From e9a321b8ccd056cc2fcdea5493ae27aa018f4fd2 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 17 Sep 2025 23:16:44 +1000 Subject: [PATCH 1/5] renamed references to pydra-* to pydra-tasks-* --- docs/source/conf.py | 2 +- pydra/tasks/freesurfer/__init__.py | 2 +- related-packages/fileformats-extras/pyproject.toml | 2 +- related-packages/fileformats/pyproject.toml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index c8872682..8509f0d4 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -8,7 +8,7 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -project = "pydra-freesurfer" +project = "pydra-tasks-freesurfer" author = "Pydra Developers" copyright = f"2022-2023, {author}" release = __version__ diff --git a/pydra/tasks/freesurfer/__init__.py b/pydra/tasks/freesurfer/__init__.py index 3117bb39..c0ea4ae5 100644 --- a/pydra/tasks/freesurfer/__init__.py +++ b/pydra/tasks/freesurfer/__init__.py @@ -15,7 +15,7 @@ from ._version import __version__ except ImportError: raise RuntimeError( - "pydra-freesurfer has not been properly installed, please run " + "pydra-tasks-freesurfer has not been properly installed, please run " f"`pip install -e {str(pkg_path)}` to install a development version" ) diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml index f97b25a3..7aad38d9 100644 --- a/related-packages/fileformats-extras/pyproject.toml +++ b/related-packages/fileformats-extras/pyproject.toml @@ -58,7 +58,7 @@ converters = [ ] [project.urls] -repository = "https://github.com/nipype/pydra-freesurfer" +repository = "https://github.com/nipype/pydra-tasks-freesurfer" [tool.hatch.version] source = "vcs" diff --git a/related-packages/fileformats/pyproject.toml b/related-packages/fileformats/pyproject.toml index 9cf2fc5a..9bf39859 100644 --- a/related-packages/fileformats/pyproject.toml +++ b/related-packages/fileformats/pyproject.toml @@ -55,7 +55,7 @@ test = [ ] [project.urls] -repository = "https://github.com/nipype/pydra-freesurfer" +repository = "https://github.com/nipype/pydra-tasks-freesurfer" [tool.hatch.version] source = "vcs" From 03b207625fbe2ab675b788328a0df8f6bb4bb9be Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Mon, 13 Oct 2025 12:04:25 +1100 Subject: [PATCH 2/5] renamed fileformats package --- .gitignore | 4 +- .../v8/longitudinal/robust_template.py | 5 +- .../freesurfer/v8/model/label_2_label.py | 4 +- .../tasks/freesurfer/v8/model/label_2_vol.py | 4 +- .../v8/model/seg_stats_recon_all.py | 4 +- .../freesurfer/v8/model/spherical_average.py | 4 +- .../v8/model/tests/test_label2label.py | 2 +- .../v8/model/tests/test_label2vol.py | 2 +- .../v8/model/tests/test_segstatsreconall.py | 2 +- .../v8/model/tests/test_sphericalaverage.py | 2 +- pydra/tasks/freesurfer/v8/petsurfer/gtmpvc.py | 4 +- .../v8/petsurfer/tests/test_gtmpvc.py | 2 +- .../v8/preprocess/concatenate_lta.py | 4 +- .../v8/preprocess/mr_is_ca_label.py | 4 +- .../freesurfer/v8/preprocess/segment_cc.py | 4 +- .../tasks/freesurfer/v8/preprocess/smooth.py | 4 +- .../preprocess/tests/test_concatenatelta.py | 2 +- .../v8/preprocess/tests/test_mriscalabel.py | 2 +- .../v8/preprocess/tests/test_smooth.py | 2 +- .../tests/test_watershedskullstrip.py | 2 +- .../v8/preprocess/watershed_skull_strip.py | 4 +- .../tasks/freesurfer/v8/registration/paint.py | 4 +- .../freesurfer/v8/registration/register.py | 4 +- .../v8/registration/tests/test_paint.py | 2 +- .../v8/registration/tests/test_register.py | 2 +- .../tasks/freesurfer/v8/utils/aparc_2_aseg.py | 4 +- pydra/tasks/freesurfer/v8/utils/contrast.py | 4 +- pydra/tasks/freesurfer/v8/utils/curvature.py | 4 +- .../freesurfer/v8/utils/curvature_stats.py | 4 +- .../tasks/freesurfer/v8/utils/euler_number.py | 4 +- .../v8/utils/extract_main_component.py | 4 +- .../tasks/freesurfer/v8/utils/fix_topology.py | 4 +- pydra/tasks/freesurfer/v8/utils/jacobian.py | 4 +- .../freesurfer/v8/utils/make_surfaces.py | 4 +- pydra/tasks/freesurfer/v8/utils/mr_is_calc.py | 4 +- .../freesurfer/v8/utils/mr_is_combine.py | 4 +- .../tasks/freesurfer/v8/utils/mr_is_expand.py | 4 +- .../freesurfer/v8/utils/mr_is_inflate.py | 4 +- .../freesurfer/v8/utils/parcellation_stats.py | 4 +- .../v8/utils/relabel_hypointensities.py | 4 +- .../v8/utils/remove_intersection.py | 4 +- pydra/tasks/freesurfer/v8/utils/sphere.py | 4 +- .../v8/utils/tests/test_aparc2aseg.py | 2 +- .../v8/utils/tests/test_contrast.py | 2 +- .../v8/utils/tests/test_curvature.py | 2 +- .../v8/utils/tests/test_curvaturestats.py | 2 +- .../v8/utils/tests/test_eulernumber.py | 2 +- .../utils/tests/test_extractmaincomponent.py | 2 +- .../v8/utils/tests/test_fixtopology.py | 2 +- .../v8/utils/tests/test_jacobian.py | 2 +- .../v8/utils/tests/test_makesurfaces.py | 2 +- .../v8/utils/tests/test_mriscalc.py | 2 +- .../v8/utils/tests/test_mriscombine.py | 2 +- .../v8/utils/tests/test_mrisexpand.py | 2 +- .../v8/utils/tests/test_mrisinflate.py | 2 +- .../v8/utils/tests/test_parcellationstats.py | 2 +- .../tests/test_relabelhypointensities.py | 2 +- .../v8/utils/tests/test_removeintersection.py | 2 +- .../freesurfer/v8/utils/tests/test_sphere.py | 2 +- .../v8/utils/tests/test_volumemask.py | 2 +- .../tasks/freesurfer/v8/utils/tkregister_2.py | 4 +- .../tasks/freesurfer/v8/utils/volume_mask.py | 4 +- .../freesurfer/medimage}/__init__.py | 49 +++++++++++++------ .../tests/test_generate_sample_data.py | 3 +- .../fileformats-extras/pyproject.toml | 17 +++---- .../freesurfer/medimage}/__init__.py | 2 +- related-packages/fileformats/pyproject.toml | 15 +++--- 67 files changed, 147 insertions(+), 130 deletions(-) rename related-packages/fileformats-extras/fileformats/extras/{medimage_freesurfer => vendor/freesurfer/medimage}/__init__.py (60%) rename related-packages/fileformats-extras/fileformats/extras/{medimage_freesurfer => vendor/freesurfer/medimage}/tests/test_generate_sample_data.py (97%) rename related-packages/fileformats/fileformats/{medimage_freesurfer => vendor/freesurfer/medimage}/__init__.py (95%) diff --git a/.gitignore b/.gitignore index cb9cc377..100b60e1 100644 --- a/.gitignore +++ b/.gitignore @@ -156,6 +156,6 @@ cython_debug/ # Generated files /pydra/tasks/freesurfer/_version.py -/related-packages/fileformats/fileformats/medimage_freesurfer/_version.py -/related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/_version.py +/related-packages/fileformats/fileformats/vendor/freesurfer/_version.py +/related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/_version.py /pydra/tasks/freesurfer/auto diff --git a/pydra/tasks/freesurfer/v8/longitudinal/robust_template.py b/pydra/tasks/freesurfer/v8/longitudinal/robust_template.py index 86c5c211..89bfc2fc 100644 --- a/pydra/tasks/freesurfer/v8/longitudinal/robust_template.py +++ b/pydra/tasks/freesurfer/v8/longitudinal/robust_template.py @@ -1,11 +1,10 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import Nifti1 -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging import os from pathlib import Path -from pathlib import Path from pydra.compose import shell import typing as ty @@ -86,7 +85,7 @@ class RobustTemplate(shell.Task["RobustTemplate.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import Nifti1 - >>> from fileformats.medimage_freesurfer import Lta + >>> from fileformats.vendor.freesurfer.medimage import Lta >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.longitudinal.robust_template import RobustTemplate diff --git a/pydra/tasks/freesurfer/v8/model/label_2_label.py b/pydra/tasks/freesurfer/v8/model/label_2_label.py index ed00f932..ce579650 100644 --- a/pydra/tasks/freesurfer/v8/model/label_2_label.py +++ b/pydra/tasks/freesurfer/v8/model/label_2_label.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -17,7 +17,7 @@ class Label2Label(shell.Task["Label2Label.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.model.label_2_label import Label2Label diff --git a/pydra/tasks/freesurfer/v8/model/label_2_vol.py b/pydra/tasks/freesurfer/v8/model/label_2_vol.py index caa3c0c7..8ab070d2 100644 --- a/pydra/tasks/freesurfer/v8/model/label_2_vol.py +++ b/pydra/tasks/freesurfer/v8/model/label_2_vol.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import Nifti1 -from fileformats.medimage_freesurfer import Dat, Label +from fileformats.vendor.freesurfer.medimage import Dat, Label import logging from pydra.tasks.freesurfer.v8.nipype_ports.utils.filemanip import fname_presuffix import os @@ -39,7 +39,7 @@ class Label2Vol(shell.Task["Label2Vol.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import Nifti1 - >>> from fileformats.medimage_freesurfer import Dat, Label + >>> from fileformats.vendor.freesurfer.medimage import Dat, Label >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.model.label_2_vol import Label2Vol diff --git a/pydra/tasks/freesurfer/v8/model/seg_stats_recon_all.py b/pydra/tasks/freesurfer/v8/model/seg_stats_recon_all.py index 6e7f92b3..7c70b365 100644 --- a/pydra/tasks/freesurfer/v8/model/seg_stats_recon_all.py +++ b/pydra/tasks/freesurfer/v8/model/seg_stats_recon_all.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pydra.tasks.freesurfer.v8.nipype_ports.utils.filemanip import fname_presuffix import os @@ -137,7 +137,7 @@ class SegStatsReconAll(shell.Task["SegStatsReconAll.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.model.seg_stats_recon_all import SegStatsReconAll diff --git a/pydra/tasks/freesurfer/v8/model/spherical_average.py b/pydra/tasks/freesurfer/v8/model/spherical_average.py index 08d0f4a9..2627d423 100644 --- a/pydra/tasks/freesurfer/v8/model/spherical_average.py +++ b/pydra/tasks/freesurfer/v8/model/spherical_average.