niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/gifti_tool.py

@@ -0,0 +1,426 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+GIFTI_TOOL_METADATA = Metadata(
+    id="4946ede9cc84ec22d01a494ff249ccac8104538c.boutiques",
+    name="gifti_tool",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+GiftiToolParameters = typing.TypedDict('GiftiToolParameters', {
+    "__STYX_TYPE__": typing.Literal["gifti_tool"],
+    "infile": InputPathType,
+    "new_numda": typing.NotRequired[float | None],
+    "new_dtype": typing.NotRequired[str | None],
+    "new_intent": typing.NotRequired[str | None],
+    "new_ndim": typing.NotRequired[float | None],
+    "new_dims": typing.NotRequired[list[float] | None],
+    "write_gifti": str,
+    "set_extern_filelist": typing.NotRequired[list[str] | None],
+    "mod_add_data": bool,
+    "verb": typing.NotRequired[float | None],
+    "show_gifti": bool,
+    "read_das": typing.NotRequired[list[float] | None],
+    "mod_gim_atr": typing.NotRequired[list[str] | None],
+    "mod_gim_meta": typing.NotRequired[list[str] | None],
+    "mod_da_atr": typing.NotRequired[list[str] | None],
+    "mod_da_meta": typing.NotRequired[list[str] | None],
+    "mod_das": typing.NotRequired[list[float] | None],
+    "new_dset": bool,
+    "compare_gifti": bool,
+    "compare_data": bool,
+    "compare_verb": typing.NotRequired[float | None],
+    "approx_gifti": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "gifti_tool": gifti_tool_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 {
+        "gifti_tool": gifti_tool_outputs,
+    }.get(t)
+
+
+class GiftiToolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `gifti_tool(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_gifti: OutputPathType
+    """Output GIFTI file"""
+
+
+def gifti_tool_params(
+    infile: InputPathType,
+    write_gifti: str,
+    new_numda: float | None = None,
+    new_dtype: str | None = None,
+    new_intent: str | None = None,
+    new_ndim: float | None = None,
+    new_dims: list[float] | None = None,
+    set_extern_filelist: list[str] | None = None,
+    mod_add_data: bool = False,
+    verb: float | None = None,
+    show_gifti: bool = False,
+    read_das: list[float] | None = None,
+    mod_gim_atr: list[str] | None = None,
+    mod_gim_meta: list[str] | None = None,
+    mod_da_atr: list[str] | None = None,
+    mod_da_meta: list[str] | None = None,
+    mod_das: list[float] | None = None,
+    new_dset: bool = False,
+    compare_gifti: bool = False,
+    compare_data: bool = False,
+    compare_verb: float | None = None,
+    approx_gifti: bool = False,
+) -> GiftiToolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Specify one or more GIFTI datasets as input.
+        write_gifti: Write out dataset as gifti image.
+        new_numda: New dataset will have NUMDA DataArray elements.
+        new_dtype: Set data type to TYPE.
+        new_intent: DA elements will have intent INTENT.
+        new_ndim: Set Dimensionality to NUMDIMS.
+        new_dims: Set dims[] to these 6 values.
+        set_extern_filelist: Store data in external files.
+        mod_add_data: Add data to empty DataArray elements.
+        verb: Set verbose level.
+        show_gifti: Show final gifti image.
+        read_das: Read DataArray list indices.
+        mod_gim_atr: Set the GIFTI NAME=VALUE attribute pair at GIFTI level.
+        mod_gim_meta: Add this pair to the GIFTI MetaData.
+        mod_da_atr: Set the DataArray NAME=VALUE attribute pair.
+        mod_da_meta: Set the DataArray NAME=VALUE pair in DA's MetaData.
+        mod_das: Specify the set of DataArrays to modify.
+        new_dset: Create a new GIFTI dataset.
+        compare_gifti: Compare two GIFTI datasets.
+        compare_data: Flag to request comparison of the data.
