From fe79dd0c155e2e4113e3f1897d35946e0d1e2080 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 10 Jan 2024 16:17:17 +1100 Subject: [PATCH] updated with latest generation of auto-gen yaml files --- nipype-auto-conv/specs/accuracy_tester.yaml | 10 ++- nipype-auto-conv/specs/bedpostx5.yaml | 4 + nipype-auto-conv/specs/classifier.yaml | 2 + nipype-auto-conv/specs/dual_regression.yaml | 3 + nipype-auto-conv/specs/feat.yaml | 2 + nipype-auto-conv/specs/feat_register.yaml | 74 ------------------- .../specs/feat_register_callables.py | 1 - nipype-auto-conv/specs/feature_extractor.yaml | 6 ++ nipype-auto-conv/specs/filmgls.yaml | 6 ++ nipype-auto-conv/specs/flameo.yaml | 4 + nipype-auto-conv/specs/fnirt.yaml | 7 +- nipype-auto-conv/specs/fslx_command.yaml | 2 + nipype-auto-conv/specs/ica__aroma.yaml | 10 +++ nipype-auto-conv/specs/melodic.yaml | 5 ++ nipype-auto-conv/specs/topup.yaml | 2 - nipype-auto-conv/specs/training.yaml | 2 +- .../specs/training_set_creator.yaml | 2 +- nipype-auto-conv/specs/x_fibres_5.yaml | 2 + 18 files changed, 61 insertions(+), 83 deletions(-) delete mode 100644 nipype-auto-conv/specs/feat_register.yaml delete mode 100644 nipype-auto-conv/specs/feat_register_callables.py diff --git a/nipype-auto-conv/specs/accuracy_tester.yaml b/nipype-auto-conv/specs/accuracy_tester.yaml index fb17bf4..a900f0c 100644 --- a/nipype-auto-conv/specs/accuracy_tester.yaml +++ b/nipype-auto-conv/specs/accuracy_tester.yaml @@ -23,10 +23,13 @@ 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. - mel_icas: generic/file+list-of - # type=inputmultiobject|default=[]: Melodic output directories trained_wts_file: generic/file # type=file|default=: trained-weights file + mel_icas: generic/directory+list-of + # type=inputmultiobject|default=[]: Melodic output directories + output_directory: generic/directory + # type=directory: Path to folder in which to store the results of the accuracy test. + # type=directory|default=: Path to folder in which to store the results of the accuracy test. metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: @@ -40,6 +43,9 @@ 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. + output_directory: generic/directory + # type=directory: Path to folder in which to store the results of the accuracy test. + # type=directory|default=: Path to folder in which to store the results of the accuracy test. callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/bedpostx5.yaml b/nipype-auto-conv/specs/bedpostx5.yaml index 92e9c8b..b25f1b6 100644 --- a/nipype-auto-conv/specs/bedpostx5.yaml +++ b/nipype-auto-conv/specs/bedpostx5.yaml @@ -53,6 +53,10 @@ inputs: # type=file|default=: b values file grad_dev: generic/file # type=file|default=: grad_dev file, if gradnonlin, -g is True + logdir: generic/directory + # type=directory|default=: + out_dir: generic/directory + # type=directory|default='bedpostx': output directory metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: diff --git a/nipype-auto-conv/specs/classifier.yaml b/nipype-auto-conv/specs/classifier.yaml index 3f29445..358635c 100644 --- a/nipype-auto-conv/specs/classifier.yaml +++ b/nipype-auto-conv/specs/classifier.yaml @@ -27,6 +27,8 @@ inputs: artifacts_list_file: generic/file # type=file: Text file listing which ICs are artifacts; can be the output from classification or can be created manually # type=file|default=: Text file listing which ICs are artifacts; can be the output from classification or can be created manually + mel_ica: generic/directory + # type=directory|default=: Melodic output directory or directories metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: diff --git a/nipype-auto-conv/specs/dual_regression.yaml b/nipype-auto-conv/specs/dual_regression.yaml index 6b873a8..3630a78 100644 --- a/nipype-auto-conv/specs/dual_regression.yaml +++ b/nipype-auto-conv/specs/dual_regression.yaml @@ -57,6 +57,9 @@ 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_dir: