Expand over sessions, update config call

.github/workflows/test.yml

@@ -91,3 +91,5 @@ jobs:
         run: poetry run poe test_labelmerge
       - name: Test using single atlas (skipping labelmerge)
         run: poetry run poe test_skip_labelmerge
+      - name: Test sessions
+        run: poetry run poe test_sessions

.gitignore

@@ -2,6 +2,9 @@
 test/data/derivatives/.snakemake/
 test/data/derivatives/config/
 test/data/derivatives/.snakebids
+test/data/derivatives_sessions/.snakemake/
+test/data/derivatives_sessions/config/
+test/data/derivatives_sessions/.snakebids
 
 # Tar files
 *.tar

pyproject.toml

@@ -69,7 +69,8 @@ test_responsemean = { shell = "python ./scattr/run.py ./test/data/bids test/data
 test_dwi = { shell = "python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ participant --dwi_dir ./test/data/derivatives/prepdwi --fs-license ./test/.fs_license -np --force-output" }
 test_labelmerge = { shell = "python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant --labelmerge_base_dir ./base_dir --labelmerge_overlay_dir ./overlay_dir --skip_brainstem --skip_thal_seg --fs-license ./test/.fs_license -np --force-output" }
 test_skip_labelmerge = { shell = "python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant --skip_labelmerge --skip_brainstem --skip_thal_seg --fs-license ./test/.fs_license -np --force-output" }
-test = ["test_base", "test_freesurfer", "test_responsemean", "test_dwi", "test_labelmerge", "test_skip_labelmerge"]
+test_sessions = { shell = "python ./scattr/run.py ./test/data/bids_sessions test/data/derivatives_sessions/ participant --fs-license ./test.fs_license -np --force-output" }
+test = ["test_base", "test_freesurfer", "test_responsemean", "test_dwi", "test_labelmerge", "test_skip_labelmerge", "test_sessions"]
 
 [tool.isort]
 profile = "black"

scattr/workflow/Snakefile

@@ -1,29 +1,26 @@
 # ---- begin snakebids boilerplate ----------------------------------------------
 
-import snakebids
-from snakebids import bids
+from snakebids import bids, generate_inputs, get_wildcard_constraints
 
 
 configfile: "config/snakebids.yml"
 
 
 # writes inputs_config.yml and updates config dict
-config.update(
-    snakebids.generate_inputs(
-        bids_dir=config["bids_dir"],
-        pybids_inputs=config["pybids_inputs"],
-        pybids_config=["bids", "derivatives"],
-        derivatives=config["derivatives"],
-        participant_label=config["participant_label"],
-        exclude_participant_label=config["exclude_participant_label"],
-        use_bids_inputs=False,
-    )
+inputs = generate_inputs(
+    bids_dir=config["bids_dir"],
+    pybids_inputs=config["pybids_inputs"],
+    pybids_config=["bids", "derivatives"],
+    derivatives=config["derivatives"],
+    participant_label=config["participant_label"],
+    exclude_participant_label=config["exclude_participant_label"],
+    use_bids_inputs=True,
 )
 
 
 # this adds constraints to the bids naming
 wildcard_constraints:
-    **snakebids.get_wildcard_constraints(config["pybids_inputs"]),
+    **get_wildcard_constraints(config["pybids_inputs"]),
 
 
 # ---- end snakebids boilerplate ------------------------------------------------
@@ -53,11 +50,11 @@ rule all:
     input:
         tck_files=expand(
             rules.filtered_tck2connectome.output.sl_assignment,
-            subject=config["input_lists"]["T1w"]["subject"],
+            zip,
+            **inputs["T1w"].input_zip_lists
         ),
         dti_files=expand(
-            rules.dwi2tensor.output.dti,
-            subject=config["input_lists"]["T1w"]["subject"],
+            rules.dwi2tensor.output.dti, zip, **inputs["T1w"].input_zip_lists
         ),
         qc_files=rules.gather_qc.input,
     params:
@@ -66,8 +63,10 @@ rule all:
                 root=str(Path(config["output_dir"]) / "mrtrix"),
                 subject="{subject}",
                 include_subject_dir=False,
+                include_session_Dir=False,
             ),
-            subject=config["input_lists"]["T1w"]["subject"],
+            zip,
+            **inputs["T1w"].input_zip_lists
         ),
     shell:  # Clean up intermediate files that left behind
         "rm -r {params.mrtrix_dir}/exclude_mask {params.mrtrix_dir}/roi_masks {params.mrtrix_dir}/unfiltered"

scattr/workflow/rules/freesurfer.smk

@@ -3,6 +3,8 @@ freesurfer_dir = str(Path(config["output_dir"]) / "freesurfer")
 if config.get("freesurfer_dir"):
     freesurfer_dir = config.get("freesurfer_dir")
 
+log_dir = str(Path(config["output_dir"]) / "logs" / "freesurfer")
+
 # Licenses
 if config.get("fs_license"):
     fs_license = config["fs_license"]
@@ -17,7 +19,13 @@ bids_fs_out = partial(
     bids,
     root=freesurfer_dir,
     datatype="anat",
-    **config["subj_wildcards"],
+    **inputs.subj_wildcards,
+)
+
+bids_log = partial(
+    bids,
+    root=log_dir,
+    **inputs["T1w"].input_wildcards,
 )
 
 # Freesurfer references (with additional in rules as necessary)
@@ -59,15 +67,16 @@ rule thalamic_segmentation:
         fs_license=fs_license,
     output:
         thal_seg=str(
-            Path(freesurfer_dir)
-            / "sub-{subject}/mri/ThalamicNuclei.v12.T1.mgz"
+            Path(bids(root=freesurfer_dir, **inputs.subj_wildcards)).parent
+            / "mri"
+            / "ThalamicNuclei.v12.T1.mgz"
         ),
     threads: 4
     resources:
         mem_mb=16000,
         time=60,
     log:
-        f"{config['output_dir']}/logs/freesurfer/sub-{{subject}}/thalamic_segmentation.log",
+        bids_log(suffix="thalamicSegmentation.log"),
     group:
         "freesurfer"
     container:
@@ -91,7 +100,9 @@ rule mgz2nii:
         if not config.get("skip_thal_seg")
         else [],
         aparcaseg=str(
-            Path(freesurfer_dir) / "sub-{subject}/mri/aparc+aseg.mgz"
+            Path(bids(root=freesurfer_dir, **inputs.subj_wildcards)).parent
+            / "mri"
+            / "aparc+aseg.mgz"
         ),
     params:
         freesurfer_dir=freesurfer_dir,
@@ -112,7 +123,7 @@ rule mgz2nii:
         mem_mb=16000,
         time=10,
     log:
-        f"{config['output_dir']}/logs/freesurfer/sub-{{subject}}/mgz2nii.log",
+        bids_log(suffix="mgz2nii.log"),
     group:
         "freesurfer"
     container:
@@ -130,7 +141,7 @@ rule fs_xfm_to_native:
     input:
         thal=rules.mgz2nii.output.thal,
         aparcaseg=rules.mgz2nii.output.aparcaseg,
-        ref=config["input_path"]["T1w"],
+        ref=inputs["T1w"].path,
     output:
         thal=bids_fs_out(
             space="T1w",
@@ -147,7 +158,7 @@ rule fs_xfm_to_native:
         mem_mb=16000,
         time=60,
     log:
-        f"{config['output_dir']}/logs/freesurfer/sub-{{subject}}/fs_xfm_to_native.log",
+        bids_log(suffix="fsXfmToNative.log"),
     group:
         "freesurfer"
     container: