niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warpcorrect.py

@@ -0,0 +1,368 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARPCORRECT_METADATA = Metadata(
+    id="ac61099f3060923f7f158e31279303a1a92afb02.boutiques",
+    name="warpcorrect",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+WarpcorrectConfigParameters = typing.TypedDict('WarpcorrectConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+WarpcorrectParameters = typing.TypedDict('WarpcorrectParameters', {
+    "__STYX_TYPE__": typing.Literal["warpcorrect"],
+    "marker": typing.NotRequired[list[float] | None],
+    "tolerance": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpcorrectConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "in": InputPathType,
+    "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 {
+        "warpcorrect": warpcorrect_cargs,
+        "config": warpcorrect_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 {
+        "warpcorrect": warpcorrect_outputs,
+    }.get(t)
+
+
+def warpcorrect_config_params(
+    key: str,
+    value: str,
+) -> WarpcorrectConfigParameters:
+    """
+    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 warpcorrect_config_cargs(
+    params: WarpcorrectConfigParameters,
+    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 WarpcorrectOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `warpcorrect(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output warp image."""
+
+
+def warpcorrect_params(
+    in_: InputPathType,
+    out: str,
+    marker: list[float] | None = None,
+    tolerance: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpcorrectConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> WarpcorrectParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input warp image.
+        out: the output warp image.
+        marker: single value or a comma separated list of values that define\
+            out of bounds voxels in the input warp image. Default: (0,0,0).
+        tolerance: numerical precision used for L2 matrix norm comparison.\
+            Default: 9.99999975e-06.
+        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__": "warpcorrect",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+        "out": out,
+    }
+    if marker is not None:
+        params["marker"] = marker
+    if tolerance is not None:
+        params["tolerance"] = tolerance
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warpcorrect_cargs(
+    params: WarpcorrectParameters,
+    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("warpcorrect")
+    if params.get("marker") is not None:
+        cargs.extend([
+            "-marker",
+            *map(str, params.get("marker"))
+        ])
+    if params.get("tolerance") is not None:
+        cargs.extend([
+            "-tolerance",
+            str(params.get("tolerance"))
+        ])
+    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")))
+    cargs.append(params.get("out"))
+    return cargs
+
+
+def warpcorrect_outputs(
+    params: WarpcorrectParameters,
+    execution: Execution,
+) -> WarpcorrectOutputs:
+    """
+    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 = WarpcorrectOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out")),
+    )
+    return ret
+
+
+def warpcorrect_execute(
+    params: WarpcorrectParameters,
+    execution: Execution,
+) -> WarpcorrectOutputs:
+    """
+    Replaces voxels in a deformation field that point to a specific out of bounds
+    location with nan,nan,nan.
+    
+    This can be used in conjunction with the warpinit command to compute a
+    MRtrix compatible deformation field from non-linear transformations
+    generated by any other registration package.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `WarpcorrectOutputs`).
+    """
+    params = execution.params(params)
+    cargs = warpcorrect_cargs(params, execution)
+    ret = warpcorrect_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warpcorrect(
+    in_: InputPathType,
+    out: str,
+    marker: list[float] | None = None,
+    tolerance: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpcorrectConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> WarpcorrectOutputs:
+    """
+    Replaces voxels in a deformation field that point to a specific out of bounds
+    location with nan,nan,nan.
+    
+    This can be used in conjunction with the warpinit command to compute a
+    MRtrix compatible deformation field from non-linear transformations
+    generated by any other registration package.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input warp image.
+        out: the output warp image.
+        marker: single value or a comma separated list of values that define\
+            out of bounds voxels in the input warp image. Default: (0,0,0).
+        tolerance: numerical precision used for L2 matrix norm comparison.\
+            Default: 9.99999975e-06.
+        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 `WarpcorrectOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPCORRECT_METADATA)
+    params = warpcorrect_params(
+        marker=marker,
+        tolerance=tolerance,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+        out=out,
+    )
+    return warpcorrect_execute(params, execution)
+
+
+__all__ = [
+    "WARPCORRECT_METADATA",
+    "WarpcorrectConfigParameters",
+    "WarpcorrectOutputs",
+    "WarpcorrectParameters",
+    "warpcorrect",
+    "warpcorrect_config_params",
+    "warpcorrect_params",
+]