+        compare_verb: Set the verbose level of comparisons.
+        approx_gifti: Approximate comparison of GIFTI datasets.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "gifti_tool",
+        "infile": infile,
+        "write_gifti": write_gifti,
+        "mod_add_data": mod_add_data,
+        "show_gifti": show_gifti,
+        "new_dset": new_dset,
+        "compare_gifti": compare_gifti,
+        "compare_data": compare_data,
+        "approx_gifti": approx_gifti,
+    }
+    if new_numda is not None:
+        params["new_numda"] = new_numda
+    if new_dtype is not None:
+        params["new_dtype"] = new_dtype
+    if new_intent is not None:
+        params["new_intent"] = new_intent
+    if new_ndim is not None:
+        params["new_ndim"] = new_ndim
+    if new_dims is not None:
+        params["new_dims"] = new_dims
+    if set_extern_filelist is not None:
+        params["set_extern_filelist"] = set_extern_filelist
+    if verb is not None:
+        params["verb"] = verb
+    if read_das is not None:
+        params["read_das"] = read_das
+    if mod_gim_atr is not None:
+        params["mod_gim_atr"] = mod_gim_atr
+    if mod_gim_meta is not None:
+        params["mod_gim_meta"] = mod_gim_meta
+    if mod_da_atr is not None:
+        params["mod_da_atr"] = mod_da_atr
+    if mod_da_meta is not None:
+        params["mod_da_meta"] = mod_da_meta
+    if mod_das is not None:
+        params["mod_das"] = mod_das
+    if compare_verb is not None:
+        params["compare_verb"] = compare_verb
+    return params
+
+
+def gifti_tool_cargs(
+    params: GiftiToolParameters,
+    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("gifti_tool")
+    cargs.extend([
+        "-infile",
+        execution.input_file(params.get("infile"))
+    ])
+    if params.get("new_numda") is not None:
+        cargs.extend([
+            "-new_numDA",
+            str(params.get("new_numda"))
+        ])
+    if params.get("new_dtype") is not None:
+        cargs.extend([
+            "-new_dtype",
+            params.get("new_dtype")
+        ])
+    if params.get("new_intent") is not None:
+        cargs.extend([
+            "-new_intent",
+            params.get("new_intent")
+        ])
+    if params.get("new_ndim") is not None:
+        cargs.extend([
+            "-new_ndim",
+            str(params.get("new_ndim"))
+        ])
+    if params.get("new_dims") is not None:
+        cargs.extend([
+            "-new_dims",
+            *map(str, params.get("new_dims"))
+        ])
+    cargs.extend([
+        "-write_gifti",
+        params.get("write_gifti")
+    ])
+    if params.get("set_extern_filelist") is not None:
+        cargs.extend([
+            "-set_extern_filelist",
+            *params.get("set_extern_filelist")
+        ])
+    if params.get("mod_add_data"):
+        cargs.append("-mod_add_data")
+    if params.get("verb") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verb"))
+        ])
+    if params.get("show_gifti"):
+        cargs.append("-show_gifti")
+    if params.get("read_das") is not None:
+        cargs.extend([
+            "-read_DAs",
+            *map(str, params.get("read_das"))
+        ])
+    if params.get("mod_gim_atr") is not None:
+        cargs.extend([
+            "-mod_gim_atr",
+            *params.get("mod_gim_atr")
+        ])
+    if params.get("mod_gim_meta") is not None:
+        cargs.extend([
+            "-mod_gim_meta",
+            *params.get("mod_gim_meta")
+        ])
+    if params.get("mod_da_atr") is not None:
+        cargs.extend([
+            "-mod_DA_atr",
+            *params.get("mod_da_atr")
+        ])
+    if params.get("mod_da_meta") is not None:
