From 71d940a4f2097c52769fd8d5ead4154e7f6ff6a9 Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Mon, 22 Jul 2024 13:56:24 -0400 Subject: [PATCH 01/17] Template inject Lflip vs R (#310) * bigbrain template laplace coords added * bugfix for using L or R template injection * lint --------- Co-authored-by: Jordan DeKraker --- hippunfold/config/snakebids.yml | 10 ++- hippunfold/workflow/rules/shape_inject.smk | 80 ++++++++++++++++------ 2 files changed, 65 insertions(+), 25 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index ce342260..8a10307c 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -384,21 +384,25 @@ template_based_segmentation: hemi: - R - L - CIVM: + dHCP: hemi: - R - L + MBMv2: hemi: - R MBMv3: hemi: - R - ABAv3: + CIVM: hemi: - R - L - dHCP: + upenn: + hemi: + - R + ABAv3: hemi: - R - L diff --git a/hippunfold/workflow/rules/shape_inject.smk b/hippunfold/workflow/rules/shape_inject.smk index f895d00f..635333a1 100644 --- a/hippunfold/workflow/rules/shape_inject.smk +++ b/hippunfold/workflow/rules/shape_inject.smk @@ -1,3 +1,36 @@ +# Template-based segmentation supports templates that have only a single hemisphere +# by mapping it to the flipped version of the other hemisphere. +# If a template has both L and R files, then we set hemi_constrained_wildcard to L|R. +# If a hemisphere is missing data, then we set it to flip that, e.g. if L missing, then use Lflip|R + +hemi_constraints = [] +if config["template"] in config["template_based_segmentation"]: + for hemi in config["hemi"]: + if hemi in config["template_based_segmentation"][config["template"]]["hemi"]: + hemi_constraints.append(hemi) + else: + hemi_constraints.append(f"{hemi}flip") + +hemi_constrained_wildcard = "{{hemi,{constraints}}}".format( + constraints="|".join(hemi_constraints) +) + + +def flipped(wildcards): + """function to map hemi in wildcards from Lflip to R, or Rflip to L, + for use in rules where e.g. the output wildcard is Lflip, but for the input, R is desired, such as + when mapping a R hemi dseg to the Lflip hemisphere of a subject.""" + + if wildcards.hemi == "L" or wildcards.hemi == "R": + return wildcards + elif wildcards.hemi == "Lflip": + wildcards.hemi = "R" + return wildcards + elif wildcards.hemi == "Rflip": + wildcards.hemi = "L" + return wildcard + + def get_input_for_shape_inject(wildcards): if config["modality"] == "cropseg": seg = bids( @@ -6,7 +39,7 @@ def get_input_for_shape_inject(wildcards): **config["subj_wildcards"], suffix="dseg.nii.gz", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) elif get_modality_key(config["modality"]) == "seg": modality_suffix = get_modality_suffix(config["modality"]) @@ -18,7 +51,7 @@ def get_input_for_shape_inject(wildcards): suffix="dseg.nii.gz", space="corobl", hemi="{hemi}", - from_="{modality_suffix}" + from_="{modality_suffix}", ).format(**wildcards, modality_suffix=modality_suffix), ) else: @@ -29,7 +62,7 @@ def get_input_for_shape_inject(wildcards): suffix="dseg.nii.gz", desc="nnunet", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) return seg @@ -42,7 +75,7 @@ def get_input_splitseg_for_shape_inject(wildcards): **config["subj_wildcards"], suffix="dsegsplit", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) elif get_modality_key(config["modality"]) == "seg": @@ -54,7 +87,7 @@ def get_input_splitseg_for_shape_inject(wildcards): suffix="dsegsplit", space="corobl", hemi="{hemi}", - from_="{modality_suffix}" + from_="{modality_suffix}", ).format(**wildcards, modality_suffix=modality_suffix) else: seg = bids( @@ -64,7 +97,7 @@ def get_input_splitseg_for_shape_inject(wildcards): suffix="dsegsplit", desc="nnunet", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ).format(**wildcards) return seg @@ -92,7 +125,7 @@ rule import_template_shape: params: template_seg=lambda wildcards, input: Path(input.template_dir) / config["template_files"][config["inject_template"]]["dseg"].format( - **wildcards + **flipped(wildcards) ), output: template_seg=bids( @@ -101,6 +134,7 @@ rule import_template_shape: space="template", **config["subj_wildcards"], desc="hipptissue", + hemi=hemi_constrained_wildcard, suffix="dseg.nii.gz" ), group: @@ -164,6 +198,7 @@ rule