General refactoring

bip/pipelines/struct_FS/FS_proc.py

@@ -26,7 +26,7 @@ def run(ctx,
         fsaverage:                  Ref,
         rh_entorhinal_exvivo_label: Out):
 
-    with redirect_logging('FS_proc', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         # We need to delete the folder because otherwise, FreeSurfer complains
         if os.path.exists(FreeSurfer_dir):

bip/pipelines/struct_FS/FS_segm.py

@@ -25,7 +25,7 @@ def run(ctx,
         FreeSurfer_dir:             Ref,
         ThalamicNuclei:             Out):
 
-    with redirect_logging('FS_segm', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         env = dict(os.environ, SUBJECTS_DIR=os.getcwd() + "/" + ctx.subject)
 

bip/pipelines/struct_FS/struct_FS.py → bip/pipelines/struct_FS/__init__.py

@@ -7,32 +7,25 @@
 # 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_FS import FS_proc, FS_segm, FS_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_FS', outdir=logs_dir):
-        pipe(FS_proc.run,
-             submit=dict(jobtime=200, name="BIP_FS_proc_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('rh_entorhinal_exvivo_label')
-        pipe(FS_segm.run,
-             submit=dict(jobtime=200, name="BIP_FS_segm_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('ThalamicNuclei')
-        pipe(FS_get_IDPs.run, 
-             submit=dict(jobtime=200, name="BIP_FS_get_IDPs_" + subj), 
-             kwargs={'ctx' : ctx})
-        targets.append('FS_IDPs')
-
-    return pipe, targets
+    pipe(FS_proc.run,
+         submit=dict(jobtime=200, name=job_name(FS_proc.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(FS_segm.run,
+         submit=dict(jobtime=200, name=job_name(FS_segm.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(FS_get_IDPs.run,
+         submit=dict(jobtime=200, name=job_name(FS_get_IDPs.run, subj)),
+         kwargs={'ctx' : ctx})

bip/pipelines/struct_T1/T1_QC_CNR_corners.py

@@ -30,7 +30,7 @@ def run(ctx,
         logs_dir:                Ref,
         tmp_dir:                 Ref):
 
-    with redirect_logging('T1_QC_CNR_corners', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(tmp_dir):
 
         roi_1_1     = tmp_dir + '/roi_1_1.nii.gz'

bip/pipelines/struct_T1/T1_QC_CNR_eyes.py

@@ -40,7 +40,7 @@ def run(ctx,
         logs_dir:              Ref,
         tmp_dir:               Ref):
 
-    with redirect_logging('T1_QC_CNR_eyes', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
         tempdir(tmp_dir):
 
         T1_brain_GM_mask_orig = tmp_dir + '/T1_brain_GM_mask_orig.nii.gz'

bip/pipelines/struct_T1/T1_QC_COG.py

@@ -24,7 +24,7 @@ def run(ctx,
         logs_dir:      Ref,
         tmp_dir:       Ref):
 
-    with redirect_logging('T1_QC_COG', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(tmp_dir):
 
         T1_tmp_5 = tmp_dir + '/T1_tmp_5.nii.gz'

bip/pipelines/struct_T1/T1_brain_extract.py

@@ -40,7 +40,7 @@ def run(ctx,
         T1_to_MNI_warp_coef:     Out,
         T1_to_MNI_warp_jac:      Out):
 
-    with redirect_logging('T1_brain_extract', outdir=logs_dir),tempdir(tmp_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir), tempdir(tmp_dir):
 
         T1_tmp_1                  = tmp_dir + '/T1_tmp_1.nii.gz'
         T1_tmp_2                  = tmp_dir + '/T1_tmp_2.nii.gz'

bip/pipelines/struct_T1/T1_defacing.py

@@ -28,7 +28,7 @@ def run(ctx,
         logs_dir:                          Ref,
         tmp_dir:                           Ref):
 
-    with redirect_logging('T1_defacing', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(tmp_dir):
 
         T1_tmp_4                  = tmp_dir + '/T1_tmp_4.nii.gz'

bip/pipelines/struct_T1/T1_fast.py

@@ -33,7 +33,7 @@ def run(ctx,
         T1_fast_WM_mask:    Out,
         T1_fast_brain_bias: Out):
 
-    with redirect_logging('T1_fast', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         #Run fast
         wrappers.fast(T1_brain, out = T1_fast_dir + '/T1_brain', b=True)

bip/pipelines/struct_T1/T1_first.py

@@ -27,7 +27,7 @@ def run(ctx,
         logs_dir:                   Ref,
         T1_first_all_fast_firstseg: Out):
 
-    with redirect_logging('T1_first', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         # Creates a link inside T1_first to T1_unbiased_brain.nii.gz
         if not os.path.exists(T1_first_unbiased_brain):

bip/pipelines/struct_T1/T1_gdc.py

@@ -12,7 +12,7 @@
 import logging
 from shutil import copyfile
 from pipe_tree import In, Out, Ref
-from bip.utils.log_utils import redirect_logging
+from bip.utils.log_utils import redirect_logging, job_name
 from gradunwarp.core.gradient_unwarp_apply import gradient_unwarp_apply
 
 log = logging.getLogger(__name__)
@@ -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_T1/T1_sienax.py

@@ -39,7 +39,7 @@ def run(ctx,
         logs_dir:                            Ref,
         tmp_dir:                             Ref):
 
-    with redirect_logging('T1_sienax', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(tmp_dir):
 
