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BUG: Error in geometry check during resampling #227

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Mar 28, 2017
Merged

BUG: Error in geometry check during resampling #227

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30 changes: 15 additions & 15 deletions radiomics/imageoperations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -322,21 +322,21 @@ def resampleImage(imageNode, maskNode, resampledPixelSpacing, interpolator=sitk.
# Step 1: Get the origin and UBound corners of the bounding box in physical space
# The additional 0.5 represents the difference between the voxel center and the voxel corner
# Upper bound index of ROI = bb[:3] + bb[3:] - 1 (LBound + Size - 1), .5 is added to get corner
physicalBounds = (maskNode.TransformContinuousIndexToPhysicalPoint(bb[3:] - .5), # Origin
maskNode.TransformContinuousIndexToPhysicalPoint(bb[:3] + bb[3:] - 0.5)) # UBound
logger.debug('ROI bounds (mm): %s', physicalBounds)

# Step 2: Determine the physical bounds of the image in a similar manner as in step 1
imageBounds = (imageNode.TransformContinuousIndexToPhysicalPoint([-0.5, -0.5, -0.5]), # Origin
imageNode.TransformContinuousIndexToPhysicalPoint(numpy.array(imageNode.GetSize()) + 0.5)) # UBound
logger.debug('Image bounds (mm): %s', imageBounds)

# Check if any of the physical bounds of the bounding box are outside the physical space of the image
# Use numpy.max and numpy.min to correct for negative directions
if numpy.any(numpy.min(imageBounds, axis=0) > numpy.min(physicalBounds, axis=0)) or \
numpy.any(numpy.max(imageBounds, axis=0) < numpy.max(physicalBounds, axis=0)):
logger.error('Physical space of bounding box is larger than physical space of image:\n\t'
'ROI physical bounds %s\n\tImage physical bounds %s', physicalBounds, imageBounds)
ROIBounds = (maskNode.TransformContinuousIndexToPhysicalPoint(bb[:3] - .5), # Origin
maskNode.TransformContinuousIndexToPhysicalPoint(bb[:3] + bb[3:] - 0.5)) # UBound
# Step 2: Translate the ROI physical bounds to the image coordinate space
ROIBounds = (imageNode.TransformPhysicalPointToContinuousIndex(ROIBounds[0]), # Origin
imageNode.TransformPhysicalPointToContinuousIndex(ROIBounds[1]))

logger.debug('ROI bounds (image coordinate space): %s', ROIBounds)

# Check if any of the ROI bounds are outside the image indices (i.e. -0.5 < ROI < Im.Size -0.5)
# The additional 0.5 is to allow for different spacings (defines the edges, not the centers of the edge-voxels
tolerance = 1e-3 # Define a tolerance to correct for machine precision errors
if numpy.any(numpy.min(ROIBounds, axis=0) < (- .5 - tolerance)) or \
numpy.any(numpy.max(ROIBounds, axis=0) > (numpy.array(imageNode.GetSize()) - .5 + tolerance)):
logger.error('Bounding box of ROI is larger than image space:\n\t'
'ROI bounds (image coordinate space) %s\n\tImage Size %s', ROIBounds, imageNode.GetSize())
return None, None

logger.debug('ROI valid, calculating resampling grid')
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