Closed cjacobs1 closed 3 years ago
@Whardian : Could you have a look at this? Would be a good first check at the codebase for you as well.
CC to @silvandeleemput
Full log:
2021-02-23T15:44:20.636018299Z THCudaCheck FAIL file=/pytorch/aten/src/THC/THCGeneral.cpp line=844 error=11 : invalid argument
2021-02-23T15:44:33.386017517Z Traceback (most recent call last):
2021-02-23T15:44:33.386051856Z File "apply.py", line 100, in <module>
2021-02-23T15:44:33.386063002Z output_json.append(extract_json_report(xmlfile=output_xml))
2021-02-23T15:44:33.386071212Z File "apply.py", line 20, in extract_json_report
2021-02-23T15:44:33.386079629Z xmlreport = LungCadReport.from_xml(ElementTree.parse(str(xmlfile)))
2021-02-23T15:44:33.386087955Z File "/home/user/xmlreport.py", line 110, in from_xml
2021-02-23T15:44:33.386096229Z cancerinfo = CancerInfo.from_xml(cancerinfo)
2021-02-23T15:44:33.386123579Z File "/home/user/xmlreport.py", line 367, in from_xml
2021-02-23T15:44:33.386135138Z referencenoduleids = tuple([int(e) for e in xml.find("./ReferenceNoduleIDs").text.split(',')])
2021-02-23T15:44:33.386143344Z AttributeError: 'NoneType' object has no attribute 'split'
I think I'll take this issue, as the xmlreport.py
should be installed from:
https://github.com/DIAGNijmegen/bodyct-nodule-evaluation
to avoid code duplication
@cjacobs1 It is indeed a case of reading an XML report with a CancerInfo section but without any ReferenceNoduleIDs
for CancerInfo. Should this be allowed? Does no reference nodules imply a low chance of cancer?
Could you provide the failing cases?
The failing cases are now in the folder I mentioned above. Yes, it is allowed that there are no reference nodule ids. That indeed implies a low chance of cancer, (although not zero because grt123 has a 'dummy' nodule as part of the solution).
I have three example cases that fail using the current version of the processor GC (v1.1.2) with the following error:
AttributeError: 'NoneType' object has no attribute 'split'
I think this may be because no nodules are detected at all?
I'll put the three cases here:
\\umcsanfsclp01.umcn.nl\radng_bodyct\software\LungCAD\grt123-failures