Merge pull request #448 from chrisfilo/fix/classifier

[RTM] disabling the classifier

CHANGES.txt

@@ -1,11 +1,12 @@
-Release x.x.x
+Release 0.9.2
 =============
 
 * [ENH] Optional ICA reports for identifying spatiotemporal artifacts (#412)
 * [ENH] Add --profile flag (#435)
 * [ENH] Crashfiles are saved in plain text to improve portability (#434)
 * [FIX] Fixes EPI mask erosion (#442)
 * [ENH] Make FSL and AFNI motion correction more comparable by using the same scheme for defining the reference image (#444)
+* [FIX] Temporarily disabling T1w quality classifier until it can be retrained on new measures (#447)
 
 
 Release 0.9.1

docs/source/index.rst

@@ -21,7 +21,6 @@ Contents
    running
    measures
    docker
-   classifier
    reports
    workflows
 

docs/source/userguide.rst

@@ -8,5 +8,4 @@ User Guide
    running
    measures
    reports
-   workflows
-   classifier
+   workflows

mriqc/bin/mriqc_clf.py

@@ -46,8 +46,8 @@ def main():
 
     g_clf = parser.add_mutually_exclusive_group()
     g_clf.add_argument('--train', nargs=2, help='training data tables, X and Y')
-    g_clf.add_argument('--load-classifier', nargs="?", default=None,
-                       const=pkgrf('mriqc', 'data/rfc-nzs-full-1.0.pklz'),
+    g_clf.add_argument('--load-classifier', nargs="?",
+                       default=pkgrf('mriqc', 'data/rfc-nzs-full-1.0.pklz'),
                        help='load pickled classifier in')
 
     parser.add_argument('--test-data', help='test data')

mriqc/bin/mriqc_run.py

@@ -280,10 +280,10 @@ def main():
 
             MRIQC_LOG.info('Summary CSV table for the %s data generated (%s)', mod, out_csv)
 
-            out_pred = generate_pred(derivatives_dir, settings['output_dir'], mod)
-            if out_pred is not None:
-                MRIQC_LOG.info('Predicted QA CSV table for the %s data generated (%s)',
-                               mod, out_pred)
+            # out_pred = generate_pred(derivatives_dir, settings['output_dir'], mod)
+            # if out_pred is not None:
+            #     MRIQC_LOG.info('Predicted QA CSV table for the %s data generated (%s)',
+            #                    mod, out_pred)
 
             out_html = op.join(reports_dir, mod + '_group.html')
             group_html(out_csv, mod,

mriqc/reports/individual.py

@@ -44,7 +44,7 @@ def individual_html(in_iqms, in_plots=None, exclude_index=0, wf_details=None):
                for k in list(BIDS_COMP.keys())]
     file_id = [comp for comp in file_id if comp is not None]
 
-    pred_qa = metadata.pop('mriqc_pred', None)
+    pred_qa = None #metadata.pop('mriqc_pred', None)
 
     # Deal with special IQMs
     if mod in ('T1w', 'T2w'):

tests/circle_outputs.txt

@@ -48,4 +48,3 @@ out/reports/sub-ds205s09_task-view_acq-LR_run-02_bold.html
 out/reports/sub-ds205s09_task-view_acq-RL_run-01_bold.html
 out/reports/T1w_group.html
 out/T1w.csv
-out/T1w_predicted_qa.csv