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pathlib import Path @@ -67,7 +67,7 @@ class SphericalAverage(shell.Task["SphericalAverage.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.model.spherical_average import SphericalAverage diff --git a/pydra/tasks/freesurfer/v8/model/tests/test_label2label.py b/pydra/tasks/freesurfer/v8/model/tests/test_label2label.py index 4f1eca2e..52645ee7 100644 --- a/pydra/tasks/freesurfer/v8/model/tests/test_label2label.py +++ b/pydra/tasks/freesurfer/v8/model/tests/test_label2label.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.model.label_2_label import Label2Label diff --git a/pydra/tasks/freesurfer/v8/model/tests/test_label2vol.py b/pydra/tasks/freesurfer/v8/model/tests/test_label2vol.py index 91459291..403800d8 100644 --- a/pydra/tasks/freesurfer/v8/model/tests/test_label2vol.py +++ b/pydra/tasks/freesurfer/v8/model/tests/test_label2vol.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import Nifti1 -from fileformats.medimage_freesurfer import Dat, Label +from fileformats.vendor.freesurfer.medimage import Dat, Label import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.model.label_2_vol import Label2Vol diff --git a/pydra/tasks/freesurfer/v8/model/tests/test_segstatsreconall.py b/pydra/tasks/freesurfer/v8/model/tests/test_segstatsreconall.py index ffe254fd..506e72be 100644 --- a/pydra/tasks/freesurfer/v8/model/tests/test_segstatsreconall.py +++ b/pydra/tasks/freesurfer/v8/model/tests/test_segstatsreconall.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.model.seg_stats_recon_all import SegStatsReconAll diff --git a/pydra/tasks/freesurfer/v8/model/tests/test_sphericalaverage.py b/pydra/tasks/freesurfer/v8/model/tests/test_sphericalaverage.py index 87538bc0..0d80320e 100644 --- a/pydra/tasks/freesurfer/v8/model/tests/test_sphericalaverage.py +++ b/pydra/tasks/freesurfer/v8/model/tests/test_sphericalaverage.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.model.spherical_average import SphericalAverage diff --git a/pydra/tasks/freesurfer/v8/petsurfer/gtmpvc.py b/pydra/tasks/freesurfer/v8/petsurfer/gtmpvc.py index 8649716a..aa718330 100644 --- a/pydra/tasks/freesurfer/v8/petsurfer/gtmpvc.py +++ b/pydra/tasks/freesurfer/v8/petsurfer/gtmpvc.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import NiftiGz -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging import os from pydra.compose import shell @@ -275,7 +275,7 @@ class GTMPVC(shell.Task["GTMPVC.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import NiftiGz - >>> from fileformats.medimage_freesurfer import Lta + >>> from fileformats.vendor.freesurfer.medimage import Lta >>> from pydra.tasks.freesurfer.v8.petsurfer.gtmpvc import GTMPVC >>> task = GTMPVC() diff --git a/pydra/tasks/freesurfer/v8/petsurfer/tests/test_gtmpvc.py b/pydra/tasks/freesurfer/v8/petsurfer/tests/test_gtmpvc.py index c006e398..cd3ee7c0 100644 --- a/pydra/tasks/freesurfer/v8/petsurfer/tests/test_gtmpvc.py +++ b/pydra/tasks/freesurfer/v8/petsurfer/tests/test_gtmpvc.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import NiftiGz -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.petsurfer.gtmpvc import GTMPVC diff --git a/pydra/tasks/freesurfer/v8/preprocess/concatenate_lta.py b/pydra/tasks/freesurfer/v8/preprocess/concatenate_lta.py index 15b4d790..dec9b83d 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/concatenate_lta.py +++ b/pydra/tasks/freesurfer/v8/preprocess/concatenate_lta.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging from pathlib import Path from pathlib import Path @@ -31,7 +31,7 @@ class ConcatenateLTA(shell.Task["ConcatenateLTA.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Lta + >>> from fileformats.vendor.freesurfer.medimage import Lta >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.preprocess.concatenate_lta import ConcatenateLTA diff --git a/pydra/tasks/freesurfer/v8/preprocess/mr_is_ca_label.py b/pydra/tasks/freesurfer/v8/preprocess/mr_is_ca_label.py index d0c29530..f2d889d6 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/mr_is_ca_label.py +++ b/pydra/tasks/freesurfer/v8/preprocess/mr_is_ca_label.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -17,7 +17,7 @@ class MRIsCALabel(shell.Task["MRIsCALabel.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.preprocess.mr_is_ca_label import MRIsCALabel diff --git a/pydra/tasks/freesurfer/v8/preprocess/segment_cc.py b/pydra/tasks/freesurfer/v8/preprocess/segment_cc.py index d73404bf..33162676 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/segment_cc.py +++ b/pydra/tasks/freesurfer/v8/preprocess/segment_cc.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging import os from pathlib import Path @@ -82,7 +82,7 @@ class SegmentCC(shell.Task["SegmentCC.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Lta + >>> from fileformats.vendor.freesurfer.medimage import Lta >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.preprocess.segment_cc import SegmentCC diff --git a/pydra/tasks/freesurfer/v8/preprocess/smooth.py b/pydra/tasks/freesurfer/v8/preprocess/smooth.py index c125f0ae..e9ee1d12 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/smooth.py +++ b/pydra/tasks/freesurfer/v8/preprocess/smooth.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory from fileformats.medimage import Nifti1 -from fileformats.medimage_freesurfer import Dat +from fileformats.vendor.freesurfer.medimage import Dat import logging from pydra.tasks.freesurfer.v8.nipype_ports.utils.filemanip import fname_presuffix from pathlib import Path @@ -33,7 +33,7 @@ class Smooth(shell.Task["Smooth.Outputs"]): >>> from fileformats.generic import Directory >>> from fileformats.medimage import Nifti1 - >>> from fileformats.medimage_freesurfer import Dat + >>> from fileformats.vendor.freesurfer.medimage import Dat >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.preprocess.smooth import Smooth diff --git a/pydra/tasks/freesurfer/v8/preprocess/tests/test_concatenatelta.py b/pydra/tasks/freesurfer/v8/preprocess/tests/test_concatenatelta.py index 0c9ae00c..3b2f6d2a 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/tests/test_concatenatelta.py +++ b/pydra/tasks/freesurfer/v8/preprocess/tests/test_concatenatelta.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.preprocess.concatenate_lta import ConcatenateLTA diff --git a/pydra/tasks/freesurfer/v8/preprocess/tests/test_mriscalabel.py b/pydra/tasks/freesurfer/v8/preprocess/tests/test_mriscalabel.py index 0a4c6f78..516b189a 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/tests/test_mriscalabel.py +++ b/pydra/tasks/freesurfer/v8/preprocess/tests/test_mriscalabel.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.preprocess.mr_is_ca_label import MRIsCALabel diff --git a/pydra/tasks/freesurfer/v8/preprocess/tests/test_smooth.py b/pydra/tasks/freesurfer/v8/preprocess/tests/test_smooth.py index f3da8b44..ddd9f31d 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/tests/test_smooth.py +++ b/pydra/tasks/freesurfer/v8/preprocess/tests/test_smooth.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory from fileformats.medimage import Nifti1 -from fileformats.medimage_freesurfer import Dat +from fileformats.vendor.freesurfer.medimage import Dat import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.preprocess.smooth import Smooth diff --git a/pydra/tasks/freesurfer/v8/preprocess/tests/test_watershedskullstrip.py b/pydra/tasks/freesurfer/v8/preprocess/tests/test_watershedskullstrip.py index 1c82d0b7..7c27fb3e 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/tests/test_watershedskullstrip.py +++ b/pydra/tasks/freesurfer/v8/preprocess/tests/test_watershedskullstrip.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.preprocess.watershed_skull_strip import ( diff --git a/pydra/tasks/freesurfer/v8/preprocess/watershed_skull_strip.py b/pydra/tasks/freesurfer/v8/preprocess/watershed_skull_strip.py index 5f096b89..90020506 100644 --- a/pydra/tasks/freesurfer/v8/preprocess/watershed_skull_strip.py +++ b/pydra/tasks/freesurfer/v8/preprocess/watershed_skull_strip.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Lta +from fileformats.vendor.freesurfer.medimage import Lta import logging import os from pathlib import Path @@ -35,7 +35,7 @@ class WatershedSkullStrip(shell.Task["WatershedSkullStrip.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Lta + >>> from fileformats.vendor.freesurfer.medimage import Lta >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.preprocess.watershed_skull_strip import WatershedSkullStrip diff --git a/pydra/tasks/freesurfer/v8/registration/paint.py b/pydra/tasks/freesurfer/v8/registration/paint.py index 40aa7d6a..ace3d417 100644 --- a/pydra/tasks/freesurfer/v8/registration/paint.py +++ b/pydra/tasks/freesurfer/v8/registration/paint.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -32,7 +32,7 @@ class Paint(shell.Task["Paint.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.registration.paint import Paint diff --git a/pydra/tasks/freesurfer/v8/registration/register.py b/pydra/tasks/freesurfer/v8/registration/register.py index aa685e14..43ab6587 100644 --- a/pydra/tasks/freesurfer/v8/registration/register.py +++ b/pydra/tasks/freesurfer/v8/registration/register.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os import os.path @@ -45,7 +45,7 @@ class Register(shell.Task["Register.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.registration.register import Register diff --git a/pydra/tasks/freesurfer/v8/registration/tests/test_paint.py b/pydra/tasks/freesurfer/v8/registration/tests/test_paint.py index 73016906..2f2ae3f6 100644 --- a/pydra/tasks/freesurfer/v8/registration/tests/test_paint.py +++ b/pydra/tasks/freesurfer/v8/registration/tests/test_paint.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.registration.paint import Paint diff --git a/pydra/tasks/freesurfer/v8/registration/tests/test_register.py b/pydra/tasks/freesurfer/v8/registration/tests/test_register.py index a605fdfa..6684b0ba 100644 --- a/pydra/tasks/freesurfer/v8/registration/tests/test_register.py +++ b/pydra/tasks/freesurfer/v8/registration/tests/test_register.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.registration.register import Register diff --git a/pydra/tasks/freesurfer/v8/utils/aparc_2_aseg.py b/pydra/tasks/freesurfer/v8/utils/aparc_2_aseg.py index f35d250d..4592f848 100644 --- a/pydra/tasks/freesurfer/v8/utils/aparc_2_aseg.py +++ b/pydra/tasks/freesurfer/v8/utils/aparc_2_aseg.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pathlib import Path @@ -58,7 +58,7 @@ class Aparc2Aseg(shell.Task["Aparc2Aseg.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.aparc_2_aseg import Aparc2Aseg diff --git a/pydra/tasks/freesurfer/v8/utils/contrast.py b/pydra/tasks/freesurfer/v8/utils/contrast.py index 999b1562..7d030496 100644 --- a/pydra/tasks/freesurfer/v8/utils/contrast.py +++ b/pydra/tasks/freesurfer/v8/utils/contrast.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Annot, White +from fileformats.vendor.freesurfer.medimage import Annot, White import logging import os from pydra.compose import shell @@ -55,7 +55,7 @@ class Contrast(shell.Task["Contrast.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Annot, White + >>> from fileformats.vendor.freesurfer.medimage import Annot, White >>> from pydra.tasks.freesurfer.v8.utils.contrast import Contrast >>> task = Contrast() diff --git a/pydra/tasks/freesurfer/v8/utils/curvature.py b/pydra/tasks/freesurfer/v8/utils/curvature.py index 5a023512..a944238e 100644 --- a/pydra/tasks/freesurfer/v8/utils/curvature.py +++ b/pydra/tasks/freesurfer/v8/utils/curvature.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pydra.compose import shell @@ -60,7 +60,7 @@ class Curvature(shell.Task["Curvature.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pydra.tasks.freesurfer.v8.utils.curvature import Curvature >>> task = Curvature() diff --git a/pydra/tasks/freesurfer/v8/utils/curvature_stats.py b/pydra/tasks/freesurfer/v8/utils/curvature_stats.py index f3dd0815..fa6e4480 100644 --- a/pydra/tasks/freesurfer/v8/utils/curvature_stats.py +++ b/pydra/tasks/freesurfer/v8/utils/curvature_stats.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pathlib import Path @@ -29,7 +29,7 @@ class CurvatureStats(shell.Task["CurvatureStats.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.curvature_stats import CurvatureStats diff --git a/pydra/tasks/freesurfer/v8/utils/euler_number.py b/pydra/tasks/freesurfer/v8/utils/euler_number.py index 9ed15a55..3f8761fd 100644 --- a/pydra/tasks/freesurfer/v8/utils/euler_number.py +++ b/pydra/tasks/freesurfer/v8/utils/euler_number.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pydra.compose import shell @@ -38,7 +38,7 @@ class EulerNumber(shell.Task["EulerNumber.Outputs"]): ------- >>> from fileformats.generic import Directory - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pydra.tasks.freesurfer.v8.utils.euler_number import EulerNumber >>> task = EulerNumber() diff --git a/pydra/tasks/freesurfer/v8/utils/extract_main_component.py b/pydra/tasks/freesurfer/v8/utils/extract_main_component.py index fe08bb78..f2db2a3d 100644 --- a/pydra/tasks/freesurfer/v8/utils/extract_main_component.py +++ b/pydra/tasks/freesurfer/v8/utils/extract_main_component.py @@ -1,4 +1,4 @@ -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -14,7 +14,7 @@ class ExtractMainComponent(shell.Task["ExtractMainComponent.Outputs"]): Examples ------- - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.extract_main_component import ExtractMainComponent diff --git a/pydra/tasks/freesurfer/v8/utils/fix_topology.py b/pydra/tasks/freesurfer/v8/utils/fix_topology.py index 274efa78..7cb21b80 100644 --- a/pydra/tasks/freesurfer/v8/utils/fix_topology.py +++ b/pydra/tasks/freesurfer/v8/utils/fix_topology.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Nofix, Orig +from fileformats.vendor.freesurfer.medimage import Nofix, Orig import logging import os from pydra.compose import shell @@ -48,7 +48,7 @@ class FixTopology(shell.Task["FixTopology.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Nofix, Orig + >>> from fileformats.vendor.freesurfer.medimage import Nofix, Orig >>> from pydra.tasks.freesurfer.v8.utils.fix_topology import FixTopology >>> task = FixTopology() diff --git a/pydra/tasks/freesurfer/v8/utils/jacobian.py b/pydra/tasks/freesurfer/v8/utils/jacobian.py index 8d104f86..7b49ecc1 100644 --- a/pydra/tasks/freesurfer/v8/utils/jacobian.py +++ b/pydra/tasks/freesurfer/v8/utils/jacobian.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -16,7 +16,7 @@ class Jacobian(shell.Task["Jacobian.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.jacobian import Jacobian diff --git a/pydra/tasks/freesurfer/v8/utils/make_surfaces.py b/pydra/tasks/freesurfer/v8/utils/make_surfaces.py index c5a85f85..085309b0 100644 --- a/pydra/tasks/freesurfer/v8/utils/make_surfaces.py +++ b/pydra/tasks/freesurfer/v8/utils/make_surfaces.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pydra.compose import shell @@ -131,7 +131,7 @@ class MakeSurfaces(shell.Task["MakeSurfaces.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pydra.tasks.freesurfer.v8.utils.make_surfaces import MakeSurfaces >>> task = MakeSurfaces() diff --git a/pydra/tasks/freesurfer/v8/utils/mr_is_calc.py b/pydra/tasks/freesurfer/v8/utils/mr_is_calc.py index fea7dcd2..85fb1c72 100644 --- a/pydra/tasks/freesurfer/v8/utils/mr_is_calc.py +++ b/pydra/tasks/freesurfer/v8/utils/mr_is_calc.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Area +from fileformats.vendor.freesurfer.medimage import Area import logging import os from pathlib import Path @@ -34,7 +34,7 @@ class MRIsCalc(shell.Task["MRIsCalc.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Area + >>> from fileformats.vendor.freesurfer.medimage import Area >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.mr_is_calc import MRIsCalc diff --git a/pydra/tasks/freesurfer/v8/utils/mr_is_combine.py b/pydra/tasks/freesurfer/v8/utils/mr_is_combine.py index c4383934..fc5d2a61 100644 --- a/pydra/tasks/freesurfer/v8/utils/mr_is_combine.py +++ b/pydra/tasks/freesurfer/v8/utils/mr_is_combine.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -16,7 +16,7 @@ class MRIsCombine(shell.Task["MRIsCombine.Outputs"]): ------- >>> from fileformats.generic import Directory - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.mr_is_combine import MRIsCombine diff --git a/pydra/tasks/freesurfer/v8/utils/mr_is_expand.py b/pydra/tasks/freesurfer/v8/utils/mr_is_expand.py index c48d7538..9c6f5ac1 100644 --- a/pydra/tasks/freesurfer/v8/utils/mr_is_expand.py +++ b/pydra/tasks/freesurfer/v8/utils/mr_is_expand.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import White +from fileformats.vendor.freesurfer.medimage import White import logging import os from pydra.compose import shell @@ -38,7 +38,7 @@ class MRIsExpand(shell.Task["MRIsExpand.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import White + >>> from fileformats.vendor.freesurfer.medimage import White >>> from pydra.tasks.freesurfer.v8.utils.mr_is_expand import MRIsExpand >>> task = MRIsExpand() diff --git a/pydra/tasks/freesurfer/v8/utils/mr_is_inflate.py b/pydra/tasks/freesurfer/v8/utils/mr_is_inflate.py index 3a19f928..c5c30721 100644 --- a/pydra/tasks/freesurfer/v8/utils/mr_is_inflate.py +++ b/pydra/tasks/freesurfer/v8/utils/mr_is_inflate.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pathlib import Path @@ -36,7 +36,7 @@ class MRIsInflate(shell.Task["MRIsInflate.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.mr_is_inflate import MRIsInflate diff --git a/pydra/tasks/freesurfer/v8/utils/parcellation_stats.py b/pydra/tasks/freesurfer/v8/utils/parcellation_stats.py index 7d786bf2..d27b4200 100644 --- a/pydra/tasks/freesurfer/v8/utils/parcellation_stats.py +++ b/pydra/tasks/freesurfer/v8/utils/parcellation_stats.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial, White +from fileformats.vendor.freesurfer.medimage import Pial, White import logging import os from pathlib import Path @@ -50,7 +50,7 @@ class ParcellationStats(shell.Task["ParcellationStats.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz - >>> from fileformats.medimage_freesurfer import Pial, White + >>> from fileformats.vendor.freesurfer.medimage import Pial, White >>> import os >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.parcellation_stats import ParcellationStats diff --git a/pydra/tasks/freesurfer/v8/utils/relabel_hypointensities.py b/pydra/tasks/freesurfer/v8/utils/relabel_hypointensities.py index dc309069..afafbeb5 100644 --- a/pydra/tasks/freesurfer/v8/utils/relabel_hypointensities.py +++ b/pydra/tasks/freesurfer/v8/utils/relabel_hypointensities.