fixes

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+count = True
+show-source = True
+statistics = True
+max_function_length = 150

.pre-commit-config.yaml

@@ -38,5 +38,5 @@ repos:
     rev: 7.1.1
     hooks:
     -   id: flake8
-        args: [--verbose]
+        args: [--config, .flake8, --verbose]
         additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear]

code/_parsers.py

@@ -62,20 +62,25 @@ def _add_common_arguments(parser: ArgumentParser) -> ArgumentParser:
 Multiple participants can be specified with a space separated list.
         """,
         nargs="+",
+        required=False,
     )
     parser.add_argument(
-        "-v",
         "--verbose",
-        dest="log_level",
-        action="append_const",
-        const=-1,
+        help="""
+        Verbosity level.
+        """,
+        choices=[0, 1, 2, 3],
+        default=2,
+        type=int,
+        nargs=1,
     )
     parser.add_argument(
         "--bids_filter_file",
         help="""
 A JSON file describing custom BIDS input filters using PyBIDS.
 For further details, please check out TBD.
         """,
+        required=False,
     )
     return parser
 
@@ -105,6 +110,12 @@ def common_parser(
         required=True,
     )
 
+    subparsers.add_parser(
+        "help",
+        help="Show cat12 script help.",
+        formatter_class=parser.formatter_class,
+    )
+
     view_parser = subparsers.add_parser(
         "view",
         help="View batch.",
@@ -125,20 +136,27 @@ def common_parser(
         formatter_class=parser.formatter_class,
     )
     segment_parser = _add_common_arguments(segment_parser)
+    segment_parser.add_argument(
+        "--reset_database",
+        help="Resets the database of the input dataset.",
+        action="store_true",
+        required=False,
+    )
+    segment_parser.add_argument(
+        "--type",
+        help="""Type of segmentation.
+ default: default CAT12 preprocessing batch;
+ default: simple processing batch;
+ 0 - longitudinal developmental;
+ 1 - longitudinal plasticity/learning;
+ 2 - longitudinal aging;
+ 3 - longitudinal save models 1 and 2;
+""",
+        choices=["default", "simple", "0", "1", "2", "3"],
+        default="default",
+        required=False,
+        type=str,
+        nargs=1,
+    )
 
     return parser
-
-
-# cat_standalone_segment_enigma.m
-# cat_standalone_segment_long.m
-# cat_standalone_resample.m
-# cat_standalone_simple.m
-# cat_standalone_tfce.m
-# cat_standalone_get_IQR.m
-# cat_standalone_smooth.m
-# cat_standalone_dicom2nii.m
-# cat_standalone_deface.m
-# cat_standalone_get_TIV.m
-# cat_standalone_segment.m
-# cat_standalone_get_quality.m
-# cat_standalone_get_ROI_values.m

code/bids_utils.py

@@ -54,7 +54,7 @@ def get_dataset_layout(
     )
 
 
-def init_derivatives_layout(output_dir) -> BIDSLayout:
+def init_derivatives_layout(output_dir: Path) -> BIDSLayout:
     """Initialize a derivatives dataset and returns its layout.
 
     :param output_dir:
@@ -64,11 +64,8 @@ def init_derivatives_layout(output_dir) -> BIDSLayout:
     :rtype: BIDSLayout
     """
     create_dir_if_absent(output_dir)
+    write_dataset_description(output_dir)
     layout_out = get_dataset_layout(output_dir)
-    layout_out = set_dataset_description(layout_out)
-    layout_out.dataset_description["DatasetType"] = "derivative"
-    layout_out.dataset_description["GeneratedBy"][0]["Name"] = "CAT12"
-    write_dataset_description(layout_out)
     return layout_out
 
 
@@ -96,64 +93,37 @@ def list_subjects(layout: BIDSLayout, subjects) -> list[str]:
     return subjects
 
 
-def set_dataset_description(
-    layout: BIDSLayout, is_derivative: bool = True
-) -> BIDSLayout:
+def write_dataset_description(output_dir) -> None:
     """Add dataset description to a layout.
 
