abspath(os.path.join(FILE_PATH, u'..', u'docs'))
-
-    folder=RAYCASTING_PRESETS_DIRECTORY= os.path.abspath(os.path.join(u".",
-                                                                  u"presets",
-                                                                  u"raycasting"))
-
-    RAYCASTING_PRESETS_COLOR_DIRECTORY = os.path.abspath(os.path.join(u".",
-                                                                  u"presets",
-                                                                  u"raycasting",
-                                                                  u"color_list"))
-
-
-# MAC App
-if not os.path.exists(ICON_DIR):
-    ICON_DIR = os.path.abspath(os.path.join(FILE_PATH, u'..', u'..', u'..', u'..', u'icons'))
-    SAMPLE_DIR = os.path.abspath(os.path.join(FILE_PATH, u'..',  u'..', u'..', u'..', u'samples'))
-    DOC_DIR = os.path.abspath(os.path.join(FILE_PATH, u'..', u'..', u'..', u'..', u'docs'))
-
-
-ID_TO_BMP = {VOL_FRONT: [_("Front"), os.path.join(ICON_DIR, u"view_front.png")],
-             VOL_BACK: [_("Back"), os.path.join(ICON_DIR, u"view_back.png")],
-             VOL_TOP: [_("Top"), os.path.join(ICON_DIR, u"view_top.png")],
-             VOL_BOTTOM: [_("Bottom"), os.path.join(ICON_DIR, u"view_bottom.png")],
-             VOL_RIGHT: [_("Right"), os.path.join(ICON_DIR, u"view_right.png")],
-             VOL_LEFT: [_("Left"), os.path.join(ICON_DIR, u"view_left.png")],
-             VOL_ISO:[_("Isometric"), os.path.join(ICON_DIR, u"view_isometric.png")]
+ID_TO_BMP = {VOL_FRONT: [_("Front"), str(inv_paths.ICON_DIR.joinpath("view_front.png"))],
+             VOL_BACK: [_("Back"), str(inv_paths.ICON_DIR.joinpath("view_back.png"))],
+             VOL_TOP: [_("Top"), str(inv_paths.ICON_DIR.joinpath("view_top.png"))],
+             VOL_BOTTOM: [_("Bottom"), str(inv_paths.ICON_DIR.joinpath("view_bottom.png"))],
+             VOL_RIGHT: [_("Right"), str(inv_paths.ICON_DIR.joinpath("view_right.png"))],
+             VOL_LEFT: [_("Left"), str(inv_paths.ICON_DIR.joinpath("view_left.png"))],
+             VOL_ISO:[_("Isometric"), str(inv_paths.ICON_DIR.joinpath("view_isometric.png"))]
              }
 
 # if 1, use vtkVolumeRaycastMapper, if 0, use vtkFixedPointVolumeRayCastMapper
@@ -427,10 +388,9 @@ RAYCASTING_FILES = {_("Airways"): "Airways.plist",
 #                    os.path.isfile(os.path.join(folder,filename))]
 
 
-USER_RAYCASTING_PRESETS_DIRECTORY = os.path.join(USER_PRESET_DIR, u'raycasting')
-RAYCASTING_TYPES = [_(filename.split(".")[0]) for filename in
-                     os.listdir(USER_RAYCASTING_PRESETS_DIRECTORY) if
-                     os.path.isfile(os.path.join(USER_RAYCASTING_PRESETS_DIRECTORY, filename))]
+RAYCASTING_TYPES = [_(filename.name.split(".")[0]) for filename in
+                    inv_paths.USER_RAYCASTING_PRESETS_DIRECTORY.glob('*') if
+                    filename.is_file()]
 RAYCASTING_TYPES += RAYCASTING_FILES.keys()
 RAYCASTING_TYPES.append(_(' Off'))
 RAYCASTING_TYPES.sort()
@@ -440,8 +400,8 @@ RAYCASTING_TOOLS = [_("Cut plane")]
 # If 0 dont't blur, 1 blur
 RAYCASTING_WWWL_BLUR = 0
 
-RAYCASTING_PRESETS_FOLDERS = (RAYCASTING_PRESETS_DIRECTORY,
-                              USER_RAYCASTING_PRESETS_DIRECTORY)
+RAYCASTING_PRESETS_FOLDERS = (inv_paths.RAYCASTING_PRESETS_DIRECTORY,
+                              inv_paths.USER_RAYCASTING_PRESETS_DIRECTORY)
 
