niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/shconv.py

@@ -0,0 +1,498 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SHCONV_METADATA = Metadata(
+    id="3c84c5743ea66d880048dc5dc975db440966a75e.boutiques",
+    name="shconv",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+ShconvVariousStringParameters = typing.TypedDict('ShconvVariousStringParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousString"],
+    "obj": str,
+})
+
+
+ShconvVariousFileParameters = typing.TypedDict('ShconvVariousFileParameters', {
+    "__STYX_TYPE__": typing.Literal["VariousFile"],
+    "obj": InputPathType,
+})
+
+
+ShconvConfigParameters = typing.TypedDict('ShconvConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+ShconvParameters = typing.TypedDict('ShconvParameters', {
+    "__STYX_TYPE__": typing.Literal["shconv"],
+    "datatype": typing.NotRequired[str | None],
+    "strides": typing.NotRequired[typing.Union[ShconvVariousStringParameters, ShconvVariousFileParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ShconvConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "odf_response": list[str],
+    "SH_out": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "shconv": shconv_cargs,
+        "VariousString": shconv_various_string_cargs,
+        "VariousFile": shconv_various_file_cargs,
+        "config": shconv_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 {
+        "shconv": shconv_outputs,
+    }.get(t)
+
+
+def shconv_various_string_params(
+    obj: str,
+) -> ShconvVariousStringParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: String object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousString",
+        "obj": obj,
+    }
+    return params
+
+
+def shconv_various_string_cargs(
+    params: ShconvVariousStringParameters,
+    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(params.get("obj"))
+    return cargs
+
+
+def shconv_various_file_params(
+    obj: InputPathType,
+) -> ShconvVariousFileParameters:
+    """
+    Build parameters.
+    
+    Args:
+        obj: File object.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "VariousFile",
+        "obj": obj,
+    }
+    return params
+
+
+def shconv_various_file_cargs(
+    params: ShconvVariousFileParameters,
+    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(execution.input_file(params.get("obj")))
+    return cargs
+
+
+def shconv_config_params(
+    key: str,
+    value: str,
+) -> ShconvConfigParameters:
+    """
+    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 shconv_config_cargs(
+    params: ShconvConfigParameters,
+    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 ShconvOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `shconv(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    sh_out: OutputPathType
+    """the output spherical harmonics coefficients image."""
+
+
+def shconv_params(
+    odf_response: list[str],
+    sh_out: str,
+    datatype: str | None = None,
+    strides: typing.Union[ShconvVariousStringParameters, ShconvVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ShconvConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> ShconvParameters:
+    """
+    Build parameters.
+    
+    Args:
+        odf_response: pairs of input ODF image and corresponding responses.
+        sh_out: the output spherical harmonics coefficients image.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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__": "shconv",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "odf_response": odf_response,
+        "SH_out": sh_out,
+    }
+    if datatype is not None:
+        params["datatype"] = datatype
+    if strides is not None:
+        params["strides"] = strides
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def shconv_cargs(
+    params: ShconvParameters,
+    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("shconv")
+    if params.get("datatype") is not None:
+        cargs.extend([
+            "-datatype",
+            params.get("datatype")
+        ])
+    if params.get("strides") is not None:
+        cargs.extend([
+            "-strides",
+            *dyn_cargs(params.get("strides")["__STYXTYPE__"])(params.get("strides"), execution)
+        ])
+    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.extend(params.get("odf_response"))
+    cargs.append(params.get("SH_out"))
+    return cargs
+
+
+def shconv_outputs(
+    params: ShconvParameters,
+    execution: Execution,
+) -> ShconvOutputs:
+    """
+    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 = ShconvOutputs(
+        root=execution.output_file("."),
+        sh_out=execution.output_file(params.get("SH_out")),
+    )
+    return ret
+
+
+def shconv_execute(
+    params: ShconvParameters,
+    execution: Execution,
+) -> ShconvOutputs:
+    """
+    Perform spherical convolution.
+    
+    Provided with matching pairs of response function and ODF images (containing
+    SH coefficients), perform spherical convolution to provide the corresponding
+    SH coefficients of the signal.
+    
+    If multiple pairs of inputs are provided, their contributions will be summed
+    into a single output.
+    
+    If the responses are multi-shell (with one line of coefficients per shell),
+    the output will be a 5-dimensional image, with the SH coefficients of the
+    signal in each shell stored at different indices along the 5th dimension.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ShconvOutputs`).
+    """
+    params = execution.params(params)
+    cargs = shconv_cargs(params, execution)
+    ret = shconv_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def shconv(
+    odf_response: list[str],
+    sh_out: str,
+    datatype: str | None = None,
+    strides: typing.Union[ShconvVariousStringParameters, ShconvVariousFileParameters] | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[ShconvConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> ShconvOutputs:
+    """
+    Perform spherical convolution.
+    
+    Provided with matching pairs of response function and ODF images (containing
+    SH coefficients), perform spherical convolution to provide the corresponding
+    SH coefficients of the signal.
+    
+    If multiple pairs of inputs are provided, their contributions will be summed
+    into a single output.
+    
+    If the responses are multi-shell (with one line of coefficients per shell),
+    the output will be a 5-dimensional image, with the SH coefficients of the
+    signal in each shell stored at different indices along the 5th dimension.
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    The spherical harmonic coefficients are stored according the conventions
+    described the main documentation, which can be found at the following link:
+    https://mrtrix.readthedocs.io/en/3.0.4/concepts/spherical_harmonics.html
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        odf_response: pairs of input ODF image and corresponding responses.
+        sh_out: the output spherical harmonics coefficients image.
+        datatype: specify output image data type. Valid choices are: float32,\
+            float32le, float32be, float64, float64le, float64be, int64, uint64,\
+            int64le, uint64le, int64be, uint64be, int32, uint32, int32le, uint32le,\
+            int32be, uint32be, int16, uint16, int16le, uint16le, int16be, uint16be,\
+            cfloat32, cfloat32le, cfloat32be, cfloat64, cfloat64le, cfloat64be,\
+            int8, uint8, bit.
+        strides: specify the strides of the output data in memory; either as a\
+            comma-separated list of (signed) integers, or as a template image from\
+            which the strides shall be extracted and used. The actual strides\
+            produced will depend on whether the output image format can support it.
+        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 `ShconvOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SHCONV_METADATA)
+    params = shconv_params(
+        datatype=datatype,
+        strides=strides,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        odf_response=odf_response,
+        sh_out=sh_out,
+    )
+    return shconv_execute(params, execution)
+
+
+__all__ = [
+    "SHCONV_METADATA",
+    "ShconvConfigParameters",
+    "ShconvOutputs",
+    "ShconvParameters",
+    "ShconvVariousFileParameters",
+    "ShconvVariousStringParameters",
+    "shconv",
+    "shconv_config_params",
+    "shconv_params",
+    "shconv_various_file_params",
+    "shconv_various_string_params",
+]