niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/gen_ss_review_table_py.py

@@ -0,0 +1,324 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+GEN_SS_REVIEW_TABLE_PY_METADATA = Metadata(
+    id="14139376af49e78f5d6fa5b8178a8e41bcf15797.boutiques",
+    name="gen_ss_review_table.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+GenSsReviewTablePyParameters = typing.TypedDict('GenSsReviewTablePyParameters', {
+    "__STYX_TYPE__": typing.Literal["gen_ss_review_table.py"],
+    "infiles": list[InputPathType],
+    "write_table": typing.NotRequired[InputPathType | None],
+    "write_outliers": typing.NotRequired[InputPathType | None],
+    "overwrite": bool,
+    "empty_is_outlier": bool,
+    "outlier_sep": typing.NotRequired[str | None],
+    "separator": typing.NotRequired[str | None],
+    "showlabs": bool,
+    "show_infiles": bool,
+    "show_keepers": bool,
+    "report_outliers": typing.NotRequired[list[str] | None],
+    "report_outliers_fill_style": typing.NotRequired[str | None],
+    "show_missing": bool,
+    "verbosity": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "gen_ss_review_table.py": gen_ss_review_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 {
+        "gen_ss_review_table.py": gen_ss_review_table_py_outputs,
+    }.get(t)
+
+
+class GenSsReviewTablePyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `gen_ss_review_table_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_table: OutputPathType | None
+    """Final table output file"""
+    output_outliers: OutputPathType | None
+    """Outliers table output file"""
+
+
+def gen_ss_review_table_py_params(
+    infiles: list[InputPathType],
+    write_table: InputPathType | None = None,
+    write_outliers: InputPathType | None = None,
+    overwrite: bool = False,
+    empty_is_outlier: bool = False,
+    outlier_sep: str | None = None,
+    separator: str | None = None,
+    showlabs: bool = False,
+    show_infiles: bool = False,
+    show_keepers: bool = False,
+    report_outliers: list[str] | None = None,
+    report_outliers_fill_style: str | None = None,
+    show_missing: bool = False,
+    verbosity: int | None = None,
+) -> GenSsReviewTablePyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infiles: Input ss_review_basic output text files to process.
+        write_table: Write final table to the given file.
+        write_outliers: Write outlier table to the given file.
+        overwrite: Overwrite the output -write_table, if it exists.
+        empty_is_outlier: Treat empty tests as outliers.
+        outlier_sep: Use SEP for the outlier table separator.
+        separator: Use SEP for the label/vals separator (default = ':').
+        showlabs: Display counts of all labels found, with parents.
+        show_infiles: Include input files in reviewtable result.
+        show_keepers: Show a table of subjects kept rather than dropped.
+        report_outliers: Report outliers where the comparison holds.
+        report_outliers_fill_style: How to fill non-outliers in the table.
+        show_missing: Display all missing keys.