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -16,7 +16,7 @@ class RelabelHypointensities(shell.Task["RelabelHypointensities.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.relabel_hypointensities import RelabelHypointensities diff --git a/pydra/tasks/freesurfer/v8/utils/remove_intersection.py b/pydra/tasks/freesurfer/v8/utils/remove_intersection.py index b004a036..09168313 100644 --- a/pydra/tasks/freesurfer/v8/utils/remove_intersection.py +++ b/pydra/tasks/freesurfer/v8/utils/remove_intersection.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -16,7 +16,7 @@ class RemoveIntersection(shell.Task["RemoveIntersection.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.remove_intersection import RemoveIntersection diff --git a/pydra/tasks/freesurfer/v8/utils/sphere.py b/pydra/tasks/freesurfer/v8/utils/sphere.py index fdc48d42..a97513c9 100644 --- a/pydra/tasks/freesurfer/v8/utils/sphere.py +++ b/pydra/tasks/freesurfer/v8/utils/sphere.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from pathlib import Path from pathlib import Path @@ -16,7 +16,7 @@ class Sphere(shell.Task["Sphere.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.sphere import Sphere diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_aparc2aseg.py b/pydra/tasks/freesurfer/v8/utils/tests/test_aparc2aseg.py index 12e16717..2120c928 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_aparc2aseg.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_aparc2aseg.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.aparc_2_aseg import Aparc2Aseg diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_contrast.py b/pydra/tasks/freesurfer/v8/utils/tests/test_contrast.py index ec832e00..c96e58b5 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_contrast.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_contrast.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Annot, White +from fileformats.vendor.freesurfer.medimage import Annot, White import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.contrast import Contrast diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_curvature.py b/pydra/tasks/freesurfer/v8/utils/tests/test_curvature.py index 1f1bdc59..6a60707e 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_curvature.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_curvature.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.curvature import Curvature diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_curvaturestats.py b/pydra/tasks/freesurfer/v8/utils/tests/test_curvaturestats.py index 92f3fa41..c0afa559 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_curvaturestats.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_curvaturestats.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.curvature_stats import CurvatureStats diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_eulernumber.py b/pydra/tasks/freesurfer/v8/utils/tests/test_eulernumber.py index 14b92c18..7b271be4 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_eulernumber.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_eulernumber.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.euler_number import EulerNumber diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_extractmaincomponent.py b/pydra/tasks/freesurfer/v8/utils/tests/test_extractmaincomponent.py index a33f5798..c0c55082 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_extractmaincomponent.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_extractmaincomponent.py @@ -1,4 +1,4 @@ -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.extract_main_component import ExtractMainComponent diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_fixtopology.py b/pydra/tasks/freesurfer/v8/utils/tests/test_fixtopology.py index 1430cca1..ec6a04ab 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_fixtopology.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_fixtopology.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Nofix, Orig +from fileformats.vendor.freesurfer.medimage import Nofix, Orig import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.fix_topology import FixTopology diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_jacobian.py b/pydra/tasks/freesurfer/v8/utils/tests/test_jacobian.py index 32bc1a88..829246eb 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_jacobian.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_jacobian.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.jacobian import Jacobian diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_makesurfaces.py b/pydra/tasks/freesurfer/v8/utils/tests/test_makesurfaces.py index ff0bd301..4bb7074e 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_makesurfaces.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_makesurfaces.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.make_surfaces import MakeSurfaces diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_mriscalc.py b/pydra/tasks/freesurfer/v8/utils/tests/test_mriscalc.py index ad079c2f..a4044a07 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_mriscalc.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_mriscalc.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Area +from fileformats.vendor.freesurfer.medimage import Area import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.mr_is_calc import MRIsCalc diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_mriscombine.py b/pydra/tasks/freesurfer/v8/utils/tests/test_mriscombine.py index b11fb0f9..0b3d8d6f 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_mriscombine.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_mriscombine.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.mr_is_combine import MRIsCombine diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_mrisexpand.py b/pydra/tasks/freesurfer/v8/utils/tests/test_mrisexpand.py index 86ac4954..67ea2bf9 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_mrisexpand.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_mrisexpand.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import White +from fileformats.vendor.freesurfer.medimage import White import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.mr_is_expand import MRIsExpand diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_mrisinflate.py b/pydra/tasks/freesurfer/v8/utils/tests/test_mrisinflate.py index 6d583b65..2d174050 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_mrisinflate.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_mrisinflate.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.mr_is_inflate import MRIsInflate diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_parcellationstats.py b/pydra/tasks/freesurfer/v8/utils/tests/test_parcellationstats.py index 5534800e..a5eb3501 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_parcellationstats.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_parcellationstats.py @@ -1,6 +1,6 @@ from fileformats.generic import Directory, File from fileformats.medimage import MghGz -from fileformats.medimage_freesurfer import Pial, White +from fileformats.vendor.freesurfer.medimage import Pial, White import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.parcellation_stats import ParcellationStats diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_relabelhypointensities.py b/pydra/tasks/freesurfer/v8/utils/tests/test_relabelhypointensities.py index 6f9fcb0f..fa91df6b 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_relabelhypointensities.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_relabelhypointensities.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.relabel_hypointensities import ( diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_removeintersection.py b/pydra/tasks/freesurfer/v8/utils/tests/test_removeintersection.py index 739fdb68..d17af7f0 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_removeintersection.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_removeintersection.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.remove_intersection import RemoveIntersection diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_sphere.py b/pydra/tasks/freesurfer/v8/utils/tests/test_sphere.py index 117b6302..59d37835 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_sphere.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_sphere.