Update to match neurodatascience/nipoppy:main (#59)

neurodatascience · Jun 13, 2024 · eaad57a · eaad57a
2 parents 307dbbd + 3f02887
commit eaad57a
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Showing 71 changed files with 1,162 additions and 1,127 deletions.
diff --git a/nipoppy_cli/nipoppy/cli/parser.py b/nipoppy_cli/nipoppy/cli/parser.py
@@ -5,12 +5,7 @@
 from pathlib import Path
 
 from nipoppy.layout import DEFAULT_LAYOUT_INFO
-from nipoppy.utils import (
-    BIDS_SESSION_PREFIX,
-    BIDS_SUBJECT_PREFIX,
-    check_participant,
-    check_session,
-)
+from nipoppy.utils import BIDS_SESSION_PREFIX, BIDS_SUBJECT_PREFIX
 
 PROGRAM_NAME = "nipoppy"
 COMMAND_INIT = "init"
@@ -51,16 +46,14 @@ def add_arg_simulate(parser: _ActionsContainer) -> _ActionsContainer:
 
 
 def add_args_participant_and_session(parser: _ActionsContainer) -> _ActionsContainer:
-    """Add --participant and --session arguments to the parser."""
+    """Add --participant-id and --session-id arguments to the parser."""
     parser.add_argument(
-        "--participant",
-        type=check_participant,
+        "--participant-id",
         required=False,
         help=f"Participant ID (with or without the {BIDS_SUBJECT_PREFIX} prefix).",
     )
     parser.add_argument(
-        "--session",
-        type=check_session,
+        "--session-id",
         required=False,
         help=f"Session ID (with or without the {BIDS_SESSION_PREFIX} prefix).",
     )
@@ -211,7 +204,7 @@ def add_subparser_dicom_reorg(
     """Add subparser for reorg command."""
     description = (
         "(Re)organize raw (DICOM) files, from the raw DICOM directory "
-        f"({DEFAULT_LAYOUT_INFO.dpath_raw_dicom}) to the organized "
+        f"({DEFAULT_LAYOUT_INFO.dpath_raw_imaging}) to the organized "
         f"sourcedata directory ({DEFAULT_LAYOUT_INFO.dpath_sourcedata})."
     )
     parser = subparsers.add_parser(

diff --git a/nipoppy_cli/nipoppy/cli/run.py b/nipoppy_cli/nipoppy/cli/run.py
@@ -67,8 +67,8 @@ def cli(argv: Sequence[str] = None) -> None:
                 pipeline_name=args.pipeline,
                 pipeline_version=args.pipeline_version,
                 pipeline_step=args.pipeline_step,
-                participant=args.participant,
-                session=args.session,
+                participant_id=args.participant_id,
+                session_id=args.session_id,
                 simulate=args.simulate,
                 **workflow_kwargs,
             )
@@ -78,8 +78,8 @@ def cli(argv: Sequence[str] = None) -> None:
                 pipeline_name=args.pipeline,
                 pipeline_version=args.pipeline_version,
                 pipeline_step=args.pipeline_step,
-                participant=args.participant,
-                session=args.session,
+                participant_id=args.participant_id,
+                session_id=args.session_id,
                 simulate=args.simulate,
                 **workflow_kwargs,
             )
@@ -88,8 +88,8 @@ def cli(argv: Sequence[str] = None) -> None:
                 dpath_root=dpath_root,
                 pipeline_name=args.pipeline,
                 pipeline_version=args.pipeline_version,
-                participant=args.participant,
-                session=args.session,
+                participant_id=args.participant_id,
+                session_id=args.session_id,
                 **workflow_kwargs,
             )
         else:

diff --git a/nipoppy_cli/nipoppy/config/main.py b/nipoppy_cli/nipoppy/config/main.py
@@ -16,8 +16,6 @@
     BIDS_SESSION_PREFIX,
     StrOrPathLike,
     apply_substitutions_to_json,
-    check_session,
-    check_session_strict,
     load_json,
 )
 
@@ -26,8 +24,13 @@ class Config(SchemaWithContainerConfig):
     """Schema for dataset configuration."""
 
