niwrap-mrtrix 0.5.0__py3-none-any.whl

niwrap_mrtrix/mrtrix/warpinvert.py

@@ -0,0 +1,370 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WARPINVERT_METADATA = Metadata(
+    id="34bd9d16c822603308c19a28bf1253af52fb2b1c.boutiques",
+    name="warpinvert",
+    package="mrtrix",
+    container_image_tag="mrtrix3/mrtrix3:3.0.4",
+)
+
+
+WarpinvertConfigParameters = typing.TypedDict('WarpinvertConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+WarpinvertParameters = typing.TypedDict('WarpinvertParameters', {
+    "__STYX_TYPE__": typing.Literal["warpinvert"],
+    "template": typing.NotRequired[InputPathType | None],
+    "displacement": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[WarpinvertConfigParameters] | 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 {
+        "warpinvert": warpinvert_cargs,
+        "config": warpinvert_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 {
+        "warpinvert": warpinvert_outputs,
+    }.get(t)
+
+
+def warpinvert_config_params(
+    key: str,
+    value: str,
+) -> WarpinvertConfigParameters:
+    """
+    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 warpinvert_config_cargs(
+    params: WarpinvertConfigParameters,
+    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 WarpinvertOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `warpinvert(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out: OutputPathType
+    """the output warp image."""
+
+
+def warpinvert_params(
+    in_: InputPathType,
+    out: str,
+    template: InputPathType | None = None,
+    displacement: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpinvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> WarpinvertParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_: the input warp image.
+        out: the output warp image.
+        template: define a template image grid for the output warp.
+        displacement: indicates that the input warp field is a displacement\
+            field; the output will also be a displacement field.
+        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__": "warpinvert",
+        "displacement": displacement,
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "in": in_,
+        "out": out,
+    }
+    if template is not None:
+        params["template"] = template
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def warpinvert_cargs(
+    params: WarpinvertParameters,
+    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("warpinvert")
+    if params.get("template") is not None:
+        cargs.extend([
+            "-template",
+            execution.input_file(params.get("template"))
+        ])
+    if params.get("displacement"):
+        cargs.append("-displacement")
+    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 warpinvert_outputs(
+    params: WarpinvertParameters,
+    execution: Execution,
+) -> WarpinvertOutputs:
+    """
+    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 = WarpinvertOutputs(
+        root=execution.output_file("."),
+        out=execution.output_file(params.get("out")),
+    )
+    return ret
+
+
+def warpinvert_execute(
+    params: WarpinvertParameters,
+    execution: Execution,
+) -> WarpinvertOutputs:
+    """
+    Invert a non-linear warp field.
+    
+    By default, this command assumes that the input warp field is a deformation
+    field, i.e. each voxel stores the corresponding position in the other image
+    (in scanner space), and the calculated output warp image will also be a
+    deformation field. If the input warp field is instead a displacment field,
+    i.e. where each voxel stores an offset from which to sample the other image
+    (but still in scanner space), then the -displacement option should be used;
+    the output warp field will additionally be calculated as a displacement
+    field in this case.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `WarpinvertOutputs`).
+    """
+    params = execution.params(params)
+    cargs = warpinvert_cargs(params, execution)
+    ret = warpinvert_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def warpinvert(
+    in_: InputPathType,
+    out: str,
+    template: InputPathType | None = None,
+    displacement: bool = False,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[WarpinvertConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> WarpinvertOutputs:
+    """
+    Invert a non-linear warp field.
+    
+    By default, this command assumes that the input warp field is a deformation
+    field, i.e. each voxel stores the corresponding position in the other image
+    (in scanner space), and the calculated output warp image will also be a
+    deformation field. If the input warp field is instead a displacment field,
+    i.e. where each voxel stores an offset from which to sample the other image
+    (but still in scanner space), then the -displacement option should be used;
+    the output warp field will additionally be calculated as a displacement
+    field in this case.
+    
+    References:
+    
+    .
+    
+    Author: MRTrix3 Developers
+    
+    URL: https://www.mrtrix.org/
+    
+    Args:
+        in_: the input warp image.
+        out: the output warp image.
+        template: define a template image grid for the output warp.
+        displacement: indicates that the input warp field is a displacement\
+            field; the output will also be a displacement field.
+        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 `WarpinvertOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WARPINVERT_METADATA)
+    params = warpinvert_params(
+        template=template,
+        displacement=displacement,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        in_=in_,
+        out=out,
+    )
+    return warpinvert_execute(params, execution)
+
+
+__all__ = [
+    "WARPINVERT_METADATA",
+    "WarpinvertConfigParameters",
+    "WarpinvertOutputs",
+    "WarpinvertParameters",
+    "warpinvert",
+    "warpinvert_config_params",
+    "warpinvert_params",
+]

niwrap_mrtrix-0.5.0.dist-info/METADATA

@@ -0,0 +1,8 @@
+Metadata-Version: 2.4
+Name: niwrap_mrtrix
+Version: 0.5.0
+Summary: NiWrap wrappers for MRTrix3.
+Author-email: CMI DAIR <dair@childmind.org>
+License-Expression: LGPL-2.1
+Requires-Python: >=3.10
+Requires-Dist: styxdefs~=0.5.0

niwrap_mrtrix-0.5.0.dist-info/RECORD

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@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any