Merge branch 'dev-v2.0.0' into master

.dryrun_test_all.sh

@@ -1,17 +1,17 @@
 #!/bin/bash
 set -euxo pipefail
 HIPPUNFOLD_CACHE_DIR=`pwd`/test_data/fake_models
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L
-hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w
-hippunfold test_data/bids_T1w test_out participant -np --modality T1w
-hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500
-hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w
-hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w
-hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template
-hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w
-hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi R 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --hemi L 
+hippunfold test_data/bids_multiT2w test_out participant -np --modality T2w 
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w 
+hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
+hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
+hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
+hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w 
+hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz 
+hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
+hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
+hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 

.gitignore

@@ -1,3 +1,160 @@
-hippunfold.egg-info
-hippunfold/.snakemake
-hippunfold/__pycache__
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

hippunfold/config/snakebids.yml

@@ -10,6 +10,7 @@ debug: False
 
 derivatives: False #will search in bids/derivatives if True; can also be path(s) to derivatives datasets
 
+
 #list of analysis levels in the bids app 
 analysis_levels: &analysis_levels
  - participant
@@ -35,8 +36,8 @@ pybids_inputs:
       suffix: 'T2w'
       extension: '.nii.gz'
       datatype: 'anat'
-      invalid_filters: 'allow'
-      space: null
+      # invalid_filters: 'allow'
+      # space: null
     wildcards:
       - subject
       - session
@@ -58,8 +59,8 @@ pybids_inputs:
       suffix: 'T1w'
       extension: '.nii.gz'
       datatype: 'anat'
-      invalid_filters: 'allow'
-      space: null
+      # invalid_filters: 'allow'
+      # space: null
     wildcards:
       - subject
       - session
@@ -75,6 +76,8 @@ pybids_inputs:
     wildcards:
       - subject
       - session
+      - acquisition
+      - run
 
   cropseg:
     filters:
@@ -86,6 +89,9 @@ pybids_inputs:
       - subject
       - session
       - hemi
+      - acquisition
+      - run
+
 
 
 
@@ -178,17 +184,11 @@ parse_args:
     help: 'Scales the default smoothing sigma for gradient and warp in greedy registration for template-based segmentation. Using a value higher than 1 will use result in a smoother warp. (default: %(default)s)'
     default: 2.0
 
-
-  --derivatives:
-    help: 'Path to the derivatives folder (e.g. for finding manual segs) (default: %(default)s) '
-    default: False
-
   --skip_preproc:
     help: 'Set this flag if your inputs (e.g. T2w, dwi) are already pre-processed (default: %(default)s)'
     default: False
     action: 'store_true'
 
-
   --skip_coreg:
     help: 'Set this flag if your inputs (e.g. T2w, dwi) are already registered to T1w space (default: %(default)s)'
     default: False
@@ -330,6 +330,20 @@ parse_args:
       - synthseg_v0.2
       - neonateT1w_v2
 
+  --enable-bids-validation:
+    help: |
+      Enable validation of BIDS dataset. BIDS validation would be performed
+      using the bids-validator plugin (if installed/enabled) or with the pybids
+      validator implementation (if bids-validator is not installed/enabled).
+    dest: "plugins.validator.skip"
+    action: "store_false"
+    default: True
+
+
+  --version:
+    help: 'Print the version of HippUnfold'
+    action: version
+    version: "1.5.2-pre.2"
 
 
 
@@ -700,6 +714,7 @@ output_density:
 
 laminar_coords_method: equivolume
 skip_preproc: False
+plugins.validator.skip: False
 nnunet_enable_tta: False
 use_gpu: False
 skip_coreg: False

hippunfold/pipeline_description.json

@@ -1,14 +1,15 @@
 {
-    "Name": "Snakemake BIDS app for hippocampal unfolding & subfield segmentation",
-    "BIDSVersion": "1.4.0",
-    "DatasetType": "derivative",
-    "GeneratedBy": [
-        {
-            "Name": "hippunfold",
-            "Version": "1.5.2-pre.2",
-            "CodeURL": "https://github.com/khanlab/hippunfold",
-            "Author": "Jordan DeKraker & Ali Khan",
-            "AuthorEmail": "[email protected]"
-        }
-    ]
+
+  "Name": "Snakemake BIDS app for hippocampal unfolding & subfield segmentation",
+  "BIDSVersion": "1.8.0",
+  "DatasetType": "derivative",
+  "GeneratedBy": [
+    {
+      "Name": "hippunfold",
+      "Version": "1.5.4",
+      "CodeURL": "https://github.com/khanlab/hippunfold",
+      "Author": "Jordan DeKraker & Ali Khan",
+      "AuthorEmail": "[email protected]"
+    }
+  ]
 }

hippunfold/run.py

@@ -1,24 +1,27 @@
 #!/usr/bin/env python3
-import os
+from pathlib import Path
 
-from snakebids.app import SnakeBidsApp
-from snakebids.cli import add_dynamic_args
+from snakebids import bidsapp, plugins
 
+if "__file__" not in globals():
+    __file__ = "../hippunfold/run.py"
 
-def get_parser():
-    """Exposes parser for sphinx doc generation, cwd is the docs dir"""
-    app = SnakeBidsApp("../hippunfold")
-    add_dynamic_args(app.parser, app.config["parse_args"], app.config["pybids_inputs"])
-    return app.parser
+
+app = bidsapp.app(
+    [
+        plugins.SnakemakeBidsApp(Path(__file__).resolve().parent),
+        plugins.BidsValidator(),
+        plugins.Version(distribution="hippunfold"),
+        plugins.CliConfig("parse_args"),
+        plugins.ComponentEdit("pybids_inputs"),
+    ]
+)
 
 
-def main():
-    app = SnakeBidsApp(
-        os.path.abspath(os.path.dirname(__file__)),
-        configfile_path="config/snakebids.yml",
-    )
-    app.run_snakemake()
+def get_parser():
+    """Exposes parser for sphinx doc generation, cwd is the docs dir."""
+    return app.build_parser().parser
 
 
 if __name__ == "__main__":
-    main()
+    app.run()