 
 ####
@@ -506,10 +466,11 @@ 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_PREFERENCES, ID_DICOM_NETWORK,
-ID_TIFF_JPG_PNG, ID_VIEW_INTERPOLATED, ID_MODE_NAVIGATION, ID_ANALYZE_IMPORT,
-ID_NIFTI_IMPORT, ID_PARREC_IMPORT] = [wx.NewId() for number in range(18)]
+ ID_PROJECT_CLOSE, ID_EXPORT_SLICE, ID_EXPORT_MASK, ID_PROJECT_INFO,
+ ID_SAVE_SCREENSHOT, ID_DICOM_LOAD_NET, ID_PRINT_SCREENSHOT,
+ ID_IMPORT_OTHERS_FILES, ID_PREFERENCES, ID_DICOM_NETWORK, ID_TIFF_JPG_PNG,
+ ID_VIEW_INTERPOLATED, ID_MODE_NAVIGATION, ID_ANALYZE_IMPORT, ID_NIFTI_IMPORT,
+ ID_PARREC_IMPORT, ID_MODE_DBS] = [wx.NewId() for number in range(21)]
 ID_EXIT = wx.ID_EXIT
 ID_ABOUT = wx.ID_ABOUT
 
@@ -546,9 +507,14 @@ ID_WATERSHED_SEGMENTATION = wx.NewId()
 ID_THRESHOLD_SEGMENTATION = wx.NewId()
 ID_FLOODFILL_SEGMENTATION = wx.NewId()
 ID_CROP_MASK = wx.NewId()
+ID_DENSITY_MEASURE = wx.NewId()
+ID_MASK_DENSITY_MEASURE = wx.NewId()
 ID_CREATE_SURFACE = wx.NewId()
 ID_CREATE_MASK = wx.NewId()
 
+ID_GOTO_SLICE = wx.NewId()
+ID_GOTO_COORD = wx.NewId()
+
 #---------------------------------------------------------
 STATE_DEFAULT = 1000
 STATE_WL = 1001
@@ -559,6 +525,9 @@ STATE_PAN = 1005
 STATE_ANNOTATE = 1006
 STATE_MEASURE_DISTANCE = 1007
 STATE_MEASURE_ANGLE = 1008
+STATE_MEASURE_DENSITY = 1009
+STATE_MEASURE_DENSITY_ELLIPSE = 1010
+STATE_MEASURE_DENSITY_POLYGON = 1011
 
 SLICE_STATE_CROSS = 3006
 SLICE_STATE_SCROLL = 3007
@@ -577,7 +546,11 @@ VOLUME_STATE_SEED = 2001
 
 TOOL_STATES = [STATE_WL, STATE_SPIN, STATE_ZOOM,
                STATE_ZOOM_SL, STATE_PAN, STATE_MEASURE_DISTANCE,
-               STATE_MEASURE_ANGLE]  #, STATE_ANNOTATE]
+               STATE_MEASURE_ANGLE, STATE_MEASURE_DENSITY_ELLIPSE,
+               STATE_MEASURE_DENSITY_POLYGON,
+               ]  #, STATE_ANNOTATE]
+
+
 
 TOOL_SLICE_STATES = [SLICE_STATE_CROSS, SLICE_STATE_SCROLL,
                      SLICE_STATE_REORIENT]
@@ -592,6 +565,9 @@ SLICE_STYLES.append(SLICE_STATE_REMOVE_MASK_PARTS)
 SLICE_STYLES.append(SLICE_STATE_SELECT_MASK_PARTS)
 SLICE_STYLES.append(SLICE_STATE_FFILL_SEGMENTATION)
 SLICE_STYLES.append(SLICE_STATE_CROP_MASK)
+SLICE_STYLES.append(STATE_MEASURE_DENSITY)
+SLICE_STYLES.append(STATE_MEASURE_DENSITY_ELLIPSE)
+SLICE_STYLES.append(STATE_MEASURE_DENSITY_POLYGON)
 
