Correcing bugs related to IDP generation

bip/pipelines/IDPs_gen/IDP_diff_TBSS.py

@@ -19,8 +19,15 @@ log = logging.getLogger(__name__)
 
 def run(ctx,
         JHUrois_FA:     In(optional=True),
+        JHUrois_MD:     In(optional=True),
+        JHUrois_MO:     In(optional=True),
+        JHUrois_L1:     In(optional=True),
+        JHUrois_L2:     In(optional=True),
+        JHUrois_L3:     In(optional=True),
+        JHUrois_ICVF:   In(optional=True),
+        JHUrois_OD:     In(optional=True),
+        JHUrois_ISOVF:  In(optional=True),
         logs_dir:       Ref,
-        JHUrois_prefix: Ref,
         IDP_diff_TBSS:  Out):
 
     with redirect_logging(job_name(run), outdir=logs_dir):
@@ -29,9 +36,9 @@ def run(ctx,
 
         result = ""
 
-        for mod in ["FA", "MD", "MO", "L1", "L2", "L3", "ICVF", "OD", "ISOVF"]:
-
-            file_name = JHUrois_prefix + mod + ".txt"
+        for file_name in [JHUrois_FA, JHUrois_MD, JHUrois_MO, JHUrois_L1,
+                          JHUrois_L2, JHUrois_L3, JHUrois_ICVF, JHUrois_OD,
+                          JHUrois_ISOVF]:
             print(file_name)
             if op.exists(file_name):
                 with open(file_name, "r", encoding="utf-8") as f:

bip/pipelines/IDPs_gen/IDP_diff_autoPtx.py

@@ -41,7 +41,7 @@ def run(ctx,
         wrappers.fslmerge("t", autoPtx_all, *list(aptx_tract_tmp.data))
         tractnorm = wrappers.fslstats(autoPtx_all, t=True).m.run()
 
-        for suffix in ['FA','L1','L2','L3','MO','MD','ICVF','OD','ISOVF']:
+        for suffix in ['FA','MD','MO','L1','L2','L3','ICVF','OD','ISOVF']:
             all_file = TBSS_prefix + suffix + ".nii.gz"
             APTX_file = aptx_txt_prefix + suffix + ".txt"
 

bip/pipelines/QC_gen/T1/QC_T1_FIRST_vols.py

+#!/usr/bin/env python
+#
+# QC_T1_FIRST_vols.py - Copying QC file with the volumes from FIRST of T1.
+#
+# 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
+#
+
+from shutil import copyfile
+from pipe_tree import In, Out
+
+def run(ctx,
+        IDP_T1_FIRST_vols: In,
+        QC_T1_FIRST_vols:  Out):
+
+    copyfile(src=IDP_T1_FIRST_vols, dst=QC_T1_FIRST_vols)

bip/pipelines/QC_gen/T1/QC_T1_SIENAX.py

+#!/usr/bin/env python
+#
+# QC_T1_SIENAX.py - Copying QC file with SIENAXvalues of T1.
+#
+# 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
+#
+
+from shutil import copyfile
+from pipe_tree import In, Out
+
+def run(ctx,
+        IDP_T1_SIENAX: In,
+        QC_T1_SIENAX:  Out):
+
+    copyfile(src=IDP_T1_SIENAX, dst=QC_T1_SIENAX)

bip/pipelines/QC_gen/T1/QC_T1_align_to_std.py

+#!/usr/bin/env python
+#
+# QC_T1_align_to_std.py - Copying QC file with alignment to std metrics.
+#
+# 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
+#
+
+from shutil import copyfile
+from pipe_tree import In, Out
+
+def run(ctx,
+        IDP_T1_align_to_std: In,
+        QC_T1_align_to_std:  Out):
+
+    copyfile(src=IDP_T1_align_to_std, dst=QC_T1_align_to_std)