template_shape_reg: space="template", **config["subj_wildcards"], desc="hipptissue", + hemi="{hemi}", suffix="dsegsplit" ), subject_seg=get_input_splitseg_for_shape_inject, @@ -183,7 +218,7 @@ rule template_shape_reg: to="subject", space="corobl", type_="ras", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), warp=bids( root=work, @@ -194,7 +229,7 @@ rule template_shape_reg: from_="template", to="subject", space="corobl", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -205,7 +240,7 @@ rule template_shape_reg: bids( root="logs", **config["subj_wildcards"], - hemi="{hemi,Lflip|R}", + hemi=hemi_constrained_wildcard, suffix="templateshapereg.txt" ), shell: @@ -222,6 +257,7 @@ rule template_shape_inject: space="template", **config["subj_wildcards"], desc="hipptissue", + hemi="{hemi}", suffix="dseg.nii.gz" ), subject_seg=get_input_for_shape_inject, @@ -235,7 +271,7 @@ rule template_shape_inject: to="subject", space="corobl", type_="ras", - hemi="{hemi}" + hemi="{hemi}", ), warp=bids( root=work, @@ -246,7 +282,7 @@ rule template_shape_inject: from_="template", to="subject", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ), params: interp_opt="-ri LABEL 0.2vox", @@ -258,14 +294,14 @@ rule template_shape_inject: suffix="dseg.nii.gz", desc="inject", space="corobl", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), log: bids( root="logs", **config["subj_wildcards"], suffix="templateshapeinject.txt", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -289,7 +325,7 @@ rule inject_init_laplace_coords: to="subject", space="corobl", type_="ras", - hemi="{hemi}" + hemi="{hemi}", ), warp=bids( root=work, @@ -300,7 +336,7 @@ rule inject_init_laplace_coords: from_="template", to="subject", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ), template_dir=Path(download_dir) / "template" / config["inject_template"], params: @@ -319,7 +355,7 @@ rule inject_init_laplace_coords: suffix="coords.nii.gz", desc="init", space="corobl", - hemi="{hemi,R|Lflip}" + hemi=hemi_constrained_wildcard, ), log: bids( @@ -329,7 +365,7 @@ rule inject_init_laplace_coords: label="{autotop}", suffix="injectcoords.txt", desc="init", - hemi="{hemi,R|Lflip}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -365,7 +401,7 @@ rule unflip_init_coords: suffix="coords.nii.gz", desc="init", space="corobl", - hemi="{hemi,L}" + hemi="{hemi,L|R}" ), container: config["singularity"]["autotop"] @@ -385,7 +421,7 @@ rule reinsert_subject_labels: suffix="dseg.nii.gz", desc="inject", space="corobl", - hemi="{hemi}" + hemi="{hemi}", ), subject_seg=get_input_for_shape_inject, params: @@ -400,7 +436,7 @@ rule reinsert_subject_labels: suffix="dseg.nii.gz", desc="postproc", space="corobl", - hemi="{hemi,Lflip|R}" + hemi=hemi_constrained_wildcard, ), group: "subj" @@ -429,7 +465,7 @@ rule unflip_postproc: suffix="dseg.nii.gz", desc="postproc", space="corobl", - hemi="{hemi,L}", + hemi="{hemi,L|R}", **config["subj_wildcards"] ), container: From bb4bcca29f8d018d998663aa273c5a6eb5a56f75 Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Mon, 22 Jul 2024 13:56:37 -0400 Subject: [PATCH 02/17] Wet-run test data (#303) * Wet-run test data * typos & clarifications --- docs/contributing/contributing.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/contributing/contributing.md b/docs/contributing/contributing.md index 79030ef0..f9e92fec 100644 --- a/docs/contributing/contributing.md +++ b/docs/contributing/contributing.md @@ -75,6 +75,10 @@ from the `hippunfold` folder that contains the cd hippunfold snakemake -np +## Wet-run testing your workflow: + +Opensource data has been made available for wet-run testing any changes to HippUnfold on OSF [here](https://osf.io/k2nme/). These are real opensource data meant ot span a wide array of HippUnfold use cases with various modalities, resolutions, developmental stages, and species. Please note that some changes to hippUnfold will impact all worflows and should be run and then visually inspected for all these cases. Other changes may impact only one workflow (e.g. adding a new template) and so the recommended run parameters should be adjusted accordingly. + ## Instructions for Compute Canada This section