Merge branch 'invesalius:master' into navigation-volume-maximize

app.py

@@ -18,8 +18,6 @@
 #    detalhes.
 # -------------------------------------------------------------------------
 
-from __future__ import print_function
-
 import argparse
 import multiprocessing
 import os
@@ -53,11 +51,7 @@
     os.environ["GDK_BACKEND"] = "x11"
 
 import wx
-
-try:
-    from wx.adv import SplashScreen
-except ImportError:
-    from wx import SplashScreen
+from wx.adv import SPLASH_CENTRE_ON_SCREEN, SPLASH_TIMEOUT, SplashScreen
 
 # import wx.lib.agw.advancedsplash as agw
 # if sys.platform.startswith('linux'):
@@ -66,6 +60,7 @@
 #    if sys.platform != 'darwin':
 #        _SplashScreen = wx.SplashScreen
 import invesalius.gui.language_dialog as lang_dlg
+import invesalius.gui.log as log
 import invesalius.i18n as i18n
 import invesalius.session as ses
 import invesalius.utils as utils
@@ -78,13 +73,8 @@
 # ------------------------------------------------------------------
 
 if sys.platform in ("linux2", "linux", "win32"):
-    try:
-        tmp_var = wx.GetXDisplay
-    except AttributeError:
-        # A workaround to make InVesalius run with wxPython4 from Ubuntu 18.04
-        wx.GetXDisplay = lambda: None
-    else:
-        del tmp_var
+    if not hasattr(wx, "GetXDisplay"):
+        setattr(wx, "GetXDisplay", lambda: None)
 
 
 session = ses.Session()
@@ -96,8 +86,6 @@
         except FileNotFoundError:
             pass
 
-import invesalius.gui.log as log
-
 
 class InVesalius(wx.App):
     """
@@ -203,7 +191,7 @@ def __init__(self):
                 icon_file = "splash_" + lang + ".png"
 
             if hasattr(sys, "frozen") and (
-                sys.frozen == "windows_exe" or sys.frozen == "console_exe"
+                getattr(sys, "frozen") == "windows_exe" or getattr(sys, "frozen") == "console_exe"
             ):
                 abs_file_path = os.path.abspath(".." + os.sep)
                 path = abs_file_path
@@ -215,10 +203,7 @@ def __init__(self):
 
             bmp = wx.Image(path).ConvertToBitmap()
 
-            try:
-                style = wx.adv.SPLASH_TIMEOUT | wx.adv.SPLASH_CENTRE_ON_SCREEN
-            except AttributeError:
-                style = wx.SPLASH_TIMEOUT | wx.SPLASH_CENTRE_ON_SCREEN
+            style = SPLASH_TIMEOUT | SPLASH_CENTRE_ON_SCREEN
 
             SplashScreen.__init__(
                 self, bitmap=bmp, splashStyle=style, milliseconds=1500, id=-1, parent=None
@@ -232,7 +217,6 @@ def Startup(self):
         # while splash is being shown
         from invesalius.control import Controller
         from invesalius.gui.frame import Frame
-        from invesalius.project import Project
 
         self.main = Frame(None)
         self.control = Controller(self.main)
@@ -289,14 +273,13 @@ def non_gui_startup(args):
     _ = i18n.InstallLanguage(lang)
 
     from invesalius.control import Controller
-    from invesalius.project import Project
 
     session = ses.Session()
     if not session.ReadConfig():
         session.CreateConfig()
         session.SetConfig("language", lang)
 
-    control = Controller(None)
+    _ = Controller(None)
 
     use_cmd_optargs(args)
 
@@ -362,6 +345,8 @@ def parse_command_line():
         help="Debug navigated TMS E-field computation",
     )
 
+    parser.add_argument("--cranioplasty", help="Creates an AI-based cranioplasty implant.")
+
     args = parser.parse_args()
     return args
 
@@ -375,24 +360,31 @@ def use_cmd_optargs(args):
         if args.save:
             Publisher.sendMessage("Save project", filepath=os.path.abspath(args.save))
             exit(0)
-
-        check_for_export(args)
-
+        if args.cranioplasty:
+            check_for_cranioplasty(args)
+        else:
+            check_for_export(args)
         return True
 
     elif args.import_folder:
         Publisher.sendMessage("Import folder", folder=args.import_folder)
         if args.save:
             Publisher.sendMessage("Save project", filepath=os.path.abspath(args.save))
             exit(0)
-        check_for_export(args)
+        if args.cranioplasty:
+            check_for_cranioplasty(args)
+        else:
+            check_for_export(args)
 
     elif args.other_file:
         Publisher.sendMessage("Open other files", filepath=args.other_file)
         if args.save:
             Publisher.sendMessage("Save project", filepath=os.path.abspath(args.save))
             exit(0)
-        check_for_export(args)
+        if args.cranioplasty:
+            check_for_cranioplasty(args)
+        else:
+            check_for_export(args)
 
     elif args.import_all:
         import invesalius.reader.dicom_reader as dcm
@@ -425,6 +417,29 @@ def use_cmd_optargs(args):
     return False
 
