Negative control error catching and angular commit syntax

README.md

@@ -48,6 +48,28 @@ The three transformations are:
 
 ## Contributing
 
+Please use the following angular commit message format:
+```
+<type>(optional scope): short summary in present tense
+
+(optional body: explains motivation for the change)
+
+(optional footer: note BREAKING CHANGES here, and issues to be closed)
+
+```
+`<type>` refers to the kind of change made and is usually one of:
+
+- `feat`: A new feature.
+- `fix`: A bug fix.
+- `docs`: Documentation changes.
+- `style`: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc).
+- `refactor`: A code change that neither fixes a bug nor adds a feature.
+- `perf`: A code change that improves performance.
+- `test`: Changes to the test framework.
+- `build`: Changes to the build process or tools.
+
+`scope` is an optional keyword that provides context for where the change was made. It can be anything relevant to your package or development workflow (e.g., it could be the module or function - name affected by the change).
+
 Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.
 
 ## License

src/readii/feature_extraction.py

@@ -93,27 +93,32 @@ def singleRadiomicFeatureExtraction(
     if negativeControl != None:
         logger.info(f"Generating {negativeControl} negative control for CT.")
         # Split negative control type into negative control and region of interest
-        if "non_roi" in negativeControl:
-            negativeControlType =  negativeControl.rsplit("_", 2)[0]
-            negativeControlRegion = "non_roi"
-        else:
-            negativeControlComponents = negativeControl.rsplit("_", 1)
-            negativeControlType = negativeControlComponents[0]
-            negativeControlRegion = negativeControlComponents[1]
-        logger.debug(f"Negative control region: {negativeControlRegion}")
-        logger.debug(f"Negative control type: {negativeControlType}")
-        # Make negative control version of ctImage
-        ctImage_nc: sitk.Image | np.ndarray = applyNegativeControl(
-            baseImage=ctImage,
-            negativeControlType=negativeControlType,
-            negativeControlRegion=negativeControlRegion,
-            roiMask=alignedROIImage,
-            randomSeed=randomSeed
-        )
+        try:
+            if "non_roi" in negativeControl:
+                negativeControlType =  negativeControl.rsplit("_", 2)[0]
+                negativeControlRegion = "non_roi"
+            else:
+                negativeControlComponents = negativeControl.rsplit("_", 1)
+                negativeControlType = negativeControlComponents[0]
+                negativeControlRegion = negativeControlComponents[1]
+            logger.debug(f"Negative control region: {negativeControlRegion}")
+            logger.debug(f"Negative control type: {negativeControlType}")
+            # Make negative control version of ctImage
+            ctImage_nc: sitk.Image | np.ndarray = applyNegativeControl(
+                baseImage=ctImage,
+                negativeControlType=negativeControlType,
+                negativeControlRegion=negativeControlRegion,
+                roiMask=alignedROIImage,
+                randomSeed=randomSeed
+            )
+        except Exception as e:
+            logger.error(f"Error generating {negativeControl} negative control for CT: {e}")
+
         croppedCT, croppedROI = imageoperations.cropToTumorMask(ctImage_nc, alignedROIImage, segBoundingBox)
     else:
         # Crop the image and mask to a bounding box around the mask to reduce volume size to process
         croppedCT, croppedROI = imageoperations.cropToTumorMask(ctImage, alignedROIImage, segBoundingBox)
+
 
     # Load PyRadiomics feature extraction parameters to use
     # Initialize feature extractor with parameters