provides an example of how to set up a `pip installed` copy From c82b8cb9bc50dd59b8da44a819b15551440b0397 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 22 Jul 2024 17:56:56 +0000 Subject: [PATCH 03/17] Bump version to 1.5.0-pre.48 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 8a10307c..75c59ee8 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.0-pre.47" + version: "1.5.0-pre.48" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 8f67d839..e791d075 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.0-pre.47", + "Version": "1.5.0-pre.48", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index d4ec5c5a..a895e24b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.0-pre.47" +version = "1.5.0-pre.48" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From bd2bd68bf1bb77f846c0fcf57a8302ea04e9c99a Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Tue, 23 Jul 2024 15:53:21 -0400 Subject: [PATCH 04/17] fix dependency versions for snakebids, pulp (#313) * fix dependency versions for snakebids, pulp * poetry lock * Revert "poetry lock" This reverts commit b2f88097a9529ce5322c7ac6fc01828bd4dc80e9. * redo poetry lock * python >3.8 * dropped testing for python <3.8 --------- Co-authored-by: Jordan DeKraker --- .github/workflows/python-testing.yml | 2 +- poetry.lock | 2264 +++++++++++--------------- pyproject.toml | 6 +- 3 files changed, 979 insertions(+), 1293 deletions(-) diff --git a/.github/workflows/python-testing.yml b/.github/workflows/python-testing.yml index 3ae96c8e..7a51a32e 100644 --- a/.github/workflows/python-testing.yml +++ b/.github/workflows/python-testing.yml @@ -35,7 +35,7 @@ jobs: needs: ["quality"] strategy: matrix: - python-version: ["3.7", "3.8", "3.9"] + python-version: ["3.8", "3.9"] steps: - name: Install non-python dependencies diff --git a/poetry.lock b/poetry.lock index c6075fa0..b9c00715 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = "*" files = [ @@ -14,25 +13,27 @@ files = [ [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, ] [package.dependencies] python-dateutil = ">=2.7.0" -typing-extensions = {version = "*", markers = "python_version < \"3.8\""} +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "astor" version = "0.8.1" description = "Read/rewrite/write Python ASTs" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" files = [ @@ -42,28 +43,24 @@ files = [ [[package]] name = "astroid" -version = "2.11.7" +version = "2.15.8" description = "An abstract syntax tree for Python with inference support." -category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7.2" files = [ - 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{file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, - {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, ] -[package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} - [package.extras] cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[docs,tests]", "pre-commit"] +dev = ["attrs[tests]", "pre-commit"] docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] tests = ["attrs[tests-no-zope]", "zope-interface"] -tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] +tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] [[package]] name = "bids-validator" -version = "1.13.1" +version = "1.14.6" description = "Validator for the Brain Imaging Data Structure" -category = "main" optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ - 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"pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" -python-versions = ">=3.7.1,<3.10" -content-hash = "38356091d070c09fd5ac91d1d9f25b5cfa8256fb8d9bdbda3e505aab8ebc21c0" +python-versions = ">=3.8,<3.10" +content-hash = "49e15674dd8aa7c835ebff1aceecbeea5902e7d1beb502df5f5f62b299204ca8" diff --git a/pyproject.toml b/pyproject.toml index a895e24b..1d030fba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,14 +5,14 @@ description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding authors = ["Jordan DeKraker & Ali Khan "] [tool.poetry.dependencies] -python = ">=3.7.1,<3.10" +python = ">=3.8,<3.10" snakemake = ">=6.0.0" -snakebids = ">=0.5.1" +snakebids = "^0.8.1" appdirs = "^1.4.4" Jinja2 = "^3.0.3" pygraphviz = "1.7" Pygments = "^2.10.0" - +pulp = "<2.8.0" [tool.poetry.dev-dependencies] flake8 = "^4.0.1" From c4ee8a3d89242c669cdad246a570d4c2798cbd8e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 23 Jul 2024 19:53:39 +0000 Subject: [PATCH 05/17] Bump version to 1.5.1-pre.49 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 75c59ee8..447e61c6 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.0-pre.48" + version: "1.5.1-pre.49" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index e791d075..11097250 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.0-pre.48", + "Version": "1.5.1-pre.49", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index 1d030fba..b416c006 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.0-pre.48" +version = "1.5.1-pre.49" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From ec556123d8f510ba83db0e8944564ce211f32e7c Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Wed, 24 Jul 2024 11:56:28 -0400 Subject: [PATCH 06/17] Import patch (#314) * moved import to where it is needed --------- Co-authored-by: Jordan DeKraker --- hippunfold/workflow/rules/common.smk | 2 ++ hippunfold/workflow/rules/nnunet.smk | 1 - 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/hippunfold/workflow/rules/common.smk b/hippunfold/workflow/rules/common.smk index 6dc2fc60..00d174ff 100644 --- a/hippunfold/workflow/rules/common.smk +++ b/hippunfold/workflow/rules/common.smk @@ -1,3 +1,5 @@ +from appdirs import AppDirs + # take mean of all scans if >1, otherwise just copy the one scan def get_avg_or_cp_scans_cmd(wildcards, input, output): if len(input) > 1: diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk index b9f20b69..a86a6623 100644 --- a/hippunfold/workflow/rules/nnunet.smk +++ b/hippunfold/workflow/rules/nnunet.smk @@ -1,5 +1,4 @@ import re -from appdirs import AppDirs def get_nnunet_input(wildcards): From ccdadc5159472f6055fab4a4f3276d3068aec52d Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 24 Jul 2024 15:56:47 +0000 Subject: [PATCH 07/17] Bump version to 1.5.2-pre.50 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 447e61c6..4fda0965 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.1-pre.49" + version: "1.5.2-pre.50" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 11097250..4a15ac27 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.1-pre.49", + "Version": "1.5.2-pre.50", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index b416c006..2be21311 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.1-pre.49" +version = "1.5.2-pre.50" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From 39e8684c63e8624fd4b0ade3ccb13f99e5c7f8a4 Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Tue, 30 Jul 2024 09:05:30 -0400 Subject: [PATCH 08/17] Update Dockerfile to latest version with dependencies (#315) --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 03364c6d..a4d5c1a6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM khanlab/autotop_deps:v0.4.4-fix +FROM khanlab/autotop_deps:v0.5.1 MAINTAINER alik@robarts.ca From 78bd548f4144e07ef3ce1c4fce084a500e9caae6 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 30 Jul 2024 13:05:49 +0000 Subject: [PATCH 09/17] Bump version to 1.5.3-pre.51 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 4fda0965..a5bd26c4 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.2-pre.50" + version: "1.5.3-pre.51" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 4a15ac27..e7ba4772 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.2-pre.50", + "Version": "1.5.3-pre.51", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index 2be21311..85dfb0b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.2-pre.50" +version = "1.5.3-pre.51" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From 259a279aa28a268163a8c28fe2815c61630d9b71 Mon Sep 17 00:00:00 2001 From: Jordan DeKraker Date: Tue, 30 Jul 2024 13:39:36 -0400 Subject: [PATCH 10/17] Jordandekraker patch 1 (#317) * Update Dockerfile to latest version with dependencies * Update Dockerfile using the new repo isntead of the old! --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index a4d5c1a6..4916a778 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM