From c15bcb46b73bffea567d682fa56612de85e99360 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:49:39 -0600 Subject: [PATCH 1/8] added exclude list as well --- petdeface/petdeface.py | 53 ++++++++++++++++++++++++++++++++++++++---- pyproject.toml | 2 +- 2 files changed, 50 insertions(+), 5 deletions(-) diff --git a/petdeface/petdeface.py b/petdeface/petdeface.py index 527d32c..a937cc3 100755 --- a/petdeface/petdeface.py +++ b/petdeface/petdeface.py @@ -201,12 +201,42 @@ def deface(args: Union[dict, argparse.Namespace]) -> None: if not check_valid_fs_license(): raise Exception("You need a valid FreeSurfer license to proceed!") - if args.participant_label: - participants = [args.participant_label] - else: + if args.subject: + subjects = args.subject + # if subject contains the string sub-, remove it to avoid redundancy as pybids will add it uses the + # right side of the sub- string as the subject label + if any("sub-" in subject for subject in subjects): + print("One or more subject contains sub- string") + subjects = [ + subject.replace("sub-", "") for subject in subjects if "sub-" in subject + ] + # raise error if a supplied subject is not contained in the dataset participants = collect_participants( args.bids_dir, bids_validate=~args.skip_bids_validator ) + for subject in subjects: + if subject not in participants: + raise FileNotFoundError( + f"sub-{subject} not found in dataset {args.bids_dir}" + ) + else: + subjects = collect_participants( + args.bids_dir, bids_validate=~args.skip_bids_validator + ) + + # check to see if any subjects are excluded from the defacing workflow + if args.excludesubject != []: + print( + f"Removing the following subjects {args.excludesubject} from the defacing workflow" + ) + args.excludesubject = [ + subject.replace("sub-", "") for subject in args.excludesubject + ] + subjects = [ + subject for subject in subjects if subject not in args.excludesubject + ] + + print(f"Subjects remaining in the defacing workflow: {subjects}") # clean up and create derivatives directories if args.output_dir == "None" or args.output_dir is None: @@ -216,7 +246,7 @@ def deface(args: Union[dict, argparse.Namespace]) -> None: petdeface_wf = Workflow(name="petdeface_wf", base_dir=output_dir) - for subject_id in participants: + for subject_id in subjects: try: single_subject_wf = init_single_subject_wf( subject_id, args.bids_dir, preview_pics=args.preview_pics @@ -268,6 +298,8 @@ def init_single_subject_wf( data = collect_anat_and_pet(bids_data) subject_data = data.get(subject_id) + if subject_data is None: + raise FileNotFoundError(f"Could not find data for subject sub-{subject_id}") # check if any t1w images exist for the pet images for pet_image, t1w_image in subject_data.items(): @@ -672,6 +704,7 @@ def __init__( remove_existing=True, # TODO: currently not implemented placement="adjacent", # TODO: currently not implemented preview_pics=True, + excludesubject=[], ): self.bids_dir = bids_dir self.remove_existing = remove_existing @@ -683,6 +716,7 @@ def __init__( self.n_procs = n_procs self.skip_bids_validator = skip_bids_validator self.preview_pics = preview_pics + self.excludesubject = excludesubject # check if freesurfer license is valid self.fs_license = check_valid_fs_license() @@ -707,6 +741,7 @@ def run(self): "placement": self.placement, "remove_existing": self.remove_existing, "preview_pics": self.preview_pics, + "excludesubject": self.excludesubject, } ) wrap_up_defacing( @@ -746,6 +781,7 @@ def cli(): "-s", help="The label of the subject to be processed.", type=str, + nargs="+", required=False, default="", ) @@ -800,6 +836,14 @@ def cli(): action="store_true", default=False, ) + parser.add_argument( + "--excludesubject", + help="Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02", + type=str, + nargs="+", + required=False, + default=[], + ) arguments = parser.parse_args() return arguments @@ -928,6 +972,7 @@ def main(): # noqa: max-complexity: 12 remove_existing=args.remove_existing, placement=args.placement, preview_pics=args.preview_pics, + excludesubject=args.excludesubject, ) petdeface.run() diff --git a/pyproject.toml b/pyproject.toml index 2e4f6de..dc1d67b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "petdeface" -version = "0.1.1" +version = "0.1.2" description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace." authors = ["Martin Nørgaard ", "Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>", "Murat Bilgel "] license = "MIT" From eec8709ca2a8ff13e460c2fab8855ecad66dbd26 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:10:10 -0600 Subject: [PATCH 2/8] update readme --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9f35194..2b3bc20 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,8 @@ This software can be installed via source or via pip from PyPi with `pip install usage: petdeface.py [-h] [--output_dir OUTPUT_DIR] [--anat_only] [--subject SUBJECT] [--session SESSION] [--docker] [--n_procs N_PROCS] [--skip_bids_validator] [--version] - [--placement PLACEMENT] [--remove_existing] input_dir + [--placement PLACEMENT] [--remove_existing] [--excludesubject] + input_dir PetDeface @@ -65,6 +66,8 @@ options: w/ defaced at input_dir 'derivatives': does all of the defacing within the derivatives folder in input_dir. --remove_existing, -r Remove existing output files in output_dir. + --excludesubject EXCLUDESUBJECT [EXCLUDESUBJECT ...] + Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02 ``` Working example usage: From 6a96610455a9442f43f3240786780dc0849d4800 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:10:49 -0600 Subject: [PATCH 3/8] update docs --- docs/usage.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/usage.rst b/docs/usage.rst index 261cb77..04887d5 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -113,6 +113,8 @@ Additional options can be found in the help menu:: e.g. replaces faced PET and T1w images w/ defaced at input_dir'derivatives': does all of the defacing within the derivatives folder in input_dir. --remove_existing, -r Remove existing output files in output_dir. + --excludesubject EXCLUDESUBJECT [EXCLUDESUBJECT ...] + Exclude a subject(s) from the defacing workflow. e.g. --excludesubject sub-01 sub-02 Docker Based ------------ From 2cc581394c795022b1b06143ffb4e448648ee545 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:14:55 -0600 Subject: [PATCH 4/8] update rtd build --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index f140e0e..aeb2b13 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,7 +15,7 @@ build: - pip install poetry - poetry config virtualenvs.create false post_install: - - poetry install + - poetry install --with=dev # Build documentation in the "docs/" directory with Sphinx sphinx: From 1f60d799b1572c9d19ffc6c1e6ffd5855e545f7a Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:20:04 -0600 Subject: [PATCH 5/8] update sphinx rtd theme --- poetry.lock | 20 +++++++++++--------- pyproject.toml | 2 +- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/poetry.lock b/poetry.lock index 066b3e4..b4d6849 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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(>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] From 83efd4f7bffec5f2f4cc8c778cc2a712343bca83 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:31:29 -0600 Subject: [PATCH 8/8] update lock and pyproject.toml --- poetry.lock | 19 ++++++++----------- pyproject.toml | 2 +- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/poetry.lock b/poetry.lock index a96508d..3d1c3ed 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1555,12 +1555,14 @@ tests = ["codecov", "pytest", "pytest-cov"] [[package]] name = "niworkflows" -version = "1.12.0.dev8+gcd633c99" +version = "1.11.0" description = "NeuroImaging Workflows provides processing tools for magnetic resonance images of the brain." optional = false -python-versions = ">=3.9" -files = [] -develop = false +python-versions = ">=3.8" +files = [ + {file = "niworkflows-1.11.0-py3-none-any.whl", hash = "sha256:f194fa958caf960ae1cba4333257eb9f0ad39efc9f23cd39f91b59495684c18c"}, + {file = "niworkflows-1.11.0.tar.gz", hash = "sha256:932bc150ea29f7d83febda9ecd05023ecd45454b532a0aec2b505ebf0a25cbc7"}, +] [package.dependencies] acres = "*" @@ -1583,6 +1585,7 @@ scipy = "*" seaborn = "*" svgutils = ">=0.3.4" templateflow = ">=0.7.2" +traits = "<6.4" transforms3d = "*" [package.extras] @@ -1593,12 +1596,6 @@ pointclouds = ["pyntcloud"] style = ["flake8 (>=3.7.0)"] tests = ["coverage (>=5.2.1)", "pytest (>=4.4)", "pytest-cov", "pytest-env", "pytest-xdist (>=1.28)", "pytest-xvfb"] -[package.source] -type = "git" -url = "https://github.com/nipreps/niworkflows.git" -reference = "HEAD" -resolved_reference = "cd633c991bc78e84c7ddfd8b48b885abe9e665f7" - [[package]] name = "nodeenv" version = "1.9.1" @@ -3230,4 +3227,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.10, <4.0" -content-hash = "e979ca8933fae0490492e21db707cc39832de351c3ae1c17633d78ff38a94f28" +content-hash = "d13eaeabc8d858d5540db6627dec495e106ff940245e5c50b9b2997e6b163b93" diff --git a/pyproject.toml b/pyproject.toml index 5e77595..2f4b675 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,9 +16,9 @@ bids_version = "1.8.0" [tool.poetry.dependencies] python = ">=3.10, <4.0" -niworkflows = { git = "https://github.com/nipreps/niworkflows.git" } setuptools = "^68.1.2" petutils = "^0.0.1" +niworkflows = "^1.11.0" [tool.poetry.group.dev.dependencies] black = "^23.7.0"