search

Resoundant / 3dmre_stats

Support for 3DMRE research applications
0 stars 0 forks source link

read_images can not work for ROI(.n1) file #1

Open judy-shang opened 3 weeks ago

judy-shang commented 3 weeks ago

Hi kkalutkiewicz, Thanks for you sharing, it helps a lot. There's a bug of the code, ROI file is bytes array and can not read by pydicom, the source code and trace is as below:

roi_stack=read_images(roi_paths)

Traceback (most recent call last): File "D:\xxx\3dmre_stats-main\mmdi3d_utils.py", line 505, in measure_mmdi3d_contrasts_in_rois(acl_path, temp_dir, inversion_3d_dir, exclude_negative_pixels) File "D:\xxx\3dmre_stats-main\mmdi3d_utils.py", line 496, in measure_mmdi3d_contrasts_in_rois contrast_data=apply_rois_to_mmdi3d_contrasts(slice_data,exclude_negative_pixels,logger) File "D:\xxx\3dmre_stats-main\mmdi3d_utils.py", line 456, in apply_rois_to_mmdi3d_contrasts roi_stack=read_images(roi_paths) File "D:\xxx\3dmre_stats-main\dicom_and_file_utils.py", line 197, in read_images ds = pydicom.read_file(slice) File "D:\Software\Python312\Lib\site-packages\pydicom\filereader.py", line 1030, in dcmread dataset = read_partial( File "D:\Software\Python312\Lib\site-packages\pydicom\filereader.py", line 778, in read_partial preamble = read_preamble(fileobj, force) File "D:\Software\Python312\Lib\site-packages\pydicom\filereader.py", line 723, in read_preamble raise InvalidDicomError( pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.

We solved the except now and it may confuse other user too, so we raised this issue, thanks for your help again.
kkalutkiewicz commented 2 weeks ago

Hi @judy-shang, thanks for raising the issue. It seems like the ROI files you are trying to open are not DICOM. If you are using Hepatogram Plus, the output data should be in DICOM. What is the data you are trying to run on?