Enhanced EEG Electrode Detection

.gitignore

@@ -1,10 +1,21 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-settings.json
-_data/*
-.DS_Store
+
+# Distribution / packaging
 *.egg
 *.egg-info/
 uv.lock
+
+# IDE / editor settings
+settings.json
+
+# macOS system files
+.DS_Store
+
+# Data directories
+_data/*
+
+# Logs and temporary files
 logs/*
+temp/*

Makefile

@@ -0,0 +1,19 @@
+# Makefile for ELK project
+
+# Default environment (production or development)
+ELK_ENV ?= production
+
+# Main target: run the project
+run: 
+	@echo "Running in $(ELK_ENV) environment..."
+	@ELK_ENV=$(ELK_ENV) uv run src/main.py
+
+# Optional: create virtual environment using uv if needed
+venv:
+	@echo "Ensuring virtual environment exists..."
+	@uv venv
+
+# Clean virtual environment (optional)
+clean:
+	@echo "Removing virtual environment..."
+	@rm -rf venv

README.md

@@ -38,15 +38,18 @@ pip install uv
 
 ## Running the App
 
-Once `uv` is installed, navigate to the project's root directory and run:
+Once the project is set up, navigate to the project root directory and use the provided Makefile to run the app:
 
-## Running the App
+```sh
+# Run with the default environment (production)
+make run
 
-Once `uv` is installed, navigate to the project's root directory and run:
+# Run in development environment
+make run ELK_ENV=development
 
