Write out QSIRecon pipeline-wise reports #7
Conversation
|
@mattcieslak this is ready to review. None of the HTML reports have anything useful except for the boilerplate, but we can deal with that in a future PR. |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #7 +/- ##
==========================================
+ Coverage 32.18% 33.28% +1.09%
==========================================
Files 56 56
Lines 6937 6780 -157
Branches 917 888 -29
==========================================
+ Hits 2233 2257 +24
+ Misses 4610 4432 -178
+ Partials 94 91 -3 ☔ View full report in Codecov by Sentry. |
There was a problem hiding this comment.
I was planning on deleting this entirely.
| qsirecon_suffixes = [] | ||
| for node_spec in workflow_spec["nodes"]: | ||
| qsirecon_suffix = node_spec.get("qsirecon_suffix", None) | ||
| qsirecon_suffixes += [qsirecon_suffix] if qsirecon_suffix else [] | ||
|
|
||
| qsirecon_suffixes = sorted(list(set(qsirecon_suffixes))) | ||
| config.loggers.cli.info(f"QSIRecon pipeline suffixes: {qsirecon_suffixes}") | ||
| failed_reports = [] | ||
| for qsirecon_suffix in qsirecon_suffixes: | ||
| suffix_dir = str(config.execution.output_dir / f"qsirecon-{qsirecon_suffix}") |
There was a problem hiding this comment.
this is a smart approach
There was a problem hiding this comment.
This might not ever be used in a recon workflow
There was a problem hiding this comment.
We just need something when there are enough sessions that we want to split the reports by session.
| qsirecon/dwiqc.json | ||
| qsirecon/sub-PNC | ||
| qsirecon/sub-PNC | ||
| qsirecon/sub-PNC.html | ||
| sub-PNC |
There was a problem hiding this comment.
Do you know why these keep getting created?
There was a problem hiding this comment.
That's where the config TOML file and any crash files will be written
* Add report config files. * Remove viz submodule. * Work on nireports. * Add viz utils back in. * More work. * Fix import. * Remove reportlets_dir. * Try to fix things. * Add qsirecon_suffix info. * Update core.py * Update run.py * Update expected outputs. * Update run.py * Update. * Update test_cli.py * Update run.py * Update expected outputs. * Update workflow.py * Update. * Fix.
Closes none. Partially reimplements PennLINC/qsiprep#761.
Probably doesn't work yet.
Changes proposed in this pull request