From 38e182cdd6dec846a01c6cf39945d6d66fdbe6dc Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 11 Jan 2024 14:54:22 +1100 Subject: [PATCH] started to manual touch up auto-conv yaml specs --- nipype-auto-conv/specs/accuracy_tester.yaml | 4 +- nipype-auto-conv/specs/apply_mask.yaml | 8 +- nipype-auto-conv/specs/apply_warp.yaml | 12 +- nipype-auto-conv/specs/fslx_command.yaml | 132 ------------------ .../specs/fslx_command_callables.py | 1 - nipype-auto-conv/specs/l2_model.yaml | 78 ----------- nipype-auto-conv/specs/l2_model_callables.py | 1 - nipype-auto-conv/specs/level_1_design.yaml | 85 ----------- .../specs/level_1_design_callables.py | 1 - .../specs/multiple_regress_design.yaml | 94 ------------- .../multiple_regress_design_callables.py | 1 - .../specs/training_set_creator.yaml | 73 ---------- .../specs/training_set_creator_callables.py | 1 - .../fileformats/medimage_fsl/__init__.py | 7 +- 14 files changed, 18 insertions(+), 480 deletions(-) delete mode 100644 nipype-auto-conv/specs/fslx_command.yaml delete mode 100644 nipype-auto-conv/specs/fslx_command_callables.py delete mode 100644 nipype-auto-conv/specs/l2_model.yaml delete mode 100644 nipype-auto-conv/specs/l2_model_callables.py delete mode 100644 nipype-auto-conv/specs/level_1_design.yaml delete mode 100644 nipype-auto-conv/specs/level_1_design_callables.py delete mode 100644 nipype-auto-conv/specs/multiple_regress_design.yaml delete mode 100644 nipype-auto-conv/specs/multiple_regress_design_callables.py delete mode 100644 nipype-auto-conv/specs/training_set_creator.yaml delete mode 100644 nipype-auto-conv/specs/training_set_creator_callables.py diff --git a/nipype-auto-conv/specs/accuracy_tester.yaml b/nipype-auto-conv/specs/accuracy_tester.yaml index a900f0c..cdd03df 100644 --- a/nipype-auto-conv/specs/accuracy_tester.yaml +++ b/nipype-auto-conv/specs/accuracy_tester.yaml @@ -25,9 +25,9 @@ inputs: # passed to the field in the automatically generated unittests. trained_wts_file: generic/file # type=file|default=: trained-weights file - mel_icas: generic/directory+list-of + mel_icas: medimage-fsl/melodic-ica+list-of # type=inputmultiobject|default=[]: Melodic output directories - output_directory: generic/directory + output_directory: Path # 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: diff --git a/nipype-auto-conv/specs/apply_mask.yaml b/nipype-auto-conv/specs/apply_mask.yaml index 617a7b3..2f98040 100644 --- a/nipype-auto-conv/specs/apply_mask.yaml +++ b/nipype-auto-conv/specs/apply_mask.yaml @@ -20,9 +20,9 @@ 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. - mask_file: generic/file + mask_file: medimage/nifti-gz # type=file|default=: binary image defining mask space - in_file: generic/file + in_file: medimage/nifti-gz # type=file|default=: image to operate on metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) @@ -37,7 +37,7 @@ 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: generic/file + out_file: medimage/nifti-gz # type=file: image written after calculations # type=file|default=: image to write callables: @@ -45,7 +45,7 @@ outputs: # to set to the `callable` attribute of output fields templates: # dict[str, str] - `output_file_template` values to be provided to output fields - out_file: out_file + out_file: out_file.nii.gz # type=file: image written after calculations # type=file|default=: image to write requirements: diff --git a/nipype-auto-conv/specs/apply_warp.yaml b/nipype-auto-conv/specs/apply_warp.yaml index 348c504..3648dec 100644 --- a/nipype-auto-conv/specs/apply_warp.yaml +++ b/nipype-auto-conv/specs/apply_warp.yaml @@ -33,17 +33,17 @@ 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: generic/file + in_file: medimage/nifti-gz # type=file|default=: image to be warped - ref_file: generic/file + ref_file: medimage/nifti-gz # type=file|default=: reference image - field_file: generic/file + field_file: medimage/nifti-gz # type=file|default=: file containing warp field - premat: generic/file + premat: Path # type=file|default=: filename for pre-transform (affine matrix) - postmat: generic/file + postmat: Path # type=file|default=: filename for post-transform (affine matrix) - mask_file: generic/file + mask_file: Path # type=file|default=: filename for mask image (in reference space) 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/fslx_command.yaml b/nipype-auto-conv/specs/fslx_command.yaml deleted file mode 100644 index 866e863..0000000 --- a/nipype-auto-conv/specs/fslx_command.yaml +++ /dev/null @@ -1,132 +0,0 @@ -# This file is used to manually specify the semi-automatic conversion of -# 'nipype.interfaces.fsl.dti.FSLXCommand' from Nipype to Pydra. -# -# Please fill-in/edit the fields below where appropriate -# -# Docs -# ---- -# -# Base support for ``xfibres`` and ``bedpostx`` -# -task_name: FSLXCommand -nipype_name: FSLXCommand -nipype_module: nipype.interfaces.fsl.dti -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. - dwi: generic/file - # type=file|default=: diffusion weighted image data file - mask: generic/file - # type=file|default=: brain binary mask file (i.e. from BET) - bvecs: generic/file - # 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: - 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. - mean_dsamples: generic/file - # type=file: Mean of distribution on diffusivity d - mean_S0samples: generic/file - # type=file: Mean of distribution on T2wbaseline signal intensity S0 - mean_tausamples: generic/file - # type=file: Mean of distribution on tau samples (only with rician noise) - 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) - dwi: - # type=file|default=: diffusion weighted image data file - mask: - # type=file|default=: brain binary mask file (i.e. from BET) - bvecs: - # type=file|default=: b vectors file - bvals: - # type=file|default=: b values file - logdir: - # type=directory|default='.': - n_fibres: - # type=range|default=2: Maximum number of fibres to fit in each voxel - model: - # type=enum|default=1|allowed[1,2,3]: use monoexponential (1, default, required for single-shell) or multiexponential (2, multi-shell) model - fudge: - # type=int|default=0: ARD fudge factor - n_jumps: - # type=int|default=5000: Num of jumps to be made by MCMC - burn_in: - # type=range|default=0: Total num of jumps at start of MCMC to be discarded - burn_in_no_ard: - # type=range|default=0: num of burnin jumps before the ard is imposed - sample_every: - # type=range|default=1: Num of jumps for each sample (MCMC) - update_proposal_every: - # type=range|default=40: Num of jumps for each update to the proposal density std (MCMC) - seed: - # type=int|default=0: seed for pseudo random number generator - no_ard: - # type=bool|default=False: Turn ARD off on all fibres - all_ard: - # type=bool|default=False: Turn ARD on on all fibres - no_spat: - # type=bool|default=False: Initialise with tensor, not spatially - non_linear: - # type=bool|default=False: Initialise with nonlinear fitting - cnlinear: - # type=bool|default=False: Initialise with constrained nonlinear fitting - rician: - # type=bool|default=False: use Rician noise modeling - f0_noard: - # type=bool|default=False: Noise floor model: add to the model an unattenuated signal compartment f0 - f0_ard: - # type=bool|default=False: Noise floor model: add to the model an unattenuated signal compartment f0 - force_dir: - # type=bool|default=True: use the actual directory name given (do not add + to make a new directory) - output_type: - # type=enum|default='NIFTI'|allowed['NIFTI','NIFTI_GZ','NIFTI_PAIR','NIFTI_PAIR_GZ']: FSL output type - args: - # type=str|default='': Additional parameters to the command - environ: - # type=dict|default={}: Environment variables - 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/fslx_command_callables.py b/nipype-auto-conv/specs/fslx_command_callables.py deleted file mode 100644 index 048758a..0000000 --- a/nipype-auto-conv/specs/fslx_command_callables.py +++ /dev/null @@ -1 +0,0 @@ -"""Module to put any functions that are referred to in FSLXCommand.yaml""" diff --git a/nipype-auto-conv/specs/l2_model.yaml b/nipype-auto-conv/specs/l2_model.yaml deleted file mode 100644 index 17c0d9c..0000000 --- a/nipype-auto-conv/specs/l2_model.yaml +++ /dev/null @@ -1,78 +0,0 @@ -# This file is used to manually specify the semi-automatic conversion of -# 'nipype.interfaces.fsl.model.L2Model' from Nipype to Pydra. -# -# Please fill-in/edit the fields below where appropriate -# -# Docs -# ---- -# Generate subject specific second level model -# -# Examples -# -------- -# -# >>> from nipype.interfaces.fsl import L2Model -# >>> model = L2Model(num_copes=3) # 3 sessions -# -# -task_name: L2Model -nipype_name: L2Model -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. - 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. - design_mat: generic/file - # type=file: design matrix file - design_con: generic/file - # type=file: design contrast file - design_grp: generic/file - # type=file: design group 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) - num_copes: - # type=range|default=1: number of copes to be combined - 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/l2_model_callables.py b/nipype-auto-conv/specs/l2_model_callables.py deleted file mode 100644 index 05b7a8c..0000000 --- a/nipype-auto-conv/specs/l2_model_callables.py +++ /dev/null @@ -1 +0,0 @@ -"""Module to put any functions that are referred to in L2Model.yaml""" diff --git a/nipype-auto-conv/specs/level_1_design.yaml b/nipype-auto-conv/specs/level_1_design.yaml deleted file mode 100644 index 227d174..0000000 --- a/nipype-auto-conv/specs/level_1_design.yaml +++ /dev/null @@ -1,85 +0,0 @@ -# This file is used to manually specify the semi-automatic conversion of -# 'nipype.interfaces.fsl.model.Level1Design' from Nipype to Pydra. -# -# Please fill-in/edit the fields below where appropriate -# -# Docs -# ---- -# Generate FEAT specific files -# -# Examples -# -------- -# -# >>> level1design = Level1Design() -# >>> level1design.inputs.interscan_interval = 2.5 -# >>> level1design.inputs.bases = {'dgamma':{'derivs': False}} -# >>> level1design.inputs.session_info = 'session_info.npz' -# >>> level1design.run() # doctest: +SKIP -# -# -task_name: Level1Design -nipype_name: Level1Design -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. - 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. - 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) - interscan_interval: - # type=float|default=0.0: Interscan interval (in secs) - session_info: - # type=any|default=None: Session specific information generated by ``modelgen.SpecifyModel`` - bases: - # type=traitcompound|default=None: name of basis function and options e.g., {'dgamma': {'derivs': True}} - orthogonalization: - # type=dict|default={}: which regressors to make orthogonal e.g., {1: {0:0,1:0,2:0}, 2: {0:1,1:1,2:0}} to make the second regressor in a 2-regressor model orthogonal to the first. - model_serial_correlations: - # type=bool|default=False: Option to model serial correlations using an autoregressive estimator (order 1). Setting this option is only useful in the context of the fsf file. If you set this to False, you need to repeat this option for FILMGLS by setting autocorr_noestimate to True - contrasts: - # type=list|default=[]: List of contrasts with each contrast being a list of the form - [('name', 'stat', [condition list], [weight list], [session list])]. if session list is None or not provided, all sessions are used. For F contrasts, the condition list should contain previously defined T-contrasts. - 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/level_1_design_callables.py b/nipype-auto-conv/specs/level_1_design_callables.py deleted file mode 100644 index 0558037..0000000 --- a/nipype-auto-conv/specs/level_1_design_callables.py +++ /dev/null @@ -1 +0,0 @@ -"""Module to put any functions that are referred to in Level1Design.yaml""" diff --git a/nipype-auto-conv/specs/multiple_regress_design.yaml b/nipype-auto-conv/specs/multiple_regress_design.yaml deleted file mode 100644 index 987f401..0000000 --- a/nipype-auto-conv/specs/multiple_regress_design.yaml +++ /dev/null @@ -1,94 +0,0 @@ -# This file is used to manually specify the semi-automatic conversion of -# 'nipype.interfaces.fsl.model.MultipleRegressDesign' from Nipype