nipype2pydra 0.4.4

基本用法

要将Nipype接口转换为Pydra任务，请运行nipype2pydra task命令，并将转换规格YAML文件和要保存生成的模块的包根传递给它，例如

$ nipype2pydra task ants_registration_registration.yaml /path/to/package/root

这将根据规格中的output_module字段在包根目录下创建一个模块文件，例如

/path/to/package/root/output/module/path

如果缺少此文件，并且nipype界面位于标准nipype.interfaces包中，那么它将被存储在pydra.tasks下，路径相同。

转换规范

虽然转换旨在尽可能自动化，但Nipype和Pydra之间存在结构差异，需要手动指定，可能需要将一些输入/输出重命名为更直观的名称。这些规范存储在YAML格式中，例如ANTs配准转换规范。

task_name: n4_bias_field_correction
nipype_name: N4BiasFieldCorrection
nipype_module: nipype.interfaces.ants.segmentation
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.
        input_image: medimage/nifti1
        mask_image: medimage/nifti1
        weight_image: medimage/nifti1
        bias_image: medimage/nifti1
    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.
        output_image: medimage/nifti1
        bias_image: medimage/nifti1
    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

在此处提供不同选项的详细描述

安装

Nipype2Pydra可以从PyPI安装Python >= 3.7，使用以下命令：

$ python3 -m pip install nipype2pydra

许可证

本作品受Creative Commons Attribution 4.0国际许可证许可。