niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/cifti_tool.py

@@ -0,0 +1,271 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CIFTI_TOOL_METADATA = Metadata(
+    id="aa87ca3b09c13211a78df0adb7766da7160abd1e.boutiques",
+    name="cifti_tool",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+CiftiToolParameters = typing.TypedDict('CiftiToolParameters', {
+    "__STYX_TYPE__": typing.Literal["cifti_tool"],
+    "input_file": InputPathType,
+    "as_cext": bool,
+    "disp_cext": bool,
+    "eval_cext": bool,
+    "eval_type": typing.NotRequired[typing.Literal["has_data", "has_bdata", "num_tokens", "show", "show_names", "show_summary", "show_text_data"] | None],
+    "output_file": typing.NotRequired[str | None],
+    "verbose_level": typing.NotRequired[float | None],
+    "verbose_read_level": typing.NotRequired[float | None],
+    "both_verbose_levels": typing.NotRequired[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 {
+        "cifti_tool": cifti_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 {
+        "cifti_tool": cifti_tool_outputs,
+    }.get(t)
+
+
+class CiftiToolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `cifti_tool(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output file for results"""
+
+
+def cifti_tool_params(
+    input_file: InputPathType,
+    as_cext: bool = False,
+    disp_cext: bool = False,
+    eval_cext: bool = False,
+    eval_type: typing.Literal["has_data", "has_bdata", "num_tokens", "show", "show_names", "show_summary", "show_text_data"] | None = None,
+    output_file: str | None = None,
+    verbose_level: float | None = None,
+    verbose_read_level: float | None = None,
+    both_verbose_levels: float | None = None,
+) -> CiftiToolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Specify input dataset.
+        as_cext: Process the input as just an extension.
+        disp_cext: Display the CIFTI extension.
+        eval_cext: Evaluate the CIFTI extension.
+        eval_type: Method for evaluation of axml elements.
+        output_file: Where to write output.
+        verbose_level: Set the verbose level.
+        verbose_read_level: Set verbose level when reading.
+        both_verbose_levels: Apply both -verb options.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "cifti_tool",
+        "input_file": input_file,
+        "as_cext": as_cext,
+        "disp_cext": disp_cext,
+        "eval_cext": eval_cext,
+    }
+    if eval_type is not None:
+        params["eval_type"] = eval_type
+    if output_file is not None:
+        params["output_file"] = output_file
+    if verbose_level is not None:
+        params["verbose_level"] = verbose_level
+    if verbose_read_level is not None:
+        params["verbose_read_level"] = verbose_read_level
+    if both_verbose_levels is not None:
+        params["both_verbose_levels"] = both_verbose_levels
+    return params
+
+
+def cifti_tool_cargs(
+    params: CiftiToolParameters,
+    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("cifti_tool")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("as_cext"):
+        cargs.append("-as_cext")
+    if params.get("disp_cext"):
+        cargs.append("-disp_cext")
+    if params.get("eval_cext"):
+        cargs.append("-eval_cext")
+    if params.get("eval_type") is not None:
+        cargs.extend([
+            "-eval_type",
+            params.get("eval_type")
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output_file")
+        ])
+    if params.get("verbose_level") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose_level"))
+        ])
+    if params.get("verbose_read_level") is not None:
+        cargs.extend([
+            "-verb_read",
+            str(params.get("verbose_read_level"))
+        ])
+    if params.get("both_verbose_levels") is not None:
+        cargs.extend([
+            "-vboth",
+            str(params.get("both_verbose_levels"))
+        ])
+    return cargs
+
+
+def cifti_tool_outputs(
+    params: CiftiToolParameters,
+    execution: Execution,
+) -> CiftiToolOutputs:
+    """
+    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 = CiftiToolOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+    )
+    return ret
+
+
+def cifti_tool_execute(
+    params: CiftiToolParameters,
+    execution: Execution,
+) -> CiftiToolOutputs:
+    """
+    Example tool for reading/writing CIFTI-2 datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `CiftiToolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = cifti_tool_cargs(params, execution)
+    ret = cifti_tool_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def cifti_tool(
+    input_file: InputPathType,
+    as_cext: bool = False,
+    disp_cext: bool = False,
+    eval_cext: bool = False,
+    eval_type: typing.Literal["has_data", "has_bdata", "num_tokens", "show", "show_names", "show_summary", "show_text_data"] | None = None,
+    output_file: str | None = None,
+    verbose_level: float | None = None,
+    verbose_read_level: float | None = None,
+    both_verbose_levels: float | None = None,
+    runner: Runner | None = None,
+) -> CiftiToolOutputs:
+    """
+    Example tool for reading/writing CIFTI-2 datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Specify input dataset.
+        as_cext: Process the input as just an extension.
+        disp_cext: Display the CIFTI extension.
+        eval_cext: Evaluate the CIFTI extension.
+        eval_type: Method for evaluation of axml elements.
+        output_file: Where to write output.
+        verbose_level: Set the verbose level.
+        verbose_read_level: Set verbose level when reading.
+        both_verbose_levels: Apply both -verb options.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `CiftiToolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CIFTI_TOOL_METADATA)
+    params = cifti_tool_params(
+        input_file=input_file,
+        as_cext=as_cext,
+        disp_cext=disp_cext,
+        eval_cext=eval_cext,
+        eval_type=eval_type,
+        output_file=output_file,
+        verbose_level=verbose_level,
+        verbose_read_level=verbose_read_level,
+        both_verbose_levels=both_verbose_levels,
+    )
+    return cifti_tool_execute(params, execution)
+
+
+__all__ = [
+    "CIFTI_TOOL_METADATA",
+    "CiftiToolOutputs",
+    "CiftiToolParameters",
+    "cifti_tool",
+    "cifti_tool_params",
+]

