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pydicom3 scipy #45

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1e46497
fix: dicom.read_file to dicom.dcmread
WillForan Mar 22, 2025
3618427
fix: scipy is a dependency (ndimage)
WillForan Mar 22, 2025
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12 changes: 6 additions & 6 deletions med2image/med2image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -494,27 +494,27 @@ def __init__(self, **kwargs):
if self._sliceToConvert != -1 or self.convertOnlySingleDICOM:
if self._b_convertMiddleSlice:
self._sliceToConvert = int(self.slices/2)
self._dcm = dicom.read_file(self.l_dcmFileNames[self._sliceToConvert],force=True)
self._dcm = dicom.dcmread(self.l_dcmFileNames[self._sliceToConvert],force=True)
self.str_inputFile = self.l_dcmFileNames[self._sliceToConvert]
if not self._b_convertMiddleSlice and self._sliceToConvert != -1:
self._dcm = dicom.read_file(self.l_dcmFileNames[self._sliceToConvert],force=True)
self._dcm = dicom.dcmread(self.l_dcmFileNames[self._sliceToConvert],force=True)
self.str_inputFile = self.l_dcmFileNames[self._sliceToConvert]
else:
self._dcm = dicom.read_file(self.str_inputFile,force=True)
self._dcm = dicom.dcmread(self.str_inputFile,force=True)
if self.convertOnlySingleDICOM:
self._sliceToConvert = 1
self._dcm = dicom.read_file(self.str_inputFile,force=True)
self._dcm = dicom.dcmread(self.str_inputFile,force=True)
self.lstr_inputFile.append(os.path.basename(self.str_inputFile))
else:
self._b_3D = True
self._dcm = dicom.read_file(self.str_inputFile,force=True)
self._dcm = dicom.dcmread(self.str_inputFile,force=True)
image = self._dcm.pixel_array
shape2D = image.shape
#print(shape2D)
self._Vnp_3DVol = np.empty( (shape2D[0], shape2D[1], self.slices) )
i = 0
for img in self.l_dcmFileNames:
self._dcm = dicom.read_file(img,force=True)
self._dcm = dicom.dcmread(img,force=True)
self.lstr_inputFile.append(os.path.basename(img))
image = self._dcm.pixel_array
self._dcmList.append(self._dcm)
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -19,7 +19,7 @@ def readme():
author_email = 'dev@babymri.org',
url = 'https://github.com/FNNDSC/med2image',
packages = ['med2image'],
install_requires = ['pfmisc', 'nibabel', 'pydicom', 'numpy', 'matplotlib', 'pillow'],
install_requires = ['pfmisc', 'nibabel', 'pydicom>=3.0.1', 'numpy', 'matplotlib', 'pillow', 'scipy'],
#test_suite = 'nose.collector',
#tests_require = ['nose'],
scripts = ['bin/med2image'],
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