-    :param layout: _description_
-    :type layout: BIDSLayout
-
-    :param is_derivative: Defaults to True
-    :type is_derivative: bool, optional
-
-    :return: Updated BIDSLayout of the dataset
-    :rtype: BIDSLayout
+    :param output_dir: output_dir
+    :type output_dir: Path
     """
     data: dict[str, Any] = {
         "Name": "dataset name",
         "BIDSVersion": "1.9.0",
-        "DatasetType": "raw",
-        "License": "CCO",
-        "Authors": ["", ""],
-        "Acknowledgements": "Special thanks to: ",
-        "HowToAcknowledge": """Please cite this paper: """,
-        "Funding": ["", ""],
-        "ReferencesAndLinks": [],
-        "DatasetDOI": "doi:",
+        "DatasetType": "derivative",
+        "License": "???",
+        "ReferencesAndLinks": ["https://doi.org/10.1101/2022.06.11.495736"],
     }
-
-    if is_derivative:
-        data["GeneratedBy"] = [
-            {
-                "Name": "bidsMReye",
-                "Version": __version__,
-                "Container": {"Type": "", "Tag": ""},
-                "Description": "",
-                "CodeURL": "",
-            },
-        ]
-
-        data["SourceDatasets"] = [
-            {
-                "DOI": "doi:",
-                "URL": "",
-                "Version": "",
-            }
-        ]
-
-    layout.dataset_description = data
-
-    return layout
-
-
-def write_dataset_description(layout: BIDSLayout) -> None:
-    """Add a dataset_description.json to a BIDS dataset.
-
-    :param layout: BIDSLayout of the dataset to update.
-    :type layout: BIDSLayout
-    """
-    output_file = Path(layout.root) / "dataset_description.json"
+    data["GeneratedBy"] = [
+        {
+            "Name": "cat12",
+            "Version": __version__,
+            "Container": {"Type": "", "Tag": __version__},
+            "Description": "",
+            "CodeURL": "",
+        },
+    ]
+    data["SourceDatasets"] = [
+        {
+            "DOI": "doi:",
+            "URL": "",
+            "Version": "",
+        }
+    ]
+
+    output_file = output_dir / "dataset_description.json"
 
     with open(output_file, "w") as ff:
-        json.dump(layout.dataset_description, ff, indent=4)
+        json.dump(data, ff, indent=4)

code/cat_logging.py

@@ -4,28 +4,22 @@
 
 import logging
 
-from defaults import default_log_level
 from rich.logging import RichHandler
 from rich.traceback import install
 
 
-def cat12_log(
-    name: str | None = None, log_level: int = logging.INFO
-) -> logging.Logger:
-    """Create log."""
+def cat12_log(name: str | None = None) -> logging.Logger:
     """Create log."""
     # let rich print the traceback
     install(show_locals=True)
 
     FORMAT = "cat12 - %(asctime)s - %(message)s"
 
-    log_level = default_log_level()
-
     if not name:
         name = "rich"
 
     logging.basicConfig(
-        level=log_level,
+        level="INFO",
         format=FORMAT,
         datefmt="[%X]",
         handlers=[

code/defaults.py

@@ -3,14 +3,9 @@
 from __future__ import annotations
 
 
-def default_log_level() -> str:
-    """Return default log level."""
-    return "INFO"
-
-
 def log_levels() -> list[str]:
     """Return a list of log levels."""
-    return ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
+    return ["ERROR", "WARNING", "INFO", "DEBUG"]
 
 
 def supported_batches() -> list[str]:
@@ -28,3 +23,18 @@ def supported_batches() -> list[str]:
         "get_quality",
         "get_ROI_values",
     ]
+
+
+# cat_standalone_segment_enigma.m
+# cat_standalone_segment_long.m
+# cat_standalone_resample.m
+# cat_standalone_simple.m
+# cat_standalone_tfce.m
+# cat_standalone_get_IQR.m
+# cat_standalone_smooth.m
+# cat_standalone_dicom2nii.m
+# cat_standalone_deface.m
+# cat_standalone_get_TIV.m
+# cat_standalone_segment.m
+# cat_standalone_get_quality.m
+# cat_standalone_get_ROI_values.m