niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/clust_exp_stat_parse_py.py

@@ -0,0 +1,346 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CLUST_EXP_STAT_PARSE_PY_METADATA = Metadata(
+    id="0ee922f117a5e881955bf4f23aba845f4aef47bb.boutiques",
+    name="ClustExp_StatParse.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ClustExpStatParsePyParameters = typing.TypedDict('ClustExpStatParsePyParameters', {
+    "__STYX_TYPE__": typing.Literal["ClustExp_StatParse.py"],
+    "statdset": InputPathType,
+    "meanbrik": float,
+    "threshbrik": float,
+    "subjdset": InputPathType,
+    "subjtable": InputPathType,
+    "master": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "pval": typing.NotRequired[float | None],
+    "minvox": typing.NotRequired[float | None],
+    "atlas": typing.NotRequired[str | None],
+    "session": typing.NotRequired[str | None],
+    "noshiny": bool,
+    "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_StatParse.py": clust_exp_stat_parse_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_StatParse.py": clust_exp_stat_parse_py_outputs,
+    }.get(t)
+
+
+class ClustExpStatParsePyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `clust_exp_stat_parse_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    table_mean: OutputPathType | None
+    """Table with all data extracted from all subjects."""
+    group_table: OutputPathType | None
+    """Table with information parsed from the statistics data set history."""
+    v_3dclust_output: OutputPathType | None
+    """Output directly from 3dclust."""
+    clusters_output: OutputPathType | None
+    """Cleaned up version of the whereami output."""
+    statinfo_output: OutputPathType | None
+    """Summary info for the shiny app."""
+    thresholded_dataset: OutputPathType | None
+    """A new data set from input statistics, thresholded at uncorrected p
+    value."""
+    thresholded_mask_dataset: OutputPathType | None
+    """Integer labeled mask of the thresholded image with cluster sizes at least
+    as big as the -MinVox."""
+    master_copy: OutputPathType | None
+    """A NIfTI copy of the master file provided that may have been resampled."""
+
+
+def clust_exp_stat_parse_py_params(
+    statdset: InputPathType,
+    meanbrik: float,
+    threshbrik: float,
+    subjdset: InputPathType,
+    subjtable: InputPathType,
+    master: InputPathType,
+    prefix: str | None = None,
+    pval: float | None = None,
+    minvox: float | None = None,
+    atlas: str | None = None,
+    session: str | None = None,
+    noshiny: bool = False,
+    overwrite: bool = False,
+) -> ClustExpStatParsePyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        statdset: Statistics dataset.
+        meanbrik: Mean subbrik (integer >= 0).
+        threshbrik: Threshold subbrik. Might be the same as MeanBrik (integer\
+            >= 0).
+        subjdset: Labeled dataset with all subjects (from @ClustExp_CatLab).
+        subjtable: Table with subject labels and input datasets.
+        master: Master data set for underlay.
+        prefix: Name for output (no path).
+        pval: Uncorrected p value for thresholding.
+        minvox: Minimum voxels in cluster.
+        atlas: Atlas name for lookup (list at: whereami -help).
+        session: Output parent folder if you don't want the current working\
+            directory.
+        noshiny: Do not create shiny app.