niwrap_afni/afni/cjpeg.py

@@ -0,0 +1,233 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CJPEG_METADATA = Metadata(
+    id="694bb4492ea6e6d5e3eefcc17b62cb000146ac38.boutiques",
+    name="cjpeg",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+CjpegParameters = typing.TypedDict('CjpegParameters', {
+    "__STYX_TYPE__": typing.Literal["cjpeg"],
+    "quality": typing.NotRequired[float | None],
+    "grayscale": bool,
+    "optimize": bool,
+    "baseline": bool,
+    "progressive": bool,
+    "outfile": str,
+    "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 {
+        "cjpeg": cjpeg_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 {
+        "cjpeg": cjpeg_outputs,
+    }.get(t)
+
+
+class CjpegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `cjpeg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """The output JPEG file"""
+
+
+def cjpeg_params(
+    outfile: str,
+    infile: InputPathType,
+    quality: float | None = None,
+    grayscale: bool = False,
+    optimize: bool = False,
+    baseline: bool = False,
+    progressive: bool = False,
+) -> CjpegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        outfile: Output JPEG file.
+        infile: Input image file.
+        quality: Quality of JPEG image (0-100).
+        grayscale: Create a grayscale JPEG file.
+        optimize: Optimize Huffman table.
+        baseline: Create a baseline JPEG file.
+        progressive: Create a progressive JPEG file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "cjpeg",
+        "grayscale": grayscale,
+        "optimize": optimize,
+        "baseline": baseline,
+        "progressive": progressive,
+        "outfile": outfile,
+        "infile": infile,
+    }
+    if quality is not None:
+        params["quality"] = quality
+    return params
+
+
+def cjpeg_cargs(
+    params: CjpegParameters,
+    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("cjpeg")
+    if params.get("quality") is not None:
+        cargs.extend([
+            "-quality",
+            str(params.get("quality"))
+        ])
+    if params.get("grayscale"):
+        cargs.append("-grayscale")
+    if params.get("optimize"):
+        cargs.append("-optimize")
+    if params.get("baseline"):
+        cargs.append("-baseline")
+    if params.get("progressive"):
+        cargs.append("-progressive")
+    cargs.append(params.get("outfile"))
+    cargs.append(execution.input_file(params.get("infile")))
+    return cargs
+
+
+def cjpeg_outputs(
+    params: CjpegParameters,
+    execution: Execution,
+) -> CjpegOutputs:
+    """
+    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 = CjpegOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("outfile")),
+    )
+    return ret
+
+
+def cjpeg_execute(
+    params: CjpegParameters,
+    execution: Execution,
+) -> CjpegOutputs:
+    """
+    Compresses an image file to a JPEG file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `CjpegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = cjpeg_cargs(params, execution)
+    ret = cjpeg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def cjpeg(
+    outfile: str,
+    infile: InputPathType,
+    quality: float | None = None,
+    grayscale: bool = False,
+    optimize: bool = False,
+    baseline: bool = False,
+    progressive: bool = False,
+    runner: Runner | None = None,
+) -> CjpegOutputs:
+    """
+    Compresses an image file to a JPEG file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        outfile: Output JPEG file.
+        infile: Input image file.
+        quality: Quality of JPEG image (0-100).
+        grayscale: Create a grayscale JPEG file.
+        optimize: Optimize Huffman table.
+        baseline: Create a baseline JPEG file.
+        progressive: Create a progressive JPEG file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `CjpegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CJPEG_METADATA)
+    params = cjpeg_params(
+        quality=quality,
+        grayscale=grayscale,
+        optimize=optimize,
+        baseline=baseline,
+        progressive=progressive,
+        outfile=outfile,
+        infile=infile,
+    )
+    return cjpeg_execute(params, execution)
+
+
+__all__ = [
+    "CJPEG_METADATA",
+    "CjpegOutputs",
+    "CjpegParameters",
+    "cjpeg",
+    "cjpeg_params",
+]