niwrap_mrtrix/mrtrix/warpinit.py

@@ -0,0 +1,356 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARPINIT_METADATA = Metadata(
+    id="4b6c806f701cb5bc6b23937491e0dab59feb77ec.boutiques",
+    name="warpinit",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+WarpinitConfigParameters = typing.TypedDict('WarpinitConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+WarpinitParameters = typing.TypedDict('WarpinitParameters', {
+    "__STYX_TYPE__": typing.Literal["warpinit"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpinitConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "template": InputPathType,
+    "warp": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "warpinit": warpinit_cargs,
+        "config": warpinit_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 {
+        "warpinit": warpinit_outputs,
+    }.get(t)
+
+
+def warpinit_config_params(
+    key: str,
+    value: str,
+) -> WarpinitConfigParameters:
+    """
+    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 warpinit_config_cargs(
+    params: WarpinitConfigParameters,
+    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 WarpinitOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `warpinit(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    warp: OutputPathType
+    """the output warp image."""
+
+
+def warpinit_params(
+    template: InputPathType,
+    warp: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpinitConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> WarpinitParameters:
+    """
+    Build parameters.
+    
+    Args:
+        template: the input template image.
+        warp: the output warp image.
+        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__": "warpinit",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "template": template,
+        "warp": warp,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warpinit_cargs(
+    params: WarpinitParameters,
+    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("warpinit")
+    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("template")))
+    cargs.append(params.get("warp"))
+    return cargs
+
+
+def warpinit_outputs(
+    params: WarpinitParameters,
+    execution: Execution,
+) -> WarpinitOutputs:
+    """
+    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 = WarpinitOutputs(
+        root=execution.output_file("."),
+        warp=execution.output_file(params.get("warp")),
+    )
+    return ret
+
+
+def warpinit_execute(
+    params: WarpinitParameters,
+    execution: Execution,
+) -> WarpinitOutputs:
+    """
+    Create an initial warp image, representing an identity transformation.
+    
+    This is useful to obtain the warp fields from other normalisation
+    applications, by applying the transformation of interest to the warp field
+    generated by this program.
+    
+    The image generated is a 4D image with the same spatial characteristics as
+    the input template image. It contains 3 volumes, with each voxel containing
+    its own x,y,z coordinates.
+    
+    Note that this command can be used to create 3 separate X,Y,Z images
+    directly (which may be useful to create images suitable for use in the
+    registration program) using the following syntax:
+    
+    $ warpinit template.mif warp-'[]'.nii
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `WarpinitOutputs`).
+    """
+    params = execution.params(params)
+    cargs = warpinit_cargs(params, execution)
+    ret = warpinit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warpinit(
+    template: InputPathType,
+    warp: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpinitConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> WarpinitOutputs:
+    """
+    Create an initial warp image, representing an identity transformation.
+    
+    This is useful to obtain the warp fields from other normalisation
+    applications, by applying the transformation of interest to the warp field
+    generated by this program.
+    
+    The image generated is a 4D image with the same spatial characteristics as
+    the input template image. It contains 3 volumes, with each voxel containing
+    its own x,y,z coordinates.
+    
+    Note that this command can be used to create 3 separate X,Y,Z images
+    directly (which may be useful to create images suitable for use in the
+    registration program) using the following syntax:
+    
+    $ warpinit template.mif warp-'[]'.nii
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        template: the input template image.
+        warp: the output warp image.
+        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 `WarpinitOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPINIT_METADATA)
+    params = warpinit_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        template=template,
+        warp=warp,
+    )
+    return warpinit_execute(params, execution)
+
+
+__all__ = [
+    "WARPINIT_METADATA",
+    "WarpinitConfigParameters",
+    "WarpinitOutputs",
+    "WarpinitParameters",
+    "warpinit",
+    "warpinit_config_params",
+    "warpinit_params",
+]