         T1_tmp_mat_1 = tmp_dir + '/tmp_mat_1.mat'

bip/pipelines/struct_T1/__init__.py

+#!/usr/bin/env python
+#
+# struct_T1.py - Pipeline with the T1w 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_T1 import T1_gdc, T1_brain_extract, T1_defacing
+from bip.pipelines.struct_T1 import T1_fast, T1_first, T1_sienax, T1_QC_COG
+from bip.pipelines.struct_T1 import T1_QC_CNR_corners, T1_QC_CNR_eyes
+
+log = logging.getLogger(__name__)
+
+def add_to_pipeline(ctx, pipe, tree):
+
+    subj = ctx.subject
+
+    pipe(T1_gdc.run,
+         submit=dict(jobtime=200, name=job_name(T1_gdc.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_brain_extract.run,
+         submit=dict(jobtime=200, name=job_name(T1_brain_extract.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_defacing.run,
+         submit=dict(jobtime=200, name=job_name(T1_defacing.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_fast.run,
+         submit=dict(jobtime=200, name=job_name(T1_fast.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_first.run,
+         submit=dict(jobtime=200, name=job_name(T1_first.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_sienax.run,
+         submit=dict(jobtime=200, name=job_name(T1_sienax.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_QC_COG.run,
+         submit=dict(jobtime=200, name=job_name(T1_QC_COG.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_QC_CNR_corners.run,
+         submit=dict(jobtime=200, name=job_name(T1_QC_CNR_corners.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(T1_QC_CNR_eyes.run,
+         submit=dict(jobtime=200, name=job_name(T1_QC_CNR_eyes.run, subj)),
+         kwargs={'ctx' : ctx})

bip/pipelines/struct_T1/struct_T1.py

-#!/usr/bin/env python
-#
-# struct_T1.py - Pipeline with the T1w 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_T1 import T1_gdc, T1_brain_extract, T1_defacing
-from bip.pipelines.struct_T1 import T1_fast, T1_first, T1_sienax, T1_QC_COG
-from bip.pipelines.struct_T1 import T1_QC_CNR_corners, T1_QC_CNR_eyes
-
-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_T1', outdir=logs_dir):
-        pipe(T1_gdc.run,
-             submit=dict(jobtime=200, name="BIP_T1_gdc_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_orig_ud_warp')
-        pipe(T1_brain_extract.run,
-             submit=dict(jobtime=200, name="BIP_T1_brain_extract_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_brain')
-        pipe(T1_defacing.run,
-             submit=dict(jobtime=200, name="BIP_T1_defacing_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_QC_face_mask_inside_brain_mask')
-        pipe(T1_fast.run,
-             submit=dict(jobtime=200, name="BIP_T1_fast_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_unbiased_brain')
-        pipe(T1_first.run,
-             submit=dict(jobtime=200, name="BIP_T1_first_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_first_all_fast_firstseg')
-        pipe(T1_sienax.run,
-             submit=dict(jobtime=200, name="BIP_T1_sienax_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_sienax_report')
-        pipe(T1_QC_COG.run,
-             submit=dict(jobtime=200, name="BIP_T1_QC_COG_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_QC_COG')
-        pipe(T1_QC_CNR_corners.run,
-             submit=dict(jobtime=200, name="BIP_T1_QC_CNR_corners_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_notNorm_QC_CNR_upper')
-        pipe(T1_QC_CNR_eyes.run,
-             submit=dict(jobtime=200, name="BIP_T1_QC_CNR_eyes_" + subj),
-             kwargs={'ctx' : ctx})
-        targets.append('T1_QC_CNR_eyes')
-
-    return pipe, targets

bip/pipelines/struct_T2_FLAIR/T2_FLAIR_apply_bfc.py

@@ -27,7 +27,7 @@ def run(ctx,
         T2_FLAIR_unbiased:       Out,
         T2_FLAIR_unbiased_brain: Out):
 
-    with redirect_logging('T2_FLAIR_apply_bfc', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         #Apply bias field correction to T2_FLAIR warped
         if os.path.isfile(T1_fast_brain_bias):

bip/pipelines/struct_T2_FLAIR/T2_FLAIR_bianca.py

@@ -44,7 +44,7 @@ def run(ctx,
         T2_FLAIR_bianca_tot_pvent_deep_volume: Out,
         T2_FLAIR_bianca_volume:                Out):
 
-    with redirect_logging('T2_FLAIR_bianca', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         # Create bianca mask
         wrappers.make_bianca_mask(T1_unbiased, T1_fast_pve_0,

bip/pipelines/struct_T2_FLAIR/T2_FLAIR_brain_extract.py

@@ -38,7 +38,7 @@ def run(ctx,
         logs_dir:                           Ref,
         tmp_dir:                            Ref):
 
-    with redirect_logging('T2_FLAIR_brain_extract', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(tmp_dir):
 
         T2_FLAIR_tmp_1_mat = tmp_dir + '/T2_FLAIR_tmp_1.mat'

bip/pipelines/struct_T2_FLAIR/T2_FLAIR_defacing.py

@@ -31,7 +31,7 @@ def run(ctx,
         logs_dir:                         Ref,
         tmp_dir:                          Ref):
 
-    with redirect_logging('T2_FLAIR_defacing', outdir=logs_dir),\
+    with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(tmp_dir):
 
         T2_FLAIR_tmp_1    = tmp_dir + '/T2_FLAIR_tmp_1nii.gz'

bip/pipelines/struct_T2_FLAIR/T2_FLAIR_gdc.py

@@ -25,7 +25,7 @@ def run(ctx,
         logs_dir:              Ref,
         T2_FLAIR_GDC:          Ref):
 
-    with redirect_logging('T2_FLAIR_gdc', outdir=logs_dir):
+    with redirect_logging(job_name(run), outdir=logs_dir):
 
         if ctx.gdc != '':
             #Calculate and apply the Gradient Distortion Unwarp