+        overwrite: Remove previous folder with same PREFIX.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ClustExp_StatParse.py",
+        "statdset": statdset,
+        "meanbrik": meanbrik,
+        "threshbrik": threshbrik,
+        "subjdset": subjdset,
+        "subjtable": subjtable,
+        "master": master,
+        "noshiny": noshiny,
+        "overwrite": overwrite,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if pval is not None:
+        params["pval"] = pval
+    if minvox is not None:
+        params["minvox"] = minvox
+    if atlas is not None:
+        params["atlas"] = atlas
+    if session is not None:
+        params["session"] = session
+    return params
+
+
+def clust_exp_stat_parse_py_cargs(
+    params: ClustExpStatParsePyParameters,
+    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_StatParse.py")
+    cargs.extend([
+        "-StatDSET",
+        execution.input_file(params.get("statdset"))
+    ])
+    cargs.extend([
+        "-MeanBrik",
+        str(params.get("meanbrik"))
+    ])
+    cargs.extend([
+        "-ThreshBrik",
+        str(params.get("threshbrik"))
+    ])
+    cargs.extend([
+        "-SubjDSET",
+        execution.input_file(params.get("subjdset"))
+    ])
+    cargs.extend([
+        "-SubjTable",
+        execution.input_file(params.get("subjtable"))
+    ])
+    cargs.extend([
+        "-master",
+        execution.input_file(params.get("master"))
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("pval") is not None:
+        cargs.extend([
+            "-p",
+            str(params.get("pval"))
+        ])
+    if params.get("minvox") is not None:
+        cargs.extend([
+            "-MinVox",
+            str(params.get("minvox"))
+        ])
+    if params.get("atlas") is not None:
+        cargs.extend([
+            "-atlas",
+            params.get("atlas")
+        ])
+    if params.get("session") is not None:
+        cargs.extend([
+            "-session",
+            params.get("session")
+        ])
+    if params.get("noshiny"):
+        cargs.append("-NoShiny")
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    return cargs
+
+
+def clust_exp_stat_parse_py_outputs(
+    params: ClustExpStatParsePyParameters,
+    execution: Execution,
+) -> ClustExpStatParsePyOutputs:
+    """
+    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 = ClustExpStatParsePyOutputs(
+        root=execution.output_file("."),
+        table_mean=execution.output_file(params.get("prefix") + "_p_uncor_" + str(params.get("pval")) + "_mean.csv") if (params.get("prefix") is not None and params.get("pval") is not None) else None,
+        group_table=execution.output_file(params.get("prefix") + "_GroupTable.csv") if (params.get("prefix") is not None) else None,
+        v_3dclust_output=execution.output_file(params.get("prefix") + "_p_uncor_" + str(params.get("pval")) + "_3dclust.1D") if (params.get("prefix") is not None and params.get("pval") is not None) else None,
+        clusters_output=execution.output_file(params.get("prefix") + "_p_uncor_" + str(params.get("pval")) + "_clusters.csv") if (params.get("prefix") is not None and params.get("pval") is not None) else None,
+        statinfo_output=execution.output_file(params.get("prefix") + "_StatInfo.csv") if (params.get("prefix") is not None) else None,
+        thresholded_dataset=execution.output_file(params.get("prefix") + "_p_uncor_" + str(params.get("pval")) + ".nii.gz") if (params.get("prefix") is not None and params.get("pval") is not None) else None,
+        thresholded_mask_dataset=execution.output_file(params.get("prefix") + "_p_uncor_" + str(params.get("pval")) + "_mask.nii.gz") if (params.get("prefix") is not None and params.get("pval") is not None) else None,
+        master_copy=execution.output_file(params.get("prefix") + "_master.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def clust_exp_stat_parse_py_execute(
+    params: ClustExpStatParsePyParameters,
+    execution: Execution,
+) -> ClustExpStatParsePyOutputs:
+    """
+    Parser for statistical data sets and subject data sets, generating several
+    outputs for further analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ClustExpStatParsePyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = clust_exp_stat_parse_py_cargs(params, execution)
+    ret = clust_exp_stat_parse_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def clust_exp_stat_parse_py(
+    statdset: InputPathType,
+    meanbrik: float,
+    threshbrik: float,
+    subjdset: InputPathType,
+    subjtable: InputPathType,
+    master: InputPathType,
+    prefix: str | None = None,
+    pval: float | None = None,
+    minvox: float | None = None,
+    atlas: str | None = None,
+    session: str | None = None,
+    noshiny: bool = False,
+    overwrite: bool = False,
+    runner: Runner | None = None,
+) -> ClustExpStatParsePyOutputs:
+    """
+    Parser for statistical data sets and subject data sets, generating several
+    outputs for further analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        statdset: Statistics dataset.
+        meanbrik: Mean subbrik (integer >= 0).
+        threshbrik: Threshold subbrik. Might be the same as MeanBrik (integer\
+            >= 0).
+        subjdset: Labeled dataset with all subjects (from @ClustExp_CatLab).
+        subjtable: Table with subject labels and input datasets.
+        master: Master data set for underlay.
+        prefix: Name for output (no path).
+        pval: Uncorrected p value for thresholding.
+        minvox: Minimum voxels in cluster.
+        atlas: Atlas name for lookup (list at: whereami -help).
