niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/fixelcorrespondence.py

@@ -0,0 +1,371 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELCORRESPONDENCE_METADATA = Metadata(
+    id="fad1be9b8243f83bbbf677ed7d4db5308a7e3c5d.boutiques",
+    name="fixelcorrespondence",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+FixelcorrespondenceConfigParameters = typing.TypedDict('FixelcorrespondenceConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+FixelcorrespondenceParameters = typing.TypedDict('FixelcorrespondenceParameters', {
+    "__STYX_TYPE__": typing.Literal["fixelcorrespondence"],
+    "angle": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcorrespondenceConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "subject_data": InputPathType,
+    "template_directory": InputPathType,
+    "output_directory": str,
+    "output_data": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fixelcorrespondence": fixelcorrespondence_cargs,
+        "config": fixelcorrespondence_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 {
+    }.get(t)
+
+
+def fixelcorrespondence_config_params(
+    key: str,
+    value: str,
+) -> FixelcorrespondenceConfigParameters:
+    """
+    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 fixelcorrespondence_config_cargs(
+    params: FixelcorrespondenceConfigParameters,
+    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 FixelcorrespondenceOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixelcorrespondence(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def fixelcorrespondence_params(
+    subject_data: InputPathType,
+    template_directory: InputPathType,
+    output_directory: str,
+    output_data: str,
+    angle: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcorrespondenceConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelcorrespondenceParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_data: the input subject fixel data file. This should be a file\
+            inside the fixel directory.
+        template_directory: the input template fixel directory.
+        output_directory: the fixel directory where the output file will be\
+            written.
+        output_data: the name of the output fixel data file. This will be\
+            placed in the output fixel directory.
+        angle: the max angle threshold for computing inter-subject fixel\
+            correspondence (Default: 45 degrees).
+        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__": "fixelcorrespondence",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "subject_data": subject_data,
+        "template_directory": template_directory,
+        "output_directory": output_directory,
+        "output_data": output_data,
+    }
+    if angle is not None:
+        params["angle"] = angle
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelcorrespondence_cargs(
+    params: FixelcorrespondenceParameters,
+    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("fixelcorrespondence")
+    if params.get("angle") is not None:
+        cargs.extend([
+            "-angle",
+            str(params.get("angle"))
+        ])
+    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("subject_data")))
+    cargs.append(execution.input_file(params.get("template_directory")))
+    cargs.append(params.get("output_directory"))
+    cargs.append(params.get("output_data"))
+    return cargs
+
+
+def fixelcorrespondence_outputs(
+    params: FixelcorrespondenceParameters,
+    execution: Execution,
+) -> FixelcorrespondenceOutputs:
+    """
+    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 = FixelcorrespondenceOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def fixelcorrespondence_execute(
+    params: FixelcorrespondenceParameters,
+    execution: Execution,
+) -> FixelcorrespondenceOutputs:
+    """
+    Obtain fixel-fixel correpondence between a subject fixel image and a template
+    fixel mask.
+    
+    It is assumed that the subject image has already been spatially normalised
+    and is aligned with the template. The output fixel image will have the same
+    fixels (and directions) of the template.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FixelcorrespondenceOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixelcorrespondence_cargs(params, execution)
+    ret = fixelcorrespondence_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelcorrespondence(
+    subject_data: InputPathType,
+    template_directory: InputPathType,
+    output_directory: str,
+    output_data: str,
+    angle: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcorrespondenceConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelcorrespondenceOutputs:
+    """
+    Obtain fixel-fixel correpondence between a subject fixel image and a template
+    fixel mask.
+    
+    It is assumed that the subject image has already been spatially normalised
+    and is aligned with the template. The output fixel image will have the same
+    fixels (and directions) of the template.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        subject_data: the input subject fixel data file. This should be a file\
+            inside the fixel directory.
+        template_directory: the input template fixel directory.
+        output_directory: the fixel directory where the output file will be\
+            written.
+        output_data: the name of the output fixel data file. This will be\
+            placed in the output fixel directory.
+        angle: the max angle threshold for computing inter-subject fixel\
+            correspondence (Default: 45 degrees).
+        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 `FixelcorrespondenceOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCORRESPONDENCE_METADATA)
+    params = fixelcorrespondence_params(
+        angle=angle,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        subject_data=subject_data,
+        template_directory=template_directory,
+        output_directory=output_directory,
+        output_data=output_data,
+    )
+    return fixelcorrespondence_execute(params, execution)
+
+
+__all__ = [
+    "FIXELCORRESPONDENCE_METADATA",
+    "FixelcorrespondenceConfigParameters",
+    "FixelcorrespondenceOutputs",
+    "FixelcorrespondenceParameters",
+    "fixelcorrespondence",
+    "fixelcorrespondence_config_params",
+    "fixelcorrespondence_params",
+]