khanlab/autotop_deps:v0.5.1 +FROM khanlab/hippunfold_deps:v0.5.1 MAINTAINER alik@robarts.ca From fe29f9c65651c20bb86bbd86141652ffc9494b21 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 30 Jul 2024 17:39:56 +0000 Subject: [PATCH 11/17] Bump version to 1.5.3-pre.52 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index a5bd26c4..fcd91a1f 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.3-pre.51" + version: "1.5.3-pre.52" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index e7ba4772..12328a83 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.3-pre.51", + "Version": "1.5.3-pre.52", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index 85dfb0b6..7683b9b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.3-pre.51" +version = "1.5.3-pre.52" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From 8230c03170c9ee3a17779dda6f59b6d55b6498ac Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 30 Jul 2024 18:38:23 +0000 Subject: [PATCH 12/17] Bump version to 1.5.4 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index fcd91a1f..cae81c88 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.3-pre.52" + version: "1.5.4" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 12328a83..ce678a4c 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.3-pre.52", + "Version": "1.5.4", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index 7683b9b6..39a8c61e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.3-pre.52" +version = "1.5.4" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From 0222393735b07b90350390dfea7c62ab143196c5 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Sun, 8 Dec 2024 22:35:10 -0500 Subject: [PATCH 13/17] fix for using T1T2w model run_inference was only accepting a single input image, this makes it accept a list of images too, and makes it so --force-nnunet-model T1T2w grabs both T1w and T2w as inputs. --- hippunfold/workflow/rules/nnunet.smk | 71 +++++++++++++++++----------- 1 file changed, 44 insertions(+), 27 deletions(-) diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk index a86a6623..6bb452ff 100644 --- a/hippunfold/workflow/rules/nnunet.smk +++ b/hippunfold/workflow/rules/nnunet.smk @@ -2,32 +2,37 @@ import re def get_nnunet_input(wildcards): - if config["modality"] == "T2w": - nii = ( - bids( - root=work, - datatype="anat", - **config["subj_wildcards"], - suffix="T2w.nii.gz", - space="corobl", - desc="preproc", - hemi="{hemi}", - ), - ) + T1w_nii = bids( + root=work, + datatype="anat", + **config["subj_wildcards"], + suffix="T1w.nii.gz", + space="corobl", + desc="preproc", + hemi="{hemi}", + ) + T2w_nii = bids( + root=work, + datatype="anat", + **config["subj_wildcards"], + suffix="T2w.nii.gz", + space="corobl", + desc="preproc", + hemi="{hemi}", + ) + if ( + config["modality"] == "T1w" + or config["modality"] == "T2w" + and config["force_nnunet_model"] == "T1T2w" + ): + return (T1w_nii, T2w_nii) + + elif config["modality"] == "T2w": + return T2w_nii elif config["modality"] == "T1w": - nii = ( - bids( - root=work, - datatype="anat", - **config["subj_wildcards"], - suffix="T1w.nii.gz", - space="corobl", - desc="preproc", - hemi="{hemi}", - ), - ) + return T1w_nii elif config["modality"] == "hippb500": - nii = bids( + return bids( root=work, datatype="dwi", hemi="{hemi}", @@ -37,7 +42,6 @@ def get_nnunet_input(wildcards): ) else: raise ValueError("modality not supported for nnunet!") - return nii def get_model_tar(): @@ -94,6 +98,19 @@ def parse_trainer_from_tar(wildcards, input): return trainer +def get_cmd_copy_inputs(wildcards, input): + in_img = input.in_img + if isinstance(in_img, str): + # we have one input image + return f"cp {in_img} tempimg/temp_0000.nii.gz" + else: + cmd = [] + # we have multiple input images + for i, img in enumerate(input.in_img): + cmd.append(f"cp {img} tempimg/temp_{i:04d}.nii.gz") + return " && ".join(cmd) + + rule run_inference: """ This rule uses either GPU or CPU . It also runs in an isolated folder (shadow), with symlinks to inputs in that folder, copying over outputs once complete, so temp files are not retained""" @@ -101,7 +118,7 @@ rule run_inference: in_img=get_nnunet_input, model_tar=get_model_tar(), params: - temp_img="tempimg/temp_0000.nii.gz", + cmd_copy_inputs=get_cmd_copy_inputs, temp_lbl="templbl/temp.nii.gz", model_dir="tempmodel", in_folder="tempimg", @@ -148,7 +165,7 @@ rule run_inference: # run inference #copy from temp output folder to final output "mkdir -p {params.model_dir} {params.in_folder} {params.out_folder} && " - "cp {input.in_img} {params.temp_img} && " + "{params.cmd_copy_inputs} && " "tar -xf {input.model_tar} -C {params.model_dir} && " "export RESULTS_FOLDER={params.model_dir} && " "export nnUNet_n_proc_DA={threads} && " From bdc02336196395324356c7c7e9a8a3a508565ce1 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Sun, 8 Dec 2024 22:38:47 -0500 Subject: [PATCH 14/17] hipp curvature was being used always, instead of wildcard this didn't affect any workflow computations, just the subsequent dscalar.nii and spec file that would have the wrong curvature map --- hippunfold/workflow/rules/gifti.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk index 2ae35706..309e380e 100644 --- a/hippunfold/workflow/rules/gifti.smk +++ b/hippunfold/workflow/rules/gifti.smk @@ -978,7 +978,7 @@ rule normalize_curvature2: space="{space}", hemi="{hemi}", desc="unnorm", - label="hipp", + label="{autotop}", **config["subj_wildcards"] ), output: From 2d0b10cf34164ca4db530986e154261b4bb1a2bc Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Sun, 8 Dec 2024 22:48:03 -0500 Subject: [PATCH 15/17] fix logical error --- hippunfold/workflow/rules/nnunet.smk | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk index 6bb452ff..ab21a4b0 100644 --- a/hippunfold/workflow/rules/nnunet.smk +++ b/hippunfold/workflow/rules/nnunet.smk @@ -20,11 +20,9 @@ def get_nnunet_input(wildcards): desc="preproc", hemi="{hemi}", ) - if ( - config["modality"] == "T1w" - or config["modality"] == "T2w" - and config["force_nnunet_model"] == "T1T2w" - ): + if (config["modality"] == "T1w" or config["modality"] == "T2w") and config[ + "force_nnunet_model" + ] == "T1T2w": return (T1w_nii, T2w_nii) elif config["modality"] == "T2w": From 253e00754773dbf8ccbdf7b1ffb194d30c1540c6 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 04:02:21 +0000 Subject: [PATCH 16/17] Bump version to 1.5.2-pre.1 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index cae81c88..037abe7b 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.4" + version: "1.5.2-pre.1" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index ce678a4c..41856087 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.4", + "Version": "1.5.2-pre.1", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index 39a8c61e..a835758f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.4" +version = "1.5.2-pre.1" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "] From 9fd29d1fd03dfe2840f96348c3255571f7a63803 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 04:02:49 +0000 Subject: [PATCH 17/17] Bump version to 1.5.2-pre.2 --- hippunfold/config/snakebids.yml | 2 +- hippunfold/pipeline_description.json | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/hippunfold/config/snakebids.yml b/hippunfold/config/snakebids.yml index 037abe7b..65044f32 100644 --- a/hippunfold/config/snakebids.yml +++ b/hippunfold/config/snakebids.yml @@ -128,7 +128,7 @@ parse_args: --version: help: 'Print the version of HippUnfold' action: version - version: "1.5.2-pre.1" + version: "1.5.2-pre.2" --modality: diff --git a/hippunfold/pipeline_description.json b/hippunfold/pipeline_description.json index 41856087..745fe333 100644 --- a/hippunfold/pipeline_description.json +++ b/hippunfold/pipeline_description.json @@ -5,7 +5,7 @@ "GeneratedBy": [ { "Name": "hippunfold", - "Version": "1.5.2-pre.1", + "Version": "1.5.2-pre.2", "CodeURL": "https://github.com/khanlab/hippunfold", "Author": "Jordan DeKraker & Ali Khan", "AuthorEmail": "ali.khan@uwo.ca" diff --git a/pyproject.toml b/pyproject.toml index a835758f..b875b20f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "hippunfold" -version = "1.5.2-pre.1" +version = "1.5.2-pre.2" description = "BIDS App for Hippocampal AutoTop (automated hippocampal unfolding and subfield segmentation)" authors = ["Jordan DeKraker & Ali Khan "]