Pixel Data is compressed in a format pydicom does not yet handle.. (CT images from HOROS or Osirix)

[rmo...@alara-expertise.fr]

Hi James,

I'm medical physicist and I try to use Pylinac locally with conda (on my macbook) and on the web to analyze my conventional scanner acquisitions made with a CATPHAN 600. I view and I exported the images with HOROS (like Osirix) and I can not manage to load them. I have the follow error message :

>>> from pylinac import CatPhan600

>>> cbct_folder = "/Users/ramiromoreno/Documents/ALARA/DVetDOC/CATPHAN/350004A/"

>>> mycbct = CatPhan600(cbct_folder)

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/Users/ramiromoreno/miniconda3/lib/python3.5/site-packages/pylinac/ct.py", line 72, in __init__

    self.dicom_stack = image.DicomImageStack(folderpath)

  File "/Users/ramiromoreno/miniconda3/lib/python3.5/site-packages/pylinac/core/image.py", line 895, in __init__

    img = DicomImage(path, dtype=dtype)

  File "/Users/ramiromoreno/miniconda3/lib/python3.5/site-packages/pylinac/core/image.py", line 668, in __init__

    self._original_dtype = self.metadata.pixel_array.dtype

  File "/Users/ramiromoreno/miniconda3/lib/python3.5/site-packages/dicom/dataset.py", line 418, in pixel_array

    return self._get_pixel_array()

  File "/Users/ramiromoreno/miniconda3/lib/python3.5/site-packages/dicom/dataset.py", line 400, in _get_pixel_array

    raise NotImplementedError("Pixel Data is compressed in a format pydicom does not yet handle. Cannot return array")

NotImplementedError: Pixel Data is compressed in a format pydicom does not yet handle. Cannot return array

>>> 

I think it comes from the dicom format because when I import your demo images directly it works but if the images are first loaded on HOROS, it does not work after reexport to dicom ..

I am a little lost !

Moreover, do you plan to implement the catphan600 analysis on the web application? for conventional CT ?

Many thanks for your work !

Ramiro MORENO

[rmo...@alara-expertise.fr]

hi James,
if i try to read and export the demo images on osirix, local and web works ok.. maybe you have a particular tag for CBCT images from linac that conventional ct do not have?

[James Kerns]

Hello Ramiro, 

      Your issue sounds like a DICOM compatibility issue. You can submit this over at the pydicom forum.

As for adding CatPhan 600 to the web app, I probably won't soon. Heroku implements size limits for their apps and with all the scientific dependencies I'm currently capped at (I believe) pylinac v0.6 on it. There are ways around this but I'm currently working on another project =/