niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/inflate_subject_new_rh.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 *
+
+INFLATE_SUBJECT_NEW_RH_METADATA = Metadata(
+    id="6ededf15eee0d58308af964a359eb602b1b300a0.boutiques",
+    name="inflate_subject_new-rh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+InflateSubjectNewRhParameters = typing.TypedDict('InflateSubjectNewRhParameters', {
+    "__STYX_TYPE__": typing.Literal["inflate_subject_new-rh"],
+    "args": 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 {
+        "inflate_subject_new-rh": inflate_subject_new_rh_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 InflateSubjectNewRhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `inflate_subject_new_rh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def inflate_subject_new_rh_params(
+    args: str | None = None,
+) -> InflateSubjectNewRhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        args: Additional command-line arguments for inflate_subject_new-rh.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "inflate_subject_new-rh",
+    }
+    if args is not None:
+        params["args"] = args
+    return params
+
+
+def inflate_subject_new_rh_cargs(
+    params: InflateSubjectNewRhParameters,
+    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 = []
+    if params.get("args") is not None:
+        cargs.extend([
+            "-rh",
+            "inflate_subject_new" + params.get("args")
+        ])
+    return cargs
+
+
+def inflate_subject_new_rh_outputs(
+    params: InflateSubjectNewRhParameters,
+    execution: Execution,
+) -> InflateSubjectNewRhOutputs:
+    """
+    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 = InflateSubjectNewRhOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def inflate_subject_new_rh_execute(
+    params: InflateSubjectNewRhParameters,
+    execution: Execution,
+) -> InflateSubjectNewRhOutputs:
+    """
+    This is a placeholder descriptor for the 'inflate_subject_new-rh' command. The
+    tool appears to be part of FreeSurfer but the specific inputs, outputs or
+    options couldn't be extracted from the help text.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `InflateSubjectNewRhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = inflate_subject_new_rh_cargs(params, execution)
+    ret = inflate_subject_new_rh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def inflate_subject_new_rh(
+    args: str | None = None,
+    runner: Runner | None = None,
+) -> InflateSubjectNewRhOutputs:
+    """
+    This is a placeholder descriptor for the 'inflate_subject_new-rh' command. The
+    tool appears to be part of FreeSurfer but the specific inputs, outputs or
+    options couldn't be extracted from the help text.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        args: Additional command-line arguments for inflate_subject_new-rh.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `InflateSubjectNewRhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_NEW_RH_METADATA)
+    params = inflate_subject_new_rh_params(
+        args=args,
+    )
+    return inflate_subject_new_rh_execute(params, execution)
+
+
+__all__ = [
+    "INFLATE_SUBJECT_NEW_RH_METADATA",
+    "InflateSubjectNewRhOutputs",
+    "InflateSubjectNewRhParameters",
+    "inflate_subject_new_rh",
+    "inflate_subject_new_rh_params",
+]

niwrap_freesurfer/freesurfer/inflate_subject_rh.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 *
+
+INFLATE_SUBJECT_RH_METADATA = Metadata(
+    id="c870a2dd4beffc1dccf8c6c63c1951a8bb440f30.boutiques",
+    name="inflate_subject-rh",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+InflateSubjectRhParameters = typing.TypedDict('InflateSubjectRhParameters', {
+    "__STYX_TYPE__": typing.Literal["inflate_subject-rh"],
+    "arguments": 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 {
+        "inflate_subject-rh": inflate_subject_rh_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 InflateSubjectRhOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `inflate_subject_rh(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def inflate_subject_rh_params(
+    arguments: str | None = None,
+) -> InflateSubjectRhParameters:
+    """
+    Build parameters.
+    
+    Args:
+        arguments: Arguments for the command. Placeholder due to lack of\
+            detailed help text.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "inflate_subject-rh",
+    }
+    if arguments is not None:
+        params["arguments"] = arguments
+    return params
+
+
+def inflate_subject_rh_cargs(
+    params: InflateSubjectRhParameters,
+    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 = []
+    if params.get("arguments") is not None:
+        cargs.extend([
+            "-rh",
+            "inflate_subject" + params.get("arguments")
+        ])
+    return cargs
+
+
+def inflate_subject_rh_outputs(
+    params: InflateSubjectRhParameters,
+    execution: Execution,
+) -> InflateSubjectRhOutputs:
+    """
+    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 = InflateSubjectRhOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def inflate_subject_rh_execute(
+    params: InflateSubjectRhParameters,
+    execution: Execution,
+) -> InflateSubjectRhOutputs:
+    """
+    Freesurfer command to perform an operation on the right hemisphere of a
+    subject's brain image data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `InflateSubjectRhOutputs`).
+    """
+    params = execution.params(params)
+    cargs = inflate_subject_rh_cargs(params, execution)
+    ret = inflate_subject_rh_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def inflate_subject_rh(
+    arguments: str | None = None,
+    runner: Runner | None = None,
+) -> InflateSubjectRhOutputs:
+    """
+    Freesurfer command to perform an operation on the right hemisphere of a
+    subject's brain image data.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        arguments: Arguments for the command. Placeholder due to lack of\
+            detailed help text.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `InflateSubjectRhOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_RH_METADATA)
+    params = inflate_subject_rh_params(
+        arguments=arguments,
+    )
+    return inflate_subject_rh_execute(params, execution)
+
+
+__all__ = [
+    "INFLATE_SUBJECT_RH_METADATA",
+    "InflateSubjectRhOutputs",
+    "InflateSubjectRhParameters",
+    "inflate_subject_rh",
+    "inflate_subject_rh_params",
+]