+        session: Output parent folder if you don't want the current working\
+            directory.
+        noshiny: Do not create shiny app.
+        overwrite: Remove previous folder with same PREFIX.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ClustExpStatParsePyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CLUST_EXP_STAT_PARSE_PY_METADATA)
+    params = clust_exp_stat_parse_py_params(
+        statdset=statdset,
+        meanbrik=meanbrik,
+        threshbrik=threshbrik,
+        subjdset=subjdset,
+        subjtable=subjtable,
+        master=master,
+        prefix=prefix,
+        pval=pval,
+        minvox=minvox,
+        atlas=atlas,
+        session=session,
+        noshiny=noshiny,
+        overwrite=overwrite,
+    )
+    return clust_exp_stat_parse_py_execute(params, execution)
+
+
+__all__ = [
+    "CLUST_EXP_STAT_PARSE_PY_METADATA",
+    "ClustExpStatParsePyOutputs",
+    "ClustExpStatParsePyParameters",
+    "clust_exp_stat_parse_py",
+    "clust_exp_stat_parse_py_params",
+]

niwrap_afni/afni/column_cat.py

@@ -0,0 +1,208 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+COLUMN_CAT_METADATA = Metadata(
+    id="22f92393a4504948631931c183a528c1437f87dc.boutiques",
+    name="column_cat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ColumnCatParameters = typing.TypedDict('ColumnCatParameters', {
+    "__STYX_TYPE__": typing.Literal["column_cat"],
+    "line_number": typing.NotRequired[float | None],
+    "separator_string": typing.NotRequired[str | None],
+    "input_files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "column_cat": column_cat_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 {
+        "column_cat": column_cat_outputs,
+    }.get(t)
+
+
+class ColumnCatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `column_cat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Redirect output of concatenation to a file"""
+
+
+def column_cat_params(
+    input_files: list[InputPathType],
+    line_number: float | None = None,
+    separator_string: str | None = None,
+) -> ColumnCatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input files to be concatenated.
+        line_number: Print only the specified line number (1-based).
+        separator_string: Use the specified string as a separator between\
+            columns.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "column_cat",
+        "input_files": input_files,
+    }
+    if line_number is not None:
+        params["line_number"] = line_number
+    if separator_string is not None:
+        params["separator_string"] = separator_string
+    return params
+
+
+def column_cat_cargs(
+    params: ColumnCatParameters,
+    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("column_cat")
+    if params.get("line_number") is not None:
+        cargs.extend([
+            "-line",
+            str(params.get("line_number"))
+        ])
+    if params.get("separator_string") is not None:
+        cargs.extend([
+            "-sep",
+            params.get("separator_string")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def column_cat_outputs(
+    params: ColumnCatParameters,
+    execution: Execution,
+) -> ColumnCatOutputs:
+    """
+    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 = ColumnCatOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("output_file.txt"),
+    )
+    return ret
+
+
+def column_cat_execute(
+    params: ColumnCatParameters,
+    execution: Execution,
+) -> ColumnCatOutputs:
+    """
+    Catenate files horizontally. Each line of output is the concatenation of each
+    current line from the input files, all on the same line, separated by a space or
+    a user-defined separator.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ColumnCatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = column_cat_cargs(params, execution)
+    ret = column_cat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def column_cat(
+    input_files: list[InputPathType],
+    line_number: float | None = None,
+    separator_string: str | None = None,
+    runner: Runner | None = None,
+) -> ColumnCatOutputs:
+    """
+    Catenate files horizontally. Each line of output is the concatenation of each
+    current line from the input files, all on the same line, separated by a space or
+    a user-defined separator.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input files to be concatenated.
+        line_number: Print only the specified line number (1-based).
+        separator_string: Use the specified string as a separator between\
+            columns.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ColumnCatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COLUMN_CAT_METADATA)
+    params = column_cat_params(
+        line_number=line_number,
+        separator_string=separator_string,
+        input_files=input_files,
+    )
+    return column_cat_execute(params, execution)
+
+
+__all__ = [
+    "COLUMN_CAT_METADATA",
+    "ColumnCatOutputs",
+    "ColumnCatParameters",
+    "column_cat",
+    "column_cat_params",
+]