 VOLUME_STYLES = TOOL_STATES + [VOLUME_STATE_SEED, STATE_MEASURE_DISTANCE,
         STATE_MEASURE_ANGLE]
@@ -612,6 +588,9 @@ STYLE_LEVEL = {SLICE_STATE_EDITOR: 1,
                STATE_DEFAULT: 0,
                STATE_MEASURE_ANGLE: 2,
                STATE_MEASURE_DISTANCE: 2,
+               STATE_MEASURE_DENSITY_ELLIPSE: 2,
+               STATE_MEASURE_DENSITY_POLYGON: 2,
+               STATE_MEASURE_DENSITY: 2,
                STATE_WL: 2,
                STATE_SPIN: 2,
                STATE_ZOOM: 2,
@@ -684,6 +663,7 @@ STATIC_REF = 0
 DYNAMIC_REF = 1
 DEFAULT_REF_MODE = DYNAMIC_REF
 REF_MODE = [_("Static ref."), _("Dynamic ref.")]
+FT_SENSOR_MODE = [_("Sensor 3"), _("Sensor 4")]
 
 DEFAULT_COIL = SELECT
 COIL = [_("Select coil:"), _("Neurosoft Figure-8"),
@@ -711,13 +691,11 @@ TIPS_IMG = [_("Select left ear in image"),
 
 BTNS_TRK = {TR1: {3: _('LET')},
             TR2: {4: _('RET')},
-            TR3: {5: _('NAT')},
-            SET: {6: _('SET')}}
+            TR3: {5: _('NAT')}}
 
 TIPS_TRK = [_("Select left ear with spatial tracker"),
             _("Select right ear with spatial tracker"),
-            _("Select nasion with spatial tracker"),
-            _("Show set coordinates in image")]
+            _("Select nasion with spatial tracker")]
 
 OBJL = wx.NewId()
 OBJR = wx.NewId()
@@ -737,11 +715,11 @@ TIPS_OBJ = [_("Select left object fiducial"),
             _("Select object center"),
             _("Attach sensor to object")]
 
-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'))
+PROBE_NAME = "1Probe"
+REF_NAME = "2Ref"
+OBJ_NAME = "3Coil"
 
 #OBJECT TRACKING
-OBJ_DIR = os.path.abspath(os.path.join(FILE_PATH, '..', 'navigation', 'objects'))
 ARROW_SCALE = 3
 ARROW_UPPER_LIMIT = 30
 #COIL_ANGLES_THRESHOLD = 3 * ARROW_SCALE

invesalius/control.py

@@ -42,6 +42,8 @@ import invesalius.gui.dialogs as dialogs
 import subprocess
 import sys
 
+from invesalius import inv_paths
+
 DEFAULT_THRESH_MODE = 0
 
 class Controller():
@@ -58,7 +60,8 @@ class Controller():
         #None, others and opened Project = 0
         #DICOM = 1
         #TIFF uCT = 2
-        self.img_type = 0 
+        self.img_type = 0
+        self.affine = None
 
         #Init session
         session = ses.Session()
@@ -108,6 +111,8 @@ class Controller():
 
         Publisher.subscribe(self.OnSaveProject, 'Save project')
 
+        Publisher.subscribe(self.Send_affine, 'Get affine matrix')
+
     def SetBitmapSpacing(self, spacing):
         proj = prj.Project()
         proj.spacing = spacing
@@ -249,6 +254,7 @@ class Controller():
     def ShowDialogCloseProject(self):
         session = ses.Session()
         st = session.project_status
+        print('Status', st, type(st))
         if st == const.PROJ_CLOSE:
             return -1
         try:
@@ -367,6 +373,7 @@ class Controller():
         session = ses.Session()
         session.CloseProject()
 
+        Publisher.sendMessage('Update status text in GUI', label=_("Ready"))
 ###########################
 
     def StartImportBitmapPanel(self, path):
@@ -656,6 +663,7 @@ class Controller():
         proj.level = self.Slice.window_level
         proj.threshold_range = int(matrix.min()), int(matrix.max())
         proj.spacing = self.Slice.spacing
+        proj.affine = self.affine.tolist()
 
         ######
         session = ses.Session()
@@ -712,7 +720,7 @@ class Controller():
            else:
                return
 
-           xyspacing = xyspacing[0] / resolution_percentage, xyspacing[1] / resolution_percentage
+       xyspacing = xyspacing[0] / resolution_percentage, xyspacing[1] / resolution_percentage
  
 
        
@@ -811,7 +819,7 @@ class Controller():
                 else:
                     return
 