     DATASET_NAME: str = Field(description="Name of the dataset")
-    VISITS: list[str] = Field(description="List of visits available in the study")
-    SESSIONS: Optional[list[str]] = Field(
+    VISIT_IDS: list[str] = Field(
+        description=(
+            "List of visits available in the study. A visit ID is an identifier "
+            "for a data collection event, not restricted to imaging data."
+        )
+    )
+    SESSION_IDS: Optional[list[str]] = Field(
         default=None,  # will be a list after validation
         description=(
             "List of BIDS-compliant sessions available in the study"
@@ -42,15 +45,15 @@ class Config(SchemaWithContainerConfig):
             ", to be used in the DICOM reorg step. Note: this field and "
             "DICOM_DIR_PARTICIPANT_FIRST cannot both be specified"
             f'. The CSV should have three columns: "{DicomDirMap.col_participant_id}"'
-            f' , "{DicomDirMap.col_session}"'
+            f' , "{DicomDirMap.col_session_id}"'
             f', and "{DicomDirMap.col_participant_dicom_dir}"'
         ),
     )
     DICOM_DIR_PARTICIPANT_FIRST: Optional[bool] = Field(
         default=None,
         description=(
             "Whether subdirectories under the raw dicom directory (default: "
-            f"{DEFAULT_LAYOUT_INFO.dpath_raw_dicom}) follow the pattern "
+            f"{DEFAULT_LAYOUT_INFO.dpath_raw_imaging}) follow the pattern "
             "<PARTICIPANT>/<SESSION> (default) or <SESSION>/<PARTICIPANT>. Note: "
             "this field and and DICOM_DIR_MAP_FILE cannot both be specified"
         ),
@@ -76,12 +79,6 @@ class Config(SchemaWithContainerConfig):
 
     model_config = ConfigDict(extra="forbid")
 
-    def _check_sessions_have_prefix(self) -> Self:
-        """Check that sessions have the BIDS prefix."""
-        for session in self.SESSIONS:
-            check_session_strict(session)
-        return self
-
     def _check_dicom_dir_options(self) -> Self:
         """Check that only one DICOM directory mapping option is given."""
         if (
@@ -137,21 +134,18 @@ def _propagate(pipeline_configs: list[PipelineConfig]):
     @classmethod
     def check_input(cls, data: Any):
         """Validate the raw input."""
-        key_sessions = "SESSIONS"
-        key_visits = "VISITS"
+        key_session_ids = "SESSION_IDS"
+        key_visit_ids = "VISIT_IDS"
         if isinstance(data, dict):
-            # if sessions are not given, infer from visits
-            if key_sessions not in data:
-                data[key_sessions] = [
-                    check_session(visit) for visit in data[key_visits]
-                ]
+            # if session_ids is not given, set to be the same as visit_ids
+            if key_session_ids not in data:
+                data[key_session_ids] = data[key_visit_ids]
 
         return data
 
     @model_validator(mode="after")
     def validate_and_process(self) -> Self:
         """Validate and process the configuration."""
-        self._check_sessions_have_prefix()
         self._check_dicom_dir_options()
         self._check_no_duplicate_pipeline()
         return self

diff --git a/nipoppy_cli/nipoppy/data/descriptors/dcm2bids-3.1.0-convert.json b/nipoppy_cli/nipoppy/data/descriptors/dcm2bids-3.1.0-convert.json
@@ -15,7 +15,7 @@
             "command-line-flag": "-d",
             "value-key": "[DICOM_DIR]",
             "default-value": [
-                "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT]]/[[NIPOPPY_SESSION]]"
+                "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT_ID]]/[[NIPOPPY_BIDS_SESSION]]"
             ]
         },
         {
@@ -26,7 +26,7 @@
             "optional": false,
             "command-line-flag": "-p",
             "value-key": "[PARTICIPANT]",
-            "default-value": "[[NIPOPPY_PARTICIPANT]]"
+            "default-value": "[[NIPOPPY_PARTICIPANT_ID]]"
         },
         {
             "name": "session",
@@ -36,7 +36,7 @@
             "optional": true,
             "command-line-flag": "-s",
             "value-key": "[SESSION]",
-            "default-value": "[[NIPOPPY_SESSION_SHORT]]"
+            "default-value": "[[NIPOPPY_SESSION_ID]]"
         },
         {
             "name": "config",

diff --git a/nipoppy_cli/nipoppy/data/descriptors/dcm2bids-3.1.0-prepare.json b/nipoppy_cli/nipoppy/data/descriptors/dcm2bids-3.1.0-prepare.json
@@ -15,7 +15,7 @@
             "command-line-flag": "-d",
             "value-key": "[DICOM_DIR]",
             "default-value": [
-                "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT]]/[[NIPOPPY_SESSION]]"
+                "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT_ID]]/[[NIPOPPY_BIDS_SESSION]]"
             ]
         },
         {