-```sh
-uv run src/main.py
-uv run src/main.py
+### Optional:
+make venv  # Creates/ensures the virtual environment exists
+make clean  # Clean the virtual environment
 ```
 
 On the first run, this command creates a virtual environment, installs all dependencies, and starts the app. This may take a moment but only happens the first time.
@@ -75,7 +78,7 @@ For help and support, please contact:
 
 ## Version
 
-The current version of the package is **0.7.1**.
+The current version of the package is **0.8.0**.
 
 ## License
 
@@ -240,7 +243,3 @@ Ensure your pull request includes:
 
 - A clear description of what the changes do and why they are necessary.
 - Any relevant issue numbers.
-
----
-
-This `README.md` provides an overview of the ELK package, including its key features, installation instructions, supported formats, authorship, contact information, current version, and license details. For any additional information or assistance, please reach out to the provided contact emails.

pyproject.toml

@@ -1,24 +1,28 @@
 [project]
-name = "electrodelocalizationkit"
-version = "0.3.1"
+name = "electrode-localization-kit"
+version = "0.8.0"
 description = "A tool for rapid EEG electrode localization using IR stereo cameras or MRI."
 readme = "README.md"
-requires-python = ">=3.11, <3.12"
-license = { file = "LICENSE" }
+license = "GPL-3.0-or-later"
+license-files = ["LICEN[CS]E"]
+requires-python = "==3.11.*"
 
 dependencies = [
-    "nibabel==5.2.1",
+    "vtk==9.2.6",
+    "PyQt6==6.7.0",
     "numpy==1.25.0",
-    "opencv_python==4.8.1.78",
     "pandas==2.2.2",
-    "PyQt6==6.7.0",
-    "PyQt6_sip==13.6.0",
+    "scipy==1.15.3",
+    "nibabel==5.2.1",
     "vedo==2023.4.6",
-    "vtk==9.2.6"
+    "PyQt6_sip==13.6.0",
+    "scikit_learn==1.7.1",
+    "scikit_image==0.25.2",
+    "opencv_python==4.8.1.78",
 ]
 
 [tool.black]
 line-length = 100
 
 [tool.ruff]
-line-length = 100
+line-length = 100

requirements.txt

@@ -8,58 +8,89 @@ deprecated==1.2.18
     # via vedo
 fonttools==4.56.0
     # via matplotlib
+imageio==2.37.0
+    # via scikit-image
+joblib==1.5.2
+    # via scikit-learn
 kiwisolver==1.4.8
     # via matplotlib
+lazy-loader==0.4
+    # via scikit-image
 matplotlib==3.10.0
     # via vtk
+networkx==3.5
+    # via scikit-image
 nibabel==5.2.1
-    # via electrodelocalizationkit (pyproject.toml)
+    # via electrode-localization-kit (pyproject.toml)
 numpy==1.25.0
     # via
-    #   electrodelocalizationkit (pyproject.toml)
+    #   electrode-localization-kit (pyproject.toml)
     #   contourpy
+    #   imageio
     #   matplotlib
     #   nibabel
     #   opencv-python
     #   pandas
+    #   scikit-image
+    #   scikit-learn
+    #   scipy
+    #   tifffile
     #   vedo
 opencv-python==4.8.1.78
-    # via electrodelocalizationkit (pyproject.toml)
+    # via electrode-localization-kit (pyproject.toml)
 packaging==24.2
     # via
+    #   lazy-loader
     #   matplotlib
     #   nibabel
+    #   scikit-image
 pandas==2.2.2
-    # via electrodelocalizationkit (pyproject.toml)
+    # via electrode-localization-kit (pyproject.toml)
 pillow==11.1.0
-    # via matplotlib
+    # via
+    #   imageio
+    #   matplotlib
+    #   scikit-image
 pygments==2.19.1
     # via vedo
 pyparsing==3.2.1
     # via matplotlib
 pyqt6==6.7.0
-    # via electrodelocalizationkit (pyproject.toml)
+    # via electrode-localization-kit (pyproject.toml)
 pyqt6-qt6==6.7.3
     # via pyqt6
 pyqt6-sip==13.6.0
     # via
-    #   electrodelocalizationkit (pyproject.toml)
+    #   electrode-localization-kit (pyproject.toml)
     #   pyqt6
 python-dateutil==2.9.0.post0
     # via
     #   matplotlib
     #   pandas
 pytz==2025.1
     # via pandas
+scikit-image==0.25.2
+    # via electrode-localization-kit (pyproject.toml)
+scikit-learn==1.7.1
+    # via electrode-localization-kit (pyproject.toml)
+scipy==1.15.3
+    # via
+    #   electrode-localization-kit (pyproject.toml)
+    #   scikit-image
+    #   scikit-learn
 six==1.17.0
     # via python-dateutil
+threadpoolctl==3.6.0
+    # via scikit-learn
+tifffile==2025.10.16
+    # via scikit-image
 tzdata==2025.1
     # via pandas
 vedo==2023.4.6
-    # via electrodelocalizationkit (pyproject.toml)
+    # via electrode-localization-kit (pyproject.toml)
 vtk==9.2.6
     # via
-    #   electrodelocalizationkit (pyproject.toml)
+    #   electrode-localization-kit (pyproject.toml)
     #   vedo
 wrapt==1.17.2
     # via deprecated

src/config/sizes.py

@@ -2,15 +2,16 @@
 Size configuration for the electrodes and flagposts.
 """
 
+
 class ElectrodeSizes:
-    HEADSCAN_ELECTRODE_SIZE = 0.02
+    HEADSCAN_ELECTRODE_SIZE = 3.5
     MRI_ELECTRODE_SIZE = 0.02
     LABEL_ELECTRODE_SIZE = 0.04
-    
+
     HEADSCAN_FLAGPOST_SIZE = 0.6
     MRI_FLAGPOST_SIZE = 0.6
     LABEL_FLAGPOST_SIZE = 0.6
-    
-    HEADSCAN_FLAGPOST_HEIGHT = 0.05
+
+    HEADSCAN_FLAGPOST_HEIGHT = 5.0
     MRI_FLAGPOST_HEIGHT = 0.05
-    LABEL_FLAGPOST_HEIGHT = 0.05
+    LABEL_FLAGPOST_HEIGHT = 0.05

src/data/loader.py

@@ -6,10 +6,13 @@
 import vedo as vd
 import nibabel as nib
 
+from processing_models.mesh.mesh_loader import MeshLoader
 
-def load_head_surface_mesh_from_file(filename: str) -> vd.Mesh:
+
+def load_head_surface_mesh_from_file(surface_file: str, texture_file: str = None) -> vd.Mesh:
     """Loads a head surface mesh from a file."""
-    return vd.Mesh(filename)
+    mesh_loader = MeshLoader(surface_file, texture_file)
+    return mesh_loader.mesh_preprocessed.clone()
 
 
 def load_mri_surface_mesh_from_file(filename: str) -> vd.Mesh:

src/data_models/cap_model.py

@@ -117,15 +117,15 @@ def insert_electrode(self, electrode: Electrode, parent=QModelIndex()) -> None:
             electrode.coordinates, electrode.modality, include_fiducials=True
         )
 
-        too_close_electrodes = [
-            d[0]
-            for d in distances
-            if (
-                d[1] <= ElectrodeSizes.HEADSCAN_ELECTRODE_SIZE / 2
-                or d[1] <= ElectrodeSizes.MRI_ELECTRODE_SIZE / 2
-                or d[1] <= ElectrodeSizes.LABEL_ELECTRODE_SIZE / 2
-            )
-        ]
+        min_distance = -1
+        if electrode.modality == ModalitiesMapping.HEADSCAN:
+            min_distance = ElectrodeSizes.HEADSCAN_ELECTRODE_SIZE / 2
+        elif electrode.modality == ModalitiesMapping.MRI:
+            min_distance = ElectrodeSizes.MRI_ELECTRODE_SIZE / 2
+        elif electrode.modality == ModalitiesMapping.REFERENCE:
+            min_distance = ElectrodeSizes.LABEL_ELECTRODE_SIZE / 2
+
+        too_close_electrodes = [d[0] for d in distances if (d[1] <= min_distance)]
 
         if len(too_close_electrodes) > 0:
             return

src/data_models/head_models.py

@@ -37,16 +37,16 @@ def __init__(self, surface_file: str, texture_file: str | None = None):
         self.texture_file = texture_file
 
         self.mesh = None
-        self.mesh = load_head_surface_mesh_from_file(surface_file)
+        self.mesh = load_head_surface_mesh_from_file(surface_file, texture_file)
 
         self.modality = ModalitiesMapping.HEADSCAN
         self.fiducials = []
 
-        self.normalization_scale = 1
+        self.normalization_scale = 1000
 
         self._registered = False
 
-        self.normalize()
+        # self.normalize()
 
         self.apply_texture()
 
@@ -56,9 +56,12 @@ def normalize(self):
     def rescale_to_original_size(self):
         self.normalization_scale = rescale_to_original_size(self.mesh, self.normalization_scale)  # type: ignore
 
-    def apply_texture(self):
+    def apply_texture(self, texture_file: str | None = None):
         if self.texture_file is not None:
             self.mesh = self.mesh.texture(self.texture_file)  # type: ignore
+        elif texture_file is not None:
+            self.texture_file = texture_file
+            self.mesh = self.mesh.texture(texture_file)
 
     def register_mesh(self, surface_registrator: BaseSurfaceRegistrator) -> np.ndarray:
         transform_matrix = surface_registrator.register()  # type: ignore

src/fileio/locations.py

@@ -28,7 +28,7 @@ def load_locations(
     #             model.remove_electrode_by_id(electrode_id)
 
     if ENV == "development":
-        files["locations"] = "sample_data/measured_electrodes.ced"
+        files["locations"] = "sample_data/electrode_locations.ced"
     else:
         file_path, _ = QFileDialog.getOpenFileName(
             None,