niwrap_freesurfer/freesurfer/inflate_subject_sc.py

@@ -0,0 +1,171 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+INFLATE_SUBJECT_SC_METADATA = Metadata(
+    id="bdd6f4bcc49d0163426eb09c58fe6f94a9a23109.boutiques",
+    name="inflate_subject_sc",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+InflateSubjectScParameters = typing.TypedDict('InflateSubjectScParameters', {
+    "__STYX_TYPE__": typing.Literal["inflate_subject_sc"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "inflate_subject_sc": inflate_subject_sc_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 {
+        "inflate_subject_sc": inflate_subject_sc_outputs,
+    }.get(t)
+
+
+class InflateSubjectScOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `inflate_subject_sc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    inflated_output: OutputPathType
+    """Inflated subject surface output."""
+
+
+def inflate_subject_sc_params(
+) -> InflateSubjectScParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "inflate_subject_sc",
+    }
+    return params
+
+
+def inflate_subject_sc_cargs(
+    params: InflateSubjectScParameters,
+    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("inflate_subject_sc")
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def inflate_subject_sc_outputs(
+    params: InflateSubjectScParameters,
+    execution: Execution,
+) -> InflateSubjectScOutputs:
+    """
+    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 = InflateSubjectScOutputs(
+        root=execution.output_file("."),
+        inflated_output=execution.output_file("[SUBJECT_DIR]/inflated_output"),
+    )
+    return ret
+
+
+def inflate_subject_sc_execute(
+    params: InflateSubjectScParameters,
+    execution: Execution,
+) -> InflateSubjectScOutputs:
+    """
+    Inferred description: Tool for inflating subject surfaces, specific details
+    unavailable.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `InflateSubjectScOutputs`).
+    """
+    params = execution.params(params)
+    cargs = inflate_subject_sc_cargs(params, execution)
+    ret = inflate_subject_sc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def inflate_subject_sc(
+    runner: Runner | None = None,
+) -> InflateSubjectScOutputs:
+    """
+    Inferred description: Tool for inflating subject surfaces, specific details
+    unavailable.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `InflateSubjectScOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_SC_METADATA)
+    params = inflate_subject_sc_params(
+    )
+    return inflate_subject_sc_execute(params, execution)
+
+
+__all__ = [
+    "INFLATE_SUBJECT_SC_METADATA",
+    "InflateSubjectScOutputs",
+    "InflateSubjectScParameters",
+    "inflate_subject_sc",
+    "inflate_subject_sc_params",
+]

niwrap_freesurfer/freesurfer/irepifitvol.py

@@ -0,0 +1,184 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IREPIFITVOL_METADATA = Metadata(
+    id="a2bd7dc06ae3c68248647867b862df791e5ba76b.boutiques",
+    name="irepifitvol",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+IrepifitvolParameters = typing.TypedDict('IrepifitvolParameters', {
+    "__STYX_TYPE__": typing.Literal["irepifitvol"],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "irepifitvol": irepifitvol_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 {
+        "irepifitvol": irepifitvol_outputs,
+    }.get(t)
+
+
+class IrepifitvolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `irepifitvol(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fitted_output: OutputPathType
+    """The resulting volume file after fitting"""
+
+
+def irepifitvol_params(
+    input_file: InputPathType,
+    output_file: str = "fitted_output",
+) -> IrepifitvolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input volume file for fitting.
+        output_file: Output volume file after fitting.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "irepifitvol",
+        "input_file": input_file,
+        "output_file": output_file,
+    }
+    return params
+
+
+def irepifitvol_cargs(
+    params: IrepifitvolParameters,
+    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("irepifitvol")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(params.get("output_file"))
+    return cargs
+
+
+def irepifitvol_outputs(
+    params: IrepifitvolParameters,
+    execution: Execution,
+) -> IrepifitvolOutputs:
+    """
+    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 = IrepifitvolOutputs(
+        root=execution.output_file("."),
+        fitted_output=execution.output_file(params.get("output_file") + ".ext"),
+    )
+    return ret
+
+
+def irepifitvol_execute(
+    params: IrepifitvolParameters,
+    execution: Execution,
+) -> IrepifitvolOutputs:
+    """
+    A tool for 3D volume fitting.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `IrepifitvolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = irepifitvol_cargs(params, execution)
+    ret = irepifitvol_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def irepifitvol(
+    input_file: InputPathType,
+    output_file: str = "fitted_output",
+    runner: Runner | None = None,
+) -> IrepifitvolOutputs:
+    """
+    A tool for 3D volume fitting.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        input_file: Input volume file for fitting.
+        output_file: Output volume file after fitting.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `IrepifitvolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IREPIFITVOL_METADATA)
+    params = irepifitvol_params(
+        input_file=input_file,
+        output_file=output_file,
+    )
+    return irepifitvol_execute(params, execution)
+
+
+__all__ = [
+    "IREPIFITVOL_METADATA",
+    "IrepifitvolOutputs",
+    "IrepifitvolParameters",
+    "irepifitvol",
+    "irepifitvol_params",
+]