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.sphere import Sphere diff --git a/pydra/tasks/freesurfer/v8/utils/tests/test_volumemask.py b/pydra/tasks/freesurfer/v8/utils/tests/test_volumemask.py index 4a341441..93a19c48 100644 --- a/pydra/tasks/freesurfer/v8/utils/tests/test_volumemask.py +++ b/pydra/tasks/freesurfer/v8/utils/tests/test_volumemask.py @@ -1,5 +1,5 @@ from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging from nipype2pydra.testing import PassAfterTimeoutWorker from pydra.tasks.freesurfer.v8.utils.volume_mask import VolumeMask diff --git a/pydra/tasks/freesurfer/v8/utils/tkregister_2.py b/pydra/tasks/freesurfer/v8/utils/tkregister_2.py index 57b52cff..ef2e46d5 100644 --- a/pydra/tasks/freesurfer/v8/utils/tkregister_2.py +++ b/pydra/tasks/freesurfer/v8/utils/tkregister_2.py @@ -1,7 +1,7 @@ import attrs from fileformats.generic import Directory, File from fileformats.medimage import MghGz, Nifti1 -from fileformats.medimage_freesurfer import Dat +from fileformats.vendor.freesurfer.medimage import Dat import logging from pydra.tasks.freesurfer.v8.nipype_ports.utils.filemanip import fname_presuffix import os @@ -96,7 +96,7 @@ class Tkregister2(shell.Task["Tkregister2.Outputs"]): >>> from fileformats.generic import Directory, File >>> from fileformats.medimage import MghGz, Nifti1 - >>> from fileformats.medimage_freesurfer import Dat + >>> from fileformats.vendor.freesurfer.medimage import Dat >>> from pathlib import Path >>> from pydra.tasks.freesurfer.v8.utils.tkregister_2 import Tkregister2 diff --git a/pydra/tasks/freesurfer/v8/utils/volume_mask.py b/pydra/tasks/freesurfer/v8/utils/volume_mask.py index 0621a051..75e212bc 100644 --- a/pydra/tasks/freesurfer/v8/utils/volume_mask.py +++ b/pydra/tasks/freesurfer/v8/utils/volume_mask.py @@ -1,6 +1,6 @@ import attrs from fileformats.generic import Directory, File -from fileformats.medimage_freesurfer import Pial +from fileformats.vendor.freesurfer.medimage import Pial import logging import os from pydra.compose import shell @@ -64,7 +64,7 @@ class VolumeMask(shell.Task["VolumeMask.Outputs"]): ------- >>> from fileformats.generic import Directory, File - >>> from fileformats.medimage_freesurfer import Pial + >>> from fileformats.vendor.freesurfer.medimage import Pial >>> from pydra.tasks.freesurfer.v8.utils.volume_mask import VolumeMask >>> task = VolumeMask() diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/__init__.py b/related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/medimage/__init__.py similarity index 60% rename from related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/__init__.py rename to related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/medimage/__init__.py index 14a7a85f..d9ef314d 100644 --- a/related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/__init__.py +++ b/related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/medimage/__init__.py @@ -1,9 +1,9 @@ -from ._version import __version__ # noqa: F401 +from .._version import __version__ # noqa: F401 from pathlib import Path import typing as ty from random import Random from fileformats.core import FileSet, SampleFileGenerator -from fileformats.medimage_freesurfer import ( +from fileformats.vendor.freesurfer.medimage import ( Inflated, Nofix, Thickness, @@ -23,24 +23,31 @@ ) - @FileSet.generate_sample_data.register -def gen_sample_inflated_data(inflated: Inflated, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_inflated_data( + inflated: Inflated, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_nofix_data(nofix: Nofix, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_nofix_data( + nofix: Nofix, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_thickness_data(thickness: Thickness, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_thickness_data( + thickness: Thickness, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_pial_data(pial: Pial, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_pial_data( + pial: Pial, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @@ -55,7 +62,9 @@ def gen_sample_xfm_data(xfm: Xfm, generator: SampleFileGenerator) -> ty.Iterable @FileSet.generate_sample_data.register -def gen_sample_ctab_data(ctab: Ctab, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_ctab_data( + ctab: Ctab, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @@ -70,17 +79,23 @@ def gen_sample_reg_data(reg: Reg, generator: SampleFileGenerator) -> ty.Iterable @FileSet.generate_sample_data.register -def gen_sample_area_data(area: Area, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_area_data( + area: Area, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_annot_data(annot: Annot, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_annot_data( + annot: Annot, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_orig_data(orig: Orig, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_orig_data( + orig: Orig, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @@ -90,15 +105,21 @@ def gen_sample_lta_data(lta: Lta, generator: SampleFileGenerator) -> ty.Iterable @FileSet.generate_sample_data.register -def gen_sample_stats_data(stats: Stats, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_stats_data( + stats: Stats, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_white_data(white: White, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_white_data( + white: White, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError @FileSet.generate_sample_data.register -def gen_sample_label_data(label: Label, generator: SampleFileGenerator) -> ty.Iterable[Path]: +def gen_sample_label_data( + label: Label, generator: SampleFileGenerator +) -> ty.Iterable[Path]: raise NotImplementedError diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/tests/test_generate_sample_data.py b/related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/medimage/tests/test_generate_sample_data.py similarity index 97% rename from related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/tests/test_generate_sample_data.py rename to related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/medimage/tests/test_generate_sample_data.py index 20ed6fc2..3ee503ea 100644 --- a/related-packages/fileformats-extras/fileformats/extras/medimage_freesurfer/tests/test_generate_sample_data.py +++ b/related-packages/fileformats-extras/fileformats/extras/vendor/freesurfer/medimage/tests/test_generate_sample_data.py @@ -1,5 +1,5 @@ import pytest -from fileformats.medimage_freesurfer import ( +from fileformats.vendor.freesurfer.medimage import ( Label, Lta, Orig, @@ -19,7 +19,6 @@ ) - @pytest.mark.xfail(reason="generate_sample_data not implemented") def test_generate_sample_label_data(): assert isinstance(Label.sample(), Label) diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml index 7aad38d9..f90a302d 100644 --- a/related-packages/fileformats-extras/pyproject.toml +++ b/related-packages/fileformats-extras/pyproject.toml @@ -3,14 +3,14 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-freesurfer-extras" +name = "fileformats-vendor-freesurfer-extras" description = "Extensions to add functionality to tool-specific *fileformats* classes" readme = "README.rst" -requires-python = ">=3.8" +requires-python = ">=3.11" dependencies = [ "fileformats", - "fileformats-medimage-freesurfer", - "pydra >= 0.23.0a" + "fileformats-vendor-freesurfer", + "pydra >= 1.0a" ] license = {file = "LICENSE"} authors = [ @@ -31,10 +31,9 @@ classifiers = [ "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Topic :: Scientific/Engineering", ] dynamic = ["version"] @@ -65,14 +64,14 @@ source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/extras/medimage_freesurfer/_version.py" +version-file = "fileformats/extras/vendor/freesurfer/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/extras/medimage_freesurfer/_version.py" +exclude = "fileformats/extras/vendor/freesurfer/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" diff --git a/related-packages/fileformats/fileformats/medimage_freesurfer/__init__.py b/related-packages/fileformats/fileformats/vendor/freesurfer/medimage/__init__.py similarity index 95% rename from related-packages/fileformats/fileformats/medimage_freesurfer/__init__.py rename to related-packages/fileformats/fileformats/vendor/freesurfer/medimage/__init__.py index b8b51a9b..2c62067f 100644 --- a/related-packages/fileformats/fileformats/medimage_freesurfer/__init__.py +++ b/related-packages/fileformats/fileformats/vendor/freesurfer/medimage/__init__.py @@ -1,4 +1,4 @@ -from ._version import __version__ # noqa: F401 +from .._version import __version__ # noqa: F401 from fileformats.generic import File diff --git a/related-packages/fileformats/pyproject.toml b/related-packages/fileformats/pyproject.toml index 9bf39859..d92a8353 100644 --- a/related-packages/fileformats/pyproject.toml +++ b/related-packages/fileformats/pyproject.toml @@ -3,10 +3,10 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "fileformats-medimage-freesurfer" +name = "fileformats-vendor-freesurfer" description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows" readme = "README.rst" -requires-python = ">=3.8" +requires-python = ">=3.11" dependencies = [ "fileformats", "fileformats-medimage" @@ -30,10 +30,9 @@ classifiers = [ "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Topic :: Scientific/Engineering", ] dynamic = ["version"] @@ -51,7 +50,7 @@ test = [ "pytest-env>=0.6.2", "pytest-cov>=2.12.1", "codecov", - "fileformats-medimage-freesurfer-extras", + "fileformats-vendor-freesurfer-extras", ] [project.urls] @@ -62,14 +61,14 @@ source = "vcs" raw-options = { root = "../.." } [tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_freesurfer/_version.py" +version-file = "fileformats/vendor/freesurfer/_version.py" [tool.hatch.build.targets.wheel] packages = ["fileformats"] [tool.black] target-version = ['py38'] -exclude = "fileformats/medimage_freesurfer/_version.py" +exclude = "fileformats/vendor/freesurfer/_version.py" [tool.codespell] ignore-words = ".codespell-ignorewords" From 7eb8e4d233fd3fcaeb5df8ff9ae4c7039f15c726 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Mon, 13 Oct 2025 12:07:05 +1100 Subject: [PATCH 3/5] updated ci-cd spec --- .github/workflows/ci-cd.