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AIM-Harvard / SlicerRadiomics

A Slicer extension to provide a GUI around pyradiomics
BSD 3-Clause "New" or "Revised" License
101 stars 47 forks source link

Error extracting features #80

Closed DanXieJY closed 5 months ago

DanXieJY commented 7 months ago

Hi, I've been trying to use the newly updated SlicerRadiomics package to extract radiomics features, but the error below prompted every time I clicked apply. There were only table titles in the tables. At first I thought it was due to the setting of my machine. But after I tried 3 different machines, including win and linux, the same thing happened. I've tried Slicer 5.3-5.6, and even manually changed the py files but nothing worked. Hope someone could help me fix this problem. Thanks!!

[2023-12-04 00:42:47] I: radiomics.script: Processing input... [2023-12-04 00:42:47] E: radiomics.script: Error extracting features! Traceback (most recent call last): File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 135, in run results = self._processCases(caseGenerator) File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 233, in _processCases setting_overrides = self._parseOverrides() File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 353, in _parseOverrides settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping'] File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/ruamel/yaml/main.py", line 1105, in safe_load error_deprecation('safe_load', 'load', arg="typ='safe', pure=True") File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/ruamel/yaml/main.py", line 1037, in error_deprecation raise AttributeError(s) AttributeError: "safe_load()" has been removed, use

yaml = YAML(typ='safe', pure=True) yaml.load(...)

instead of file "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 353

settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']

pieper commented 7 months ago

It looks like this needs to be updated to use the new syntax - is that what you tried?

https://github.com/AIM-Harvard/pyradiomics/blob/master/radiomics/scripts/__init__.py#L353

DanXieJY commented 7 months ago

It looks like this needs to be updated to use the new syntax - is that what you tried?

https://github.com/AIM-Harvard/pyradiomics/blob/master/radiomics/scripts/__init__.py#L353

Yes, I've tried that but the new error prompted:

[2023-12-05 00:21:16] E: radiomics.script: Error extracting features! Traceback (most recent call last): File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 135, in run results = self._processCases(caseGenerator) File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 233, in _processCases setting_overrides = self._parseOverrides() File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 353, in _parseOverrides yaml = YAML(typ='safe', pure=True) NameError: name 'YAML' is not defined

pieper commented 7 months ago

It looks like with this tool you need to explicitly import the YAML object:

https://yaml.readthedocs.io/en/latest/basicuse/#basic-usage

If you get it working could you post a pull request?

DanXieJY commented 7 months ago

It looks like with this tool you need to explicitly import the YAML object:

https://yaml.readthedocs.io/en/latest/basicuse/#basic-usage

If you get it working could you post a pull request?

Thank you for the quick response. I tried adding "from ruamel.yaml import YAML" to the top of the init.py file, but another error came. Sorry I'm very new to this area and hope for further guidance.

RadiomicsCLI standard error:

[2023-12-05 11:12:38] I: radiomics.script: Starting PyRadiomics (version: 3.1.0a2.post8+g6a761c4) [2023-12-05 11:12:38] I: radiomics.script: Processing input... [2023-12-05 11:12:38] E: radiomics.script: Error extracting features! Traceback (most recent call last): File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 136, in run results = self._processCases(caseGenerator) File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 234, in _processCases setting_overrides = self._parseOverrides() File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/init.py", line 355, in _parseOverrides yaml.load(...) File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/ruamel/yaml/main.py", line 449, in load constructor, parser = self.get_constructor_parser(stream) File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/ruamel/yaml/main.py", line 500, in get_constructor_parser self.reader.stream = stream File "/root/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/ruamel/yaml/reader.py", line 113, in stream raise YAMLStreamError('stream argument needs to have a read() method') ruamel.yaml.error.YAMLStreamError: stream argument needs to have a read() method

pieper commented 7 months ago

I'm not too familiar with this package either, but based on the message I think you need to pass it an open file not the name of the file. So something like:

schemaFile, schemaFuncs = radiomics.getParameterValidationFiles()
with open(schemaFile) as schema:
    settingsSchema = yaml.safe(schema)['mapping']['setting']['mapping']

If you can't find a combination that works, next time post your changed code along with the error message to make debugging clearer.

DanXieJY commented 7 months ago

I'm not too familiar with this package either, but based on the message I think you need to pass it an open file not the name of the file. So something like:

schemaFile, schemaFuncs = radiomics.getParameterValidationFiles()
with open(schemaFile) as schema:
    settingsSchema = yaml.safe(schema)['mapping']['setting']['mapping']

If you can't find a combination that works, next time post your changed code along with the error message to make debugging clearer.

I finally made it run successfully!! Thank you for the precious advice. Below is what I changed to https://github.com/AIM-Harvard/pyradiomics/blob/master/radiomics/scripts/__init__.py

  1. Add the code below to the top of the file: from ruamel.yaml import YAML
  2. Add the code below before line 353: yaml = YAML(typ='safe', pure=True)
  3. Change what was in line 353 to: settingsSchema = yaml.load(schema)['mapping']['setting']['mapping']
pieper commented 7 months ago

Thanks for reporting back with the solution 👍

Would you be able to make a pull request to update the repository with these changes?

DanXieJY commented 6 months ago

Thanks for reporting back with the solution 👍

Would you be able to make a pull request to update the repository with these changes?

For sure! I am now trying to pull a request. Thanks again for the help!

CC-DrDU commented 5 months ago

Hi there. Recently I've been trying to use the SlicerRadiomics to extract radiomics features and I also got this problem. I only got table title in the result table. I'm using a Slicer 5.7.0 and a SlicerRadiomics version c29d8a7 (2024-01-01) on Windows 11. So how can I fix this problem or bypass the problem? Thank you for your attention!

pieper commented 5 months ago

I tried yesterday with the windows stable and got a more recent radiomics code that worked.

I wasn't able to get a more recent build for the current stable 5.6.1 though, so maybe there's a configuration issue or something wrong with the extension update mechanism. @jcfr or @lassoan have you seen extension update issues?

lassoan commented 5 months ago

Most likely the problem is that the SlicerRadiomics superbuild specifies pyradiomics version using the branch name origin/master instead of a hash. The package manager is smart enough that it will not download and build a package again if it has that package already.

The fix is to change origin/master to the latest hash (146e3bd0971336913f9c9f49ce535bc4663ca5c2) in External_python-pyradiomics.cmake.

pieper commented 5 months ago

Thanks Andras, let's give that a try. 👍

https://github.com/AIM-Harvard/SlicerRadiomics/commit/30e27987d918f2b0b6a65dba2f910fbe681e8f69

CC-DrDU commented 5 months ago

Thank you all for your remarkable work. I've downloaded the Slicer 5.0.2 and used the compatible SlicerRadiomics, and it worked well on my computer. I guess I should stick to the older version for now. Thanks again!

lassoan commented 5 months ago

The fix works well! You can update SlicerRadiomics extension in the Extensions Manager in Slicer-6.1.