-                xyspacing = xyspacing[0] / resolution_percentage, xyspacing[1] / resolution_percentage
+            xyspacing = xyspacing[0] / resolution_percentage, xyspacing[1] / resolution_percentage
 
             self.matrix, scalar_range, self.filename = image_utils.dcm2memmap(filelist, size,
                                                                         orientation, resolution_percentage)
@@ -859,6 +867,10 @@ class Controller():
         self.matrix, scalar_range, self.filename = image_utils.img2memmap(group)
 
         hdr = group.header
+        if group.affine.any():
+            self.affine = group.affine
+            Publisher.sendMessage('Update affine matrix',
+                                  affine=self.affine, status=True)
         hdr.set_data_dtype('int16')
         dims = hdr.get_zooms()
         dimsf = tuple([float(s) for s in dims])
@@ -879,6 +891,11 @@ class Controller():
                               threshold_range=scalar_range)
         return self.matrix, self.filename
 
+    def Send_affine(self):
+        if self.affine is not None:
+            Publisher.sendMessage('Update affine matrix',
+                                  affine=self.affine, status=True)
+
     def LoadImagedataInfo(self):
         proj = prj.Project()
 
@@ -905,13 +922,13 @@ class Controller():
     def LoadRaycastingPreset(self, preset_name):
         if preset_name != const.RAYCASTING_OFF_LABEL:
             if preset_name in const.RAYCASTING_FILES.keys():
-                path = os.path.join(const.RAYCASTING_PRESETS_DIRECTORY,
+                path = os.path.join(inv_paths.RAYCASTING_PRESETS_DIRECTORY,
                                     const.RAYCASTING_FILES[preset_name])
             else:
-                path = os.path.join(const.RAYCASTING_PRESETS_DIRECTORY,
+                path = os.path.join(inv_paths.RAYCASTING_PRESETS_DIRECTORY,
                                         preset_name+".plist")
                 if not os.path.isfile(path):
-                    path = os.path.join(const.USER_RAYCASTING_PRESETS_DIRECTORY,
+                    path = os.path.join(inv_paths.USER_RAYCASTING_PRESETS_DIRECTORY,
                                     preset_name+".plist")
             preset = plistlib.readPlist(path)
             prj.Project().raycasting_preset = preset
@@ -925,7 +942,7 @@ class Controller():
     def SaveRaycastingPreset(self, preset_name):
         preset = prj.Project().raycasting_preset
         preset['name'] = preset_name
-        preset_dir = os.path.join(const.USER_RAYCASTING_PRESETS_DIRECTORY,
+        preset_dir = os.path.join(inv_paths.USER_RAYCASTING_PRESETS_DIRECTORY,
                                   preset_name + '.plist')
         plistlib.writePlist(preset, preset_dir)
 

invesalius/data/converters.py

@@ -21,7 +21,7 @@ import numpy
 import vtk
 from vtk.util import numpy_support
 
-def to_vtk(n_array, spacing, slice_number, orientation):
+def to_vtk(n_array, spacing, slice_number, orientation, origin=(0, 0, 0), padding=(0, 0, 0)):
 
     if orientation == "SAGITTAL":
         orientation = "SAGITAL"
@@ -32,20 +32,22 @@ def to_vtk(n_array, spacing, slice_number, orientation):
         dy, dx = n_array.shape
         dz = 1
 
+    px, py, pz = padding
+
     v_image = numpy_support.numpy_to_vtk(n_array.flat)
 
     if orientation == 'AXIAL':
-        extent = (0, dx -1, 0, dy -1, slice_number, slice_number + dz - 1)
+        extent = (0 - px , dx -1 - px, 0 - py, dy - 1 - py, slice_number - pz, slice_number + dz - 1 - pz)
     elif orientation == 'SAGITAL':
         dx, dy, dz = dz, dx, dy
-        extent = (slice_number, slice_number + dx - 1, 0, dy - 1, 0, dz - 1)
+        extent = (slice_number - px, slice_number + dx - 1 - px, 0 - py, dy - 1 - py, 0 - pz, dz - 1 - pz)
     elif orientation == 'CORONAL':
         dx, dy, dz = dx, dz, dy
-        extent = (0, dx - 1, slice_number, slice_number + dy - 1, 0, dz - 1)
+        extent = (0 - px, dx - 1 - px, slice_number - py, slice_number + dy - 1 - py, 0 - pz, dz - 1 - pz)
 
