niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__grayplot.py

@@ -0,0 +1,189 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__GRAYPLOT_METADATA = Metadata(
+    id="3d444976676cbb4979c872f1285979b9e0bd687d.boutiques",
+    name="@grayplot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VGrayplotParameters = typing.TypedDict('VGrayplotParameters', {
+    "__STYX_TYPE__": typing.Literal["@grayplot"],
+    "dirname": str,
+    "allorder": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@grayplot": v__grayplot_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 {
+        "@grayplot": v__grayplot_outputs,
+    }.get(t)
+
+
+class VGrayplotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__grayplot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    grayplot_img: OutputPathType
+    """Output grayplot image"""
+
+
+def v__grayplot_params(
+    dirname: str,
+    allorder: bool = False,
+) -> VGrayplotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dirname: Directory containing afni_proc.py results.
+        allorder: Create grayplots for all ordering methods.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@grayplot",
+        "dirname": dirname,
+        "allorder": allorder,
+    }
+    return params
+
+
+def v__grayplot_cargs(
+    params: VGrayplotParameters,
+    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("@grayplot")
+    cargs.append(params.get("dirname"))
+    if params.get("allorder"):
+        cargs.append("-ALLorder")
+    return cargs
+
+
+def v__grayplot_outputs(
+    params: VGrayplotParameters,
+    execution: Execution,
+) -> VGrayplotOutputs:
+    """
+    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 = VGrayplotOutputs(
+        root=execution.output_file("."),
+        grayplot_img=execution.output_file("Grayplot.errts.*.png"),
+    )
+    return ret
+
+
+def v__grayplot_execute(
+    params: VGrayplotParameters,
+    execution: Execution,
+) -> VGrayplotOutputs:
+    """
+    Script to read files from an afni_proc.py results directory and produce a
+    grayplot from the errts dataset(s), combined with a motion magnitude indicator
+    graph.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VGrayplotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__grayplot_cargs(params, execution)
+    ret = v__grayplot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__grayplot(
+    dirname: str,
+    allorder: bool = False,
+    runner: Runner | None = None,
+) -> VGrayplotOutputs:
+    """
+    Script to read files from an afni_proc.py results directory and produce a
+    grayplot from the errts dataset(s), combined with a motion magnitude indicator
+    graph.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dirname: Directory containing afni_proc.py results.
+        allorder: Create grayplots for all ordering methods.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VGrayplotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__GRAYPLOT_METADATA)
+    params = v__grayplot_params(
+        dirname=dirname,
+        allorder=allorder,
+    )
+    return v__grayplot_execute(params, execution)
+
+
+__all__ = [
+    "VGrayplotOutputs",
+    "VGrayplotParameters",
+    "V__GRAYPLOT_METADATA",
+    "v__grayplot",
+    "v__grayplot_params",
+]

niwrap_afni/afni/v__help_afni.py

@@ -0,0 +1,165 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__HELP_AFNI_METADATA = Metadata(
+    id="87ebd1e4083856099825a6ef50fde5abb2dad615.boutiques",
+    name="@help.AFNI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VHelpAfniParameters = typing.TypedDict('VHelpAfniParameters', {
+    "__STYX_TYPE__": typing.Literal["@help.AFNI"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@help.AFNI": v__help_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 {
+    }.get(t)
+
+
+class VHelpAfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__help_afni(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__help_afni_params(
+) -> VHelpAfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@help.AFNI",
+    }
+    return params
+
+
+def v__help_afni_cargs(
+    params: VHelpAfniParameters,
+    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("@help.AFNI")
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v__help_afni_outputs(
+    params: VHelpAfniParameters,
+    execution: Execution,
+) -> VHelpAfniOutputs:
+    """
+    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 = VHelpAfniOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__help_afni_execute(
+    params: VHelpAfniParameters,
+    execution: Execution,
+) -> VHelpAfniOutputs:
+    """
+    A script to retrieve and search AFNI's help page for all programs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VHelpAfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__help_afni_cargs(params, execution)
+    ret = v__help_afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__help_afni(
+    runner: Runner | None = None,
+) -> VHelpAfniOutputs:
+    """
+    A script to retrieve and search AFNI's help page for all programs.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VHelpAfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__HELP_AFNI_METADATA)
+    params = v__help_afni_params(
+    )
+    return v__help_afni_execute(params, execution)
+
+
+__all__ = [
+    "VHelpAfniOutputs",
+    "VHelpAfniParameters",
+    "V__HELP_AFNI_METADATA",
+    "v__help_afni",
+    "v__help_afni_params",
+]

