diff --git a/med2image/med2image.py b/med2image/med2image.py index 9c3474d..f484992 100755 --- a/med2image/med2image.py +++ b/med2image/med2image.py @@ -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) diff --git a/setup.py b/setup.py index b2e6f34..ea38d00 100644 --- a/setup.py +++ b/setup.py @@ -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'],