Problem:
If I try to do something like nii = dicom2nifti.dicom_series_to_nifti(dcm_path, output_file=None), I'll get a ImageFileError: Filespec "None" does not look right for class <class 'nibabel.nifti1.Nifti1Image'> error (for the complete error, see below).
Solution:
The error comes from the lack of a simple check in the dicom2nifti.image_reorientation.reorient_image function.
The provided solution adds this simple check wheather to overwrite the output_file.
File ~/miniconda3/envs/brain/lib/python3.8/site-packages/nibabel/filename_parser.py:114, in types_filenames(template_fname, types_exts, trailing_suffixes, enforce_extensions, match_case)
113 if not isinstance(template_fname, str):
--> 114 raise TypesFilenamesError('Need file name as input '
115 'to set_filenames')
116 if template_fname.endswith('.'):
TypesFilenamesError: Need file name as input to set_filenames
During handling of the above exception, another exception occurred:
ImageFileError Traceback (most recent call last)
Input In [16], in <cell line: 1>()
----> 1 nii["NII"].to_filename(None)
Relates to issue #33
Problem:
If I try to do something like
nii = dicom2nifti.dicom_series_to_nifti(dcm_path, output_file=None), I'll get aImageFileError: Filespec "None" does not look right for class <class 'nibabel.nifti1.Nifti1Image'>error (for the complete error, see below).Solution:
The error comes from the lack of a simple check in the
dicom2nifti.image_reorientation.reorient_imagefunction.The provided solution adds this simple check wheather to overwrite the
output_file.Full error:
TypesFilenamesError Traceback (most recent call last) File ~/miniconda3/envs/brain/lib/python3.8/site-packages/nibabel/filebasedimages.py:299, in FileBasedImage.filespec_to_file_map(klass, filespec) 298 try: --> 299 filenames = types_filenames( 300 filespec, klass.files_types, 301 trailing_suffixes=klass._compressed_suffixes) 302 except TypesFilenamesError:
File ~/miniconda3/envs/brain/lib/python3.8/site-packages/nibabel/filename_parser.py:114, in types_filenames(template_fname, types_exts, trailing_suffixes, enforce_extensions, match_case) 113 if not isinstance(template_fname, str): --> 114 raise TypesFilenamesError('Need file name as input ' 115 'to set_filenames') 116 if template_fname.endswith('.'):
TypesFilenamesError: Need file name as input to set_filenames
During handling of the above exception, another exception occurred:
ImageFileError Traceback (most recent call last) Input In [16], in <cell line: 1>() ----> 1 nii["NII"].to_filename(None)
File ~/miniconda3/envs/brain/lib/python3.8/site-packages/nibabel/filebasedimages.py:332, in FileBasedImage.to_filename(self, filename) 318 def to_filename(self, filename): 319 """ Write image to files implied by filename string 320 321 Parameters (...) 330 None 331 """ --> 332 self.file_map = self.filespec_to_file_map(filename) 333 self.to_file_map()
File ~/miniconda3/envs/brain/lib/python3.8/site-packages/nibabel/filebasedimages.py:303, in FileBasedImage.filespec_to_file_map(klass, filespec) 299 filenames = types_filenames( 300 filespec, klass.files_types, 301 trailing_suffixes=klass._compressed_suffixes) 302 except TypesFilenamesError: --> 303 raise ImageFileError( 304 f'Filespec "{filespec}" does not look right for class {klass}') 305 file_map = {} 306 for key, fname in filenames.items():
ImageFileError: Filespec "None" does not look right for class <class 'nibabel.nifti1.Nifti1Image'>