niwrap-freesurfer 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/fscalc_fsl.py

@@ -1,196 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FSCALC_FSL_METADATA = Metadata(
-    id="a318448c0ae9ee2486a72de6136c2f2bdab8a57e.boutiques",
-    name="fscalc.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FscalcFslParameters = typing.TypedDict('FscalcFslParameters', {
-    "__STYX_TYPE__": typing.Literal["fscalc.fsl"],
-    "input_file": InputPathType,
-    "output_file": str,
-    "additional_options": typing.NotRequired[str | None],
-})
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fscalc.fsl": fscalc_fsl_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "fscalc.fsl": fscalc_fsl_outputs,
-    }.get(t)
-
-
-class FscalcFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `fscalc_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    output_file: OutputPathType
-    """Output file"""
-
-
-def fscalc_fsl_params(
-    input_file: InputPathType,
-    output_file: str,
-    additional_options: str | None = None,
-) -> FscalcFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        input_file: Input image file readable by Freesurfer.
-        output_file: Output image file writable by Freesurfer.
-        additional_options: Additional fslmaths-specific options.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "fscalc.fsl",
-        "input_file": input_file,
-        "output_file": output_file,
-    }
-    if additional_options is not None:
-        params["additional_options"] = additional_options
-    return params
-
-
-def fscalc_fsl_cargs(
-    params: FscalcFslParameters,
-    execution: Execution,
-) -> list[str]:
-    """
-    Build command-line arguments from parameters.
-    
-    Args:
-        params: The parameters.
-        execution: The execution object for resolving input paths.
-    Returns:
-        Command-line arguments.
-    """
-    cargs = []
-    cargs.append("fscalc.fsl")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("additional_options") is not None:
-        cargs.append(params.get("additional_options"))
-    return cargs
-
-
-def fscalc_fsl_outputs(
-    params: FscalcFslParameters,
-    execution: Execution,
-) -> FscalcFslOutputs:
-    """
-    Build outputs object containing output file paths and possibly stdout/stderr.
-    
-    Args:
-        params: The parameters.
-        execution: The execution object for resolving input paths.
-    Returns:
-        Outputs object.
-    """
-    ret = FscalcFslOutputs(
-        root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
-    )
-    return ret
-
-
-def fscalc_fsl_execute(
-    params: FscalcFslParameters,
-    execution: Execution,
-) -> FscalcFslOutputs:
-    """
-    A Freesurfer wrapper around fslmaths, allowing input and output formats
-    compatible with Freesurfer.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FscalcFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = fscalc_fsl_cargs(params, execution)
-    ret = fscalc_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def fscalc_fsl(
-    input_file: InputPathType,
-    output_file: str,
-    additional_options: str | None = None,
-    runner: Runner | None = None,
-) -> FscalcFslOutputs:
-    """
-    A Freesurfer wrapper around fslmaths, allowing input and output formats
-    compatible with Freesurfer.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        input_file: Input image file readable by Freesurfer.
-        output_file: Output image file writable by Freesurfer.
-        additional_options: Additional fslmaths-specific options.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FscalcFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSCALC_FSL_METADATA)
-    params = fscalc_fsl_params(
-        input_file=input_file,
-        output_file=output_file,
-        additional_options=additional_options,
-    )
-    return fscalc_fsl_execute(params, execution)
-
-
-__all__ = [
-    "FSCALC_FSL_METADATA",
-    "FscalcFslOutputs",
-    "FscalcFslParameters",
-    "fscalc_fsl",
-    "fscalc_fsl_params",
-]

niwrap_freesurfer/freesurfer/fsfirst_fsl.py

@@ -1,166 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FSFIRST_FSL_METADATA = Metadata(
-    id="fe4368d67f0bf44514ba8d3556dd0dd0df276d60.boutiques",
-    name="fsfirst.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FsfirstFslParameters = typing.TypedDict('FsfirstFslParameters', {
-    "__STYX_TYPE__": typing.Literal["fsfirst.fsl"],
-})
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fsfirst.fsl": fsfirst_fsl_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
-
-
-class FsfirstFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `fsfirst_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-
-
-def fsfirst_fsl_params(
-) -> FsfirstFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "fsfirst.fsl",
-    }
-    return params
-
-
-def fsfirst_fsl_cargs(
-    params: FsfirstFslParameters,
-    execution: Execution,
-) -> list[str]:
-    """
-    Build command-line arguments from parameters.
-    
-    Args:
-        params: The parameters.
-        execution: The execution object for resolving input paths.
-    Returns:
-        Command-line arguments.
-    """
-    cargs = []
-    cargs.append("fsfirst.fsl")
-    return cargs
-
-
-def fsfirst_fsl_outputs(
-    params: FsfirstFslParameters,
-    execution: Execution,
-) -> FsfirstFslOutputs:
-    """
-    Build outputs object containing output file paths and possibly stdout/stderr.
-    
-    Args:
-        params: The parameters.
-        execution: The execution object for resolving input paths.
-    Returns:
-        Outputs object.
-    """
-    ret = FsfirstFslOutputs(
-        root=execution.output_file("."),
-    )
-    return ret
-
-
-def fsfirst_fsl_execute(
-    params: FsfirstFslParameters,
-    execution: Execution,
-) -> FsfirstFslOutputs:
-    """
-    The tool intended for FSL's FIRST module, responsible for model-based
-    segmentation and registration of subcortical structures.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FsfirstFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = fsfirst_fsl_cargs(params, execution)
-    ret = fsfirst_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def fsfirst_fsl(
-    runner: Runner | None = None,
-) -> FsfirstFslOutputs:
-    """
-    The tool intended for FSL's FIRST module, responsible for model-based
-    segmentation and registration of subcortical structures.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FsfirstFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSFIRST_FSL_METADATA)
-    params = fsfirst_fsl_params(
-    )
-    return fsfirst_fsl_execute(params, execution)
-
-
-__all__ = [
-    "FSFIRST_FSL_METADATA",
-    "FsfirstFslOutputs",
-    "FsfirstFslParameters",
-    "fsfirst_fsl",
-    "fsfirst_fsl_params",
-]