to Pydra. -# -# Please fill-in/edit the fields below where appropriate -# -# Docs -# ---- -# Generate multiple regression design -# -# .. note:: -# FSL does not demean columns for higher level analysis. -# -# Please see `FSL documentation -# `_ -# for more details on model specification for higher level analysis. -# -# Examples -# -------- -# -# >>> from nipype.interfaces.fsl import MultipleRegressDesign -# >>> model = MultipleRegressDesign() -# >>> model.inputs.contrasts = [['group mean', 'T',['reg1'],[1]]] -# >>> model.inputs.regressors = dict(reg1=[1, 1, 1], reg2=[2.,-4, 3]) -# >>> model.run() # doctest: +SKIP -# -# -task_name: MultipleRegressDesign -nipype_name: MultipleRegressDesign -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. - 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. - design_mat: generic/file - # type=file: design matrix file - design_con: generic/file - # type=file: design t-contrast file - design_fts: generic/file - # type=file: design f-contrast file - design_grp: generic/file - # type=file: design group 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) - contrasts: - # type=list|default=[]: List of contrasts with each contrast being a list of the form - [('name', 'stat', [condition list], [weight list])]. if session list is None or not provided, all sessions are used. For F contrasts, the condition list should contain previously defined T-contrasts without any weight list. - regressors: - # type=dict|default={}: dictionary containing named lists of regressors - groups: - # type=list|default=[]: list of group identifiers (defaults to single group) - 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/multiple_regress_design_callables.py b/nipype-auto-conv/specs/multiple_regress_design_callables.py deleted file mode 100644 index d429231..0000000 --- a/nipype-auto-conv/specs/multiple_regress_design_callables.py +++ /dev/null @@ -1 +0,0 @@ -"""Module to put any functions that are referred to in MultipleRegressDesign.yaml""" diff --git a/nipype-auto-conv/specs/training_set_creator.yaml b/nipype-auto-conv/specs/training_set_creator.yaml deleted file mode 100644 index d9bb524..0000000 --- a/nipype-auto-conv/specs/training_set_creator.yaml +++ /dev/null @@ -1,73 +0,0 @@ -# This file is used to manually specify the semi-automatic conversion of -# 'nipype.interfaces.fsl.fix.TrainingSetCreator' from Nipype to Pydra. -# -# Please fill-in/edit the fields below where appropriate -# -# Docs -# ---- -# Goes through set of provided melodic output directories, to find all -# the ones that have a hand_labels_noise.txt file in them. -# -# This is outsourced as a separate class, so that the pipeline is -# rerun every time a handlabeled file has been changed, or a new one -# created. -# -# -task_name: TrainingSetCreator -nipype_name: TrainingSetCreator -nipype_module: nipype.interfaces.fsl.fix -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. - 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) -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. - 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) - mel_icas_in: - # type=inputmultiobject|default=[]: Melodic output directories - 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/training_set_creator_callables.py b/nipype-auto-conv/specs/training_set_creator_callables.py deleted file mode 100644 index b585309..0000000 --- a/nipype-auto-conv/specs/training_set_creator_callables.py +++ /dev/null @@ -1 +0,0 @@ -"""Module to put any functions that are referred to in TrainingSetCreator.yaml""" diff --git a/related-packages/fileformats/fileformats/medimage_fsl/__init__.py b/related-packages/fileformats/fileformats/medimage_fsl/__init__.py index d6ea01b..c8301dd 100644 --- a/related-packages/fileformats/fileformats/medimage_fsl/__init__.py +++ b/related-packages/fileformats/fileformats/medimage_fsl/__init__.py @@ -1,5 +1,10 @@ -from fileformats.generic import File +from fileformats.generic import File, Directory + class Con(File): ext = ".con" binary = True + + +class MelodicIca(Directory): + """Directory containing output from Melodic ICA"""