niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__build_afni_xlib.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 *
+
+V__BUILD_AFNI_XLIB_METADATA = Metadata(
+    id="335ac2386eff0dba38cfaae81dacca730457f4a7.boutiques",
+    name="@build_afni_Xlib",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VBuildAfniXlibParameters = typing.TypedDict('VBuildAfniXlibParameters', {
+    "__STYX_TYPE__": typing.Literal["@build_afni_Xlib"],
+    "localinstall": bool,
+    "debug_symbols": bool,
+    "lib64": bool,
+    "packages": list[str],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@build_afni_Xlib": v__build_afni_xlib_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 VBuildAfniXlibOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__build_afni_xlib(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__build_afni_xlib_params(
+    packages: list[str],
+    localinstall: bool = False,
+    debug_symbols: bool = False,
+    lib64: bool = False,
+) -> VBuildAfniXlibParameters:
+    """
+    Build parameters.
+    
+    Args:
+        packages: Packages to compile and install (e.g., lesstif, openmotif,\
+            libXt).
+        localinstall: Install under each package directory.
+        debug_symbols: Compile with -g to add symbols.
+        lib64: Install libs under lib64 (default is lib).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@build_afni_Xlib",
+        "localinstall": localinstall,
+        "debug_symbols": debug_symbols,
+        "lib64": lib64,
+        "packages": packages,
+    }
+    return params
+
+
+def v__build_afni_xlib_cargs(
+    params: VBuildAfniXlibParameters,
+    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("@build_afni_Xlib")
+    if params.get("localinstall"):
+        cargs.append("-localinstall")
+    if params.get("debug_symbols"):
+        cargs.append("-g")
+    if params.get("lib64"):
+        cargs.append("-lib64")
+    cargs.extend(params.get("packages"))
+    return cargs
+
+
+def v__build_afni_xlib_outputs(
+    params: VBuildAfniXlibParameters,
+    execution: Execution,
+) -> VBuildAfniXlibOutputs:
+    """
+    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 = VBuildAfniXlibOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__build_afni_xlib_execute(
+    params: VBuildAfniXlibParameters,
+    execution: Execution,
+) -> VBuildAfniXlibOutputs:
+    """
+    Compile and install lesstif, openmotif, and/or libXt.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VBuildAfniXlibOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__build_afni_xlib_cargs(params, execution)
+    ret = v__build_afni_xlib_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__build_afni_xlib(
+    packages: list[str],
+    localinstall: bool = False,
+    debug_symbols: bool = False,
+    lib64: bool = False,
+    runner: Runner | None = None,
+) -> VBuildAfniXlibOutputs:
+    """
+    Compile and install lesstif, openmotif, and/or libXt.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        packages: Packages to compile and install (e.g., lesstif, openmotif,\
+            libXt).
+        localinstall: Install under each package directory.
+        debug_symbols: Compile with -g to add symbols.
+        lib64: Install libs under lib64 (default is lib).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VBuildAfniXlibOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__BUILD_AFNI_XLIB_METADATA)
+    params = v__build_afni_xlib_params(
+        localinstall=localinstall,
+        debug_symbols=debug_symbols,
+        lib64=lib64,
+        packages=packages,
+    )
+    return v__build_afni_xlib_execute(params, execution)
+
+
+__all__ = [
+    "VBuildAfniXlibOutputs",
+    "VBuildAfniXlibParameters",
+    "V__BUILD_AFNI_XLIB_METADATA",
+    "v__build_afni_xlib",
+    "v__build_afni_xlib_params",
+]