niwrap_freesurfer/freesurfer/fslmaths_fsl.py

@@ -1,196 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FSLMATHS_FSL_METADATA = Metadata(
-    id="1ba348f3e9fa1acbe3b64d58f1387f609d1c083e.boutiques",
-    name="fslmaths.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FslmathsFslParameters = typing.TypedDict('FslmathsFslParameters', {
-    "__STYX_TYPE__": typing.Literal["fslmaths.fsl"],
-    "first_input": InputPathType,
-    "operations_and_inputs": str,
-    "output_image": str,
-})
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fslmaths.fsl": fslmaths_fsl_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "fslmaths.fsl": fslmaths_fsl_outputs,
-    }.get(t)
-
-
-class FslmathsFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `fslmaths_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    output_file: OutputPathType
-    """The resultant output image after applying the specified operations."""
-
-
-def fslmaths_fsl_params(
-    first_input: InputPathType,
-    operations_and_inputs: str,
-    output_image: str,
-) -> FslmathsFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        first_input: First input image for fslmaths operations.
-        operations_and_inputs: Operations and inputs to be applied on the first\
-            image.
-        output_image: Output image file.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "fslmaths.fsl",
-        "first_input": first_input,
-        "operations_and_inputs": operations_and_inputs,
-        "output_image": output_image,
-    }
-    return params
-
-
-def fslmaths_fsl_cargs(
-    params: FslmathsFslParameters,
-    execution: Execution,
-) -> list[str]:
-    """
-    Build command-line arguments from parameters.
-    
-    Args:
-        params: The parameters.
-        execution: The execution object for resolving input paths.
-    Returns:
-        Command-line arguments.
-    """
-    cargs = []
-    cargs.append("fslmaths")
-    cargs.append(execution.input_file(params.get("first_input")))
-    cargs.append(params.get("operations_and_inputs"))
-    cargs.append(params.get("output_image"))
-    return cargs
-
-
-def fslmaths_fsl_outputs(
-    params: FslmathsFslParameters,
-    execution: Execution,
-) -> FslmathsFslOutputs:
-    """
-    Build outputs object containing output file paths and possibly stdout/stderr.
-    
-    Args:
-        params: The parameters.
-        execution: The execution object for resolving input paths.
-    Returns:
-        Outputs object.
-    """
-    ret = FslmathsFslOutputs(
-        root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_image") + ".nii.gz"),
-    )
-    return ret
-
-
-def fslmaths_fsl_execute(
-    params: FslmathsFslParameters,
-    execution: Execution,
-) -> FslmathsFslOutputs:
-    """
-    FSLmaths: part of FMRIB Software Library (FSL) for manipulating images via
-    various mathematical operations.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FslmathsFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = fslmaths_fsl_cargs(params, execution)
-    ret = fslmaths_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def fslmaths_fsl(
-    first_input: InputPathType,
-    operations_and_inputs: str,
-    output_image: str,
-    runner: Runner | None = None,
-) -> FslmathsFslOutputs:
-    """
-    FSLmaths: part of FMRIB Software Library (FSL) for manipulating images via
-    various mathematical operations.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        first_input: First input image for fslmaths operations.
-        operations_and_inputs: Operations and inputs to be applied on the first\
-            image.
-        output_image: Output image file.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FslmathsFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSLMATHS_FSL_METADATA)
-    params = fslmaths_fsl_params(
-        first_input=first_input,
-        operations_and_inputs=operations_and_inputs,
-        output_image=output_image,
-    )
-    return fslmaths_fsl_execute(params, execution)
-
-
-__all__ = [
-    "FSLMATHS_FSL_METADATA",
-    "FslmathsFslOutputs",
-    "FslmathsFslParameters",
-    "fslmaths_fsl",
-    "fslmaths_fsl_params",
-]