+        cargs.extend([
+            "-mod_DA_meta",
+            *params.get("mod_da_meta")
+        ])
+    if params.get("mod_das") is not None:
+        cargs.extend([
+            "-mod_DAs",
+            *map(str, params.get("mod_das"))
+        ])
+    if params.get("new_dset"):
+        cargs.append("-new_dset")
+    if params.get("compare_gifti"):
+        cargs.append("-compare_gifti")
+    if params.get("compare_data"):
+        cargs.append("-compare_data")
+    if params.get("compare_verb") is not None:
+        cargs.extend([
+            "-compare_verb",
+            str(params.get("compare_verb"))
+        ])
+    if params.get("approx_gifti"):
+        cargs.append("-approx_gifti")
+    return cargs
+
+
+def gifti_tool_outputs(
+    params: GiftiToolParameters,
+    execution: Execution,
+) -> GiftiToolOutputs:
+    """
+    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 = GiftiToolOutputs(
+        root=execution.output_file("."),
+        output_gifti=execution.output_file(params.get("write_gifti")),
+    )
+    return ret
+
+
+def gifti_tool_execute(
+    params: GiftiToolParameters,
+    execution: Execution,
+) -> GiftiToolOutputs:
+    """
+    Tool for creating, displaying, modifying, or comparing GIFTI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `GiftiToolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = gifti_tool_cargs(params, execution)
+    ret = gifti_tool_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def gifti_tool(
+    infile: InputPathType,
+    write_gifti: str,
+    new_numda: float | None = None,
+    new_dtype: str | None = None,
+    new_intent: str | None = None,
+    new_ndim: float | None = None,
+    new_dims: list[float] | None = None,
+    set_extern_filelist: list[str] | None = None,
+    mod_add_data: bool = False,
+    verb: float | None = None,
+    show_gifti: bool = False,
+    read_das: list[float] | None = None,
+    mod_gim_atr: list[str] | None = None,
+    mod_gim_meta: list[str] | None = None,
+    mod_da_atr: list[str] | None = None,
+    mod_da_meta: list[str] | None = None,
+    mod_das: list[float] | None = None,
+    new_dset: bool = False,
+    compare_gifti: bool = False,
+    compare_data: bool = False,
+    compare_verb: float | None = None,
+    approx_gifti: bool = False,
+    runner: Runner | None = None,
+) -> GiftiToolOutputs:
+    """
+    Tool for creating, displaying, modifying, or comparing GIFTI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Specify one or more GIFTI datasets as input.
+        write_gifti: Write out dataset as gifti image.
+        new_numda: New dataset will have NUMDA DataArray elements.
+        new_dtype: Set data type to TYPE.
+        new_intent: DA elements will have intent INTENT.
+        new_ndim: Set Dimensionality to NUMDIMS.
+        new_dims: Set dims[] to these 6 values.
+        set_extern_filelist: Store data in external files.
+        mod_add_data: Add data to empty DataArray elements.
+        verb: Set verbose level.
+        show_gifti: Show final gifti image.
+        read_das: Read DataArray list indices.
+        mod_gim_atr: Set the GIFTI NAME=VALUE attribute pair at GIFTI level.
+        mod_gim_meta: Add this pair to the GIFTI MetaData.
+        mod_da_atr: Set the DataArray NAME=VALUE attribute pair.
+        mod_da_meta: Set the DataArray NAME=VALUE pair in DA's MetaData.
+        mod_das: Specify the set of DataArrays to modify.
+        new_dset: Create a new GIFTI dataset.
+        compare_gifti: Compare two GIFTI datasets.
+        compare_data: Flag to request comparison of the data.
+        compare_verb: Set the verbose level of comparisons.