diff --git a/nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json b/nipoppy_cli/nipoppy/data/descriptors/fmriprep-20.2.7.json
@@ -63,7 +63,7 @@
             "list": true,
             "command-line-flag": "--participant-label",
             "default-value": [
-                "[[NIPOPPY_PARTICIPANT]]"
+                "[[NIPOPPY_PARTICIPANT_ID]]"
             ]
         },
         {
@@ -451,7 +451,7 @@
             "type": "String",
             "value-key": "[FS_SUBJECTS_DIR]",
             "command-line-flag": "--fs-subjects-dir",
-            "default-value": "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_SESSION]]"
+            "default-value": "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_BIDS_SESSION]]"
         },
         {
             "id": "hires",
@@ -606,14 +606,14 @@
             "CONTAINER_CONFIG": {
                 "ARGS": [
                     "--bind",
-                    "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_SESSION]]"
+                    "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_BIDS_SESSION]]"
                 ]
             }
         },
         "nipoppy_old": {
             "paths_to_tar": [
-                "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]/fmriprep/sub-[[NIPOPPY_PARTICIPANT]]/ses-[[NIPOPPY_SESSION]]",
-                "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_SESSION]]/sub-[[NIPOPPY_PARTICIPANT]]"
+                "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]/fmriprep/sub-[[NIPOPPY_PARTICIPANT_ID]]/ses-[[NIPOPPY_BIDS_SESSION]]",
+                "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/6.0.1/output/[[NIPOPPY_BIDS_SESSION]]/sub-[[NIPOPPY_PARTICIPANT_ID]]"
             ]
         }
     }

diff --git a/nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json b/nipoppy_cli/nipoppy/data/descriptors/fmriprep-23.1.3.json
@@ -54,7 +54,7 @@
             "list": true,
             "command-line-flag": "--participant-label",
             "default-value": [
-                "[[NIPOPPY_PARTICIPANT]]"
+                "[[NIPOPPY_PARTICIPANT_ID]]"
             ]
         },
         {
@@ -509,7 +509,7 @@
             "type": "String",
             "value-key": "[FS_SUBJECTS_DIR]",
             "command-line-flag": "--fs-subjects-dir",
-            "default-value": "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_SESSION]]"
+            "default-value": "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_BIDS_SESSION]]"
         },
         {
             "id": "hires",
@@ -663,14 +663,14 @@
             "CONTAINER_CONFIG": {
                 "ARGS": [
                     "--bind",
-                    "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_SESSION]]"
+                    "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_BIDS_SESSION]]"
                 ]
             }
         },
         "nipoppy_old": {
             "paths_to_tar": [
-                "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]/sub-[[NIPOPPY_PARTICIPANT]]/ses-[[NIPOPPY_SESSION]]",
-                "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_SESSION]]/sub-[[NIPOPPY_PARTICIPANT]]"
+                "[[NIPOPPY_DPATH_PIPELINE_OUTPUT]]/sub-[[NIPOPPY_PARTICIPANT_ID]]/ses-[[NIPOPPY_BIDS_SESSION]]",
+                "[[NIPOPPY_DPATH_DERIVATIVES]]/freesurfer/7.3.2/output/[[NIPOPPY_BIDS_SESSION]]/sub-[[NIPOPPY_PARTICIPANT_ID]]"
             ]
         }
     }

diff --git a/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2-convert.json b/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2-convert.json
@@ -22,7 +22,7 @@
             "optional": true,
             "command-line-flag": "-d",
             "value-key": "[DICOM_DIR_TEMPLATE]",
-            "default-value": "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT]]/[[NIPOPPY_SESSION]]/*"
+            "default-value": "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT_ID]]/[[NIPOPPY_BIDS_SESSION]]/*"
         },
         {
             "name": "files",
@@ -41,7 +41,7 @@
             "optional": true,
             "command-line-flag": "-s",
             "value-key": "[SUBJS]",
-            "default-value": "[[NIPOPPY_PARTICIPANT]]"
+            "default-value": "[[NIPOPPY_PARTICIPANT_ID]]"
         },
         {
             "name": "converter",
@@ -120,7 +120,7 @@
             "optional": true,
             "command-line-flag": "-ss",
             "value-key": "[SESSION]",
-            "default-value": "[[NIPOPPY_SESSION]]"
+            "default-value": "[[NIPOPPY_BIDS_SESSION]]"
         },
         {
             "name": "bids_options",

diff --git a/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2-prepare.json b/nipoppy_cli/nipoppy/data/descriptors/heudiconv-0.12.2-prepare.json
@@ -22,7 +22,7 @@
             "optional": true,
             "command-line-flag": "-d",
             "value-key": "[DICOM_DIR_TEMPLATE]",
-            "default-value": "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT]]/[[NIPOPPY_SESSION]]/*"
+            "default-value": "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT_ID]]/[[NIPOPPY_BIDS_SESSION]]/*"
         },
         {
             "name": "files",
@@ -41,7 +41,7 @@
             "optional": true,
             "command-line-flag": "-s",
             "value-key": "[SUBJS]",
-            "default-value": "[[NIPOPPY_PARTICIPANT]]"
+            "default-value": "[[NIPOPPY_PARTICIPANT_ID]]"
         },
         {
             "name": "converter",
@@ -121,7 +121,7 @@
             "optional": true,
             "command-line-flag": "-ss",
             "value-key": "[SESSION]",
-            "default-value": "[[NIPOPPY_SESSION]]"
+            "default-value": "[[NIPOPPY_BIDS_SESSION]]"
         },
         {
             "name": "bids_options",

