Merge branch 'master' into minors-visualization-nav

mo-gaafar · Jul 14, 2024 · 297a6c6 · 297a6c6
2 parents a3a4136 + c18da9f
commit 297a6c6
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diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,20 @@
+name: pre-commit
+on:
+  pull_request
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - id: file_changes
+      uses: trilom/file-changes-action@v1.2.4
+      with:
+        prNumber: ${{ github.event.number }}
+        output: ' '
+    - uses: pre-commit/action@v2.0.3
+      name: ruff-pre-commit-run
+      with: 
+        extra_args: --files ${{ steps.file_changes.outputs.files }}
diff --git a/environment.yml b/environment.yml
@@ -2,37 +2,40 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python=3.11
+  - python==3.11
   - cython==3.0.10
-  - pillow==9.4.0
+  - pillow==10.3.0
   - pypubsub==4.0.3
-  - h5py==3.8.0
-  - imageio==2.31.1
-  - nibabel==5.1.0
-  - numpy==1.24.3
-  - psutil==5.9.4
+  - h5py==3.11.0
+  - imageio==2.34.2
+  - nibabel==5.2.1
+  - numpy==1.26.4
+  - psutil==6.0.0
   - pyserial==3.5
-  - pytorch==2.0.1
-  - requests==2.31.0
-  - scipy==1.10.1
-  - vtk==9.2.6
+  - pytorch==2.3.1
+  - requests==2.32.3
+  - scipy==1.14.0
+  - vtk==9.3.0
   - mido==1.2.10
-  - nest-asyncio==1.5.6
+  - nest-asyncio==1.6.0
   - pip
   - pip:
-    - aioconsole==0.6.1
-    - opencv-python==4.7.0.72
-    - python-gdcm==3.0.22
-    - python-rtmidi==1.4.9
-    - python-socketio[client]==5.8.0
-    - pyacvd==0.2.9
-    - pyclaron==0.0.4
-    - polhemusFT==0.0.3
-    - polhemus==0.0.3
+    - matplotlib==3.9.0
+    - aioconsole==0.7.1
+    - opencv-python==4.10.0.84
+    - python-gdcm==3.0.24
+    - python-rtmidi==1.5.8
+    - python-socketio[client]==5.11.3
+    - pyacvd==0.2.11
+    - pyclaron
+    - polhemusFT
+    - polhemus
     - pypolaris==0.0.7
-    - scikit-image==0.21.0
+    - scikit-image==0.24.0
+    - scikit-learn==1.5.0
     - Trekker==0.9
-    - uvicorn[standard]==0.22.0
+    - uvicorn[standard]==0.30.1
     - wxPython==4.2.1
-    - ruff~=0.4.5
+    - mypy==1.10.1
+    - ruff~=0.5.0
     - pre-commit~=3.7.1
diff --git a/invesalius/constants.py b/invesalius/constants.py
@@ -186,8 +186,10 @@
 #Colors for errors and positives
 RED_COLOR_FLOAT = (0.99, 0.55, 0.38)
 GREEN_COLOR_FLOAT = (0.40, 0.76, 0.65)
+YELLOW_COLOR_FLOAT = (1.0, 0.77, 0.0)
 RED_COLOR_RGB = (252, 141, 98)
 GREEN_COLOR_RGB = (102, 194, 165)
+YELLOW_COLOR_RGB = (255, 196, 0)
 
 # Volume view angle
 VOL_FRONT = wx.NewIdRef()
@@ -746,6 +748,7 @@
 DEFAULT_REF_MODE = DYNAMIC_REF
 REF_MODE = [_("Static ref."), _("Dynamic ref.")]
 FT_SENSOR_MODE = [_("Sensor 3"), _("Sensor 4")]
+TRACKERS_WITH_SENSOR_OPTIONS = [FASTRAK, ISOTRAKII, PATRIOT, DEBUGTRACKRANDOM, DEBUGTRACKAPPROACH]
 
 DEFAULT_COIL = SELECT
 COIL = [_("Select coil:"), _("Neurosoft Figure-8"),
@@ -760,6 +763,7 @@
 SET = wx.NewIdRef()
 
 FIDUCIAL_LABELS = ["Left Ear: ", "Right Ear: ", "Nose: "]
+FIDUCIAL_REGISTRATION_ORDER = [0, 2, 1]
 IMAGE_FIDUCIALS = [
     {
         'button_id': IR1,
@@ -817,6 +821,9 @@
 OBJA = wx.NewIdRef()
 OBJF = wx.NewIdRef()
 
+OBJECT_FIDUCIAL_ANTERIOR = 2
+OBJECT_FIDUCIAL_FIXED = 3
+
 OBJECT_FIDUCIALS = [
     {
         'fiducial_index': 0,
@@ -831,13 +838,13 @@
         'tip': _("Select right object fiducial"),
     },
     {
-        'fiducial_index': 2,
+        'fiducial_index': OBJECT_FIDUCIAL_ANTERIOR,
         'button_id': OBJA,
         'label': _('Anterior'),
         'tip': _("Select anterior object fiducial"),
     },
     {
-        'fiducial_index': 3,
+        'fiducial_index': OBJECT_FIDUCIAL_FIXED,
         'button_id': OBJF,
         'label': _('Fixed'),
         'tip': _("Attach sensor to object"),