bip/pipelines/QC_gen/T1/QC_T1_generator.py

+#!/usr/bin/env python
+#
+# QC_diff_autoPtx.py - Generating QC file with autoPtx metrics
+#
+# 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.path as op
+import json
+import logging
+from pipe_tree import In, Out, Ref
+from bip.utils.log_utils import redirect_logging, job_name
+
+log = logging.getLogger(__name__)
+
+def run(ctx,
+        QC_T1_align_to_std: In(optional=True),
+        QC_T1_noise_ratio:  In(optional=True),
+        QC_T1_SIENAX:       In(optional=True),
+        QC_T1_FIRST_vols:   In(optional=True),
+        logs_dir:           Ref,
+        QC_T1:              Out):
+
+    with redirect_logging(job_name(run), outdir=logs_dir):
+
+        result = ""
+        QC_json_file = ctx.get_data("QC/QC_T1.json")
+
+        with open(QC_json_file, "r", encoding="utf-8") as f:
+            QC_dict = json.load(f)
+
+        for QC_file in [QC_T1_align_to_std, QC_T1_noise_ratio, QC_T1_SIENAX,
+                        QC_T1_FIRST_vols]:
+
+            plain_name = op.basename(QC_file).replace(".txt", "")
+            num_QC = len(QC_dict[plain_name])
+            result_nans = ("NaN " * num_QC).strip()
+
+            if QC_file is not None and op.exists(QC_file):
+                with open(QC_file, "r", encoding="utf-8") as f:
+                    QC_l = f.read().strip().split()
+                if len(QC_l) != num_QC:
+                    result += " " + result_nans
+                else:
+                    result += " " + " ".join(QC_l)
+
+            else:
+                result += " " + result_nans
+
+        result = result.replace("  ", " ").strip()
+
+        print(result)
+
+        with open(QC_T1, 'wt', encoding="utf-8") as f:
+            f.write(f'{result}\n')

bip/pipelines/QC_gen/T1/QC_T1_noise_ratio.py

+#!/usr/bin/env python
+#
+# QC_T1_noise_ratio.py - Copying QC file with noise ratio of T1.
+#
+# 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
+#
+
+from shutil import copyfile
+from pipe_tree import In, Out
+
+def run(ctx,
+        IDP_T1_noise_ratio: In,
+        QC_T1_noise_ratio:  Out):
+
+    copyfile(src=IDP_T1_noise_ratio, dst=QC_T1_noise_ratio)

bip/pipelines/QC_gen/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,R1735
+#
+
+import logging
+from bip.utils.log_utils    import job_name
+from bip.pipelines.QC_gen.T1 import QC_T1_align_to_std
+from bip.pipelines.QC_gen.T1 import QC_T1_noise_ratio
+from bip.pipelines.QC_gen.T1 import QC_T1_SIENAX
+from bip.pipelines.QC_gen.T1 import QC_T1_FIRST_vols
+from bip.pipelines.QC_gen.T1 import QC_T1_generator
+
+log = logging.getLogger(__name__)
+
+def add_to_pipeline(ctx, pipe, tree):
+
+    subj = ctx.subject
+
+    pipe(QC_T1_align_to_std.run,
+         submit=dict(jobtime=200, name=job_name(QC_T1_align_to_std.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(QC_T1_noise_ratio.run,
+         submit=dict(jobtime=200, name=job_name(QC_T1_noise_ratio.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(QC_T1_SIENAX.run,
+         submit=dict(jobtime=200, name=job_name(QC_T1_SIENAX.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(QC_T1_FIRST_vols.run,
+         submit=dict(jobtime=200, name=job_name(QC_T1_FIRST_vols.run, subj)),
+         kwargs={'ctx' : ctx})
+    pipe(QC_T1_generator.run,
+         submit=dict(jobtime=200, name=job_name(QC_T1_generator.run, subj)),
+         kwargs={'ctx' : ctx})

