niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/dirmerge.py

@@ -0,0 +1,365 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DIRMERGE_METADATA = Metadata(
+    id="92c50a190c4f14115f8c861044c931f1316999ca.boutiques",
+    name="dirmerge",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+DirmergeConfigParameters = typing.TypedDict('DirmergeConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+DirmergeParameters = typing.TypedDict('DirmergeParameters', {
+    "__STYX_TYPE__": typing.Literal["dirmerge"],
+    "unipolar_weight": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirmergeConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "subsets": int,
+    "bvalue_files": list[str],
+    "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 {
+        "dirmerge": dirmerge_cargs,
+        "config": dirmerge_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 {
+        "dirmerge": dirmerge_outputs,
+    }.get(t)
+
+
+def dirmerge_config_params(
+    key: str,
+    value: str,
+) -> DirmergeConfigParameters:
+    """
+    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 dirmerge_config_cargs(
+    params: DirmergeConfigParameters,
+    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 DirmergeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dirmerge(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output directions file, with each row listing the X Y Z gradient
+    directions, the b-value, and an index representing the phase encode
+    direction"""
+
+
+def dirmerge_params(
+    subsets: int,
+    bvalue_files: list[str],
+    out: str,
+    unipolar_weight: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirmergeConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DirmergeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subsets: the number of subsets (eg. phase encoding directions) per\
+            b-value.
+        bvalue_files: the b-value and sets of corresponding files, in order.
+        out: the output directions file, with each row listing the X Y Z\
+            gradient directions, the b-value, and an index representing the phase\
+            encode direction.
+        unipolar_weight: set the weight given to the unipolar electrostatic\
+            repulsion model compared to the bipolar model (default: 0.2).
+        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__": "dirmerge",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "subsets": subsets,
+        "bvalue_files": bvalue_files,
+        "out": out,
+    }
+    if unipolar_weight is not None:
+        params["unipolar_weight"] = unipolar_weight
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dirmerge_cargs(
+    params: DirmergeParameters,
+    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("dirmerge")
+    if params.get("unipolar_weight") is not None:
+        cargs.extend([
+            "-unipolar_weight",
+            str(params.get("unipolar_weight"))
+        ])
+    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(str(params.get("subsets")))
+    cargs.extend(params.get("bvalue_files"))
+    cargs.append(params.get("out"))
+    return cargs
+
+
+def dirmerge_outputs(
+    params: DirmergeParameters,
+    execution: Execution,
+) -> DirmergeOutputs:
+    """
+    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 = DirmergeOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out")),
+    )
+    return ret
+
+
+def dirmerge_execute(
+    params: DirmergeParameters,
+    execution: Execution,
+) -> DirmergeOutputs:
+    """
+    Splice / merge multiple sets of directions in such a way as to maintain
+    near-optimality upon truncation.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DirmergeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dirmerge_cargs(params, execution)
+    ret = dirmerge_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dirmerge(
+    subsets: int,
+    bvalue_files: list[str],
+    out: str,
+    unipolar_weight: float | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirmergeConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DirmergeOutputs:
+    """
+    Splice / merge multiple sets of directions in such a way as to maintain
+    near-optimality upon truncation.
+    
+    
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        subsets: the number of subsets (eg. phase encoding directions) per\
+            b-value.
+        bvalue_files: the b-value and sets of corresponding files, in order.
+        out: the output directions file, with each row listing the X Y Z\
+            gradient directions, the b-value, and an index representing the phase\
+            encode direction.
+        unipolar_weight: set the weight given to the unipolar electrostatic\
+            repulsion model compared to the bipolar model (default: 0.2).
+        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 `DirmergeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRMERGE_METADATA)
+    params = dirmerge_params(
+        unipolar_weight=unipolar_weight,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        subsets=subsets,
+        bvalue_files=bvalue_files,
+        out=out,
+    )
+    return dirmerge_execute(params, execution)
+
+
+__all__ = [
+    "DIRMERGE_METADATA",
+    "DirmergeConfigParameters",
+    "DirmergeOutputs",
+    "DirmergeParameters",
+    "dirmerge",
+    "dirmerge_config_params",
+    "dirmerge_params",
+]

niwrap_mrtrix/mrtrix/dirorder.py

@@ -0,0 +1,347 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DIRORDER_METADATA = Metadata(
+    id="822332bcb7593b804c24d6da3c7da0a1eb44ba1a.boutiques",
+    name="dirorder",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+DirorderConfigParameters = typing.TypedDict('DirorderConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+DirorderParameters = typing.TypedDict('DirorderParameters', {
+    "__STYX_TYPE__": typing.Literal["dirorder"],
+    "cartesian": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirorderConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": 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 {
+        "dirorder": dirorder_cargs,
+        "config": dirorder_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 {
+        "dirorder": dirorder_outputs,
+    }.get(t)
+
+
+def dirorder_config_params(
+    key: str,
+    value: str,
+) -> DirorderConfigParameters:
+    """
+    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 dirorder_config_cargs(
+    params: DirorderConfigParameters,
+    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 DirorderOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dirorder(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """the output directions file"""
+
+
+def dirorder_params(
+    input_: InputPathType,
+    output: str,
+    cartesian: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirorderConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> DirorderParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: the input directions file.
+        output: the output directions file.
+        cartesian: Output the directions in Cartesian coordinates [x y z]\
+            instead of [az el].
+        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__": "dirorder",
+        "cartesian": cartesian,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "input": input_,
+        "output": output,
+    }
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def dirorder_cargs(
+    params: DirorderParameters,
+    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("dirorder")
+    if params.get("cartesian"):
+        cargs.append("-cartesian")
+    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")))
+    cargs.append(params.get("output"))
+    return cargs
+
+
+def dirorder_outputs(
+    params: DirorderParameters,
+    execution: Execution,
+) -> DirorderOutputs:
+    """
+    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 = DirorderOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("output")),
+    )
+    return ret
+
+
+def dirorder_execute(
+    params: DirorderParameters,
+    execution: Execution,
+) -> DirorderOutputs:
+    """
+    Reorder a set of directions to ensure near-uniformity upon truncation.
+    
+    The intent of this command is to reorder a set of gradient directions such
+    that if a scan is terminated prematurely, at any point, the acquired
+    directions will still be close to optimally distributed on the half-sphere.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DirorderOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dirorder_cargs(params, execution)
+    ret = dirorder_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dirorder(
+    input_: InputPathType,
+    output: str,
+    cartesian: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[DirorderConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> DirorderOutputs:
+    """
+    Reorder a set of directions to ensure near-uniformity upon truncation.
+    
+    The intent of this command is to reorder a set of gradient directions such
+    that if a scan is terminated prematurely, at any point, the acquired
+    directions will still be close to optimally distributed on the half-sphere.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        input_: the input directions file.
+        output: the output directions file.
+        cartesian: Output the directions in Cartesian coordinates [x y z]\
+            instead of [az el].
+        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 `DirorderOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRORDER_METADATA)
+    params = dirorder_params(
+        cartesian=cartesian,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        input_=input_,
+        output=output,
+    )
+    return dirorder_execute(params, execution)
+
+
+__all__ = [
+    "DIRORDER_METADATA",
+    "DirorderConfigParameters",
+    "DirorderOutputs",
+    "DirorderParameters",
+    "dirorder",
+    "dirorder_config_params",
+    "dirorder_params",
+]