General refactoring

bip/pipelines/struct_T2_FLAIR/__init__.py

+#!/usr/bin/env python
+#
+# struct_T2_FLAIR.py - Pipeline with the T2 FLAIR processing.
+#
+# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
+#
+# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
+#
+
+import logging
+from bip.utils.log_utils           import job_name
+from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_gdc, T2_FLAIR_brain_extract
+from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_defacing, T2_FLAIR_apply_bfc
+from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_bianca
+
+log = logging.getLogger(__name__)
+
+def add_to_pipeline(ctx, pipe, tree):
+
+    subj = ctx.subject
+
+    pipe(T2_FLAIR_gdc.run,
+         submit=dict(jobtime=200, name=job_name(T2_FLAIR_gdc.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T2_FLAIR_brain_extract.run,
+         submit=dict(jobtime=200, name=job_name(T2_FLAIR_brain_extract.run,
+                                                subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T2_FLAIR_defacing.run,
+         submit=dict(jobtime=200, name=job_name(T2_FLAIR_defacing.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T2_FLAIR_apply_bfc.run,
+         submit=dict(jobtime=200, name=job_name(T2_FLAIR_apply_bfc.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T2_FLAIR_bianca.run,
+         submit=dict(jobtime=200, name=job_name(T2_FLAIR_bianca.run, subj)),
+         kwargs={'ctx' : ctx})

bip/pipelines/struct_T2_FLAIR/struct_T2_FLAIR.py

-#!/usr/bin/env python
-#
-# struct_T2_FLAIR.py - Pipeline with the T2 FLAIR processing.
-#
-# Author: Fidel Alfaro Almagro <fidel.alfaroalmagro@ndcn.ox.ac.uk>
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-# Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
-#
-# pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
-#
-
-import logging
-from bip.utils.log_utils           import redirect_logging
-from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_gdc, T2_FLAIR_brain_extract
-from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_defacing, T2_FLAIR_apply_bfc
-from bip.pipelines.struct_T2_FLAIR import T2_FLAIR_bianca
-
-log = logging.getLogger(__name__)
-
-def add_to_pipeline(ctx, pipe, tree, targets):
-
-    logs_dir=tree.get('logs_dir')
-
-    subj = ctx.subject 
-
-    with redirect_logging('pipe_struct_T2_FLAIR', outdir=logs_dir):
-        pipe(T2_FLAIR_gdc.run,
-             submit=dict(jobtime=200, name="BIP_T2_FLAIR_gdc_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T2_FLAIR_orig_ud_warp')
-        pipe(T2_FLAIR_brain_extract.run,
-             submit=dict(jobtime=200, name="BIP_T2_FLAIR_brain_extract_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T2_FLAIR_brain')
-        pipe(T2_FLAIR_defacing.run,
-             submit=dict(jobtime=200, name="BIP_T2_FLAIR_defacing_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T2_FLAIR_defacing_mask')
-        pipe(T2_FLAIR_apply_bfc.run,
-             submit=dict(jobtime=200, name="BIP_T2_FLAIR_apply_bfc_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T2_FLAIR_unbiased_brain')
-        pipe(T2_FLAIR_bianca.run,
-             submit=dict(jobtime=200, name="BIP_T2_FLAIR_bianca_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T2_FLAIR_bianca_volume')
-
-
-    return pipe, targets

bip/pipelines/struct_asl/struct_asl.py → bip/pipelines/struct_asl/__init__.py

@@ -7,28 +7,22 @@
 # Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
 #
 # pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
 #
 
 import logging
-from bip.utils.log_utils      import redirect_logging
+from bip.utils.log_utils      import job_name
 from bip.pipelines.struct_asl import asl_proc, asl_get_IDPs
 
 log = logging.getLogger(__name__)
 
-def add_to_pipeline(ctx, pipe, tree, targets):
+def add_to_pipeline(ctx, pipe, tree):
 
