niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/transformconvert.py

@@ -0,0 +1,346 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TRANSFORMCONVERT_METADATA = Metadata(
+    id="75054a4be3e9dc5460e5441d97e2350d859886dd.boutiques",
+    name="transformconvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+TransformconvertConfigParameters = typing.TypedDict('TransformconvertConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+TransformconvertParameters = typing.TypedDict('TransformconvertParameters', {
+    "__STYX_TYPE__": typing.Literal["transformconvert"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TransformconvertConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[str],
+    "operation": str,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "transformconvert": transformconvert_cargs,
+        "config": transformconvert_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 {
+        "transformconvert": transformconvert_outputs,
+    }.get(t)
+
+
+def transformconvert_config_params(
+    key: str,
+    value: str,
+) -> TransformconvertConfigParameters:
+    """
+    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 transformconvert_config_cargs(
+    params: TransformconvertConfigParameters,
+    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 TransformconvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `transformconvert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output transformation matrix."""
+
+
+def transformconvert_params(
+    input_: list[str],
+    operation: str,
+    output: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TransformconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TransformconvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input(s) for the specified operation.
+        operation: the operation to perform, one of:\
+            flirt_import, itk_import.
+        output: the output transformation 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__": "transformconvert",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "operation": operation,
+        "output": output,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def transformconvert_cargs(
+    params: TransformconvertParameters,
+    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("transformconvert")
+    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("input"))
+    cargs.append(params.get("operation"))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def transformconvert_outputs(
+    params: TransformconvertParameters,
+    execution: Execution,
+) -> TransformconvertOutputs:
+    """
+    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 = TransformconvertOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def transformconvert_execute(
+    params: TransformconvertParameters,
+    execution: Execution,
+) -> TransformconvertOutputs:
+    """
+    Convert linear transformation matrices.
+    
+    This command allows to convert transformation matrices provided by other
+    registration softwares to a format usable in MRtrix3. Example usages are
+    provided below.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TransformconvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = transformconvert_cargs(params, execution)
+    ret = transformconvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def transformconvert(
+    input_: list[str],
+    operation: str,
+    output: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TransformconvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TransformconvertOutputs:
+    """
+    Convert linear transformation matrices.
+    
+    This command allows to convert transformation matrices provided by other
+    registration softwares to a format usable in MRtrix3. Example usages are
+    provided below.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input(s) for the specified operation.
+        operation: the operation to perform, one of:\
+            flirt_import, itk_import.
+        output: the output transformation 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 `TransformconvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRANSFORMCONVERT_METADATA)
+    params = transformconvert_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        operation=operation,
+        output=output,
+    )
+    return transformconvert_execute(params, execution)
+
+
+__all__ = [
+    "TRANSFORMCONVERT_METADATA",
+    "TransformconvertConfigParameters",
+    "TransformconvertOutputs",
+    "TransformconvertParameters",
+    "transformconvert",
+    "transformconvert_config_params",
+    "transformconvert_params",
+]

niwrap_mrtrix/mrtrix/tsfdivide.py

@@ -0,0 +1,340 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TSFDIVIDE_METADATA = Metadata(
+    id="4ccdf692559c43f81a4682ec0171e369f074e7b7.boutiques",
+    name="tsfdivide",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+TsfdivideConfigParameters = typing.TypedDict('TsfdivideConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+TsfdivideParameters = typing.TypedDict('TsfdivideParameters', {
+    "__STYX_TYPE__": typing.Literal["tsfdivide"],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[TsfdivideConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input1": InputPathType,
+    "input2": InputPathType,
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tsfdivide": tsfdivide_cargs,
+        "config": tsfdivide_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 {
+        "tsfdivide": tsfdivide_outputs,
+    }.get(t)
+
+
+def tsfdivide_config_params(
+    key: str,
+    value: str,
+) -> TsfdivideConfigParameters:
+    """
+    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 tsfdivide_config_cargs(
+    params: TsfdivideConfigParameters,
+    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 TsfdivideOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tsfdivide(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output track scalar file"""
+
+
+def tsfdivide_params(
+    input1: InputPathType,
+    input2: InputPathType,
+    output: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TsfdivideConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> TsfdivideParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input1: the first input track scalar file.
+        input2: the second input track scalar file.
+        output: the output track scalar file.
+        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__": "tsfdivide",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input1": input1,
+        "input2": input2,
+        "output": output,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def tsfdivide_cargs(
+    params: TsfdivideParameters,
+    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("tsfdivide")
+    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("input1")))
+    cargs.append(execution.input_file(params.get("input2")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def tsfdivide_outputs(
+    params: TsfdivideParameters,
+    execution: Execution,
+) -> TsfdivideOutputs:
+    """
+    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 = TsfdivideOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def tsfdivide_execute(
+    params: TsfdivideParameters,
+    execution: Execution,
+) -> TsfdivideOutputs:
+    """
+    Divide corresponding values in track scalar files.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TsfdivideOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tsfdivide_cargs(params, execution)
+    ret = tsfdivide_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tsfdivide(
+    input1: InputPathType,
+    input2: InputPathType,
+    output: str,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[TsfdivideConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> TsfdivideOutputs:
+    """
+    Divide corresponding values in track scalar files.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input1: the first input track scalar file.
+        input2: the second input track scalar file.
+        output: the output track scalar file.
+        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 `TsfdivideOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TSFDIVIDE_METADATA)
+    params = tsfdivide_params(
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input1=input1,
+        input2=input2,
+        output=output,
+    )
+    return tsfdivide_execute(params, execution)
+
+
+__all__ = [
+    "TSFDIVIDE_METADATA",
+    "TsfdivideConfigParameters",
+    "TsfdivideOutputs",
+    "TsfdivideParameters",
+    "tsfdivide",
+    "tsfdivide_config_params",
+    "tsfdivide_params",
+]