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merged 2 commits into from
Jun 27, 2023
Merged

fix #6630 #6660

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d246bbf
fix #6630
function2-llx Jun 27, 2023
2b33b12
fix the ITK reference link by the way
function2-llx Jun 27, 2023
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16 changes: 8 additions & 8 deletions monai/data/image_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,7 @@ def read(self, data: Sequence[PathLike] | PathLike, **kwargs):
data: file name or a list of file names to read,
kwargs: additional args for `itk.imread` API, will override `self.kwargs` for existing keys.
More details about available args:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/itkExtras.py
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/itk/support/extras.py

"""
img_ = []
Expand All @@ -230,7 +230,7 @@ def read(self, data: Sequence[PathLike] | PathLike, **kwargs):
name = f"{name}"
if Path(name).is_dir():
# read DICOM series
# https://itk.org/ITKExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage
# https://examples.itk.org/src/io/gdcm/readdicomseriesandwrite3dimage/documentation
names_generator = itk.GDCMSeriesFileNames.New()
names_generator.SetUseSeriesDetails(True)
names_generator.AddSeriesRestriction("0008|0021") # Series Date
Expand Down Expand Up @@ -512,19 +512,19 @@ def _combine_dicom_series(self, data: Iterable):
first_array = self._get_array_data(first_slice)
shape = first_array.shape
spacing = getattr(first_slice, "PixelSpacing", [1.0, 1.0, 1.0])
pos = getattr(first_slice, "ImagePositionPatient", (0.0, 0.0, 0.0))[2]
prev_pos = getattr(first_slice, "ImagePositionPatient", (0.0, 0.0, 0.0))[2]
stack_array = [first_array]
for idx in range(1, len(slices)):
slc_array = self._get_array_data(slices[idx])
slc_shape = slc_array.shape
slc_spacing = getattr(first_slice, "PixelSpacing", (1.0, 1.0, 1.0))
slc_pos = getattr(first_slice, "ImagePositionPatient", (0.0, 0.0, float(idx)))[2]
if spacing != slc_spacing:
slc_spacing = getattr(slices[idx], "PixelSpacing", (1.0, 1.0, 1.0))
slc_pos = getattr(slices[idx], "ImagePositionPatient", (0.0, 0.0, float(idx)))[2]
if not np.allclose(slc_spacing, spacing):
warnings.warn(f"the list contains slices that have different spacings {spacing} and {slc_spacing}.")
if shape != slc_shape:
warnings.warn(f"the list contains slices that have different shapes {shape} and {slc_shape}.")
average_distance += abs(pos - slc_pos)
pos = slc_pos
average_distance += abs(prev_pos - slc_pos)
prev_pos = slc_pos
stack_array.append(slc_array)

if len(slices) > 1:
Expand Down