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PathologyDataScience / HistomicsML2

A tool for training machine-learning models with whole-slide imaging datasets
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Data import issue #61

Closed slee172 closed 4 years ago

slee172 commented 4 years ago

@Reasat I have finished creating the dataset and my project directory structure looks like this image I think I have to select 'myproject' as the base project However, I don't see the option in http://localhost/HistomicsML/data.html Screenshot from 2020-10-13 17-21-51

slee172 commented 4 years ago

I think this can be resolved by running the docker images on the correct directory. It seems like you "run" the docker on your home directory. I would suggest you to "run" the docker under the HistomicsML directory. The "Project directory" selection tab will search all directories under the "HistomicsML" directory.

Reasat commented 4 years ago

Thanks for opening this as a separate issue. I have run the docker under the HistomicsML directory. And I can locate the 'myproject' directory. And it automatically locates the slide_info.csv. But when I click submit it says, "localhost says Cannot create slide list"

slee172 commented 4 years ago

@Reasat Good to hear that you confirmed the directory.

I think that the error text "Cannot create slide list" indicates that the system cannot create the "slidelist.txt" file under the "/datasets/myproject" directory.

You may have to check two things.

  1. slide_info.csv file is correct.
  2. the "myproject" directory has a write permission.

You can refer to "Web server docker container needs a permission to access the directories: myproject1, myproject2, …, classifiers, so make sure that the directories support a writable permission (e.g. chmod 777 /master/myproject1)." in https://histomicsml2.readthedocs.io/en/latest/data-import.html

Reasat commented 4 years ago

Thanks! Allowing permission solved the import step. But in the next stage, I am facing this Screenshot from 2020-10-13 21-53-44 Note that in the generated slide_info.csv the location of the file is written down as /datasets/myproject/tif/CMU-1-JP2K-33005.svs.dzi.tif but the actual file name in the tif folder is CMU-1-JP2K-33005.dzi.tif (without svs). Tried with both filenames, but got the same error.

slee172 commented 4 years ago

I think the Data Import issue has been resolved.

I will move the issue of displaying a slide to another issue.