niwrap_mrtrix/mrtrix/fixelcrop.py

@@ -0,0 +1,348 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIXELCROP_METADATA = Metadata(
+    id="df585f30c2a7738dc8886c2e7c7172b7e6cdc09c.boutiques",
+    name="fixelcrop",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+FixelcropConfigParameters = typing.TypedDict('FixelcropConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+FixelcropParameters = typing.TypedDict('FixelcropParameters', {
+    "__STYX_TYPE__": typing.Literal["fixelcrop"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcropConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input_fixel_directory": InputPathType,
+    "input_fixel_mask": InputPathType,
+    "output_fixel_directory": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fixelcrop": fixelcrop_cargs,
+        "config": fixelcrop_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 {
+        "fixelcrop": fixelcrop_outputs,
+    }.get(t)
+
+
+def fixelcrop_config_params(
+    key: str,
+    value: str,
+) -> FixelcropConfigParameters:
+    """
+    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 fixelcrop_config_cargs(
+    params: FixelcropConfigParameters,
+    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 FixelcropOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fixelcrop(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_fixel_directory: OutputPathType
+    """the output directory to store the cropped directions and data files"""
+
+
+def fixelcrop_params(
+    input_fixel_directory: InputPathType,
+    input_fixel_mask: InputPathType,
+    output_fixel_directory: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcropConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> FixelcropParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_fixel_directory: input fixel directory, all data files and\
+            directions file will be cropped and saved in the output fixel directory.
+        input_fixel_mask: the input fixel data file defining which fixels to\
+            crop. Fixels with zero values will be removed.
+        output_fixel_directory: the output directory to store the cropped\
+            directions and data files.
+        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__": "fixelcrop",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input_fixel_directory": input_fixel_directory,
+        "input_fixel_mask": input_fixel_mask,
+        "output_fixel_directory": output_fixel_directory,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def fixelcrop_cargs(
+    params: FixelcropParameters,
+    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("fixelcrop")
+    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("input_fixel_directory")))
+    cargs.append(execution.input_file(params.get("input_fixel_mask")))
+    cargs.append(params.get("output_fixel_directory"))
+    return cargs
+
+
+def fixelcrop_outputs(
+    params: FixelcropParameters,
+    execution: Execution,
+) -> FixelcropOutputs:
+    """
+    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 = FixelcropOutputs(
+        root=execution.output_file("."),
+        output_fixel_directory=execution.output_file(params.get("output_fixel_directory")),
+    )
+    return ret
+
+
+def fixelcrop_execute(
+    params: FixelcropParameters,
+    execution: Execution,
+) -> FixelcropOutputs:
+    """
+    Crop/remove fixels from sparse fixel image using a binary fixel mask.
+    
+    The mask must be input as a fixel data file the same dimensions as the fixel
+    data file(s) to be cropped.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FixelcropOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fixelcrop_cargs(params, execution)
+    ret = fixelcrop_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fixelcrop(
+    input_fixel_directory: InputPathType,
+    input_fixel_mask: InputPathType,
+    output_fixel_directory: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[FixelcropConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> FixelcropOutputs:
+    """
+    Crop/remove fixels from sparse fixel image using a binary fixel mask.
+    
+    The mask must be input as a fixel data file the same dimensions as the fixel
+    data file(s) to be cropped.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_fixel_directory: input fixel directory, all data files and\
+            directions file will be cropped and saved in the output fixel directory.
+        input_fixel_mask: the input fixel data file defining which fixels to\
+            crop. Fixels with zero values will be removed.
+        output_fixel_directory: the output directory to store the cropped\
+            directions and data files.
+        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 `FixelcropOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCROP_METADATA)
+    params = fixelcrop_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_fixel_directory=input_fixel_directory,
+        input_fixel_mask=input_fixel_mask,
+        output_fixel_directory=output_fixel_directory,
+    )
+    return fixelcrop_execute(params, execution)
+
+
+__all__ = [
+    "FIXELCROP_METADATA",
+    "FixelcropConfigParameters",
+    "FixelcropOutputs",
+    "FixelcropParameters",
+    "fixelcrop",
+    "fixelcrop_config_params",
+    "fixelcrop_params",
+]