 
+def check_for_cranioplasty(args):
+    import invesalius.constants as const
+    from invesalius.i18n import tr as _
+
+    if args.cranioplasty:
+        from invesalius.data import slice_
+        from invesalius.project import Project
+
+        # create cranium mask
+        Publisher.sendMessage("Update threshold limits", threshold_range=(226, 3071))
+        Publisher.sendMessage("Appy threshold all slices")
+
+        # create implant mask
+        Publisher.sendMessage("Create implant for cranioplasty")
+
+        path_ = args.export
+
+        # convert masks to surfaces and exports them.
+        Publisher.sendMessage(
+            "Export all surfaces separately", folder=path_, filetype=const.FILETYPE_STL
+        )
+
+
 def sanitize(text):
     text = str(text).strip().replace(" ", "_")
     return re.sub(r"(?u)[^-\w.]", "", text)
@@ -441,9 +456,9 @@ def check_for_export(args, suffix="", remove_surfaces=False):
 
         if suffix:
             if args.export.endswith(".stl"):
-                path_ = "{}-{}.stl".format(args.export[:-4], suffix)
+                path_ = f"{args.export[:-4]}-{suffix}.stl"
             else:
-                path_ = "{}-{}.stl".format(args.export, suffix)
+                path_ = f"{args.export}-{suffix}.stl"
         else:
             path_ = args.export
 
@@ -455,9 +470,9 @@ def check_for_export(args, suffix="", remove_surfaces=False):
 
             for threshold_name, threshold_range in Project().presets.thresh_ct.items():
                 if isinstance(threshold_range[0], int):
-                    path_ = "{}-{}-{}.stl".format(args.export_to_all, suffix, threshold_name)
+                    path_ = f"{args.export_to_all}-{suffix}-{threshold_name}.stl"
                     export(path_, threshold_range, remove_surface=True)
-        except:
+        except Exception:
             traceback.print_exc()
         finally:
             exit(0)
@@ -469,14 +484,15 @@ def check_for_export(args, suffix="", remove_surfaces=False):
         export_filename = args.export_project
         if suffix:
             export_filename, ext = os.path.splitext(export_filename)
-            export_filename = "{}-{}{}".format(export_filename, suffix, ext)
+            export_filename = f"{export_filename}-{suffix}{ext}"
 
         prj.export_project(export_filename, save_masks=args.save_masks)
-        print("Saved {}".format(export_filename))
+        print(f"Saved {export_filename}")
 
 
 def export(path_, threshold_range, remove_surface=False):
     import invesalius.constants as const
+    from invesalius.i18n import tr as _
 
     Publisher.sendMessage("Set threshold values", threshold_range=threshold_range)
 
@@ -504,7 +520,7 @@ def print_events(topic=Publisher.AUTO_TOPIC, **msg_data):
     """
     Print pubsub messages
     """
-    utils.debug("%s\n\tParameters: %s" % (topic, msg_data))
+    utils.debug(f"{topic}\n\tParameters: {msg_data}")
 
 
 def init():
@@ -517,7 +533,7 @@ def init():
     multiprocessing.freeze_support()
 
     # Needed in win 32 exe
-    if hasattr(sys, "frozen") and sys.platform.startswith("win"):
+    if hasattr(sys, "frozen") and sys.platform == "win32":
         # Click in the .inv3 file support
         root = winreg.HKEY_CLASSES_ROOT
         key = "InVesalius 3.1\InstallationDir"
@@ -532,9 +548,9 @@ def init():
         if inv_paths.OLD_USER_INV_DIR.exists():
             inv_paths.copy_old_files()
 
-    if hasattr(sys, "frozen") and sys.frozen == "windows_exe":
+    if hasattr(sys, "frozen") and getattr(sys, "frozen") == "windows_exe":
         # Set system standard error output to file
-        path = inv_paths.USER_LOG_DIR.join("stderr.log")
+        path = inv_paths.USER_LOG_DIR.joinpath("stderr.log")
         sys.stderr = open(path, "w")
 
 
@@ -586,7 +602,7 @@ def main(connection=None, remote_host=None):
     if args.no_gui:
         non_gui_startup(args)
     else:
-        application = InVesalius(0)
+        application = InVesalius(False)
         application.MainLoop()
 
