niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/tckresample.py

@@ -0,0 +1,580 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TCKRESAMPLE_METADATA = Metadata(
+    id="985698dc2451e564202878939f3e4388fbe9d151.boutiques",
+    name="tckresample",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+TckresampleLineParameters = typing.TypedDict('TckresampleLineParameters', {
+    "__STYX_TYPE__": typing.Literal["line"],
+    "num": int,
+    "start": list[float],
+    "end": list[float],
+})
+
+
+TckresampleArcParameters = typing.TypedDict('TckresampleArcParameters', {
+    "__STYX_TYPE__": typing.Literal["arc"],
+    "num": int,
+    "start": list[float],
+    "mid": list[float],
+    "end": list[float],
+})
+
+
+TckresampleConfigParameters = typing.TypedDict('TckresampleConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+TckresampleParameters = typing.TypedDict('TckresampleParameters', {
+    "__STYX_TYPE__": typing.Literal["tckresample"],
+    "upsample": typing.NotRequired[int | None],
+    "downsample": typing.NotRequired[int | None],
+    "step_size": typing.NotRequired[float | None],
+    "num_points": typing.NotRequired[int | None],
+    "endpoints": bool,
+    "line": typing.NotRequired[TckresampleLineParameters | None],
+    "arc": typing.NotRequired[TckresampleArcParameters | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TckresampleConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in_tracks": InputPathType,
+    "out_tracks": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tckresample": tckresample_cargs,
+        "line": tckresample_line_cargs,
+        "arc": tckresample_arc_cargs,
+        "config": tckresample_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 {
+        "tckresample": tckresample_outputs,
+    }.get(t)
+
+
+def tckresample_line_params(
+    num: int,
+    start: list[float],
+    end: list[float],
+) -> TckresampleLineParameters:
+    """
+    Build parameters.
+    
+    Args:
+        num: resample tracks at 'num' equidistant locations along a line\
+            between 'start' and 'end' (specified as comma-separated 3-vectors in\
+            scanner coordinates).
+        start: resample tracks at 'num' equidistant locations along a line\
+            between 'start' and 'end' (specified as comma-separated 3-vectors in\
+            scanner coordinates).
+        end: resample tracks at 'num' equidistant locations along a line\
+            between 'start' and 'end' (specified as comma-separated 3-vectors in\
+            scanner coordinates).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "line",
+        "num": num,
+        "start": start,
+        "end": end,
+    }
+    return params
+
+
+def tckresample_line_cargs(
+    params: TckresampleLineParameters,
+    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("-line")
+    cargs.append(str(params.get("num")))
+    cargs.append(",".join(map(str, params.get("start"))))
+    cargs.append(",".join(map(str, params.get("end"))))
+    return cargs
+
+
+def tckresample_arc_params(
+    num: int,
+    start: list[float],
+    mid: list[float],
+    end: list[float],
+) -> TckresampleArcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        num: resample tracks at 'num' equidistant locations along a circular\
+            arc specified by points 'start', 'mid' and 'end' (specified as\
+            comma-separated 3-vectors in scanner coordinates).
+        start: resample tracks at 'num' equidistant locations along a circular\
+            arc specified by points 'start', 'mid' and 'end' (specified as\
+            comma-separated 3-vectors in scanner coordinates).
+        mid: resample tracks at 'num' equidistant locations along a circular\
+            arc specified by points 'start', 'mid' and 'end' (specified as\
+            comma-separated 3-vectors in scanner coordinates).
+        end: resample tracks at 'num' equidistant locations along a circular\
+            arc specified by points 'start', 'mid' and 'end' (specified as\
+            comma-separated 3-vectors in scanner coordinates).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "arc",
+        "num": num,
+        "start": start,
+        "mid": mid,
+        "end": end,
+    }
+    return params
+
+
+def tckresample_arc_cargs(
+    params: TckresampleArcParameters,
+    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("-arc")
+    cargs.append(str(params.get("num")))
+    cargs.append(",".join(map(str, params.get("start"))))
+    cargs.append(",".join(map(str, params.get("mid"))))
+    cargs.append(",".join(map(str, params.get("end"))))
+    return cargs
+
+
+def tckresample_config_params(
+    key: str,
+    value: str,
+) -> TckresampleConfigParameters:
+    """
+    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 tckresample_config_cargs(
+    params: TckresampleConfigParameters,
+    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 TckresampleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tckresample(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_tracks: OutputPathType
+    """the output resampled tracks"""
+
+
+def tckresample_params(
+    in_tracks: InputPathType,
+    out_tracks: str,
+    upsample: int | None = None,
+    downsample: int | None = None,
+    step_size: float | None = None,
+    num_points: int | None = None,
+    endpoints: bool = False,
+    line: TckresampleLineParameters | None = None,
+    arc: TckresampleArcParameters | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckresampleConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TckresampleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_tracks: the input track file.
+        out_tracks: the output resampled tracks.
+        upsample: increase the density of points along the length of each\
+            streamline by some factor (may improve mapping streamlines to ROIs,\
+            and/or visualisation).
+        downsample: increase the density of points along the length of each\
+            streamline by some factor (decreases required storage space).
+        step_size: re-sample the streamlines to a desired step size (in mm).
+        num_points: re-sample each streamline to a fixed number of points.
+        endpoints: only output the two endpoints of each streamline.
+        line: resample tracks at 'num' equidistant locations along a line\
+            between 'start' and 'end' (specified as comma-separated 3-vectors in\
+            scanner coordinates).
+        arc: resample tracks at 'num' equidistant locations along a circular\
+            arc specified by points 'start', 'mid' and 'end' (specified as\
+            comma-separated 3-vectors in scanner coordinates).
