Merge pull request #299 from JoostJM/update-resampling

Allow a 0 value for output spacing when resampling

CHANGES.rst

@@ -12,6 +12,10 @@ New Features
 - Add a row by row customization of the extraction label in the batch processing command line script, as well as both
   batchprocessing examples.
   (`#262 <https://github.com/Radiomics/pyradiomics/pull/262>`_)
+- Allow value 0 for a resampled pixel spacing (per dimension). Values of 0 are replaced by the spacing for that
+  dimension as it is in the original (non-resampled) mask. This allows resampling over a subset of dimension (e.g. only
+  in-plane resampling when out-of-plane spacing is set to 0).
+  (`#299 <https://github.com/Radiomics/pyradiomics/pull/299>`_)
 
 Bug fixes
 #########

docs/customization.rst

@@ -128,7 +128,9 @@ Feature Extractor Level
 
 *Resampling the image*
 
-- resampledPixelSpacing [None]: List of 3 floats (> 0), sets the size of the voxel in (x, y, z) plane when resampling.
+- resampledPixelSpacing [None]: List of 3 floats (>= 0), sets the size of the voxel in (x, y, z) plane when resampling.
+  A value of 0 is replaced with the spacing for that dimension as it is in the original (non-resampled) mask, thereby
+  enabling only in-plane resampling, for example.
 - interpolator [sitkBSpline]: Simple ITK constant or string name thereof, sets interpolator to use for resampling.
   Enumerated value, possible values:
 

radiomics/imageoperations.py

@@ -414,6 +414,9 @@ def resampleImage(imageNode, maskNode, resampledPixelSpacing, interpolator=sitk.
   'imageNode' and 'maskNode' are SimpleITK Objects, and 'resampledPixelSpacing' is the output pixel spacing (sequence of
   3 elements).
 
+  If only in-plane resampling is required, set the output pixel spacing for the out-of-plane dimension (usually the last
+  dimension) to 0. Spacings with a value of 0 are replaced by the spacing as it is in the original mask.
+
   Only part of the image and labelmap are resampled. The resampling grid is aligned to the input origin, but only voxels
   covering the area of the image ROI (defined by the bounding box) and the padDistance are resampled. This results in a
   resampled and partially cropped image and mask. Additional padding is required as some filters also sample voxels
@@ -443,14 +446,13 @@ def resampleImage(imageNode, maskNode, resampledPixelSpacing, interpolator=sitk.
   if imageNode is None or maskNode is None:
     return None, None  # this function is expected to always return a tuple of 2 elements
 
-  logger.debug('Comparing resampled spacing to original spacing (image and mask')
   maskSpacing = numpy.array(maskNode.GetSpacing())
   imageSpacing = numpy.array(imageNode.GetSpacing())
 
-  # If current spacing is equal to resampledPixelSpacing, no interpolation is needed
-  if numpy.array_equal(maskSpacing, resampledPixelSpacing) and numpy.array_equal(imageSpacing, resampledPixelSpacing):
-    logger.info('New spacing equal to old, no resampling required')
-    return imageNode, maskNode
+  # If spacing for a direction is set to 0, use the original spacing (enables "only in-slice" resampling)
+  logger.debug('Where resampled spacing is set to 0, set it to the original spacing (mask)')
+  resampledPixelSpacing = numpy.array(resampledPixelSpacing)
+  resampledPixelSpacing = numpy.where(resampledPixelSpacing == 0, maskSpacing, resampledPixelSpacing)
 
   # Check if the maskNode contains a valid ROI. If ROI is valid, the bounding box needed to calculate the resampling
   # grid is returned.
@@ -463,6 +465,13 @@ def resampleImage(imageNode, maskNode, resampledPixelSpacing, interpolator=sitk.
   maskSize = numpy.array(maskNode.GetSize())
   resampledPixelSpacing = numpy.where(bb[3:] != 1, resampledPixelSpacing, maskSpacing)
 
+  # If current spacing is equal to resampledPixelSpacing, no interpolation is needed
+  # Tolerance = 1e-5 + 1e-8*abs(resampledSpacing)
+  logger.debug('Comparing resampled spacing to original spacing (image and mask')
+  if numpy.allclose(maskSpacing, resampledPixelSpacing) and numpy.allclose(imageSpacing, resampledPixelSpacing):
+    logger.info('New spacing equal to old, no resampling required')
+    return imageNode, maskNode
+
   spacingRatio = maskSpacing / resampledPixelSpacing
 
   # Determine bounds of cropped volume in terms of new Index coordinate space,

radiomics/schemas/paramSchema.yaml

@@ -43,9 +43,9 @@ mapping:
           min-ex: 0
       resampledPixelSpacing:
         seq:
-          - type: int
+          - type: float
             range:
-              min-ex: 0
+              min: 0
       interpolator:
         type: any
         func: checkInterpolator