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BUG: Fixed resizing for wavelet filtering (resizing was scrambling image) #346

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Feb 21, 2018
Merged

BUG: Fixed resizing for wavelet filtering (resizing was scrambling image) #346

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BUG: Fixed resizing for wavelet filtering. Resizing does not scramble…
michaelschwier Feb 16, 2018
67845cf
ENH: changed pad mode from constant to wrap
michaelschwier Feb 21, 2018
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8 changes: 4 additions & 4 deletions radiomics/imageoperations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -745,9 +745,9 @@ def _swt3(inputImage, wavelet='coif1', level=1, start_level=0, axes=(2, 1, 0)):
raise ValueError('Expected 3D data array')

original_shape = matrix.shape
adjusted_shape = tuple([dim + 1 if dim % 2 != 0 else dim for dim in original_shape])
padding = tuple([(0, 1 if dim % 2 != 0 else 0) for dim in original_shape])
data = matrix.copy()
data.resize(adjusted_shape, refcheck=False)
data = numpy.pad(data, padding, 'constant')
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As discussed, should change boudnary mode to wrap.

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done


if not isinstance(wavelet, pywt.Wavelet):
wavelet = pywt.Wavelet(wavelet)
Expand All @@ -764,14 +764,14 @@ def _swt3(inputImage, wavelet='coif1', level=1, start_level=0, axes=(2, 1, 0)):
dec_im = {}
for decName, decImage in six.iteritems(dec):
decTemp = decImage.copy()
decTemp = numpy.resize(decTemp, original_shape)
decTemp = decTemp[[slice(None, -1 if dim % 2 != 0 else None) for dim in original_shape]]
sitkImage = sitk.GetImageFromArray(decTemp)
sitkImage.CopyInformation(inputImage)
dec_im[str(decName).replace('a', 'L').replace('d', 'H')] = sitkImage

ret.append(dec_im)

data = numpy.resize(data, original_shape)
data = data[[slice(None, -1 if dim % 2 != 0 else None) for dim in original_shape]]
approximation = sitk.GetImageFromArray(data)
approximation.CopyInformation(inputImage)

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