+        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__": "tckresample",
+        "endpoints": endpoints,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in_tracks": in_tracks,
+        "out_tracks": out_tracks,
+    }
+    if upsample is not None:
+        params["upsample"] = upsample
+    if downsample is not None:
+        params["downsample"] = downsample
+    if step_size is not None:
+        params["step_size"] = step_size
+    if num_points is not None:
+        params["num_points"] = num_points
+    if line is not None:
+        params["line"] = line
+    if arc is not None:
+        params["arc"] = arc
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tckresample_cargs(
+    params: TckresampleParameters,
+    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("tckresample")
+    if params.get("upsample") is not None:
+        cargs.extend([
+            "-upsample",
+            str(params.get("upsample"))
+        ])
+    if params.get("downsample") is not None:
+        cargs.extend([
+            "-downsample",
+            str(params.get("downsample"))
+        ])
+    if params.get("step_size") is not None:
+        cargs.extend([
+            "-step_size",
+            str(params.get("step_size"))
+        ])
+    if params.get("num_points") is not None:
+        cargs.extend([
+            "-num_points",
+            str(params.get("num_points"))
+        ])
+    if params.get("endpoints"):
+        cargs.append("-endpoints")
+    if params.get("line") is not None:
+        cargs.extend(dyn_cargs(params.get("line")["__STYXTYPE__"])(params.get("line"), execution))
+    if params.get("arc") is not None:
+        cargs.extend(dyn_cargs(params.get("arc")["__STYXTYPE__"])(params.get("arc"), 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.append(execution.input_file(params.get("in_tracks")))
+    cargs.append(params.get("out_tracks"))
+    return cargs
+
+
+def tckresample_outputs(
+    params: TckresampleParameters,
+    execution: Execution,
+) -> TckresampleOutputs:
+    """
+    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 = TckresampleOutputs(
+        root=execution.output_file("."),
+        out_tracks=execution.output_file(params.get("out_tracks")),
+    )
+    return ret
+
+
+def tckresample_execute(
+    params: TckresampleParameters,
+    execution: Execution,
+) -> TckresampleOutputs:
+    """
+    Resample each streamline in a track file to a new set of vertices.
+    
+    It is necessary to specify precisely ONE of the command-line options for
+    controlling how this resampling takes place; this may be either increasing
+    or decreasing the number of samples along each streamline, or may involve
+    changing the positions of the samples according to some specified
+    trajectory.
+    
+    Note that because the length of a streamline is calculated based on the sums
+    of distances between adjacent vertices, resampling a streamline to a new set
+    of vertices will typically change the quantified length of that streamline;
+    the magnitude of the difference will typically depend on the discrepancy in
+    the number of vertices, with less vertices leading to a shorter length (due
+    to taking chordal lengths of curved trajectories).
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TckresampleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tckresample_cargs(params, execution)
+    ret = tckresample_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tckresample(
+    in_tracks: InputPathType,
+    out_tracks: str,
+    upsample: int | None = None,
+    downsample: int | None = None,
+    step_size: float | None = None,
+    num_points: int | None = None,
+    endpoints: bool = False,
+    line: TckresampleLineParameters | None = None,
+    arc: TckresampleArcParameters | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TckresampleConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TckresampleOutputs:
+    """
+    Resample each streamline in a track file to a new set of vertices.
+    
+    It is necessary to specify precisely ONE of the command-line options for
+    controlling how this resampling takes place; this may be either increasing
+    or decreasing the number of samples along each streamline, or may involve
+    changing the positions of the samples according to some specified
+    trajectory.
+    
+    Note that because the length of a streamline is calculated based on the sums
+    of distances between adjacent vertices, resampling a streamline to a new set
+    of vertices will typically change the quantified length of that streamline;
+    the magnitude of the difference will typically depend on the discrepancy in
+    the number of vertices, with less vertices leading to a shorter length (due
+    to taking chordal lengths of curved trajectories).
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_tracks: the input track file.
+        out_tracks: the output resampled tracks.
+        upsample: increase the density of points along the length of each\
+            streamline by some factor (may improve mapping streamlines to ROIs,\
+            and/or visualisation).
+        downsample: increase the density of points along the length of each\
+            streamline by some factor (decreases required storage space).
+        step_size: re-sample the streamlines to a desired step size (in mm).
+        num_points: re-sample each streamline to a fixed number of points.
+        endpoints: only output the two endpoints of each streamline.
+        line: resample tracks at 'num' equidistant locations along a line\
+            between 'start' and 'end' (specified as comma-separated 3-vectors in\
+            scanner coordinates).
+        arc: resample tracks at 'num' equidistant locations along a circular\
+            arc specified by points 'start', 'mid' and 'end' (specified as\
+            comma-separated 3-vectors in scanner coordinates).
+        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 `TckresampleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TCKRESAMPLE_METADATA)
+    params = tckresample_params(
+        upsample=upsample,
+        downsample=downsample,
+        step_size=step_size,
+        num_points=num_points,
+        endpoints=endpoints,
+        line=line,
+        arc=arc,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_tracks=in_tracks,
+        out_tracks=out_tracks,
+    )
+    return tckresample_execute(params, execution)
+
+
+__all__ = [
+    "TCKRESAMPLE_METADATA",
+    "TckresampleArcParameters",
+    "TckresampleConfigParameters",
+    "TckresampleLineParameters",
+    "TckresampleOutputs",
+    "TckresampleParameters",
+    "tckresample",
+    "tckresample_arc_params",
+    "tckresample_config_params",
+    "tckresample_line_params",
+    "tckresample_params",
+]