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml index 961764ef..6dc80c21 100644 --- a/.github/workflows/ci-cd.yaml +++ b/.github/workflows/ci-cd.yaml @@ -129,11 +129,11 @@ jobs: - name: Install task package run: | pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]" - python -c "import fileformats.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" + python -c "import fileformats.vendor.freesurfer.medimage as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')" - name: Test fileformats with pytest run: >- - pytest ./related-packages -sv --cov fileformats.medimage_freesurfer - --cov fileformats.extras.medimage_freesurfer --cov-report xml . + pytest ./related-packages -sv --cov fileformats.vendor.freesurfer.medimage + --cov fileformats.extras.vendor.freesurfer.medimage --cov-report xml . deploy-fileformats: needs: [build, test, fileformats-test] From e6c573ba2250d74ada44c31d4ebddf66a338c6ae Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Mon, 13 Oct 2025 13:21:53 +1100 Subject: [PATCH 4/5] cleaned up references to fileformats package --- nipype-auto-conv/specs/interfaces/aparc_2_aseg.yaml | 6 +++--- nipype-auto-conv/specs/interfaces/concatenate_lta.yaml | 4 ++-- nipype-auto-conv/specs/interfaces/contrast.yaml | 4 ++-- nipype-auto-conv/specs/interfaces/curvature.yaml | 2 +- nipype-auto-conv/specs/interfaces/curvature_stats.yaml | 4 ++-- nipype-auto-conv/specs/interfaces/em_register.yaml | 2 +- nipype-auto-conv/specs/interfaces/euler_number.yaml | 2 +- .../specs/interfaces/extract_main_component.yaml | 2 +- nipype-auto-conv/specs/interfaces/fix_topology.yaml | 4 ++-- nipype-auto-conv/specs/interfaces/gtmpvc.yaml | 2 +- nipype-auto-conv/specs/interfaces/jacobian.yaml | 2 +- nipype-auto-conv/specs/interfaces/label_2_label.yaml | 4 ++-- nipype-auto-conv/specs/interfaces/label_2_vol.yaml | 2 +- nipype-auto-conv/specs/interfaces/make_surfaces.yaml | 2 +- nipype-auto-conv/specs/interfaces/mr_is_ca_label.yaml | 6 +++--- nipype-auto-conv/specs/interfaces/mr_is_calc.yaml | 2 +- nipype-auto-conv/specs/interfaces/mr_is_expand.yaml | 2 +- nipype-auto-conv/specs/interfaces/mr_is_inflate.yaml | 2 +- nipype-auto-conv/specs/interfaces/paint.yaml | 2 +- nipype-auto-conv/specs/interfaces/parcellation_stats.yaml | 6 +++--- nipype-auto-conv/specs/interfaces/register.yaml | 6 +++--- .../specs/interfaces/relabel_hypointensities.yaml | 2 +- .../specs/interfaces/remove_intersection.yaml | 2 +- nipype-auto-conv/specs/interfaces/seg_stats.yaml | 2 +- .../specs/interfaces/seg_stats_recon_all.yaml | 8 ++++---- nipype-auto-conv/specs/interfaces/segment_cc.yaml | 2 +- nipype-auto-conv/specs/interfaces/smooth.yaml | 2 +- nipype-auto-conv/specs/interfaces/sphere.yaml | 2 +- nipype-auto-conv/specs/interfaces/spherical_average.yaml | 4 ++-- nipype-auto-conv/specs/interfaces/tkregister_2.yaml | 2 +- nipype-auto-conv/specs/interfaces/volume_mask.yaml | 4 ++-- .../specs/interfaces/watershed_skull_strip.yaml | 2 +- pyproject.toml | 2 +- 33 files changed, 51 insertions(+), 51 deletions(-) diff --git a/nipype-auto-conv/specs/interfaces/aparc_2_aseg.yaml b/nipype-auto-conv/specs/interfaces/aparc_2_aseg.yaml index 7ce3308d..2e4fb1db 100644 --- a/nipype-auto-conv/specs/interfaces/aparc_2_aseg.yaml +++ b/nipype-auto-conv/specs/interfaces/aparc_2_aseg.yaml @@ -63,13 +63,13 @@ inputs: # type=file|default=: Implicit input filled file. Only required with FS v5.3. lh_annotation: generic/file # type=file|default=: Input file must be /label/lh.aparc.annot - lh_pial: fileformats.medimage_freesurfer.Pial + lh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/lh.pial lh_ribbon: medimage/mgh-gz # type=file|default=: Input file must be /mri/lh.ribbon.mgz - lh_white: fileformats.medimage_freesurfer.Pial + lh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/lh.white - rh_annotation: fileformats.medimage_freesurfer.Pial + rh_annotation: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /label/rh.aparc.annot rh_pial: generic/file # type=file|default=: Input file must be /surf/rh.pial diff --git a/nipype-auto-conv/specs/interfaces/concatenate_lta.yaml b/nipype-auto-conv/specs/interfaces/concatenate_lta.yaml index dd1cb089..e676f281 100644 --- a/nipype-auto-conv/specs/interfaces/concatenate_lta.yaml +++ b/nipype-auto-conv/specs/interfaces/concatenate_lta.yaml @@ -47,7 +47,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_lta1: fileformats.medimage_freesurfer.Lta + in_lta1: fileformats.vendor.freesurfer.medimage.Lta # type=file|default=: maps some src1 to dst1 subjects_dir: generic/directory # type=directory|default=: subjects directory @@ -71,7 +71,7 @@ outputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - out_file: fileformats.medimage_freesurfer.Lta + out_file: fileformats.vendor.freesurfer.medimage.Lta # type=file: the combined LTA maps: src1 to dst2 = LTA2*LTA1 # type=file|default=: the combined LTA maps: src1 to dst2 = LTA2*LTA1 callables: diff --git a/nipype-auto-conv/specs/interfaces/contrast.yaml b/nipype-auto-conv/specs/interfaces/contrast.yaml index 3c13671b..5d935674 100644 --- a/nipype-auto-conv/specs/interfaces/contrast.yaml +++ b/nipype-auto-conv/specs/interfaces/contrast.yaml @@ -37,7 +37,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - annotation: fileformats.medimage_freesurfer.Annot + annotation: fileformats.vendor.freesurfer.medimage.Annot # type=file|default=: Input annotation file must be /label/.aparc.annot cortex: generic/file # type=file|default=: Input cortex label must be /label/.cortex.label @@ -49,7 +49,7 @@ inputs: # type=directory|default=: subjects directory thickness: generic/file # type=file|default=: Input file must be /surf/?h.thickness - white: fileformats.medimage_freesurfer.White + white: fileformats.vendor.freesurfer.medimage.White # type=file|default=: Input file must be /surf/.white callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/nipype-auto-conv/specs/interfaces/curvature.yaml b/nipype-auto-conv/specs/interfaces/curvature.yaml index 748c88b3..a8376c39 100644 --- a/nipype-auto-conv/specs/interfaces/curvature.yaml +++ b/nipype-auto-conv/specs/interfaces/curvature.yaml @@ -33,7 +33,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.Pial + in_file: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for Curvature subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/curvature_stats.yaml b/nipype-auto-conv/specs/interfaces/curvature_stats.yaml index 2e93873e..e3678bc6 100644 --- a/nipype-auto-conv/specs/interfaces/curvature_stats.yaml +++ b/nipype-auto-conv/specs/interfaces/curvature_stats.yaml @@ -58,7 +58,7 @@ inputs: # passed to the field in the automatically generated unittests. curvfile1: generic/file # type=file|default=: Input file for CurvatureStats - curvfile2: fileformats.medimage_freesurfer.Pial + curvfile2: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for CurvatureStats subjects_dir: generic/directory # type=directory|default=: subjects directory @@ -80,7 +80,7 @@ outputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - out_file: fileformats.medimage_freesurfer.Stats + out_file: fileformats.vendor.freesurfer.medimage.Stats # type=file: Output curvature stats file # type=file|default=: Output curvature stats file callables: diff --git a/nipype-auto-conv/specs/interfaces/em_register.yaml b/nipype-auto-conv/specs/interfaces/em_register.yaml index 8c3ef93b..525bdf65 100644 --- a/nipype-auto-conv/specs/interfaces/em_register.yaml +++ b/nipype-auto-conv/specs/interfaces/em_register.yaml @@ -59,7 +59,7 @@ outputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - out_file: fileformats.medimage_freesurfer.Lta + out_file: fileformats.vendor.freesurfer.medimage.Lta # type=file: output transform # type=file|default=: output transform callables: diff --git a/nipype-auto-conv/specs/interfaces/euler_number.yaml b/nipype-auto-conv/specs/interfaces/euler_number.yaml index 963344b7..fe7f45b8 100644 --- a/nipype-auto-conv/specs/interfaces/euler_number.yaml +++ b/nipype-auto-conv/specs/interfaces/euler_number.yaml @@ -30,7 +30,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.Pial + in_file: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for EulerNumber subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/extract_main_component.yaml b/nipype-auto-conv/specs/interfaces/extract_main_component.yaml index 4fc35138..809d67ed 100644 --- a/nipype-auto-conv/specs/interfaces/extract_main_component.yaml +++ b/nipype-auto-conv/specs/interfaces/extract_main_component.yaml @@ -30,7 +30,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.Pial + in_file: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: input surface file callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/nipype-auto-conv/specs/interfaces/fix_topology.yaml b/nipype-auto-conv/specs/interfaces/fix_topology.yaml index 3d5addd9..45d8d985 100644 --- a/nipype-auto-conv/specs/interfaces/fix_topology.yaml +++ b/nipype-auto-conv/specs/interfaces/fix_topology.yaml @@ -42,11 +42,11 @@ inputs: # type=file|default=: Implicit input brain.mgz in_inflated: generic/file # type=file|default=: Undocumented input file .inflated - in_orig: fileformats.medimage_freesurfer.Orig + in_orig: fileformats.vendor.freesurfer.medimage.Orig # type=file|default=: Undocumented input file .orig in_wm: generic/file # type=file|default=: Implicit input wm.mgz - sphere: fileformats.medimage_freesurfer.Nofix + sphere: fileformats.vendor.freesurfer.medimage.Nofix # type=file|default=: Sphere input file subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/gtmpvc.yaml b/nipype-auto-conv/specs/interfaces/gtmpvc.yaml index 90b84fbc..7254f9d5 100644 --- a/nipype-auto-conv/specs/interfaces/gtmpvc.yaml +++ b/nipype-auto-conv/specs/interfaces/gtmpvc.yaml @@ -55,7 +55,7 @@ inputs: # type=file|default=: input volume - source data to pvc mask_file: generic/file # type=file|default=: ignore areas outside of the mask (in input vol space) - reg_file: fileformats.medimage_freesurfer.Lta + reg_file: fileformats.vendor.freesurfer.medimage.Lta # type=file|default=: LTA registration file that maps PET to anatomical segmentation: generic/file # type=file|default=: segfile : anatomical segmentation to define regions for GTM diff --git a/nipype-auto-conv/specs/interfaces/jacobian.yaml b/nipype-auto-conv/specs/interfaces/jacobian.yaml index 14fc8deb..37a393c3 100644 --- a/nipype-auto-conv/specs/interfaces/jacobian.yaml +++ b/nipype-auto-conv/specs/interfaces/jacobian.yaml @@ -33,7 +33,7 @@ inputs: # passed to the field in the automatically generated unittests. in_mappedsurf: generic/file # type=file|default=: Mapped surface - in_origsurf: fileformats.medimage_freesurfer.Pial + in_origsurf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Original surface subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/label_2_label.yaml b/nipype-auto-conv/specs/interfaces/label_2_label.yaml index 934f9f55..b4376b4a 100644 --- a/nipype-auto-conv/specs/interfaces/label_2_label.yaml +++ b/nipype-auto-conv/specs/interfaces/label_2_label.yaml @@ -49,9 +49,9 @@ inputs: # type=file|default=: Source label source_sphere_reg: generic/file # type=file|default=: Implicit input .sphere.reg - source_white: fileformats.medimage_freesurfer.Pial + source_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input .white - sphere_reg: fileformats.medimage_freesurfer.Pial + sphere_reg: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input .sphere.reg subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/label_2_vol.yaml b/nipype-auto-conv/specs/interfaces/label_2_vol.yaml index eecb7bd4..b6e681b8 100644 --- a/nipype-auto-conv/specs/interfaces/label_2_vol.yaml +++ b/nipype-auto-conv/specs/interfaces/label_2_vol.yaml @@ -36,7 +36,7 @@ inputs: # type=file|default=: file with each frame is nhits for a label map_label_stat: generic/file # type=file|default=: map the label stats field into the vol - reg_file: fileformats.medimage_freesurfer.Dat + reg_file: fileformats.vendor.freesurfer.medimage.Dat # type=file|default=: tkregister style matrix VolXYZ = R*LabelXYZ reg_header: generic/file # type=file|default=: label template volume diff --git a/nipype-auto-conv/specs/interfaces/make_surfaces.yaml b/nipype-auto-conv/specs/interfaces/make_surfaces.yaml index b61d5b40..cefef373 100644 --- a/nipype-auto-conv/specs/interfaces/make_surfaces.yaml +++ b/nipype-auto-conv/specs/interfaces/make_surfaces.yaml @@ -49,7 +49,7 @@ inputs: # type=file|default=: Implicit input file filled.mgz in_label: generic/file # type=file|default=: Implicit input label/.aparc.annot - in_orig: fileformats.medimage_freesurfer.Pial + in_orig: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input file .orig in_white: generic/file # type=file|default=: Implicit input that is sometimes used diff --git a/nipype-auto-conv/specs/interfaces/mr_is_ca_label.yaml b/nipype-auto-conv/specs/interfaces/mr_is_ca_label.yaml index 1f61ee3f..585cf810 100644 --- a/nipype-auto-conv/specs/interfaces/mr_is_ca_label.yaml +++ b/nipype-auto-conv/specs/interfaces/mr_is_ca_label.yaml @@ -46,7 +46,7 @@ inputs: # passed to the field in the automatically generated unittests. aseg: generic/file # type=file|default=: Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file - canonsurf: fileformats.medimage_freesurfer.Pial + canonsurf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input canonical surface file classifier: generic/file # type=file|default=: Classifier array input file @@ -54,11 +54,11 @@ inputs: # type=file|default=: implicit input {hemisphere}.curv label: generic/file # type=file|default=: Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file - smoothwm: fileformats.medimage_freesurfer.Pial + smoothwm: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: implicit input {hemisphere}.smoothwm subjects_dir: generic/directory # type=directory|default=: subjects directory - sulc: fileformats.medimage_freesurfer.Pial + sulc: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: implicit input {hemisphere}.sulc callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/nipype-auto-conv/specs/interfaces/mr_is_calc.yaml b/nipype-auto-conv/specs/interfaces/mr_is_calc.yaml index ede76b0f..287e8896 100644 --- a/nipype-auto-conv/specs/interfaces/mr_is_calc.yaml +++ b/nipype-auto-conv/specs/interfaces/mr_is_calc.yaml @@ -42,7 +42,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file1: fileformats.medimage_freesurfer.Area + in_file1: fileformats.vendor.freesurfer.medimage.Area # type=file|default=: Input file 1 in_file2: generic/file # type=file|default=: Input file 2 diff --git a/nipype-auto-conv/specs/interfaces/mr_is_expand.yaml b/nipype-auto-conv/specs/interfaces/mr_is_expand.yaml index b86212dd..297367ae 100644 --- a/nipype-auto-conv/specs/interfaces/mr_is_expand.yaml +++ b/nipype-auto-conv/specs/interfaces/mr_is_expand.yaml @@ -34,7 +34,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.White + in_file: fileformats.vendor.freesurfer.medimage.White # type=file|default=: Surface to expand subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/mr_is_inflate.yaml b/nipype-auto-conv/specs/interfaces/mr_is_inflate.yaml index 4afb1810..4b0bc460 100644 --- a/nipype-auto-conv/specs/interfaces/mr_is_inflate.yaml +++ b/nipype-auto-conv/specs/interfaces/mr_is_inflate.yaml @@ -31,7 +31,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.Pial + in_file: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for MRIsInflate subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/paint.yaml b/nipype-auto-conv/specs/interfaces/paint.yaml index 7859f0e6..780ecfeb 100644 --- a/nipype-auto-conv/specs/interfaces/paint.yaml +++ b/nipype-auto-conv/specs/interfaces/paint.yaml @@ -37,7 +37,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_surf: fileformats.medimage_freesurfer.Pial + in_surf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Surface file with grid (vertices) onto which the template data is to be sampled or 'painted' subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/parcellation_stats.yaml b/nipype-auto-conv/specs/interfaces/parcellation_stats.yaml index 3867cf60..525ea356 100644 --- a/nipype-auto-conv/specs/interfaces/parcellation_stats.yaml +++ b/nipype-auto-conv/specs/interfaces/parcellation_stats.yaml @@ -61,9 +61,9 @@ inputs: # type=file|default=: Input file must be /surf/lh.pial lh_white: generic/file # type=file|default=: Input file must be /surf/lh.white - rh_pial: fileformats.medimage_freesurfer.Pial + rh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/rh.pial - rh_white: fileformats.medimage_freesurfer.White + rh_white: fileformats.vendor.freesurfer.medimage.White # type=file|default=: Input file must be /surf/rh.white ribbon: medimage/mgh-gz # type=file|default=: Input file must be /mri/ribbon.mgz @@ -91,7 +91,7 @@ outputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - out_color: fileformats.medimage_freesurfer.Ctab + out_color: fileformats.vendor.freesurfer.medimage.Ctab # type=file: Output annotation files's colortable to text file # type=file|default=: Output annotation files's colortable to text file out_table: generic/file diff --git a/nipype-auto-conv/specs/interfaces/register.yaml b/nipype-auto-conv/specs/interfaces/register.yaml index b4caabf5..8f2981f5 100644 --- a/nipype-auto-conv/specs/interfaces/register.yaml +++ b/nipype-auto-conv/specs/interfaces/register.yaml @@ -36,9 +36,9 @@ inputs: # passed to the field in the automatically generated unittests. in_smoothwm: generic/file # type=file|default=: Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm - in_sulc: fileformats.medimage_freesurfer.Pial + in_sulc: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Undocumented mandatory input file ${SUBJECTS_DIR}/surf/{hemisphere}.sulc - in_surf: fileformats.medimage_freesurfer.Pial + in_surf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Surface to register, often {hemi}.sphere subjects_dir: generic/directory # type=directory|default=: subjects directory @@ -60,7 +60,7 @@ outputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - out_file: fileformats.medimage_freesurfer.Reg + out_file: fileformats.vendor.freesurfer.medimage.Reg # type=file: Output surface file to capture registration # type=file|default=: Output surface file to capture registration callables: diff --git a/nipype-auto-conv/specs/interfaces/relabel_hypointensities.yaml b/nipype-auto-conv/specs/interfaces/relabel_hypointensities.yaml index 8be14235..4ba87aaa 100644 --- a/nipype-auto-conv/specs/interfaces/relabel_hypointensities.yaml +++ b/nipype-auto-conv/specs/interfaces/relabel_hypointensities.yaml @@ -35,7 +35,7 @@ inputs: # passed to the field in the automatically generated unittests. aseg: generic/file # type=file|default=: Input aseg file - lh_white: fileformats.medimage_freesurfer.Pial + lh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input file must be lh.white rh_white: generic/file # type=file|default=: Implicit input file must be rh.white diff --git a/nipype-auto-conv/specs/interfaces/remove_intersection.yaml b/nipype-auto-conv/specs/interfaces/remove_intersection.yaml index 18bbe3e4..668211c5 100644 --- a/nipype-auto-conv/specs/interfaces/remove_intersection.yaml +++ b/nipype-auto-conv/specs/interfaces/remove_intersection.yaml @@ -30,7 +30,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.Pial + in_file: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for RemoveIntersection subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/seg_stats.yaml b/nipype-auto-conv/specs/interfaces/seg_stats.yaml index d63a5b2f..9708cc10 100644 --- a/nipype-auto-conv/specs/interfaces/seg_stats.yaml +++ b/nipype-auto-conv/specs/interfaces/seg_stats.yaml @@ -77,7 +77,7 @@ outputs: sf_avg_file: generic/file # type=file: Text file with func statistics averaged over segs and framss # type=traitcompound|default=None: Save mean across space and time - summary_file: fileformats.medimage_freesurfer.Stats + summary_file: fileformats.vendor.freesurfer.medimage.Stats # type=file: Segmentation summary statistics table # type=file|default=: Segmentation stats summary table file callables: diff --git a/nipype-auto-conv/specs/interfaces/seg_stats_recon_all.yaml b/nipype-auto-conv/specs/interfaces/seg_stats_recon_all.yaml index 71b4fc10..0a1e4456 100644 --- a/nipype-auto-conv/specs/interfaces/seg_stats_recon_all.yaml +++ b/nipype-auto-conv/specs/interfaces/seg_stats_recon_all.yaml @@ -80,11 +80,11 @@ inputs: # type=file|default=: Compensate for partial voluming presurf_seg: medimage/mgh-gz # type=file|default=: Input segmentation volume - rh_orig_nofix: fileformats.medimage_freesurfer.Pial + rh_orig_nofix: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input rh.orig.nofix - rh_pial: fileformats.medimage_freesurfer.Pial + rh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/rh.pial - rh_white: fileformats.medimage_freesurfer.Pial + rh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file must be /surf/rh.white ribbon: medimage/mgh-gz # type=file|default=: Input file mri/ribbon.mgz @@ -119,7 +119,7 @@ outputs: sf_avg_file: generic/file # type=file: Text file with func statistics averaged over segs and framss # type=traitcompound|default=None: Save mean across space and time - summary_file: fileformats.medimage_freesurfer.Stats + summary_file: fileformats.vendor.freesurfer.medimage.Stats # type=file: Segmentation summary statistics table # type=file|default=: Segmentation stats summary table file callables: diff --git a/nipype-auto-conv/specs/interfaces/segment_cc.yaml b/nipype-auto-conv/specs/interfaces/segment_cc.yaml index f7cf1279..706dd018 100644 --- a/nipype-auto-conv/specs/interfaces/segment_cc.yaml +++ b/nipype-auto-conv/specs/interfaces/segment_cc.yaml @@ -65,7 +65,7 @@ outputs: out_file: generic/file # type=file: Output segmentation including corpus collosum # type=file|default=: Filename to write aseg including CC - out_rotation: fileformats.medimage_freesurfer.Lta + out_rotation: fileformats.vendor.freesurfer.medimage.Lta # type=file: Output lta rotation file # type=file|default=: Global filepath for writing rotation lta callables: diff --git a/nipype-auto-conv/specs/interfaces/smooth.yaml b/nipype-auto-conv/specs/interfaces/smooth.yaml index 7e2d2cdf..7ce3f470 100644 --- a/nipype-auto-conv/specs/interfaces/smooth.yaml +++ b/nipype-auto-conv/specs/interfaces/smooth.yaml @@ -41,7 +41,7 @@ inputs: # passed to the field in the automatically generated unittests. in_file: medimage/nifti1 # type=file|default=: source volume - reg_file: fileformats.medimage_freesurfer.Dat + reg_file: fileformats.vendor.freesurfer.medimage.Dat # type=file|default=: registers volume to surface anatomical subjects_dir: generic/directory # type=directory|default=: subjects directory diff --git a/nipype-auto-conv/specs/interfaces/sphere.yaml b/nipype-auto-conv/specs/interfaces/sphere.yaml index 4fd47875..d456865d 100644 --- a/nipype-auto-conv/specs/interfaces/sphere.yaml +++ b/nipype-auto-conv/specs/interfaces/sphere.yaml @@ -30,7 +30,7 @@ inputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - in_file: fileformats.medimage_freesurfer.Pial + in_file: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input file for Sphere in_smoothwm: generic/file # type=file|default=: Input surface required when -q flag is not selected diff --git a/nipype-auto-conv/specs/interfaces/spherical_average.yaml b/nipype-auto-conv/specs/interfaces/spherical_average.yaml index 9d33d71a..91b2ac5a 100644 --- a/nipype-auto-conv/specs/interfaces/spherical_average.yaml +++ b/nipype-auto-conv/specs/interfaces/spherical_average.yaml @@ -41,7 +41,7 @@ inputs: # passed to the field in the automatically generated unittests. in_orig: generic/file # type=file|default=: Original surface filename - in_surf: fileformats.medimage_freesurfer.Pial + in_surf: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Input surface file subjects_dir: generic/directory # type=directory|default=: subjects directory @@ -63,7 +63,7 @@ outputs: # from the nipype interface, but you may want to be more specific, particularly # for file types, where specifying the format also specifies the file that will be # passed to the field in the automatically generated unittests. - out_file: fileformats.medimage_freesurfer.Out + out_file: fileformats.vendor.freesurfer.medimage.Out # type=file: Output label # type=file|default=: Output filename callables: diff --git a/nipype-auto-conv/specs/interfaces/tkregister_2.yaml b/nipype-auto-conv/specs/interfaces/tkregister_2.yaml index 09eb8a0b..4038dcd6 100644 --- a/nipype-auto-conv/specs/interfaces/tkregister_2.yaml +++ b/nipype-auto-conv/specs/interfaces/tkregister_2.yaml @@ -81,7 +81,7 @@ outputs: # type=file: FSL-style registration file lta_file: generic/file # type=file: LTA-style registration file - reg_file: fileformats.medimage_freesurfer.Dat + reg_file: fileformats.vendor.freesurfer.medimage.Dat # type=file: freesurfer-style registration file # type=file|default='register.dat': freesurfer-style registration file callables: diff --git a/nipype-auto-conv/specs/interfaces/volume_mask.yaml b/nipype-auto-conv/specs/interfaces/volume_mask.yaml index 48a4efb8..d1a59a32 100644 --- a/nipype-auto-conv/specs/interfaces/volume_mask.yaml +++ b/nipype-auto-conv/specs/interfaces/volume_mask.yaml @@ -49,9 +49,9 @@ inputs: # type=file|default=: Implicit aseg.mgz segmentation. Specify a different aseg by using the 'in_aseg' input. in_aseg: generic/file # type=file|default=: Input aseg file for VolumeMask - lh_pial: fileformats.medimage_freesurfer.Pial + lh_pial: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input left pial surface - lh_white: fileformats.medimage_freesurfer.Pial + lh_white: fileformats.vendor.freesurfer.medimage.Pial # type=file|default=: Implicit input left white matter surface rh_pial: generic/file # type=file|default=: Implicit input right pial surface diff --git a/nipype-auto-conv/specs/interfaces/watershed_skull_strip.yaml b/nipype-auto-conv/specs/interfaces/watershed_skull_strip.yaml index 0d97e979..5dba26ee 100644 --- a/nipype-auto-conv/specs/interfaces/watershed_skull_strip.yaml +++ b/nipype-auto-conv/specs/interfaces/watershed_skull_strip.yaml @@ -49,7 +49,7 @@ inputs: # type=file|default=: input volume subjects_dir: generic/directory # type=directory|default=: subjects directory - transform: fileformats.medimage_freesurfer.Lta + transform: fileformats.vendor.freesurfer.medimage.Lta # type=file|default=: undocumented callable_defaults: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` diff --git a/pyproject.toml b/pyproject.toml index 9743e9ca..e0090940 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,7 +13,7 @@ dependencies = [ "fileformats >=0.15.4", "fileformats-datascience >=0.3.2", "fileformats-medimage >=0.10.5", - "fileformats-medimage_freesurfer", + "fileformats.vendor.freesurfer.medimage", "looseversion>=1.3.0", ] license = { file = "LICENSE" } From 11e26a4c788aef2a63126fa19a656311a6a467af Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Mon, 13 Oct 2025 13:31:19 +1100 Subject: [PATCH 5/5] fixing up fileformats references --- pyproject.toml | 4 ++-- related-packages/fileformats-extras/pyproject.toml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e0090940..58ac2aca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,13 +7,13 @@ name = "pydra-tasks-freesurfer" description = "Pydra tasks package for freesurfer" readme = "README.md" requires-python = ">=3.11" -keywords = ["freesirfer", "neuroimaging", "pydra", "segmentation"] +keywords = ["freesurfer", "neuroimaging", "pydra", "segmentation"] dependencies = [ "pydra >=1.0a2", "fileformats >=0.15.4", "fileformats-datascience >=0.3.2", "fileformats-medimage >=0.10.5", - "fileformats.vendor.freesurfer.medimage", + "fileformats-vendor-freesurfer", "looseversion>=1.3.0", ] license = { file = "LICENSE" } diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml index f90a302d..06ad4ce0 100644 --- a/related-packages/fileformats-extras/pyproject.toml +++ b/related-packages/fileformats-extras/pyproject.toml @@ -70,7 +70,7 @@ version-file = "fileformats/extras/vendor/freesurfer/_version.py" packages = ["fileformats"] [tool.black] -target-version = ['py38'] +target-version = ['py311'] exclude = "fileformats/extras/vendor/freesurfer/_version.py" [tool.codespell]