 

environment.yml

@@ -2,7 +2,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python==3.11
+  - python==3.11.10
   - cython==3.0.10
   - pillow==10.3.0
   - pypubsub==4.0.3
@@ -12,7 +12,6 @@ dependencies:
   - numpy==1.26.4
   - psutil==6.0.0
   - pyserial==3.5
-  - pytorch==2.3.1
   - requests==2.32.3
   - scipy==1.14.0
   - vtk==9.3.0
@@ -33,6 +32,7 @@ dependencies:
     - pypolaris==0.0.7
     - scikit-image==0.24.0
     - scikit-learn==1.5.0
+    - torch==2.3.1
     - Trekker==0.9
     - uvicorn[standard]==0.30.1
     - wxPython==4.2.1

invesalius/control.py

@@ -45,6 +45,7 @@
 from invesalius import inv_paths, plugins
 from invesalius.i18n import tr as _
 from invesalius.pubsub import pub as Publisher
+from invesalius.segmentation.deep_learning import segment
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -124,6 +125,9 @@ def __bind_events(self) -> None:
 
         Publisher.subscribe(self.LoadProject, "Load project data")
 
+        # for call cranioplasty implant by command line
+        Publisher.subscribe(segment.run_cranioplasty_implant, "Create implant for cranioplasty")
+
     def SetBitmapSpacing(self, spacing: Tuple[float, float, float]) -> None:
         proj = prj.Project()
         proj.spacing = spacing
@@ -384,8 +388,6 @@ def SaveProject(self, path: Optional["str | Path"] = None, compress: bool = Fals
             if isinstance(filename, str):
                 filename = utils.decode(filename, const.FS_ENCODE)
 
-            proj = prj.Project()
-
             # Update progress dialog
             Publisher.sendMessage(
                 "Update Progress bar", value=30, msg="Preparing to save project..."
@@ -702,13 +704,13 @@ def CreateBitmapProject(self, bmp_data, rec_data, matrix, matrix_filename):
 
         name = rec_data[0]
         orientation = rec_data[1]
-        sp_x = float(rec_data[2])
-        sp_y = float(rec_data[3])
-        sp_z = float(rec_data[4])
-        interval = int(rec_data[5])
+        # sp_x = float(rec_data[2])
+        # sp_y = float(rec_data[3])
+        # sp_z = float(rec_data[4])
+        # interval = int(rec_data[5])
 
-        bits = bmp_data.GetFirstPixelSize()
-        sx, sy = size = bmp_data.GetFirstBitmapSize()
+        # bits = bmp_data.GetFirstPixelSize()
+        # sx, sy = size = bmp_data.GetFirstBitmapSize()
 
         proj = prj.Project()
         proj.name = name
@@ -988,20 +990,20 @@ def OpenDicomGroup(
 
         size = dicom.image.size
         bits = dicom.image.bits_allocad
-        sop_class_uid = dicom.acquisition.sop_class_uid
+        # sop_class_uid = dicom.acquisition.sop_class_uid
         xyspacing = dicom.image.spacing
         orientation = dicom.image.orientation_label
-        samples_per_pixel = dicom.image.samples_per_pixel
+        # samples_per_pixel = dicom.image.samples_per_pixel
 
         wl = float(dicom.image.level)
         ww = float(dicom.image.window)
 
-        if sop_class_uid == "1.2.840.10008.5.1.4.1.1.7":  # Secondary Capture Image Storage
-            use_dcmspacing = 1
-        else:
-            use_dcmspacing = 0
+        # if sop_class_uid == "1.2.840.10008.5.1.4.1.1.7":  # Secondary Capture Image Storage
+        #     use_dcmspacing = 1
+        # else:
+        #     use_dcmspacing = 0
 
-        imagedata = None
+        # imagedata = None
 
         if dicom.image.number_of_frames == 1:
             sx, sy = size

invesalius/data/actor_factory.py

@@ -10,7 +10,7 @@
 from invesalius import inv_paths
 
 
-class ActorFactory(object):
+class ActorFactory:
     def __init__(self):
         pass
 

invesalius/data/brainmesh_handler.py

@@ -3,7 +3,7 @@
 
 # import os
 import pyvista
-from vtkmodules.vtkCommonColor import vtkColorSeries, vtkNamedColors
+from vtkmodules.vtkCommonColor import vtkColorSeries
 
 # import Trekker
 from vtkmodules.vtkCommonCore import (

invesalius/data/coordinates.py

@@ -21,7 +21,7 @@
 from math import cos, sin
 from random import uniform
 from time import sleep
-from typing import TYPE_CHECKING, Any, List, Optional, Sequence, Tuple, Union
+from typing import TYPE_CHECKING, List, Optional, Sequence, Tuple, Union
 
 import numpy as np
 import wx
@@ -621,7 +621,7 @@ def dynamic_reference(probe, reference):
     # a: rotation of plane (X, Y) around Z axis (azimuth)
     # b: rotation of plane (X', Z) around Y' axis (elevation)
     # a: rotation of plane (Y', Z') around X'' axis (roll)
-    m_rot = np.mat(
+    m_rot = np.asmatrix(
         [
             [
                 cos(a) * cos(b),