niwrap_afni/afni/v__center_distance.py

@@ -0,0 +1,187 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__CENTER_DISTANCE_METADATA = Metadata(
+    id="e8ff28117986ef062e78754067cfab3c33d4cd86.boutiques",
+    name="@Center_Distance",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VCenterDistanceParameters = typing.TypedDict('VCenterDistanceParameters', {
+    "__STYX_TYPE__": typing.Literal["@Center_Distance"],
+    "dset1": InputPathType,
+    "dset2": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@Center_Distance": v__center_distance_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 {
+        "@Center_Distance": v__center_distance_outputs,
+    }.get(t)
+
+
+class VCenterDistanceOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__center_distance(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    distance_output: OutputPathType
+    """The calculated distance between the centers of DSET_1 and DSET_2"""
+
+
+def v__center_distance_params(
+    dset1: InputPathType,
+    dset2: InputPathType,
+) -> VCenterDistanceParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset1: First dataset file (e.g. file1.nii.gz).
+        dset2: Second dataset file (e.g. file2.nii.gz).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@Center_Distance",
+        "dset1": dset1,
+        "dset2": dset2,
+    }
+    return params
+
+
+def v__center_distance_cargs(
+    params: VCenterDistanceParameters,
+    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("@Center_Distance")
+    cargs.extend([
+        "-dset",
+        execution.input_file(params.get("dset1"))
+    ])
+    cargs.append(execution.input_file(params.get("dset2")))
+    return cargs
+
+
+def v__center_distance_outputs(
+    params: VCenterDistanceParameters,
+    execution: Execution,
+) -> VCenterDistanceOutputs:
+    """
+    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 = VCenterDistanceOutputs(
+        root=execution.output_file("."),
+        distance_output=execution.output_file("distance.txt"),
+    )
+    return ret
+
+
+def v__center_distance_execute(
+    params: VCenterDistanceParameters,
+    execution: Execution,
+) -> VCenterDistanceOutputs:
+    """
+    Tool to calculate the distance between the centers of two datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VCenterDistanceOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__center_distance_cargs(params, execution)
+    ret = v__center_distance_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__center_distance(
+    dset1: InputPathType,
+    dset2: InputPathType,
+    runner: Runner | None = None,
+) -> VCenterDistanceOutputs:
+    """
+    Tool to calculate the distance between the centers of two datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset1: First dataset file (e.g. file1.nii.gz).
+        dset2: Second dataset file (e.g. file2.nii.gz).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VCenterDistanceOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CENTER_DISTANCE_METADATA)
+    params = v__center_distance_params(
+        dset1=dset1,
+        dset2=dset2,
+    )
+    return v__center_distance_execute(params, execution)
+
+
+__all__ = [
+    "VCenterDistanceOutputs",
+    "VCenterDistanceParameters",
+    "V__CENTER_DISTANCE_METADATA",
+    "v__center_distance",
+    "v__center_distance_params",
+]

niwrap_afni/afni/v__chauffeur_afni.py

@@ -0,0 +1,204 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__CHAUFFEUR_AFNI_METADATA = Metadata(
+    id="7bd1968eb762331f9eaee48a7484852a7e447634.boutiques",
+    name="@chauffeur_afni",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VChauffeurAfniParameters = typing.TypedDict('VChauffeurAfniParameters', {
+    "__STYX_TYPE__": typing.Literal["@chauffeur_afni"],
+    "ulay": InputPathType,
+    "olay": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@chauffeur_afni": v__chauffeur_afni_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 {
+        "@chauffeur_afni": v__chauffeur_afni_outputs,
+    }.get(t)
+
+
+class VChauffeurAfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__chauffeur_afni(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image: OutputPathType
+    """Generated montage image"""
+    cluster_report: OutputPathType
+    """Clusterization report"""
+    whereami_report: OutputPathType
+    """Whereami report for clusterized data"""
+
+
+def v__chauffeur_afni_params(
+    ulay: InputPathType,
+    prefix: str,
+    olay: InputPathType | None = None,
+) -> VChauffeurAfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+        ulay: Name of underlay dataset (required); can be 3D or 4D set.
+        prefix: Prefix for output files (required).
+        olay: Name of overlay dataset (optional).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@chauffeur_afni",
+        "ulay": ulay,
+        "prefix": prefix,
+    }
+    if olay is not None:
+        params["olay"] = olay
+    return params
+
+
+def v__chauffeur_afni_cargs(
+    params: VChauffeurAfniParameters,
+    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("@chauffeur_afni")
+    cargs.append(execution.input_file(params.get("ulay")))
+    if params.get("olay") is not None:
+        cargs.append(execution.input_file(params.get("olay")))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.append("[options]")
+    return cargs
+
+
+def v__chauffeur_afni_outputs(
+    params: VChauffeurAfniParameters,
+    execution: Execution,
+) -> VChauffeurAfniOutputs:
+    """
+    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 = VChauffeurAfniOutputs(
+        root=execution.output_file("."),
+        output_image=execution.output_file(params.get("prefix") + ".png"),
+        cluster_report=execution.output_file(params.get("prefix") + "_clust_rep.txt"),
+        whereami_report=execution.output_file(params.get("prefix") + "_clust_whereami.txt"),
+    )
+    return ret
+
+
+def v__chauffeur_afni_execute(
+    params: VChauffeurAfniParameters,
+    execution: Execution,
+) -> VChauffeurAfniOutputs:
+    """
+    Automated QC snapshots generator in AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VChauffeurAfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__chauffeur_afni_cargs(params, execution)
+    ret = v__chauffeur_afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__chauffeur_afni(
+    ulay: InputPathType,
+    prefix: str,
+    olay: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> VChauffeurAfniOutputs:
+    """
+    Automated QC snapshots generator in AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        ulay: Name of underlay dataset (required); can be 3D or 4D set.
+        prefix: Prefix for output files (required).
+        olay: Name of overlay dataset (optional).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VChauffeurAfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CHAUFFEUR_AFNI_METADATA)
+    params = v__chauffeur_afni_params(
+        ulay=ulay,
+        olay=olay,
+        prefix=prefix,
+    )
+    return v__chauffeur_afni_execute(params, execution)
+
+
+__all__ = [
+    "VChauffeurAfniOutputs",
+    "VChauffeurAfniParameters",
+    "V__CHAUFFEUR_AFNI_METADATA",
+    "v__chauffeur_afni",
+    "v__chauffeur_afni_params",
+]