Starting with IDP scripts

bip/main.py

@@ -26,6 +26,7 @@ from bip.pipelines.dMRI_fieldmap   import dMRI_fieldmap
 from bip.pipelines.fMRI_task       import fMRI_task
 from bip.pipelines.fMRI_rest       import fMRI_rest
 from bip.pipelines.dMRI_diff       import dMRI_diff
+from bip.pipelines.IDPs_gen        import IDPs_gen
 
 log = logging.getLogger('bip.main')
 
@@ -343,6 +344,7 @@ def main():
     pipe, targets = fMRI_task.add_to_pipeline(ctx, pipe, tree, targets)
     pipe, targets = fMRI_rest.add_to_pipeline(ctx, pipe, tree, targets)
     pipe, targets = dMRI_diff.add_to_pipeline(ctx, pipe, tree, targets)
+    pipe, targets = IDPs_gen.add_to_pipeline(ctx, pipe, tree, targets)
 
     # The skip-missing flag deals with cases where the subject is missing
     # the data of some modalities. For more details, check:

bip/pipelines/IDPs_gen/IDP_subject_ID.py

+#!/usr/bin/env python
+#
+# IDP_subject_ID.py - Generating IDP file with the subject ID.
+#
+# 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 pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+        T1_orig:        In,
+        IDP_subject_ID: Out,
+        logs_dir:       Ref):
+
+    with redirect_logging('IDP_subject_ID', outdir=logs_dir):
+        with open(IDP_subject_ID, 'wt', encoding="utf-8") as f:
+            f.write(f'{ctx.subject}\n')

bip/pipelines/IDPs_gen/IDP_subject_centre.py

+#!/usr/bin/env python
+#
+# IDP_subject_centre.py - Generating IDP file with the acquisition centre.
+#
+# 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 os
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+        T1_orig:            In,
+        T1_dcm_txt:         In,
+        dMRI_dcm_txt:       Ref,
+        rfMRI_dcm_txt:      Ref,
+        SWI_dcm_txt:        Ref,
+        T2_dcm_txt:         Ref,
+        tfMRI_dcm_txt:      Ref,
+        logs_dir:           Ref,
+        IDP_subject_centre: Out):
+
+    line = ""
+
+    for file_name in [T1_dcm_txt, T2_dcm_txt, rfMRI_dcm_txt, SWI_dcm_txt, 
+                      dMRI_dcm_txt, tfMRI_dcm_txt]:
+
+        if os.path.exists(file_name):
+            with open(file_name, 'rt', encoding="utf-8") as f:
+                cont = f.readlines()
+                for x in cont:
+                    if x.startswith("(0008, 0081) Institution Address"):
+                        line = x.replace("(0008, 0081) Institution Address", "")
+                        line = line.strip().replace("ST: ", "").strip()
+                        line = line.replace("'","").replace(",","__").replace(" ","_")
+                        break
+        if line != "":
+            break
+
+    if line != "":
+        # TODO: Allow users to change the file with the sites
+        with open(ctx.get_data("IDPs/sites_UKBB.json"), "r", encoding="utf-8") as f:
+            sites = json.load(f)
+
+    centre = sites[line]
+
+    with redirect_logging('IDP_subject_centre', outdir=logs_dir):
+        with open(IDP_subject_centre, 'wt', encoding="utf-8") as f:
+            f.write(f'{centre}\n')

bip/pipelines/IDPs_gen/IDPs_gen.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.IDPs_gen import IDP_subject_ID
+from bip.pipelines.IDPs_gen import IDP_subject_centre
+
+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_IDPs_gen', outdir=logs_dir):
+        pipe(IDP_subject_ID.run,
+             submit=dict(jobtime=200, name="BIP_IDPs_subject_ID_" + subj),
+             kwargs={'ctx' : ctx})
+        targets.append('IDP_subject_ID')
+        pipe(IDP_subject_centre.run,
+             submit=dict(jobtime=200, name="BIP_IDP_subject_centre_" + subj),
+             kwargs={'ctx' : ctx})
+        targets.append('IDP_subject_centre')
+
+    return pipe, targets