bip/pipelines/dMRI_diff/diff_bedpostx.py

@@ -36,8 +36,7 @@ def run(ctx,
         bedpostx_nodif_brain:      Out,
         bedpostx_nodif_brain_mask: Out,
         bedpostx_nvox:             Out,
-        bedpostx_eye:              Out,
-        bp_logs_dir:               Out):
+        bedpostx_eye:              Out):
 
     with redirect_logging(job_name(run), outdir=logs_dir):
 

bip/pipelines/dMRI_diff/diff_noddi.py

@@ -48,10 +48,10 @@ def run(ctx,
         # In case the kernels were already calculated for this study:
         # TODO: Verify that this is regular UKB data.
         # Otherwise, this should not be done
-        if not op.exists(op.join(os.getcwd(), 'kernels/')):
+        if not op.exists(op.join(os.getcwd(), 'kernels')):
             with lockdir(dirname=os.getcwd(), delay=10):
                 # 2 checks will be needed
-                if not op.exists(op.join(os.getcwd(), 'kernels/')):
+                if not op.exists(op.join(os.getcwd(), 'kernels')):
                     if op.exists(ctx.get_data('dMRI/kernels.zip')):
                         with zipfile.ZipFile(ctx.get_data('dMRI/kernels.zip'),
                                              'r') as zip_ref:

bip/pipelines/dMRI_diff/diff_tbss.py

@@ -25,6 +25,8 @@ log = logging.getLogger(__name__)
 def run(ctx,
         FA:                          In,
         ISOVF:                       In(optional=True),
+        OD:                          In(optional=True),
+        ICVF:                        In(optional=True),
         logs_dir:                    Ref,
         tmp_dir:                     Ref,
         TBSS_MNI_to_dti_FA_warp_msf: Ref,
@@ -51,7 +53,15 @@ def run(ctx,
         TBSS_mean_FA_skeleton:       Out,
         TBSS_mean_FA_skeleton_mask:  Out,
         TBSS_all_FA_skeletonised:    Out,
-        JHUrois_FA:                  Out):
+        JHUrois_FA:                  Out,
+        JHUrois_MD:                  Out,
+        JHUrois_MO:                  Out,
+        JHUrois_L1:                  Out,
+        JHUrois_L2:                  Out,
+        JHUrois_L3:                  Out,
+        JHUrois_ICVF:                Out,
+        JHUrois_OD:                  Out,
+        JHUrois_ISOVF:               Out,):
 
     with redirect_logging(job_name(run), outdir=logs_dir),\
          tempdir(op.join(tmp_dir, job_name(run))) as tmp_dir:
@@ -148,7 +158,7 @@ def run(ctx,
             f.write(f'{mean}')
 
         # Applying to the outputs of both dtifit and noddi
-        dict_suffix = {dtifit_prefix: ['L1', 'L2', 'L3', 'MO', 'MD'],
+        dict_suffix = {dtifit_prefix: ['MO', 'MD', 'L1', 'L2', 'L3'],
                        NODDI_prefix: ['ICVF', 'OD', 'ISOVF']}
 
         for prefix in dict_suffix:
@@ -169,3 +179,7 @@ def run(ctx,
                     mean = wrappers.fslstats(d_output_skel, K=atlas).M.run()
 
                     np.savetxt(d_output_txt, mean, fmt="%0.8f")
+                else:
+                    num_tracts = ctx.get('dMRI_TBSS_num_tracts', 48)
+                    str_NaNs = ["NaN" for _ in range(num_tracts)]
+                    print("[" + " ".join(str_NaNs) + "]\n")

bip/pipelines/struct_FS/FS_get_IDPs.py

@@ -26,7 +26,7 @@ def run(ctx,
         FreeSurfer_dir:             In,
         logs_dir:                   Ref,
         FS_IDPs:                    Out,
-        FS_headers_info:            Out):
+        FS_headers_info:            Ref):
 
     with redirect_logging(job_name(run), outdir=logs_dir):