niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/xsanatreg.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+XSANATREG_METADATA = Metadata(
+    id="fa7d0e1f8dd94e54884aa8dac608dad32d5de507.boutiques",
+    name="xsanatreg",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+XsanatregParameters = typing.TypedDict('XsanatregParameters', {
+    "__STYX_TYPE__": typing.Literal["xsanatreg"],
+    "src_cordir": str,
+    "targ_cordir": str,
+    "transform_file": str,
+    "temp_directory": typing.NotRequired[str | None],
+    "source_minc": typing.NotRequired[str | None],
+    "target_minc": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+    "version": bool,
+    "umask": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "xsanatreg": xsanatreg_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)
+
+
+class XsanatregOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `xsanatreg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def xsanatreg_params(
+    src_cordir: str,
+    targ_cordir: str,
+    transform_file: str,
+    temp_directory: str | None = None,
+    source_minc: str | None = None,
+    target_minc: str | None = None,
+    no_cleanup: bool = False,
+    version: bool = False,
+    umask: str | None = None,
+) -> XsanatregParameters:
+    """
+    Build parameters.
+    
+    Args:
+        src_cordir: Directory of source COR volume.
+        targ_cordir: Directory of target COR volume.
+        transform_file: File in which to store the transformation.
+        temp_directory: Directory for temporary storage, defaults to /tmp.
+        source_minc: File name for source minc, set automatically if not\
+            specified.
+        target_minc: File name for target minc, set automatically if not\
+            specified.
+        no_cleanup: Do not delete temporary minc files.
+        version: Print version and exit.
+        umask: Set file mode creation mask.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "xsanatreg",
+        "src_cordir": src_cordir,
+        "targ_cordir": targ_cordir,
+        "transform_file": transform_file,
+        "no_cleanup": no_cleanup,
+        "version": version,
+    }
+    if temp_directory is not None:
+        params["temp_directory"] = temp_directory
+    if source_minc is not None:
+        params["source_minc"] = source_minc
+    if target_minc is not None:
+        params["target_minc"] = target_minc
+    if umask is not None:
+        params["umask"] = umask
+    return params
+
+
+def xsanatreg_cargs(
+    params: XsanatregParameters,
+    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("xsanatreg")
+    cargs.extend([
+        "-src",
+        params.get("src_cordir")
+    ])
+    cargs.extend([
+        "-targ",
+        params.get("targ_cordir")
+    ])
+    cargs.extend([
+        "-xfm",
+        params.get("transform_file")
+    ])
+    if params.get("temp_directory") is not None:
+        cargs.extend([
+            "-tmpdir",
+            params.get("temp_directory")
+        ])
+    if params.get("source_minc") is not None:
+        cargs.extend([
+            "-srcminc",
+            params.get("source_minc")
+        ])
+    if params.get("target_minc") is not None:
+        cargs.extend([
+            "-targminc",
+            params.get("target_minc")
+        ])
+    if params.get("no_cleanup"):
+        cargs.append("-nocleanup")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("umask") is not None:
+        cargs.extend([
+            "-umask",
+            params.get("umask")
+        ])
+    return cargs
+
+
+def xsanatreg_outputs(
+    params: XsanatregParameters,
+    execution: Execution,
+) -> XsanatregOutputs:
+    """
+    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 = XsanatregOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def xsanatreg_execute(
+    params: XsanatregParameters,
+    execution: Execution,
+) -> XsanatregOutputs:
+    """
+    A tool for registering source and target COR volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `XsanatregOutputs`).
+    """
+    params = execution.params(params)
+    cargs = xsanatreg_cargs(params, execution)
+    ret = xsanatreg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def xsanatreg(
+    src_cordir: str,
+    targ_cordir: str,
+    transform_file: str,
+    temp_directory: str | None = None,
+    source_minc: str | None = None,
+    target_minc: str | None = None,
+    no_cleanup: bool = False,
+    version: bool = False,
+    umask: str | None = None,
+    runner: Runner | None = None,
+) -> XsanatregOutputs:
+    """
+    A tool for registering source and target COR volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        src_cordir: Directory of source COR volume.
+        targ_cordir: Directory of target COR volume.
+        transform_file: File in which to store the transformation.
+        temp_directory: Directory for temporary storage, defaults to /tmp.
+        source_minc: File name for source minc, set automatically if not\
+            specified.
+        target_minc: File name for target minc, set automatically if not\
+            specified.
+        no_cleanup: Do not delete temporary minc files.
+        version: Print version and exit.
+        umask: Set file mode creation mask.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `XsanatregOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XSANATREG_METADATA)
+    params = xsanatreg_params(
+        src_cordir=src_cordir,
+        targ_cordir=targ_cordir,
+        transform_file=transform_file,
+        temp_directory=temp_directory,
+        source_minc=source_minc,
+        target_minc=target_minc,
+        no_cleanup=no_cleanup,
+        version=version,
+        umask=umask,
+    )
+    return xsanatreg_execute(params, execution)
+
+
+__all__ = [
+    "XSANATREG_METADATA",
+    "XsanatregOutputs",
+    "XsanatregParameters",
+    "xsanatreg",
+    "xsanatreg_params",
+]