generic/directory + # type=directory: + # type=directory|default='output': This directory will be created to hold all output and logfiles callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/feat.yaml b/nipype-auto-conv/specs/feat.yaml index 94af3ad..3862605 100644 --- a/nipype-auto-conv/specs/feat.yaml +++ b/nipype-auto-conv/specs/feat.yaml @@ -35,6 +35,8 @@ 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. + feat_dir: generic/directory + # type=directory: callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/feat_register.yaml b/nipype-auto-conv/specs/feat_register.yaml deleted file mode 100644 index fadda16..0000000 --- a/nipype-auto-conv/specs/feat_register.yaml +++ /dev/null @@ -1,74 +0,0 @@ -# This file is used to manually specify the semi-automatic conversion of -# 'nipype.interfaces.fsl.model.FEATRegister' from Nipype to Pydra. -# -# Please fill-in/edit the fields below where appropriate -# -# Docs -# ---- -# Register feat directories to a specific standard -task_name: FEATRegister -nipype_name: FEATRegister -nipype_module: nipype.interfaces.fsl.model -inputs: - omit: - # list[str] - fields to omit from the Pydra interface - rename: - # dict[str, str] - fields to rename in the Pydra interface - types: - # dict[str, type] - override inferred types (use "mime-like" string for file-format types, - # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred - # 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. - feat_dirs: generic/file+list-of - # type=inputmultiobject|default=[]: Lower level feat dirs - reg_image: generic/file - # type=file|default=: image to register to (will be treated as standard) - metadata: - # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) -outputs: - omit: - # list[str] - fields to omit from the Pydra interface - rename: - # dict[str, str] - fields to rename in the Pydra interface - types: - # dict[str, type] - override inferred types (use "mime-like" string for file-format types, - # e.g. 'medimage/nifti-gz'). For most fields the type will be correctly inferred - # 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. - fsf_file: generic/file - # type=file: FSL feat specification file - callables: - # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` - # to set to the `callable` attribute of output fields - templates: - # dict[str, str] - `output_file_template` values to be provided to output fields - requirements: - # dict[str, list[str]] - input fields that are required to be provided for the output field to be present -tests: -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - feat_dirs: - # type=inputmultiobject|default=[]: Lower level feat dirs - reg_image: - # type=file|default=: image to register to (will be treated as standard) - reg_dof: - # type=int|default=12: registration degrees of freedom - imports: - # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file -doctests: [] diff --git a/nipype-auto-conv/specs/feat_register_callables.py b/nipype-auto-conv/specs/feat_register_callables.py deleted file mode 100644 index 8271252..0000000 --- a/nipype-auto-conv/specs/feat_register_callables.py +++ /dev/null @@ -1 +0,0 @@ -"""Module to put any functions that are referred to in FEATRegister.yaml""" diff --git a/nipype-auto-conv/specs/feature_extractor.yaml b/nipype-auto-conv/specs/feature_extractor.yaml index 0e017da..2b83416 100644 --- a/nipype-auto-conv/specs/feature_extractor.yaml +++ b/nipype-auto-conv/specs/feature_extractor.yaml @@ -22,6 +22,9 @@ 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. + mel_ica: generic/directory + # type=directory: Melodic output directory or directories + # type=directory|default=: Melodic output directory or directories metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: @@ -35,6 +38,9 @@ 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. + mel_ica: generic/directory + # type=directory: Melodic output directory or directories + # type=directory|default=: Melodic output directory or directories callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/filmgls.yaml b/nipype-auto-conv/specs/filmgls.yaml index 2df9dc4..155c8a7 100644 --- a/nipype-auto-conv/specs/filmgls.yaml +++ b/nipype-auto-conv/specs/filmgls.yaml @@ -55,6 +55,9 @@ inputs: # type=file|default=: input data file design_file: generic/file # type=file|default=: design matrix file + results_dir: generic/directory + # type=directory: directory storing model estimation output + # type=directory|default='results': directory to store results in metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: @@ -78,6 +81,9 @@ outputs: # type=file: The FILM autocorrelation parameters logfile: generic/file # type=file: FILM run logfile + results_dir: generic/directory + # type=directory: directory storing model estimation output + # type=directory|default='results': directory to store results in callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/flameo.yaml b/nipype-auto-conv/specs/flameo.yaml index b3d3c8d..c7b2cf2 100644 --- a/nipype-auto-conv/specs/flameo.yaml +++ b/nipype-auto-conv/specs/flameo.yaml @@ -55,6 +55,8 @@ inputs: # type=file|default=: ascii matrix specifying f-contrasts cov_split_file: datascience/text-matrix # type=file|default=: ascii matrix specifying the groups the covariance is split into + log_dir: generic/directory + # type=directory|default='stats': metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: @@ -68,6 +70,8 @@ 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. + stats_dir: generic/directory + # type=directory: directory storing model estimation output callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/fnirt.yaml b/nipype-auto-conv/specs/fnirt.yaml index cca2254..506b06f 100644 --- a/nipype-auto-conv/specs/fnirt.yaml +++ b/nipype-auto-conv/specs/fnirt.yaml @@ -227,8 +227,9 @@ tests: in_fwhm: '[8, 4, 2, 2]' # type=list|default=[]: FWHM (in mm) of gaussian smoothing kernel for input volume, default [6, 4, 2, 2] subsampling_scheme: '[4, 2, 1, 1]' - warp_resolution: '(6, 6, 6)' # type=list|default=[]: sub-sampling scheme, list, default [4, 2, 1, 1] + warp_resolution: (6, 6, 6) + # type=tuple|default=(0, 0, 0): (approximate) resolution (in mm) of warp basis in x-, y- and z-direction, default 10, 10, 10 imports: &id001 # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item # consisting of 'module', 'name', and optionally 'alias' keys @@ -256,8 +257,10 @@ doctests: # '.mock()' method of the corresponding class is used instead. in_fwhm: '[8, 4, 2, 2]' # type=list|default=[]: FWHM (in mm) of gaussian smoothing kernel for input volume, default [6, 4, 2, 2] - subsampling_scheme: '[4, 2, 1, 1] Specify the resolution of the warps >>> fnirt_mprage.inputs.warp_resolution = (6, 6, 6)' + subsampling_scheme: '[4, 2, 1, 1]' # type=list|default=[]: sub-sampling scheme, list, default [4, 2, 1, 1] + warp_resolution: (6, 6, 6) + # type=tuple|default=(0, 0, 0): (approximate) resolution (in mm) of warp basis in x-, y- and z-direction, default 10, 10, 10 imports: *id001 # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item # consisting of 'module', 'name', and optionally 'alias' keys diff --git a/nipype-auto-conv/specs/fslx_command.yaml b/nipype-auto-conv/specs/fslx_command.yaml index 9670198..866e863 100644 --- a/nipype-auto-conv/specs/fslx_command.yaml +++ b/nipype-auto-conv/specs/fslx_command.yaml @@ -30,6 +30,8 @@ inputs: # type=file|default=: b vectors file bvals: generic/file # type=file|default=: b values file + logdir: generic/directory + # type=directory|default='.': metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: diff --git a/nipype-auto-conv/specs/ica__aroma.yaml b/nipype-auto-conv/specs/ica__aroma.yaml index a88cfbe..a637cc3 100644 --- a/nipype-auto-conv/specs/ica__aroma.yaml +++ b/nipype-auto-conv/specs/ica__aroma.yaml @@ -56,6 +56,13 @@ inputs: # type=file|default=: File name of the