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Support channeled dicom slices #16

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merged 6 commits into from
May 14, 2020
Merged

Support channeled dicom slices #16

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9b29a87
Refactored _merge_slice_pixel_arrays to support channelled slices, e.…
jond01 May 11, 2020
cb0d926
Merge remote-tracking branch 'innolitics/master' into issues11+12_fix
jond01 May 11, 2020
1ab1954
Added SamplesPerPixel to invariant_properties and MockSlice
jond01 May 13, 2020
7cc1961
Added test for combining RGB dicom slices
jond01 May 13, 2020
899d277
Fixed Rows <-> Columns from pixel_array shape (tests)
jond01 May 13, 2020
6a8b0b4
Merge branch 'master' of https://github.com/innolitics/dicom-numpy
jond01 May 14, 2020
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28 changes: 14 additions & 14 deletions dicom_numpy/combine_slices.py
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Expand Up @@ -75,27 +75,27 @@ def combine_slices(slice_datasets, rescale=None):


def _merge_slice_pixel_arrays(slice_datasets, rescale=None):
first_dataset = slice_datasets[0]
num_rows = first_dataset.Rows
num_columns = first_dataset.Columns
num_slices = len(slice_datasets)

sorted_slice_datasets = _sort_by_slice_position(slice_datasets)

if rescale is None:
rescale = any(_requires_rescaling(d) for d in sorted_slice_datasets)

if rescale:
voxels = np.empty((num_columns, num_rows, num_slices), dtype=np.float32, order='F')
for k, dataset in enumerate(sorted_slice_datasets):
first_dataset = sorted_slice_datasets[0]
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I won't have a chance to read through this in detail until later, but two comments:

  1. We should add a test
  2. What happens if some slices are RGB and others aren't? Would the error message make the problem clear to a user?

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@johndgiese johndgiese May 11, 2020 •
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BTW thanks for making a PR for this---it will definitely make dicom-numpy more useful and generic!

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My pleasure :)

  1. Yes, will add a bit later
  2. I do not think it is a legitimate situation (?). My guess is that along with Rows, Columns, BitsStored - the attribute SamplesPerPixel is necessary for calculating pixel_array (and its shape) from PixelData. If there are some slices with different shape, they cannot be combined.
    The current error will be something related to numpy's incompatible shapes.
    In order to avoid it, maybe we should add SamplesPerPixel to the invariant_properties list? (in _validate_slices_form_uniform_grid)

slice_dtype = first_dataset.pixel_array.dtype
slice_shape = first_dataset.pixel_array.T.shape
num_slices = len(sorted_slice_datasets)

voxels_shape = slice_shape + (num_slices,)
voxels_dtype = np.float32 if rescale else slice_dtype
voxels = np.empty(voxels_shape, dtype=voxels_dtype, order='F')

for k, dataset in enumerate(sorted_slice_datasets):
pixel_array = dataset.pixel_array.T
if rescale:
slope = float(getattr(dataset, 'RescaleSlope', 1))
intercept = float(getattr(dataset, 'RescaleIntercept', 0))
voxels[:, :, k] = dataset.pixel_array.T.astype(np.float32) * slope + intercept
else:
dtype = first_dataset.pixel_array.dtype
voxels = np.empty((num_columns, num_rows, num_slices), dtype=dtype, order='F')
for k, dataset in enumerate(sorted_slice_datasets):
voxels[:, :, k] = dataset.pixel_array.T
pixel_array = pixel_array.astype(np.float32) * slope + intercept
voxels[..., k] = pixel_array

return voxels

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