niwrap_freesurfer/freesurfer/zero_lt_4dfp.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ZERO_LT_4DFP_METADATA = Metadata(
+    id="5af9fb53b5beb7937f30eebe316bb87929b7202b.boutiques",
+    name="zero_lt_4dfp",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+ZeroLt4dfpParameters = typing.TypedDict('ZeroLt4dfpParameters', {
+    "__STYX_TYPE__": typing.Literal["zero_lt_4dfp"],
+    "flt_value": float,
+    "file_4dfp": InputPathType,
+    "outroot": typing.NotRequired[str | None],
+    "endianness": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "zero_lt_4dfp": zero_lt_4dfp_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 {
+        "zero_lt_4dfp": zero_lt_4dfp_outputs,
+    }.get(t)
+
+
+class ZeroLt4dfpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `zero_lt_4dfp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_4dfp: OutputPathType | None
+    """Output 4dfp file with values less than the threshold zeroed."""
+
+
+def zero_lt_4dfp_params(
+    flt_value: float,
+    file_4dfp: InputPathType,
+    outroot: str | None = None,
+    endianness: str | None = None,
+) -> ZeroLt4dfpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        flt_value: Floating point threshold value. Values less than this in the\
+            4dfp file will be zeroed.
+        file_4dfp: Input 4dfp file.
+        outroot: Output root name for 4dfp file. If not specified, defaults to\
+            input file root with 'z' appended.
+        endianness: Specify output endian format: 'b' for big endian or 'l' for\
+            little endian. Defaults to input endian.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "zero_lt_4dfp",
+        "flt_value": flt_value,
+        "file_4dfp": file_4dfp,
+    }
+    if outroot is not None:
+        params["outroot"] = outroot
+    if endianness is not None:
+        params["endianness"] = endianness
+    return params
+
+
+def zero_lt_4dfp_cargs(
+    params: ZeroLt4dfpParameters,
+    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("zero_lt_4dfp")
+    cargs.append(str(params.get("flt_value")))
+    cargs.append(execution.input_file(params.get("file_4dfp")))
+    if params.get("outroot") is not None:
+        cargs.append(params.get("outroot"))
+    if params.get("endianness") is not None:
+        cargs.extend([
+            "-@",
+            params.get("endianness")
+        ])
+    return cargs
+
+
+def zero_lt_4dfp_outputs(
+    params: ZeroLt4dfpParameters,
+    execution: Execution,
+) -> ZeroLt4dfpOutputs:
+    """
+    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 = ZeroLt4dfpOutputs(
+        root=execution.output_file("."),
+        output_4dfp=execution.output_file(params.get("outroot") + ".4dfp") if (params.get("outroot") is not None) else None,
+    )
+    return ret
+
+
+def zero_lt_4dfp_execute(
+    params: ZeroLt4dfpParameters,
+    execution: Execution,
+) -> ZeroLt4dfpOutputs:
+    """
+    A tool to process 4dfp image files by zeroing values less than a given float
+    threshold.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ZeroLt4dfpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = zero_lt_4dfp_cargs(params, execution)
+    ret = zero_lt_4dfp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def zero_lt_4dfp(
+    flt_value: float,
+    file_4dfp: InputPathType,
+    outroot: str | None = None,
+    endianness: str | None = None,
+    runner: Runner | None = None,
+) -> ZeroLt4dfpOutputs:
+    """
+    A tool to process 4dfp image files by zeroing values less than a given float
+    threshold.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        flt_value: Floating point threshold value. Values less than this in the\
+            4dfp file will be zeroed.
+        file_4dfp: Input 4dfp file.
+        outroot: Output root name for 4dfp file. If not specified, defaults to\
+            input file root with 'z' appended.
+        endianness: Specify output endian format: 'b' for big endian or 'l' for\
+            little endian. Defaults to input endian.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ZeroLt4dfpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ZERO_LT_4DFP_METADATA)
+    params = zero_lt_4dfp_params(
+        flt_value=flt_value,
+        file_4dfp=file_4dfp,
+        outroot=outroot,
+        endianness=endianness,
+    )
+    return zero_lt_4dfp_execute(params, execution)
+
+
+__all__ = [
+    "ZERO_LT_4DFP_METADATA",
+    "ZeroLt4dfpOutputs",
+    "ZeroLt4dfpParameters",
+    "zero_lt_4dfp",
+    "zero_lt_4dfp_params",
+]

niwrap_freesurfer-0.5.0.dist-info/METADATA

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