Usage

Example PyHIST run command: bash pyhist.py \ --patch-size 64 \ --output-downsample 16 \ --save-patches \ --save-tilecrossed-image \ --info "verbose" \ --output /data/apps/tests/pyhist/output \ /data/apps/tests/pyhist/GTEX-1117F-0126.svs

Things to note:

  • The HiPerGator module for PyHIST has been set up in a manner that does not require you to invoke Python to run the script. If you are following the examples in the authors' tutorial, drop the python or python3 from the command. In the example above, you can see that the command is just pyhist.py ....
  • The full path must be specified= for the input file and the output directory. In the above example this is /data/apps/tests/pyhist/GTEX-1117F-0126.svs and /data/apps/tests/pyhist/output respectively. Your paths will likely look something like /blue/yourgroup/yourusename/yourdir/.... If you do not specify the full path, the script will try to write to unexpected directories and will fail.
  • You must always include the --output option to specify the full path to the output directory. As above, the default action (if you leave this option off) will attempt to save the output to a directory that will likely fail. Including this option will ensure that your output goes to your intended directory.