steinbock classify ilastik prepare #110
Comments
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hi, i installed it from pip install under python 3.8, and I am using M1 chip MacBook. Thanks |
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Alright, it seems that the default Ilastik project file does not get shipped with binary distributions of steinbock from PyPI. I will release a fix with the next version. Until then, please use the Docker version of steinbock or manually download the Ilastik project file from https://github.com/BodenmillerGroup/steinbock/tree/main/steinbock/classification/ilastik/data. EDIT: now opened a separate issue for this problem: #111 In general, especially when using the Ilastik/CellProfiler-based approach for segmentation, I recommend to use the Docker version of steinbock, as it ships with tested versions of Ilastik & CellProfiler. As stated here, directly installing steinbock from PyPI is intended for advanced use in Python scripts only. |
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Thanks, but while I may have another issue, is this due to the compatibility of M1 chip? steinbock --version |
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While there may indeed be problems with docker/tensorflow/deepcell on M1 systems (see here), your error is because of
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jwindhager
added
support
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while when i put the path in still not running good, you were saying there is no way I can run it on M1 chip? docker run -v /Users/yangfan/Documents/steinbock/data -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -u WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested Options: Commands: |
You seem to have accidentally deleted the colon (
What's the steinbock command you're trying to run? What's the error message?
Steinbock SHOULD run without issues on M1 systems, but you MAY run into problems with DeepCell-related functionality. The Ilastik/CellProfiler functionality should work, though. |
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Thanks a lot for pointing out my stupid problems, I can successfully run the code. (base) yangfan@s-MacBook-Pro data % steinbock apps ilastik WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested Thread 0x0000004039cc2700 (most recent call first): Thread 0x000000402fbe9700 (most recent call first): Thread 0x0000004006136700 (most recent call first): Thread 0x0000004006937700 (most recent call first): Thread 0x0000004009138700 (most recent call first): Current thread 0x0000004002d6d340 (most recent call first): |
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No worries! Did you start xquartz before executing the command, as described in the installation instructions for MacOS? |
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Thanks for this, while I finally got the ilastik pop-up, but there's no project file can be found in all folders. |
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The Ilastik project file should've been generated by the |
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no errors this one steinbock classify ilastik prepare --cropsize 50 --seed 123 |
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Are you using the identical steinbock |
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yes, i just copied the commands and run. I re-run it from the beginning and I got the pixel_classifier.ilp file in the folder, but still nothing there when using steinbock apps ilastik |
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Could you please share the alias, the commands and the command output here? Thanks |
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i made a picture, hope you can understand |
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Thanks! From Ilastik, the |
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alias steinbock="docker run -v /Users/yangfan/Documents/steinbock/xx:data -v /tmp/.X11-unix:/tmp/.X11-unix -v ~/.Xauthority:/home/steinbock/.Xauthority:ro -u this command returns
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Sorry, missed a slash, edited my comment now. |
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Thanks, while still errors， I feel so frustrated 😭 and wasted lots of your valuable time, maybe i am just not that smart enough to pull this off |
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No worries, you can do this! Did you remember to start xquartz before running above commands? |
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yes. opening all the time, |
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The only difference between these two alias I noticed is "DISPLAY=$(hostname):0" this part, |
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Ah, my bad, you're on a Mac, not on Linux. Apologies! Please indeed use |
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Well, after i re-install everything, I finally can make this run!!! Thank you so much for your help and also your patience! |
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Glad it works now! To answer your question: at this point, I cannot really think of situations in which you'd like to combine both Ilastik/CellProfiler and DeepCell for nuclear segmentation. But it's science after all, so I wouldn't be surprised if there was a use case for this at some point ;-) |
Dear developer,
This steinbock gonna make IMC life so easy, while when i am following the instructions, I got an error when I performed the ilastik prepare
steinbock classify ilastik prepare --cropsize 50 --seed 123
ilastik_img/20210305_NE_mockData1_001.h5
ilastik_img/20210305_NE_mockData1_002.h5
ilastik_img/20210305_NE_mockData1_003.h5
ilastik_img/20210305_NE_mockData2_001.h5
ilastik_img/20210305_NE_mockData2_002.h5
ilastik_img/20210305_NE_mockData2_003.h5
ilastik_img/20210305_NE_mockData3_001.h5
ilastik_img/20210305_NE_mockData3_002.h5
ilastik_img/20210305_NE_mockData3_003.h5
ilastik_img/20210305_NE_mockData4_001.h5
ilastik_img/20210305_NE_mockData4_002.h5
ilastik_img/20210305_NE_mockData4_003.h5
ilastik_img/20210305_NE_mockData5_001.h5
ilastik_img/20210305_NE_mockData5_002.h5
ilastik_img/20210305_NE_mockData5_003.h5
ilastik_crops/20210305_NE_mockData1_001_x1_y47_w50_h50.h5
ilastik_crops/20210305_NE_mockData1_002_x46_y2_w50_h50.h5
ilastik_crops/20210305_NE_mockData1_003_x45_y7_w50_h50.h5
ilastik_crops/20210305_NE_mockData2_001_x39_y22_w50_h50.h5
ilastik_crops/20210305_NE_mockData2_002_x22_y12_w50_h50.h5
ilastik_crops/20210305_NE_mockData2_003_x19_y47_w50_h50.h5
ilastik_crops/20210305_NE_mockData3_001_x35_y46_w50_h50.h5
ilastik_crops/20210305_NE_mockData3_002_x30_y16_w50_h50.h5
ilastik_crops/20210305_NE_mockData3_003_x85_y34_w50_h50.h5
ilastik_crops/20210305_NE_mockData4_001_x17_y7_w50_h50.h5
ilastik_crops/20210305_NE_mockData4_002_x1_y20_w50_h50.h5
ilastik_crops/20210305_NE_mockData4_003_x30_y14_w50_h50.h5
ilastik_crops/20210305_NE_mockData5_001_x15_y39_w50_h50.h5
ilastik_crops/20210305_NE_mockData5_002_x107_y18_w50_h50.h5
ilastik_crops/20210305_NE_mockData5_003_x54_y83_w50_h50.h5
Traceback (most recent call last):
File "/usr/local/bin/steinbock", line 8, in
sys.exit(steinbock_cmd_group())
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.9/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/steinbock/classification/_cli/ilastik.py", line 168, in prepare_cmd
ilastik.create_and_save_ilastik_project(ilastik_crop_files, ilastik_project_file)
File "/usr/local/lib/python3.9/site-packages/steinbock/classification/ilastik/_ilastik.py", line 219, in create_and_save_ilastik_project
shutil.copyfile(_project_file_template, ilastik_project_file)
File "/usr/local/Cellar/[email protected]/3.9.6/Frameworks/Python.framework/Versions/3.9/lib/python3.9/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.9/site-packages/steinbock/classification/ilastik/data/pixel_classifier.ilp'
Can you help me with it? Thanks
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