+        approx_gifti: Approximate comparison of GIFTI datasets.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `GiftiToolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GIFTI_TOOL_METADATA)
+    params = gifti_tool_params(
+        infile=infile,
+        new_numda=new_numda,
+        new_dtype=new_dtype,
+        new_intent=new_intent,
+        new_ndim=new_ndim,
+        new_dims=new_dims,
+        write_gifti=write_gifti,
+        set_extern_filelist=set_extern_filelist,
+        mod_add_data=mod_add_data,
+        verb=verb,
+        show_gifti=show_gifti,
+        read_das=read_das,
+        mod_gim_atr=mod_gim_atr,
+        mod_gim_meta=mod_gim_meta,
+        mod_da_atr=mod_da_atr,
+        mod_da_meta=mod_da_meta,
+        mod_das=mod_das,
+        new_dset=new_dset,
+        compare_gifti=compare_gifti,
+        compare_data=compare_data,
+        compare_verb=compare_verb,
+        approx_gifti=approx_gifti,
+    )
+    return gifti_tool_execute(params, execution)
+
+
+__all__ = [
+    "GIFTI_TOOL_METADATA",
+    "GiftiToolOutputs",
+    "GiftiToolParameters",
+    "gifti_tool",
+    "gifti_tool_params",
+]

niwrap_afni/afni/gltsymtest.py

@@ -0,0 +1,193 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+GLTSYMTEST_METADATA = Metadata(
+    id="ee7f3e82da13db7db87fe98e1283b73580005843.boutiques",
+    name="GLTsymtest",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+GltsymtestParameters = typing.TypedDict('GltsymtestParameters', {
+    "__STYX_TYPE__": typing.Literal["GLTsymtest"],
+    "badonly": bool,
+    "varlist": str,
+    "expr": 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 {
+        "GLTsymtest": gltsymtest_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 GltsymtestOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `gltsymtest(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def gltsymtest_params(
+    varlist: str,
+    expr: list[str],
+    badonly: bool = False,
+) -> GltsymtestParameters:
+    """
+    Build parameters.
+    
+    Args:
+        varlist: A list of allowed variable names in the expression, separated\
+            by commas, semicolons, and/or spaces.
+        expr: GLT symbolic expression(s), enclosed in quotes.
+        badonly: A flag to only output BAD messages rather than all messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "GLTsymtest",
+        "badonly": badonly,
+        "varlist": varlist,
+        "expr": expr,
+    }
+    return params
+
+
+def gltsymtest_cargs(
+    params: GltsymtestParameters,
+    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("GLTsymtest")
+    if params.get("badonly"):
+        cargs.append("-badonly")
+    cargs.append(params.get("varlist"))
+    cargs.extend(params.get("expr"))
+    return cargs
+
+
+def gltsymtest_outputs(
+    params: GltsymtestParameters,
+    execution: Execution,
+) -> GltsymtestOutputs:
+    """
+    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 = GltsymtestOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def gltsymtest_execute(
+    params: GltsymtestParameters,
+    execution: Execution,
+) -> GltsymtestOutputs:
+    """
+    A tool to test the validity of '-gltsym' strings for use with 3dDeconvolve or
+    3dREMLfit.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `GltsymtestOutputs`).
+    """
+    params = execution.params(params)
+    cargs = gltsymtest_cargs(params, execution)
+    ret = gltsymtest_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def gltsymtest(
+    varlist: str,
+    expr: list[str],
+    badonly: bool = False,
+    runner: Runner | None = None,
+) -> GltsymtestOutputs:
+    """
+    A tool to test the validity of '-gltsym' strings for use with 3dDeconvolve or
+    3dREMLfit.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        varlist: A list of allowed variable names in the expression, separated\
+            by commas, semicolons, and/or spaces.
+        expr: GLT symbolic expression(s), enclosed in quotes.
+        badonly: A flag to only output BAD messages rather than all messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `GltsymtestOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GLTSYMTEST_METADATA)
+    params = gltsymtest_params(
+        badonly=badonly,
+        varlist=varlist,
+        expr=expr,
+    )
+    return gltsymtest_execute(params, execution)
+
+
+__all__ = [
+    "GLTSYMTEST_METADATA",
+    "GltsymtestOutputs",
+    "GltsymtestParameters",
+    "gltsymtest",
+    "gltsymtest_params",
+]