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scipion-em / scipion-em-imod

Plugin to use some of the Tomography tools from IMOD in Scipion
GNU General Public License v3.0
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CTF correction step: generating defocus file failed #276

Closed wlugmayr closed 3 months ago

wlugmayr commented 3 months ago

When going over the June 2024 tutorial (2D CTF correction) using CTF auto on 40 frames:

stdout.log 00097: FINISHED: convertInputStep, step 1, time 2024-06-14 10:20:04.623320 00098: STARTED: generateDefocusFile, step 2, time 2024-06-14 10:20:04.638512 00099: Trying to generate defocus file at Runs/001922_ProtImodCtfCorrection/tmp/TS_03/TS_03.defocus 00100: FAILED: generateDefocusFile, step 2, time 2024-06-14 10:20:04.652169

stderr.log 00001: Traceback (most recent call last): 00002: File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 203, in run 00003: self._run() 00004: File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 254, in _run 00005: resultFiles = self._runFunc() 00006: File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 250, in _runFunc 00007: return self._func(*self._args) 00008: File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/imod/protocols/protocol_ctfCorrection.py", line 173, in generateDefocusFile 00009: utils.generateDefocusIMODFileFromObject(ctfTomoSeries, defocusFilePath, inputTiltSeries=ts) 00010: File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/imod/utils.py", line 665, in generateDefocusIMODFileFromObject 00011: defocusUDict = generateDefocusUDictionary(ctfTomoSeries) 00012: File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/imod/utils.py", line 860, in generateDefocusUDictionary 00013: index = ctfTomo.getIndex().get() 00014: AttributeError: 'int' object has no attribute 'get' 00015: Protocol failed: 'int' object has no attribute 'get'

azazellochg commented 3 months ago

Thanks @wlugmayr , this has been fixed in devel branch and just waiting to be released.

wlugmayr commented 3 months ago

Well does not really fit here, but when I was searching if the error comes from myself I realized that the recent June 2024 tutorial is not consistent. Once the input was imod - Automatic CTF estimation.CTFTomoSeries and later (now correct): imod - CTF estimation (auto).CTFTomoSeries So I was not sure if I did the right thing and maybe future readers are also uncertain if they have choosen the right CTF task.

azazellochg commented 3 months ago

I see, thanks. I'll update the picture in the tutorial

azazellochg commented 3 months ago

Done! New pdf should appear on the website soon. Otherwise, Scipion_Tutorial_Tomogram_Reconstruction.pdf