+        verbosity: Verbosity level.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "gen_ss_review_table.py",
+        "infiles": infiles,
+        "overwrite": overwrite,
+        "empty_is_outlier": empty_is_outlier,
+        "showlabs": showlabs,
+        "show_infiles": show_infiles,
+        "show_keepers": show_keepers,
+        "show_missing": show_missing,
+    }
+    if write_table is not None:
+        params["write_table"] = write_table
+    if write_outliers is not None:
+        params["write_outliers"] = write_outliers
+    if outlier_sep is not None:
+        params["outlier_sep"] = outlier_sep
+    if separator is not None:
+        params["separator"] = separator
+    if report_outliers is not None:
+        params["report_outliers"] = report_outliers
+    if report_outliers_fill_style is not None:
+        params["report_outliers_fill_style"] = report_outliers_fill_style
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def gen_ss_review_table_py_cargs(
+    params: GenSsReviewTablePyParameters,
+    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("gen_ss_review_table.py")
+    cargs.extend([execution.input_file(f) for f in params.get("infiles")])
+    if params.get("write_table") is not None:
+        cargs.extend([
+            "-write_table",
+            execution.input_file(params.get("write_table"))
+        ])
+    if params.get("write_outliers") is not None:
+        cargs.extend([
+            "-write_outliers",
+            execution.input_file(params.get("write_outliers"))
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("empty_is_outlier"):
+        cargs.append("-empty_is_outlier")
+    if params.get("outlier_sep") is not None:
+        cargs.extend([
+            "-outlier_sep",
+            params.get("outlier_sep")
+        ])
+    if params.get("separator") is not None:
+        cargs.extend([
+            "-separator",
+            params.get("separator")
+        ])
+    if params.get("showlabs"):
+        cargs.append("-showlabs")
+    if params.get("show_infiles"):
+        cargs.append("-show_infiles")
+    if params.get("show_keepers"):
+        cargs.append("-show_keepers")
+    if params.get("report_outliers") is not None:
+        cargs.extend([
+            "-report_outliers",
+            *params.get("report_outliers")
+        ])
+    if params.get("report_outliers_fill_style") is not None:
+        cargs.extend([
+            "-report_outliers_fill_style",
+            params.get("report_outliers_fill_style")
+        ])
+    if params.get("show_missing"):
+        cargs.append("-show_missing")
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    return cargs
+
+
+def gen_ss_review_table_py_outputs(
+    params: GenSsReviewTablePyParameters,
+    execution: Execution,
+) -> GenSsReviewTablePyOutputs:
+    """
+    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 = GenSsReviewTablePyOutputs(
+        root=execution.output_file("."),
+        output_table=execution.output_file(pathlib.Path(params.get("write_table")).name) if (params.get("write_table") is not None) else None,
+        output_outliers=execution.output_file(pathlib.Path(params.get("write_outliers")).name) if (params.get("write_outliers") is not None) else None,
+    )
+    return ret
+
+
+def gen_ss_review_table_py_execute(
+    params: GenSsReviewTablePyParameters,
+    execution: Execution,
+) -> GenSsReviewTablePyOutputs:
+    """
+    Generate a table from ss_review_basic output files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `GenSsReviewTablePyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = gen_ss_review_table_py_cargs(params, execution)
+    ret = gen_ss_review_table_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def gen_ss_review_table_py(
+    infiles: list[InputPathType],
+    write_table: InputPathType | None = None,
+    write_outliers: InputPathType | None = None,
+    overwrite: bool = False,
+    empty_is_outlier: bool = False,
+    outlier_sep: str | None = None,
+    separator: str | None = None,
+    showlabs: bool = False,
+    show_infiles: bool = False,
+    show_keepers: bool = False,
+    report_outliers: list[str] | None = None,
+    report_outliers_fill_style: str | None = None,
+    show_missing: bool = False,
+    verbosity: int | None = None,
+    runner: Runner | None = None,
+) -> GenSsReviewTablePyOutputs:
+    """
+    Generate a table from ss_review_basic output files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infiles: Input ss_review_basic output text files to process.
+        write_table: Write final table to the given file.
+        write_outliers: Write outlier table to the given file.
+        overwrite: Overwrite the output -write_table, if it exists.
+        empty_is_outlier: Treat empty tests as outliers.
+        outlier_sep: Use SEP for the outlier table separator.
+        separator: Use SEP for the label/vals separator (default = ':').
+        showlabs: Display counts of all labels found, with parents.
+        show_infiles: Include input files in reviewtable result.
+        show_keepers: Show a table of subjects kept rather than dropped.
+        report_outliers: Report outliers where the comparison holds.
+        report_outliers_fill_style: How to fill non-outliers in the table.
+        show_missing: Display all missing keys.