-    logs_dir=tree.get('logs_dir')
+    subj = ctx.subject
 
-    subj = ctx.subject 
-
-    with redirect_logging('pipe_struct_asl', outdir=logs_dir):
-        pipe(asl_proc.run,
-             submit=dict(jobtime=200, name="BIP_asl_proc_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('region_analysis_gm_csv')
-        pipe(asl_get_IDPs.run,
-             submit=dict(jobtime=200, name="BIP_asl_get_IDPs_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('ASL_IDPs')
-
-    return pipe, targets
+    pipe(asl_proc.run,
+         submit=dict(jobtime=200, name=job_name(asl_proc.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(asl_get_IDPs.run,
+         submit=dict(jobtime=200, name=job_name(asl_get_IDPs.run, subj)),
+         kwargs={'ctx' : ctx})

bip/pipelines/struct_asl/asl_get_IDPs.py

@@ -22,7 +22,7 @@ def run(ctx,
         ASL_region_analysis_dir: Ref,
         ASL_IDPs:                Out):
 
-    with redirect_logging('asl_get_IDPs', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         result = ctx.subject
 

bip/pipelines/struct_asl/asl_proc.py

@@ -55,7 +55,7 @@ def run(ctx,
         ASL_std_ACBV_calib:            Out,
         region_analysis_gm_csv:        Out):
 
-    with redirect_logging('asl_proc', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         BBASL_ROI_DIR = ctx.get_data("asl/ukb_rois/")
 

bip/pipelines/struct_swMRI/struct_swMRI.py → bip/pipelines/struct_swMRI/__init__.py

@@ -7,24 +7,19 @@
 # Author: Michiel Cottaar <michiel.cottaar@ndcn.ox.ac.uk>
 #
 # pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
+# pylint: disable=W0613
 #
 
 import logging
-from bip.utils.log_utils        import redirect_logging
+from bip.utils.log_utils        import job_name
 from bip.pipelines.struct_swMRI import swMRI_proc
 
 log = logging.getLogger(__name__)
 
-def add_to_pipeline(ctx, pipe, tree, targets):
+def add_to_pipeline(ctx, pipe, tree):
 
-    logs_dir=tree.get('logs_dir')
+    subj = ctx.subject
 
-    subj = ctx.subject 
-
-    with redirect_logging('pipe_struct_swMRI', outdir=logs_dir):
-        pipe(swMRI_proc.run,
-            submit=dict(jobtime=200, name="BIP_swMRI_proc_" + subj),
-            kwargs={'ctx' : ctx})
-        targets.append('SWI')
-
-    return pipe, targets
+    pipe(swMRI_proc.run,
+        submit=dict(jobtime=200, name=job_name(swMRI_proc.run, subj)),
+        kwargs={'ctx' : ctx})

bip/pipelines/struct_swMRI/swMRI_gdc.py

@@ -24,7 +24,7 @@ def run(ctx,
         logs_dir:                Ref,
         T1_GDC:                  Ref):
 
-    with redirect_logging('T1_gdc', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         if ctx.gdc != '':
             #Calculate and apply the Gradient Distortion Unwarp

bip/pipelines/struct_swMRI/swMRI_proc.py

@@ -51,7 +51,7 @@ def run(ctx,
         T1_to_SWI_mat:              Out,
         filtered_phase:             Out):
 
-    with redirect_logging('swMRI_proc', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         with open(SWI_num_coils, 'r', encoding="utf-8") as f:
             num_coils = int(f.read())

bip/utils/log_utils.py

@@ -22,13 +22,10 @@ from subprocess import check_output
 from fsl import wrappers
 
 
-def run_command(logger, command, **kwargs): This fails
-#def run_command(logger, command, env):
+def run_command(logger, command, **kwargs): 
     try:
         logger.info(command.strip())
-        # This fails
         job_output = check_output(command,shell=True,**kwargs).decode('UTF-8')
-        #job_output = check_output(command,shell=True,env=env).decode('UTF-8')
         logger.info('Output: \t' + job_output.strip())
 
     except Exception as e:
@@ -40,6 +37,10 @@ def run_command(logger, command, **kwargs): This fails
 
     return job_output.strip()
 
+def job_name(function, *args):
+    func = function.__module__.removeprefix('bip.pipelines.')
+    return '_'.join([func] + list(args))
+
 
 def create_formatter():
     """Create a logging.Formatter. """