QuantUS-OpenSource · OmidChaghaneh · Feb 20, 2026 · Mar 31, 2026 · Apr 15, 2026 · davidspector67
diff --git a/src/__init__.py b/src/__init__.py
diff --git a/src/data_objs/image.py b/src/data_objs/image.py
@@ -15,3 +15,11 @@ def __init__(self, scan_path: str):
         self.frame_rate: float # Hz
         self.intensities_for_analysis: np.ndarray # linearized intensity values
         self.extras_dict: dict = {} # dictionary for any extra information inputted by plugins
+
+        # Visualization defaults (Moved from CeusSeg)
+        self.clahe_clip_limit: float = 1.2
+        self.gamma: float = 1.5
+        self.width_scale_axial: float = 1.0
+        self.width_scale_sagittal: float = 1.0
+        self.width_scale_coronal: float = 1.0
+        self.use_philips_ceus: bool = False
diff --git a/src/data_objs/seg.py b/src/data_objs/seg.py
@@ -9,4 +9,3 @@ class CeusSeg:
     def __init__(self):
         self.seg_name: str
         self.seg_mask: np.ndarray
-        self.pixdim: List[float]  # voxel spacing in mm
diff --git a/src/image_preprocessing/__init__.py b/src/image_preprocessing/__init__.py
diff --git a/src/image_preprocessing/functions.py b/src/image_preprocessing/functions.py
@@ -0,0 +1,2 @@
+from .image_preprocessors.enhance_clahe import enhance_clahe
+from .image_preprocessors.enhance_gamma import enhance_gamma
diff --git a/src/image_preprocessing/image_preprocessors/__init__.py b/src/image_preprocessing/image_preprocessors/__init__.py
diff --git a/src/seg_loading/README.md b/src/seg_loading/README.md
@@ -19,10 +19,9 @@ class CeusSeg:
     def __init__(self):
         self.seg_name: str
         self.seg_mask: np.ndarray
-        self.pixdim: List[float]  # voxel spacing in mm
 ```
 
-The pixel dimensions, segmentation name, and binary mask are all that must be saved in a segmentation parser.
+The segmentation name and binary mask are all that must be saved in a segmentation parser.
 
 ### Plugin Structure
 

diff --git a/src/seg_loading/seg_loaders/load_bolus_mask.py b/src/seg_loading/seg_loaders/load_bolus_mask.py
@@ -32,7 +32,7 @@ def load_bolus_mask(image_data: UltrasoundImage, seg_path: str, **kwargs) -> Ceu
 
     out = CeusSeg()
     out.seg_mask = bolus_seg
-    out.pixdim = image_data.pixdim
+
     if seg_path.endswith('.nii.gz'):
         out.seg_name = Path(seg_path).name[:-7]  # Remove '.nii.gz'
     else:

diff --git a/src/seg_loading/seg_loaders/nifti.py b/src/seg_loading/seg_loaders/nifti.py
@@ -19,9 +19,9 @@ def nifti(image_data: UltrasoundImage, seg_path: str, **kwargs) -> CeusSeg:
     out.seg_mask = np.asarray(seg.dataobj, dtype=np.uint8)
 
     if out.seg_mask.ndim == 3: # 2D + time
-        out.pixdim = seg.header.get_zooms()[:2]
+        image_data.pixdim = list(seg.header.get_zooms()[:2])
     elif out.seg_mask.ndim == 4: # 3D + time
-        out.pixdim = seg.header.get_zooms()[:3]
+        image_data.pixdim = list(seg.header.get_zooms()[:3])
 
     if seg_path.endswith('.nii.gz'):
         out.seg_name = Path(seg_path).name[:-7]  # Remove '.nii.gz'

diff --git a/src/time_series_analysis/options.py b/src/time_series_analysis/options.py
@@ -59,10 +59,17 @@ def get_analysis_types() -> Tuple[dict, dict]:
                 pass
 
     functions = {}
-    for file in (Path(__file__).parent / "curve_types" / "curve_definitions").iterdir():
-        module = importlib.import_module(f'.curve_types.curve_definitions.{file.stem}', package=__package__)
-        for name, obj in inspect.getmembers(module, inspect.isfunction):
-            if not name.startswith("_") and obj.__module__ == module.__name__:
-                functions[name] = obj
+    curve_defs_path = Path(__file__).parent / "curve_types" / "curve_definitions"
+    if curve_defs_path.exists():
+        for file in curve_defs_path.iterdir():
+            if file.suffix == ".py" and not file.name.startswith("_"):
+                try:
+                    module = importlib.import_module(f'.curve_types.curve_definitions.{file.stem}', package=__package__)
+                    for name, obj in inspect.getmembers(module, inspect.isfunction):
+                        if not name.startswith("_") and obj.__module__ == module.__name__:
+                            functions[name] = obj
+                except Exception as e:
+                    print(f"Error loading curve definition {file.name}: {e}")
+                    pass
 
     return types, functions
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		from .image_preprocessors.enhance_clahe import enhance_clahe
davidspector67 Apr 12, 2026 • edited Loading Copy link Copy Markdown Contributor Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. I understand that this addition is likely used to call from the frontend, but such a connection between the backend and frontend would violate the MVC architecture. I'll look through the frontend PR next but would it be possible to remove this file? OmidChaghaneh Apr 15, 2026 Copy link Copy Markdown Contributor Author Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. I believe the CLAHE settings have been completely replaced by the P high and P low parameters in Yuanshan’s branch (60-3D-Motion-Compensation). The main issue is that different developments take time, and merging requests also introduces delays. In the meantime, some features from already developed branches may become outdated, conflict with newer changes, or require rework before integration. Do you think it would be a good idea to keep this PR open until Yuanshan’s PR is also ready?
		from .image_preprocessors.enhance_gamma import enhance_gamma
Comment on lines +1 to +2 Copilot AI Apr 2, 2026 Copy link Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. `functions.py` only re-exports `enhance_clahe`/`enhance_gamma`, but nothing in the repo imports `src.image_preprocessing.functions` (so this module appears unused) and it omits the other preprocessors in `image_preprocessors/`. Consider removing it, or making it a deliberate public API by exporting all preprocessors (and/or documenting intended usage) so it doesn't become dead/partial duplication of the dynamic plugin discovery in `options.get_im_preproc_funcs()`. Copilot uses AI. Check for mistakes.