diff --git a/nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json b/nipoppy_cli/nipoppy/data/descriptors/mriqc-23.1.0.json
@@ -82,7 +82,7 @@
             "list": true,
             "command-line-flag": "--participant-label",
             "default-value": [
-                "[[NIPOPPY_PARTICIPANT]]"
+                "[[NIPOPPY_PARTICIPANT_ID]]"
             ]
         },
         {
@@ -93,7 +93,7 @@
             "type": "String",
             "value-key": "[SESSION_ID]",
             "command-line-flag": "--session-id",
-            "default-value": "[[NIPOPPY_SESSION_SHORT]]"
+            "default-value": "[[NIPOPPY_SESSION_ID]]"
         },
         {
             "id": "run_id",

diff --git a/nipoppy_cli/nipoppy/data/examples/sample_global_config-all_pipelines.json b/nipoppy_cli/nipoppy/data/examples/sample_global_config-all_pipelines.json
@@ -1,12 +1,12 @@
 {
     "DATASET_NAME": "<DATASET_NAME>",
-    "VISITS": [
+    "VISIT_IDS": [
         "<VISIT_LABEL>",
         "<OTHER_VISIT_LABEL>"
     ],
-    "SESSIONS": [
-        "ses-<SESSION_LABEL>",
-        "ses-<OTHER_SESSION_LABEL>"
+    "SESSION_IDS": [
+        "<SESSION_LABEL>",
+        "<OTHER_SESSION_LABEL>"
     ],
     "SUBSTITUTIONS": {
         "[[NIPOPPY_DPATH_CONTAINERS]]": "<PATH_TO_CONTAINER_STORE_DIRECTORY>",

diff --git a/nipoppy_cli/nipoppy/data/examples/sample_global_config-latest_pipelines.json b/nipoppy_cli/nipoppy/data/examples/sample_global_config-latest_pipelines.json
@@ -1,12 +1,12 @@
 {
     "DATASET_NAME": "<DATASET_NAME>",
-    "VISITS": [
+    "VISIT_IDS": [
         "<VISIT_LABEL>",
         "<OTHER_VISIT_LABEL>"
     ],
-    "SESSIONS": [
-        "ses-<SESSION_LABEL>",
-        "ses-<OTHER_SESSION_LABEL>"
+    "SESSION_IDS": [
+        "<SESSION_LABEL>",
+        "<OTHER_SESSION_LABEL>"
     ],
     "SUBSTITUTIONS": {
         "[[NIPOPPY_DPATH_CONTAINERS]]": "<PATH_TO_CONTAINER_STORE_DIRECTORY>",

diff --git a/nipoppy_cli/nipoppy/data/examples/sample_manifest.csv b/nipoppy_cli/nipoppy/data/examples/sample_manifest.csv
@@ -1,7 +1,7 @@
-participant_id,visit,session,datatype
-01,BL,ses-BL,"['anat']"
+participant_id,visit_id,session_id,datatype
+01,BL,BL,"['anat']"
 01,M06,,
-01,M12,ses-M12,"['anat']"
-02,BL,ses-BL,"['anat','dwi']"
+01,M12,M12,"['anat']"
+02,BL,BL,"['anat','dwi']"
 02,M06,,
-02,M12,ses-M12,"['anat','dwi']"
+02,M12,M12,"['anat','dwi']"
diff --git a/nipoppy_cli/nipoppy/data/examples/sample_tracker_configs/mriqc-23.1.0.json b/nipoppy_cli/nipoppy/data/examples/sample_tracker_configs/mriqc-23.1.0.json
@@ -2,8 +2,8 @@
     {
         "NAME": "pipeline_complete",
         "PATHS": [
-            "[[NIPOPPY_BIDS_ID]]/[[NIPOPPY_SESSION]]/anat/[[NIPOPPY_BIDS_ID]]_[[NIPOPPY_SESSION]]_*_T1w.json",
-            "[[NIPOPPY_BIDS_ID]]_[[NIPOPPY_SESSION]]_*_T1w.html"
+            "[[NIPOPPY_BIDS_PARTICIPANT]]/[[NIPOPPY_BIDS_SESSION]]/anat/[[NIPOPPY_BIDS_PARTICIPANT]]_[[NIPOPPY_BIDS_SESSION]]_*_T1w.json",
+            "[[NIPOPPY_BIDS_PARTICIPANT]]_[[NIPOPPY_BIDS_SESSION]]_*_T1w.html"
         ]
     }
 ]