enh: keep track of templateflow home / demote some log traces

Author: oesteban

fmriprep/config.py

@@ -123,6 +123,7 @@
     from time import strftime
     from niworkflows.utils.spaces import SpatialReferences as _SRs, Reference as _Ref
     from nipype import logging as nlogging, __version__ as _nipype_ver
+    from templateflow import __version__ as _tf_ver
     from . import __version__
 
 
@@ -154,6 +155,11 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
 if _fs_license is None and os.getenv('FREESURFER_HOME'):
     _fs_license = os.path.join(os.getenv('FREESURFER_HOME'), 'license.txt')
 
+_templateflow_home = Path(os.getenv(
+    'TEMPLATEFLOW_HOME',
+    os.path.join(os.getenv('HOME'), '.cache', 'templateflow'))
+)
+
 
 class _Config:
     """An abstract class forbidding instantiation."""
@@ -279,6 +285,9 @@ class execution(_Config):
     """List of participant identifiers that are to be preprocessed."""
     task_id = None
     """Select a particular task from all available in the dataset."""
+    templateflow_home = _templateflow_home
+    """The root folder of the TemplateFlow client."""
+    templateflow_version = _tf_ver
     version = __version__
     """*fMRIPrep*'s version."""
     work_dir = Path('work').absolute()
@@ -295,6 +304,7 @@ class execution(_Config):
         'layout',
         'log_dir',
         'output_dir',
+        'templateflow_home',
         'work_dir',
     )
 
@@ -303,6 +313,8 @@ class execution(_Config):
 del _fs_license
 del _exec_env
 del _nipype_ver
+del _templateflow_home
+del _tf_ver
 
 
 class workflow(_Config):

fmriprep/workflows/base.py

@@ -295,6 +295,11 @@ def init_single_subject_wf(subject_id):
               ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')]),
         ])
 
+    # Dump a copy of the config file into the log directory
+    log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
+        / 'log' / config.execution.run_uuid
+    log_dir.mkdir(exist_ok=True, parents=True)
+    config.to_filename(log_dir / 'fmriprep.toml')
     return workflow
 
 

fmriprep/workflows/bold/base.py

@@ -166,9 +166,9 @@ def init_func_preproc_wf(bold_file):
         bold_tlen, mem_gb = _create_mem_gb(ref_file)
 
     wf_name = _get_wf_name(ref_file)
-    config.loggers.workflow.log(
-        25, ('Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
-             'Memory resampled/largemem=%.2f/%.2f GB.'),
+    config.loggers.workflow.debug(
+        'Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
+        'Memory resampled/largemem=%.2f/%.2f GB.',
         ref_file, mem_gb['filesize'], bold_tlen, mem_gb['resampled'], mem_gb['largemem'])
 
     sbref_file = None
@@ -771,8 +771,7 @@ def init_func_preproc_wf(bold_file):
     # Freesurfer
     freesurfer_spaces = spaces.get_fs_spaces()
     if freesurfer and freesurfer_spaces:
-        config.loggers.workflow.log(
-            25, 'Creating BOLD surface-sampling workflow.')
+        config.loggers.workflow.debug('Creating BOLD surface-sampling workflow.')
         bold_surf_wf = init_bold_surf_wf(
             mem_gb=mem_gb['resampled'],
             surface_spaces=freesurfer_spaces,