     # Generating the vtkImageData
     image = vtk.vtkImageData()
-    image.SetOrigin(0, 0, 0)
+    image.SetOrigin(origin)
     image.SetSpacing(spacing)
     image.SetDimensions(dx, dy, dz)
     # SetNumberOfScalarComponents and SetScalrType were replaced by

invesalius/data/coordinates.py

@@ -54,37 +54,22 @@ def GetCoordinates(trck_init, trck_id, ref_mode):
 
 def ClaronCoord(trck_init, trck_id, ref_mode):
     trck = trck_init[0]
-    scale = np.array([1.0, 1.0, -1.0])
-    coord = None
-    k = 0
-    # TODO: try to replace 'while' and use some Claron internal computation
+    trck.Run()
+    scale = np.array([1.0, 1.0, 1.0])
 
-    if ref_mode:
-        while k < 20:
-            try:
-                trck.Run()
-                probe = np.array([trck.PositionTooltipX1, trck.PositionTooltipY1,
-                                  trck.PositionTooltipZ1, trck.AngleX1, trck.AngleY1, trck.AngleZ1])
-                reference = np.array([trck.PositionTooltipX2, trck.PositionTooltipY2,
-                                      trck.PositionTooltipZ2, trck.AngleZ2,  trck.AngleY2, trck.AngleX2])
-                k = 30
-            except AttributeError:
-                k += 1
-                print("wait, collecting coordinates ...")
-        if k == 30:
-            coord = dynamic_reference(probe, reference)
-            coord = (coord[0] * scale[0], coord[1] * scale[1], coord[2] * scale[2], coord[3], coord[4], coord[5])
-    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])
+    coord1 = np.array([float(trck.PositionTooltipX1)*scale[0], float(trck.PositionTooltipY1)*scale[1],
+                      float(trck.PositionTooltipZ1)*scale[2],
+                      float(trck.AngleZ1), float(trck.AngleY1), float(trck.AngleX1)])
 
-                k = 30
-            except AttributeError:
-                k += 1
-                print("wait, collecting coordinates ...")
+    coord2 = np.array([float(trck.PositionTooltipX2)*scale[0], float(trck.PositionTooltipY2)*scale[1],
+                       float(trck.PositionTooltipZ2)*scale[2],
+                       float(trck.AngleZ2), float(trck.AngleY2), float(trck.AngleX2)])
+
+    coord3 = np.array([float(trck.PositionTooltipX3) * scale[0], float(trck.PositionTooltipY3) * scale[1],
+                       float(trck.PositionTooltipZ3) * scale[2],
+                       float(trck.AngleZ3), float(trck.AngleY3), float(trck.AngleX3)])
+
+    coord = np.vstack([coord1, coord2, coord3])
 
     Publisher.sendMessage('Sensors ID', probe_id=trck.probeID, ref_id=trck.refID)
 
@@ -124,7 +109,10 @@ def PolhemusWrapperCoord(trck, trck_id, ref_mode):
         coord3 = np.array([float(trck.PositionTooltipX3) * scale[0], float(trck.PositionTooltipY3) * scale[1],
                            float(trck.PositionTooltipZ3) * scale[2],
                            float(trck.AngleX3), float(trck.AngleY3), float(trck.AngleZ3)])
-        coord = np.vstack([coord, coord3])
+        coord4 = np.array([float(trck.PositionTooltipX4) * scale[0], float(trck.PositionTooltipY4) * scale[1],
+                           float(trck.PositionTooltipZ4) * scale[2],
+                           float(trck.AngleX4), float(trck.AngleY4), float(trck.AngleZ4)])
+        coord = np.vstack([coord, coord3, coord4])
 
     if trck.StylusButton:
         Publisher.sendMessage('PLH Stylus Button On')
@@ -174,33 +162,31 @@ def PolhemusSerialCoord(trck_init, trck_id, ref_mode):
     # 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")
+    trck_init.write(str.encode("P"))
+    scale = 10. * np.array([1., 1.0, 1.0])
     lines = trck_init.readlines()
 
-    coord = None
-
-    if lines[0][0] != '0':
+    if lines is None:
         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:
-                    print("error!!")
-
-            coord = data[0:6]
+        data = lines[0]
+        data = data.replace(str.encode('-'), str.encode(' -'))
+        data = [s for s in data.split()]
+        data = [float(s) for s in data[1:len(data)]]
+        probe = np.array([data[0] * scale[0], data[1] * scale[1], data[2] * scale[2], data[3], data[4], data[5]])
+
+        if ref_mode:
+            data2 = lines[1]
+            data2 = data2.replace(str.encode('-'), str.encode(' -'))
+            data2 = [s for s in data2.split()]
+            data2 = [float(s) for s in data2[1:len(data2)]]
+            reference = np.array(
+                [data2[0] * scale[0], data2[1] * scale[1], data2[2] * scale[2], data2[3], data2[4], data2[5]])
+        else:
+            reference = np.zeros(6)
+
+        coord = np.vstack([probe, reference])
+
     return coord
 
