A collection of diagnostics tools for Ilastik.
- A parameter-optimization script
src/paramOpt.py
that runs cross-validation tests to find the optimal number of trees and features. - A simple test script
src/runningTimeProf.py
that isolates feature computation and prediction in order to profile the time for each of these stages individually. - A script
trackingCsvDiagnostics.py
to read and diagnose the conservation-tracking csv result files.
- Download and install the latest versions of ilastik and lazyflow.
- IMPORTANT: Change directory to the parent folder that contains the project (.ilp) file.
- Run the parameter-optimization script with the following command:
>>>python paramOpt.py --run_command=<ilastik-run-command> --project-file=<ilp-project-file>
- Download and install the latest versions of ilastik and lazyflow.
- Run the profiling script with the following command:
>>>python runningTimeProf.py <project-file> <data-file> <threads-enabled> <thread-number>
The file trackingCsvDiagnostics.py
allows the user to plot different tracking parameters contained in the csv files. Here's a list of the arguments available.
Argument | Description --- | --- | --- | -h, --help | show this help message and exit --file FILE | Name of conservation-tracking csv file. --lineage-ids | Plot the lineage IDs. --tracks | Plot the tracks of all the objects in the file. --object-num | Plot the number of objects per frame. --errors | Plot the errors per frame. These errors include appearing IDs and repeated IDs. --collisions | Plot the number of collisions per frame. --bounding-rect BOUNDINGRECT | Plot the bounding rectangles for the choose frame.
- Download and install the latest versions of ilastik and lazyflow.
- Run the tracking diagnostics script with the test csv file with the following command:
>>>python trackingCsvDiagnostics.py --tracks