niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warp2metric.py

@@ -0,0 +1,449 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARP2METRIC_METADATA = Metadata(
+    id="7c25f1be081ec7621f562b1f88e03c6ae513109c.boutiques",
+    name="warp2metric",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+Warp2metricFcParameters = typing.TypedDict('Warp2metricFcParameters', {
+    "__STYX_TYPE__": typing.Literal["fc"],
+    "template_fixel_directory": InputPathType,
+    "output_fixel_directory": str,
+    "output_fixel_data": str,
+})
+
+
+Warp2metricConfigParameters = typing.TypedDict('Warp2metricConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Warp2metricParameters = typing.TypedDict('Warp2metricParameters', {
+    "__STYX_TYPE__": typing.Literal["warp2metric"],
+    "fc": typing.NotRequired[Warp2metricFcParameters | None],
+    "jmat": typing.NotRequired[str | None],
+    "jdet": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Warp2metricConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "warp2metric": warp2metric_cargs,
+        "fc": warp2metric_fc_cargs,
+        "config": warp2metric_config_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 {
+        "warp2metric": warp2metric_outputs,
+    }.get(t)
+
+
+def warp2metric_fc_params(
+    template_fixel_directory: InputPathType,
+    output_fixel_directory: str,
+    output_fixel_data: str,
+) -> Warp2metricFcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        template_fixel_directory: use an input template fixel image to define\
+            fibre orientations and output a fixel image describing the change in\
+            fibre cross-section (FC) in the perpendicular plane to the fixel\
+            orientation. e.g. warp2metric warp.mif -fc fixel_template_directory\
+            output_fixel_directory fc.mif.
+        output_fixel_directory: use an input template fixel image to define\
+            fibre orientations and output a fixel image describing the change in\
+            fibre cross-section (FC) in the perpendicular plane to the fixel\
+            orientation. e.g. warp2metric warp.mif -fc fixel_template_directory\
+            output_fixel_directory fc.mif.
+        output_fixel_data: use an input template fixel image to define fibre\
+            orientations and output a fixel image describing the change in fibre\
+            cross-section (FC) in the perpendicular plane to the fixel orientation.\
+            e.g. warp2metric warp.mif -fc fixel_template_directory\
+            output_fixel_directory fc.mif.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fc",
+        "template_fixel_directory": template_fixel_directory,
+        "output_fixel_directory": output_fixel_directory,
+        "output_fixel_data": output_fixel_data,
+    }
+    return params
+
+
+def warp2metric_fc_cargs(
+    params: Warp2metricFcParameters,
+    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("-fc")
+    cargs.append(execution.input_file(params.get("template_fixel_directory")))
+    cargs.append(params.get("output_fixel_directory"))
+    cargs.append(params.get("output_fixel_data"))
+    return cargs
+
+
+def warp2metric_config_params(
+    key: str,
+    value: str,
+) -> Warp2metricConfigParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def warp2metric_config_cargs(
+    params: Warp2metricConfigParameters,
+    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("-config")
+    cargs.append(params.get("key"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class Warp2metricOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `warp2metric(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    jmat: OutputPathType | None
+    """output a Jacobian matrix image stored in column-major order along the 4th
+    dimension.Note the output jacobian describes the warp gradient w.r.t the
+    scanner space coordinate system """
+    jdet: OutputPathType | None
+    """output the Jacobian determinant instead of the full matrix """
+
+
+def warp2metric_params(
+    in_: InputPathType,
+    fc: Warp2metricFcParameters | None = None,
+    jmat: str | None = None,
+    jdet: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Warp2metricConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Warp2metricParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input deformation field.
+        fc: use an input template fixel image to define fibre orientations and\
+            output a fixel image describing the change in fibre cross-section (FC)\
+            in the perpendicular plane to the fixel orientation. e.g. warp2metric\
+            warp.mif -fc fixel_template_directory output_fixel_directory fc.mif.