 
@@ -225,9 +211,12 @@ def DebugCoord(trk_init, trck_id, ref_mode):
     coord3 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
                        uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
 
+    coord4 = np.array([uniform(1, 200), uniform(1, 200), uniform(1, 200),
+                       uniform(-180.0, 180.0), uniform(-180.0, 180.0), uniform(-180.0, 180.0)])
+
     Publisher.sendMessage('Sensors ID', probe_id=int(uniform(0, 5)), ref_id=int(uniform(0, 5)))
 
-    return np.vstack([coord1, coord2, coord3])
+    return np.vstack([coord1, coord2, coord3, coord4])
 
 
 def dynamic_reference(probe, reference):

invesalius/data/editor.py

@@ -117,9 +117,7 @@ class Editor:
         #    a = (int(self.txtThresI.GetValue()), int(self.txtThresF.GetValue()))
         #    self.editor.SetOperationType(op, a)
             wx, wy, wz = self.From3dToImagePixel(pos, (x, y, z))
-            print "Comecei"
             self.DoOperation(wx, wy, wz)
-            print "Terminei"
             Publisher.sendMessage('Update images', self.image)
             Publisher.sendMessage('Update viewer', None)
 
@@ -135,7 +133,6 @@ class Editor:
         """
         x, y, z = pPos
         bounds = self.actor.GetBounds()
-        print bounds
 
         #c = vtk.vtkCoordinate()
         #c.SetCoordinateSystemToWorld()
@@ -228,15 +225,11 @@ class Editor:
         cursor = self.cursor
         b = [0,0,0,0,0,0]
         self.actor.GetDisplayBounds(b)
-        print "To Paint", xc, yc, zc
-        print "Bounds", b
-        print "dimensions", self.image.GetDimensions()
         xs, ys, zs = self.image.GetSpacing()
         try:
             zs = (b[-1]-b[-2]) / self.image.GetDimensions()[2]
         except ZeroDivisionError:
             pass
-        print xs, ys, zs
         if self.orientation == AXIAL:
             o = lambda x, y: (xc + x, y + yc, zc)
         elif self.orientation == CORONAL:

invesalius/data/imagedata_utils.py

@@ -37,6 +37,8 @@ import invesalius.reader.bitmap_reader as bitmap_reader
 import invesalius.utils as utils
 import invesalius.data.converters as converters
 
+from invesalius import inv_paths
+
 if sys.platform == 'win32':
     try:
         import win32api
@@ -335,7 +337,7 @@ def CreateImageData(filelist, zspacing, xyspacing,size,
     message = _("Generating multiplanar visualization...")
 
     if not const.VTK_WARNING:
-        log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
+        log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
         fow = vtk.vtkFileOutputWindow()
         fow.SetFileName(log_path)
         ow = vtk.vtkOutputWindow()
@@ -440,7 +442,7 @@ class ImageCreator:
         message = _("Generating multiplanar visualization...")
 
         if not const.VTK_WARNING:
-            log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
+            log_path = os.path.join(inv_paths.USER_LOG_DIR, 'vtkoutput.txt')
             fow = vtk.vtkFileOutputWindow()
             fow.SetFileName(log_path)
             ow = vtk.vtkOutputWindow()

invesalius/data/interpolation.pyx

@@ -4,7 +4,7 @@ import numpy as np
 cimport numpy as np
 cimport cython
 
-from libc.math cimport floor, ceil, sqrt, fabs, round, sin, M_PI
+from libc.math cimport floor, ceil, sqrt, fabs, sin, M_PI
 from cython.parallel import prange
 
 DEF LANCZOS_A = 4
@@ -81,7 +81,7 @@ cdef double[64][64] temp = [
 @cython.cdivision(True)
 @cython.wraparound(False)
 cdef double nearest_neighbour_interp(image_t[:, :, :] V, double x, double y, double z) nogil:
-    return V[<int>round(z), <int>round(y), <int>round(x)]
+    return V[<int>(z), <int>(y), <int>(x)]
 
 @cython.boundscheck(False) # turn of bounds-checking for entire function
 @cython.cdivision(True)