niwrap_afni/afni/clust_exp_hist_table_py.py

@@ -0,0 +1,218 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CLUST_EXP_HIST_TABLE_PY_METADATA = Metadata(
+    id="a706e0c184974ad6ed86360994f032d1d4e5296f.boutiques",
+    name="ClustExp_HistTable.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ClustExpHistTablePyParameters = typing.TypedDict('ClustExpHistTablePyParameters', {
+    "__STYX_TYPE__": typing.Literal["ClustExp_HistTable.py"],
+    "stat_dset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "session": typing.NotRequired[str | None],
+    "overwrite": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ClustExp_HistTable.py": clust_exp_hist_table_py_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 {
+        "ClustExp_HistTable.py": clust_exp_hist_table_py_outputs,
+    }.get(t)
+
+
+class ClustExpHistTablePyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `clust_exp_hist_table_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    group_table: OutputPathType | None
+    """Table with information parsed from the statistics dataset history."""
+
+
+def clust_exp_hist_table_py_params(
+    stat_dset: InputPathType,
+    prefix: str | None = None,
+    session: str | None = None,
+    overwrite: bool = False,
+) -> ClustExpHistTablePyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        stat_dset: Statistics dataset.
+        prefix: Name for output (no path). Default is GroupOut.
+        session: Output parent folder if you don't want the current working\
+            directory. Default is ./.
+        overwrite: Remove previous folder with same PREFIX.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ClustExp_HistTable.py",
+        "stat_dset": stat_dset,
+        "overwrite": overwrite,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if session is not None:
+        params["session"] = session
+    return params
+
+
+def clust_exp_hist_table_py_cargs(
+    params: ClustExpHistTablePyParameters,
+    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("ClustExp_HistTable.py")
+    cargs.extend([
+        "-StatDSET",
+        execution.input_file(params.get("stat_dset"))
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("session") is not None:
+        cargs.extend([
+            "-session",
+            params.get("session")
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    return cargs
+
+
+def clust_exp_hist_table_py_outputs(
+    params: ClustExpHistTablePyParameters,
+    execution: Execution,
+) -> ClustExpHistTablePyOutputs:
+    """
+    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 = ClustExpHistTablePyOutputs(
+        root=execution.output_file("."),
+        group_table=execution.output_file(params.get("prefix") + "_GroupTable.csv") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def clust_exp_hist_table_py_execute(
+    params: ClustExpHistTablePyParameters,
+    execution: Execution,
+) -> ClustExpHistTablePyOutputs:
+    """
+    Script to extract the data table from history of datasets from 3dttest++, 3dMVM,
+    or 3dLME.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ClustExpHistTablePyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = clust_exp_hist_table_py_cargs(params, execution)
+    ret = clust_exp_hist_table_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def clust_exp_hist_table_py(
+    stat_dset: InputPathType,
+    prefix: str | None = None,
+    session: str | None = None,
+    overwrite: bool = False,
+    runner: Runner | None = None,
+) -> ClustExpHistTablePyOutputs:
+    """
+    Script to extract the data table from history of datasets from 3dttest++, 3dMVM,
+    or 3dLME.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        stat_dset: Statistics dataset.
+        prefix: Name for output (no path). Default is GroupOut.
+        session: Output parent folder if you don't want the current working\
+            directory. Default is ./.
+        overwrite: Remove previous folder with same PREFIX.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ClustExpHistTablePyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CLUST_EXP_HIST_TABLE_PY_METADATA)
+    params = clust_exp_hist_table_py_params(
+        stat_dset=stat_dset,
+        prefix=prefix,
+        session=session,
+        overwrite=overwrite,
+    )
+    return clust_exp_hist_table_py_execute(params, execution)
+
+
+__all__ = [
+    "CLUST_EXP_HIST_TABLE_PY_METADATA",
+    "ClustExpHistTablePyOutputs",
+    "ClustExpHistTablePyParameters",
+    "clust_exp_hist_table_py",
+    "clust_exp_hist_table_py_params",
+]