No such file or directory error

[Med-Rokaimi]

Hey,
I'm trying to implement your amazing tutorial but keeps giving me this error.
FileNotFoundError: [Errno 2] No such file or directory: 'D:/manifest-1654812109500/Duke-Breast-Cancer-MRI/Breast_MRI_001/1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538/1.3.6.1.4.1.14519.5.2.1.185777849803665244536713316058283493877/1-01.dcm'
this is my paths definition:

data_path = 'D:/manifest-1654812109500'
boxes_path = 'D:/Annotation_Boxes.csv'
mapping_path = 'D:/Breast-Cancer-MRI-filepath_filename-mapping.csv'
target_png_dir = 'png_out'
if not os.path.exists(target_png_dir):
	 #os.makedirs(target_png_dir)

the completed message:

FileNotFoundError                         Traceback (most recent call last)
~\AppData\Local\Temp\7\ipykernel_8036\3333985462.py in save_dcm_slice(dcm_fname, label, vol_idx)
     14         try:
---> 15             dcm = pydicom.dcmread(dcm_fname)
     16         except FileNotFoundError:

C:\ProgramData\Anaconda3\lib\site-packages\pydicom\filereader.py in dcmread(fp, defer_size, stop_before_pixels, force, specific_tags)
    992         logger.debug("Reading file '{0}'".format(fp))
--> 993         fp = open(fp, 'rb')
    994     elif fp is None or not hasattr(fp, "read") or not hasattr(fp, "seek"):

FileNotFoundError: [Errno 2] No such file or directory: 'D:/manifest-1654812109500\\Duke-Breast-Cancer-MRI/Breast_MRI_001/1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538/1.3.6.1.4.1.14519.5.2.1.185777849803665244536713316058283493877/1-001.dcm'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
~\AppData\Local\Temp\7\ipykernel_8036\536749713.py in <module>
     39                 if ct_negative >= N_class:
     40                         continue
---> 41                 save_dcm_slice(dcm_fname, 0, vol_idx)
     42                 ct_negative += 1

~\AppData\Local\Temp\7\ipykernel_8036\3333985462.py in save_dcm_slice(dcm_fname, label, vol_idx)
     25             dcm_fname_split[-1] = dcm_fname_end
     26             dcm_fname = '/'.join(dcm_fname_split)
---> 27             dcm = pydicom.dcmread(dcm_fname)
     28 
     29 

C:\ProgramData\Anaconda3\lib\site-packages\pydicom\filereader.py in dcmread(fp, defer_size, stop_before_pixels, force, specific_tags)
    991         caller_owns_file = False
    992         logger.debug("Reading file '{0}'".format(fp))
--> 993         fp = open(fp, 'rb')
    994     elif fp is None or not hasattr(fp, "read") or not hasattr(fp, "seek"):
    995         raise TypeError("dcmread: Expected a file path or a file-like, "

FileNotFoundError: [Errno 2] No such file or directory: 'D:/manifest-1654812109500\\Duke-Breast-Cancer-MRI/Breast_MRI_001/1.3.6.1.4.1.14519.5.2.1.186051521067863971269584893740842397538/1.3.6.1.4.1.14519.5.2.1.185777849803665244536713316058283493877/1-01.dcm'

The error is occurring because the Dicom files are stored with other paths, not the default you set in your code
1-001.dcm
for example:
D:\manifest-1654812109500\Duke-Breast-Cancer-MRI\Breast_MRI_001\01-01-1990-NA-MRI BREAST BILATERAL WWO-97538\8.000000-ax dyn 2nd pass-92755

Is there an easy way please to deal with this path issue ?

[nickk124]

Hi, sorry for the late reply. I think this may be because it seems that you're running on Windows. I just commited a fix for the code to be OS agnostic (a few lines before used linux path separation), in 316cb28.

Does that fix things?