Reminder: If any changes are done in this branch (e.g. in notebook), MyBinder needs to rebuild the Dockerfile (otherwise clicking the link above will only load the previously built Docker image, i.e. without the new changes). The easiest (and unfortunatly, not clean) way to do this is to add a space before the backward slash on this line of the Dockerfile (this change in the RUN stage is recognised by MyBinder, and thus this entire stage and all the following ones are rebuilt).
Changes done so far:
Converted the batch_processing.sh script into a Jupyter Notebook
Added verbosity flag (False clears the output of the cells, except for figures, but currently True for debugging)
Plotted all the QC plots (for the functions that have that functionality), with their overlay + some transparency.
Refactored most hardcoded file and folder names, and instead set the prefixes in a cell with all config params and generate (i.e. concat) the filenames when called.
Separated most CLI calls to their own cells (they could be reconsolidated in one or fewer cells, but it was easier to handle both less verbosity but retain the plots this way).
At this point, @jcohenadad maybe you could give offer guidance on what other plots (if any) you think would be useful to visualise in such a pipeline, how you want to display your final results, and some documentation (before the pipeline, at each step, and/or at the figures/results).
Resolves #2
MyBinder link pointing to the notebook & this branch: https://mybinder.org/v2/gh/sct-pipeline/binder-example/jupyter?urlpath=lab/tree/batch_processing.ipynb
Reminder: If any changes are done in this branch (e.g. in notebook), MyBinder needs to rebuild the Dockerfile (otherwise clicking the link above will only load the previously built Docker image, i.e. without the new changes). The easiest (and unfortunatly, not clean) way to do this is to add a space before the backward slash on this line of the Dockerfile (this change in the
RUNstage is recognised by MyBinder, and thus this entire stage and all the following ones are rebuilt).Changes done so far:
At this point, @jcohenadad maybe you could give offer guidance on what other plots (if any) you think would be useful to visualise in such a pipeline, how you want to display your final results, and some documentation (before the pipeline, at each step, and/or at the figures/results).