+        jmat: output a Jacobian matrix image stored in column-major order along\
+            the 4th dimension.Note the output jacobian describes the warp gradient\
+            w.r.t the scanner space coordinate system.
+        jdet: output the Jacobian determinant instead of the full matrix.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "warp2metric",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+    }
+    if fc is not None:
+        params["fc"] = fc
+    if jmat is not None:
+        params["jmat"] = jmat
+    if jdet is not None:
+        params["jdet"] = jdet
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warp2metric_cargs(
+    params: Warp2metricParameters,
+    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("warp2metric")
+    if params.get("fc") is not None:
+        cargs.extend(dyn_cargs(params.get("fc")["__STYXTYPE__"])(params.get("fc"), execution))
+    if params.get("jmat") is not None:
+        cargs.extend([
+            "-jmat",
+            params.get("jmat")
+        ])
+    if params.get("jdet") is not None:
+        cargs.extend([
+            "-jdet",
+            params.get("jdet")
+        ])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    if params.get("config") is not None:
+        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("in")))
+    return cargs
+
+
+def warp2metric_outputs(
+    params: Warp2metricParameters,
+    execution: Execution,
+) -> Warp2metricOutputs:
+    """
+    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 = Warp2metricOutputs(
+        root=execution.output_file("."),
+        jmat=execution.output_file(params.get("jmat")) if (params.get("jmat") is not None) else None,
+        jdet=execution.output_file(params.get("jdet")) if (params.get("jdet") is not None) else None,
+    )
+    return ret
+
+
+def warp2metric_execute(
+    params: Warp2metricParameters,
+    execution: Execution,
+) -> Warp2metricOutputs:
+    """
+    Compute fixel-wise or voxel-wise metrics from a 4D deformation field.
+    
+    
+    
+    References:
+    
+    Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway,
+    GR. Connelly, A.Investigating White Matter Fibre Density and Morphology
+    using Fixel-Based Analysis. Neuroimage, 2017, 144, 58-73, doi:
+    10.1016/j.neuroimage.2016.09.029.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Warp2metricOutputs`).
+    """
+    params = execution.params(params)
+    cargs = warp2metric_cargs(params, execution)
+    ret = warp2metric_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warp2metric(
+    in_: InputPathType,
+    fc: Warp2metricFcParameters | None = None,
+    jmat: str | None = None,
+    jdet: str | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Warp2metricConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Warp2metricOutputs:
+    """
+    Compute fixel-wise or voxel-wise metrics from a 4D deformation field.
+    
+    
+    
+    References:
+    
+    Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway,
+    GR. Connelly, A.Investigating White Matter Fibre Density and Morphology
+    using Fixel-Based Analysis. Neuroimage, 2017, 144, 58-73, doi:
+    10.1016/j.neuroimage.2016.09.029.
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input deformation field.
+        fc: use an input template fixel image to define fibre orientations and\
+            output a fixel image describing the change in fibre cross-section (FC)\
+            in the perpendicular plane to the fixel orientation. e.g. warp2metric\
+            warp.mif -fc fixel_template_directory output_fixel_directory fc.mif.
+        jmat: output a Jacobian matrix image stored in column-major order along\
+            the 4th dimension.Note the output jacobian describes the warp gradient\
+            w.r.t the scanner space coordinate system.
+        jdet: output the Jacobian determinant instead of the full matrix.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Warp2metricOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARP2METRIC_METADATA)
+    params = warp2metric_params(
+        fc=fc,
+        jmat=jmat,
+        jdet=jdet,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+    )
+    return warp2metric_execute(params, execution)
+
+
+__all__ = [
+    "WARP2METRIC_METADATA",
+    "Warp2metricConfigParameters",
+    "Warp2metricFcParameters",
+    "Warp2metricOutputs",
+    "Warp2metricParameters",
+    "warp2metric",
+    "warp2metric_config_params",
+    "warp2metric_fc_params",
+    "warp2metric_params",
+]