niwrap_afni/afni/v__is_oblique.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__IS_OBLIQUE_METADATA = Metadata(
+    id="2e3c80c4806683277ce568a5d838cb3d495df099.boutiques",
+    name="@isOblique",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VIsObliqueParameters = typing.TypedDict('VIsObliqueParameters', {
+    "__STYX_TYPE__": typing.Literal["@isOblique"],
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@isOblique": v__is_oblique_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 {
+        "@isOblique": v__is_oblique_outputs,
+    }.get(t)
+
+
+class VIsObliqueOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__is_oblique(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    result: OutputPathType
+    """Output result indicating if the file is oblique or plumb"""
+
+
+def v__is_oblique_params(
+    infile: InputPathType,
+) -> VIsObliqueParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input file (e.g., Hello+orig.HEAD).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@isOblique",
+        "infile": infile,
+    }
+    return params
+
+
+def v__is_oblique_cargs(
+    params: VIsObliqueParameters,
+    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("@isOblique")
+    cargs.append(execution.input_file(params.get("infile")))
+    return cargs
+
+
+def v__is_oblique_outputs(
+    params: VIsObliqueParameters,
+    execution: Execution,
+) -> VIsObliqueOutputs:
+    """
+    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 = VIsObliqueOutputs(
+        root=execution.output_file("."),
+        result=execution.output_file("oblique_check_result.txt"),
+    )
+    return ret
+
+
+def v__is_oblique_execute(
+    params: VIsObliqueParameters,
+    execution: Execution,
+) -> VIsObliqueOutputs:
+    """
+    Determine if a file is oblique or plumb.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VIsObliqueOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__is_oblique_cargs(params, execution)
+    ret = v__is_oblique_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__is_oblique(
+    infile: InputPathType,
+    runner: Runner | None = None,
+) -> VIsObliqueOutputs:
+    """
+    Determine if a file is oblique or plumb.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input file (e.g., Hello+orig.HEAD).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VIsObliqueOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__IS_OBLIQUE_METADATA)
+    params = v__is_oblique_params(
+        infile=infile,
+    )
+    return v__is_oblique_execute(params, execution)
+
+
+__all__ = [
+    "VIsObliqueOutputs",
+    "VIsObliqueParameters",
+    "V__IS_OBLIQUE_METADATA",
+    "v__is_oblique",
+    "v__is_oblique_params",
+]

niwrap_afni/afni/v__iso_masks.py

@@ -0,0 +1,185 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__ISO_MASKS_METADATA = Metadata(
+    id="efb13b19016645aff7a7273058c6f68edcfc682d.boutiques",
+    name="@IsoMasks",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VIsoMasksParameters = typing.TypedDict('VIsoMasksParameters', {
+    "__STYX_TYPE__": typing.Literal["@IsoMasks"],
+    "input_dataset": InputPathType,
+    "isovals": typing.NotRequired[list[float] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@IsoMasks": v__iso_masks_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 VIsoMasksOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__iso_masks(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__iso_masks_params(
+    input_dataset: InputPathType,
+    isovals: list[float] | None = None,
+) -> VIsoMasksParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset for creating isosurfaces.
+        isovals: Isovalue thresholds for creating isosurfaces.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@IsoMasks",
+        "input_dataset": input_dataset,
+    }
+    if isovals is not None:
+        params["isovals"] = isovals
+    return params
+
+
+def v__iso_masks_cargs(
+    params: VIsoMasksParameters,
+    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("@IsoMasks")
+    cargs.extend([
+        "-mask",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    if params.get("isovals") is not None:
+        cargs.extend(map(str, params.get("isovals")))
+    return cargs
+
+
+def v__iso_masks_outputs(
+    params: VIsoMasksParameters,
+    execution: Execution,
+) -> VIsoMasksOutputs:
+    """
+    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 = VIsoMasksOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__iso_masks_execute(
+    params: VIsoMasksParameters,
+    execution: Execution,
+) -> VIsoMasksOutputs:
+    """
+    Creates isosurfaces from isovolume envelopes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VIsoMasksOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__iso_masks_cargs(params, execution)
+    ret = v__iso_masks_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__iso_masks(
+    input_dataset: InputPathType,
+    isovals: list[float] | None = None,
+    runner: Runner | None = None,
+) -> VIsoMasksOutputs:
+    """
+    Creates isosurfaces from isovolume envelopes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset for creating isosurfaces.
+        isovals: Isovalue thresholds for creating isosurfaces.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VIsoMasksOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ISO_MASKS_METADATA)
+    params = v__iso_masks_params(
+        input_dataset=input_dataset,
+        isovals=isovals,
+    )
+    return v__iso_masks_execute(params, execution)
+
+
+__all__ = [
+    "VIsoMasksOutputs",
+    "VIsoMasksParameters",
+    "V__ISO_MASKS_METADATA",
+    "v__iso_masks",
+    "v__iso_masks_params",
+]