+        verbosity: Verbosity level.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `GenSsReviewTablePyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GEN_SS_REVIEW_TABLE_PY_METADATA)
+    params = gen_ss_review_table_py_params(
+        infiles=infiles,
+        write_table=write_table,
+        write_outliers=write_outliers,
+        overwrite=overwrite,
+        empty_is_outlier=empty_is_outlier,
+        outlier_sep=outlier_sep,
+        separator=separator,
+        showlabs=showlabs,
+        show_infiles=show_infiles,
+        show_keepers=show_keepers,
+        report_outliers=report_outliers,
+        report_outliers_fill_style=report_outliers_fill_style,
+        show_missing=show_missing,
+        verbosity=verbosity,
+    )
+    return gen_ss_review_table_py_execute(params, execution)
+
+
+__all__ = [
+    "GEN_SS_REVIEW_TABLE_PY_METADATA",
+    "GenSsReviewTablePyOutputs",
+    "GenSsReviewTablePyParameters",
+    "gen_ss_review_table_py",
+    "gen_ss_review_table_py_params",
+]

niwrap_afni/afni/get_afni_model_prf.py

@@ -0,0 +1,196 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+GET_AFNI_MODEL_PRF_METADATA = Metadata(
+    id="cb7d3b9ba2d4dd13509959e5b0788f67b7ac9d2f.boutiques",
+    name="get_afni_model_PRF",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+GetAfniModelPrfParameters = typing.TypedDict('GetAfniModelPrfParameters', {
+    "__STYX_TYPE__": typing.Literal["get_afni_model_PRF"],
+    "amplitude": float,
+    "x_coord": float,
+    "y_coord": float,
+    "sigma": float,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "get_afni_model_PRF": get_afni_model_prf_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 GetAfniModelPrfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `get_afni_model_prf(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def get_afni_model_prf_params(
+    amplitude: float,
+    x_coord: float,
+    y_coord: float,
+    sigma: float,
+) -> GetAfniModelPrfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        amplitude: Amplitude for the AFNI model.
+        x_coord: X-coordinate for the AFNI model.
+        y_coord: Y-coordinate for the AFNI model.
+        sigma: Sigma value for the AFNI model.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "get_afni_model_PRF",
+        "amplitude": amplitude,
+        "x_coord": x_coord,
+        "y_coord": y_coord,
+        "sigma": sigma,
+    }
+    return params
+
+
+def get_afni_model_prf_cargs(
+    params: GetAfniModelPrfParameters,
+    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("get_afni_model_PRF")
+    cargs.append(str(params.get("amplitude")))
+    cargs.append(str(params.get("x_coord")))
+    cargs.append(str(params.get("y_coord")))
+    cargs.append(str(params.get("sigma")))
+    return cargs
+
+
+def get_afni_model_prf_outputs(
+    params: GetAfniModelPrfParameters,
+    execution: Execution,
+) -> GetAfniModelPrfOutputs:
+    """
+    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 = GetAfniModelPrfOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def get_afni_model_prf_execute(
+    params: GetAfniModelPrfParameters,
+    execution: Execution,
+) -> GetAfniModelPrfOutputs:
+    """
+    A tool to get AFNI model parameters assuming a PRF framework.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `GetAfniModelPrfOutputs`).
+    """
+    params = execution.params(params)
+    cargs = get_afni_model_prf_cargs(params, execution)
+    ret = get_afni_model_prf_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def get_afni_model_prf(
+    amplitude: float,
+    x_coord: float,
+    y_coord: float,
+    sigma: float,
+    runner: Runner | None = None,
+) -> GetAfniModelPrfOutputs:
+    """
+    A tool to get AFNI model parameters assuming a PRF framework.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        amplitude: Amplitude for the AFNI model.
+        x_coord: X-coordinate for the AFNI model.
+        y_coord: Y-coordinate for the AFNI model.
+        sigma: Sigma value for the AFNI model.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `GetAfniModelPrfOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GET_AFNI_MODEL_PRF_METADATA)
+    params = get_afni_model_prf_params(
+        amplitude=amplitude,
+        x_coord=x_coord,
+        y_coord=y_coord,
+        sigma=sigma,
+    )
+    return get_afni_model_prf_execute(params, execution)
+
+
+__all__ = [
+    "GET_AFNI_MODEL_PRF_METADATA",
+    "GetAfniModelPrfOutputs",
+    "GetAfniModelPrfParameters",
+    "get_afni_model_prf",
+    "get_afni_model_prf_params",
+]