warp-file describing the non-linear registration (e.g. FSL FNIRT) of the structural data to MNI152 space (.nii.gz) motion_parameters: text/text-file # type=file|default=: motion parameters file + feat_dir: generic/directory + # type=directory|default=: If a feat directory exists and temporal filtering has not been run yet, ICA_AROMA can use the files in this directory. + out_dir: generic/directory + # type=directory: directory contains (in addition to the denoised files): melodic.ica + classified_motion_components + classification_overview + feature_scores + melodic_ic_mni) + # type=directory|default='out': output directory + melodic_dir: generic/directory + # type=directory|default=: path to MELODIC directory if MELODIC has already been run metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: @@ -73,6 +80,9 @@ outputs: # type=file: if generated: aggressively denoised volume nonaggr_denoised_file: generic/file # type=file: if generated: non aggressively denoised volume + out_dir: generic/directory + # type=directory: directory contains (in addition to the denoised files): melodic.ica + classified_motion_components + classification_overview + feature_scores + melodic_ic_mni) + # type=directory|default='out': output directory callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/melodic.yaml b/nipype-auto-conv/specs/melodic.yaml index fb02987..9e355f6 100644 --- a/nipype-auto-conv/specs/melodic.yaml +++ b/nipype-auto-conv/specs/melodic.yaml @@ -77,6 +77,11 @@ 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_dir: generic/directory + # type=directory: + # type=directory|default=: output directory name + report_dir: generic/directory + # type=directory: callables: # dict[str, str] - names of methods/callable classes defined in the adjacent `*_callables.py` # to set to the `callable` attribute of output fields diff --git a/nipype-auto-conv/specs/topup.yaml b/nipype-auto-conv/specs/topup.yaml index d4c21ec..bfb37c4 100644 --- a/nipype-auto-conv/specs/topup.yaml +++ b/nipype-auto-conv/specs/topup.yaml @@ -45,8 +45,6 @@ inputs: # type=file|default=: name of 4D file with images encoding_file: text/text-file # type=file|default=: name of text file with PE directions/times - readout_times: generic/file+list-of - # type=inputmultiobject|default=[]: readout times (dwell times by # phase-encode steps minus 1) out_base: generic/file # type=file|default=: base-name of output files (spline coefficients (Hz) and movement parameters) out_field: generic/file diff --git a/nipype-auto-conv/specs/training.yaml b/nipype-auto-conv/specs/training.yaml index 91531b1..6491ff2 100644 --- a/nipype-auto-conv/specs/training.yaml +++ b/nipype-auto-conv/specs/training.yaml @@ -22,7 +22,7 @@ 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. - mel_icas: generic/file+list-of + mel_icas: generic/directory+list-of # type=inputmultiobject|default=[]: Melodic output directories metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) diff --git a/nipype-auto-conv/specs/training_set_creator.yaml b/nipype-auto-conv/specs/training_set_creator.yaml index 04f170d..d9bb524 100644 --- a/nipype-auto-conv/specs/training_set_creator.yaml +++ b/nipype-auto-conv/specs/training_set_creator.yaml @@ -27,7 +27,7 @@ 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. - mel_icas_in: generic/file+list-of + mel_icas_in: generic/directory+list-of # type=inputmultiobject|default=[]: Melodic output directories metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) diff --git a/nipype-auto-conv/specs/x_fibres_5.yaml b/nipype-auto-conv/specs/x_fibres_5.yaml index 7756753..1cbf74a 100644 --- a/nipype-auto-conv/specs/x_fibres_5.yaml +++ b/nipype-auto-conv/specs/x_fibres_5.yaml @@ -33,6 +33,8 @@ inputs: # type=file|default=: b vectors file bvals: generic/file # type=file|default=: b values file + logdir: generic/directory + # type=directory|default='.': metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: