stacktrace in ./cip_vascular_analysis.sh

[Jason Brown]

Hi, I found this group email distribution on the Github page, I'm working with Dr. Lindsay Forbes at the University of Colorado.

We're stuck on this stacktrace error. Is the problem with our data, or is there any other recommendation for getting unblocked? Her # is 919-609-7530.

thank you, - Jason

Logs:

CIPDocker $ ./cip_vascular_analysis.sh DICOM_subset /<obfuscated_path>/host

DICOM_subset.nrrd exists.

Segmentation already computed.

Vessel particles already computed.

Reading polydata...

Reading label map...

Writing labeled particles...

DONE.

Traceback (most recent call last):

  File "/ChestImagingPlatform/cip_python/phenotypes/vasculature_phenotypes.py", line 505, in <module>

    v_df,figure,profiles=vasculature_pheno.execute(vessel,options.cid,spacing=spacing)

  File "/ChestImagingPlatform/cip_python/phenotypes/vasculature_phenotypes.py", line 192, in execute

    array_v[ff]=vtk_to_numpy(tmp)

  File "/root/miniconda2/lib/python2.7/site-packages/vtkmodules/util/numpy_support.py", line 216, in vtk_to_numpy

    typ = vtk_array.GetDataType()

AttributeError: 'NoneType' object has no attribute 'GetDataType'

cp: cannot stat '/tmp/DICOM_subset_vascularPhenotypes.csv': No such file or directory

d9804c4a1d5c34c084c31c2a558cf686cf5c4c7c4ed5d989d00b5f2e35d50aac

d9804c4a1d5c34c084c31c2a558cf686cf5c4c7c4ed5d989d00b5f2e35d50aac

Stacktrace error here: https://github.com/acil-bwh/CIPDocker/blob/300c67864b36fffd14ce6acf6e9350fbf31937c2/cip_vascular_analysis.sh#L67

python error here: https://github.com/Slicer/ChestImagingPlatform/blob/7b06fcb39b4f5bfbe56ee8a4cf258cd94330bc70/cip_python/phenotypes/vasculature_phenotypes.py#L192

Full debug logs here (latest at bottom): https://docs.google.com/document/d/1mx1SzRtdIyl69VcgBpi_5i7FvknZErV6PKr43R0T9KQ/edit?usp=sharing

--

Jason Kingsley Brown
Jasonking...@gmail.com | 847.421.3493