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Negative control error handling #39

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Merged
merged 2 commits into from
Sep 25, 2024
Merged

Negative control error handling #39

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d9d8069
feat(feature_extraction): add logging for error raised when cropping …
strixy16 Sep 25, 2024
e1a9888
fix(feature_extraction): actually raise an exception for negative con…
strixy16 Sep 25, 2024
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60 changes: 32 additions & 28 deletions src/readii/feature_extraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,35 +90,39 @@ def singleRadiomicFeatureExtraction(
if correctedROIImage is not None:
alignedROIImage = correctedROIImage

try:
if negativeControl != None:
logger.info(f"Generating {negativeControl} negative control for CT.")
# Split negative control type into negative control and region of interest
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}")
raise

if negativeControl != None:
logger.info(f"Generating {negativeControl} negative control for CT.")
# Split negative control type into negative control and region of interest
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)
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)
except Exception as e:
logger.error(f"Error cropping image and mask: {e}")
raise

# Load PyRadiomics feature extraction parameters to use
# Initialize feature extractor with parameters
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