Create a module to keep invesalius path (invesalius#183)

* created a file to keep all the inv paths

* frame and task_slice using inv_paths

* task slice, surface, export and data_notebook using invesalius.inv_paths

* clut_raycasting using inv_paths

* using pathlib in frame

* dicom reader using inv_paths

* neuronavigation using inv_paths

* session using inv_paths

* dialogs using inv_paths

Author: tfmoraes

app.py

@@ -65,21 +65,9 @@
 import invesalius.session as ses
 import invesalius.utils as utils
 
-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)
+from invesalius import inv_paths
 
-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()
 
 # ------------------------------------------------------------------
 
@@ -510,17 +498,14 @@ def 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

invesalius/constants.py

@@ -24,6 +24,7 @@
 import itertools
 
 from invesalius import utils
+from invesalius import inv_paths
 
 #from invesalius.project import Project
 INVESALIUS_VERSION = "3.1.1"
@@ -335,59 +336,13 @@
 # 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
@@ -433,10 +388,9 @@
 #                    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()
@@ -446,8 +400,8 @@
 # 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)
 
 
 ####
@@ -761,14 +715,11 @@
             _("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 subprocess
 import sys
 
+from invesalius import inv_paths
+
 DEFAULT_THRESH_MODE = 0
 
 class Controller():
@@ -920,13 +922,13 @@ def LoadImagedataInfo(self):
     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
@@ -940,7 +942,7 @@ def LoadRaycastingPreset(self, preset_name):
     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/imagedata_utils.py

@@ -37,6 +37,8 @@
 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 @@ def CreateImageData(self, filelist, zspacing, size, bits):
         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/trackers.py

@@ -61,15 +61,16 @@ def DefaultTracker(tracker_id):
 
 def ClaronTracker(tracker_id):
     import invesalius.constants as const
+    from invesalius import inv_paths
 
     trck_init = None
     try:
         import pyclaron
 
         lib_mode = 'wrapper'
         trck_init = pyclaron.pyclaron()
-        trck_init.CalibrationDir = const.CAL_DIR.encode(const.FS_ENCODE)
-        trck_init.MarkerDir = const.MAR_DIR.encode(const.FS_ENCODE)
+        trck_init.CalibrationDir = inv_paths.CAL_DIR.encode(const.FS_ENCODE)
+        trck_init.MarkerDir = inv_paths.MAR_DIR.encode(const.FS_ENCODE)
         trck_init.NumberFramesProcessed = 1
         trck_init.FramesExtrapolated = 0
         trck_init.PROBE_NAME = const.PROBE_NAME.encode(const.FS_ENCODE)

invesalius/data/viewer_volume.py

@@ -42,6 +42,8 @@
 import invesalius.style as st
 import invesalius.utils as utils
 
+from invesalius import inv_paths
+
 if sys.platform == 'win32':
     try:
         import win32api
@@ -873,7 +875,7 @@ def CreateTargetAim(self):
 
         self.m_img_vtk = m_img_vtk
 
-        filename = os.path.join(const.OBJ_DIR, "aim.stl")
+        filename = os.path.join(inv_paths.OBJ_DIR, "aim.stl")
 
         reader = vtk.vtkSTLReader()
         reader.SetFileName(filename)
@@ -898,7 +900,7 @@ def CreateTargetAim(self):
         self.aim_actor = aim_actor
         self.ren.AddActor(aim_actor)
 
-        obj_polydata = self.CreateObjectPolyData(os.path.join(const.OBJ_DIR, "magstim_fig8_coil_no_handle.stl"))
+        obj_polydata = self.CreateObjectPolyData(os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil_no_handle.stl"))
 
         transform = vtk.vtkTransform()
         transform.RotateZ(90)
@@ -1148,7 +1150,7 @@ def CreateObjectPolyData(self, filename):
                 wx.MessageBox(_("File format not reconized by InVesalius"), _("Import surface error"))
                 return
         else:
-            filename = os.path.join(const.OBJ_DIR, "magstim_fig8_coil.stl")
+            filename = os.path.join(inv_paths.OBJ_DIR, "magstim_fig8_coil.stl")
             reader = vtk.vtkSTLReader()
 
         if _has_win32api:

invesalius/data/volume.py

@@ -33,6 +33,8 @@
 from vtk.util import numpy_support
 import invesalius.session as ses
 
+from invesalius import inv_paths
+
 
 Kernels = { 
     "Basic Smooth 5x5" : [1.0, 1.0, 1.0, 1.0, 1.0,
@@ -352,7 +354,7 @@ def Create8bColorTable(self, scale):
         color_preset = self.config['CLUT']
         if color_preset != "No CLUT":
             p = plistlib.readPlist(
-                os.path.join(const.RAYCASTING_PRESETS_DIRECTORY,
+                os.path.join(inv_paths.RAYCASTING_PRESETS_DIRECTORY,
                              'color_list', color_preset + '.plist'))
             r = p['Red']
             g = p['Green']