niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_roi_row.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 *
+
+FAT_ROI_ROW_METADATA = Metadata(
+    id="027b80948cf0bd1ac046353e98ebb2ca04186002.boutiques",
+    name="fat_roi_row",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatRoiRowParameters = typing.TypedDict('FatRoiRowParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_roi_row"],
+    "roi": str,
+    "matrix_files": typing.NotRequired[str | None],
+    "list_file": typing.NotRequired[InputPathType | None],
+    "extern_labs_no": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_roi_row": fat_roi_row_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 {
+        "fat_roi_row": fat_roi_row_outputs,
+    }.get(t)
+
+
+class FatRoiRowOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_roi_row(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Selected ROI row output file in .row format."""
+
+
+def fat_roi_row_params(
+    roi: str,
+    matrix_files: str | None = None,
+    list_file: InputPathType | None = None,
+    extern_labs_no: bool = False,
+) -> FatRoiRowParameters:
+    """
+    Build parameters.
+    
+    Args:
+        roi: Specify which ROI's row of connectivity you want to select out. If\
+            labeltables were used, you may select the ROI by either the string\
+            label or the ROI mask number.
+        matrix_files: Provide the set of matrix (*.grid or *.netcc) files by\
+            searchable path. This can be a globbable entry in quotes containing\
+            wildcard characters.
+        list_file: Provide the set of matrix (*.grid or *.netcc) files by\
+            explicit path in a text file. The LIST text file must contain at least\
+            one column with the path to subject matrix file.
+        extern_labs_no: Switch to turn off the writing/usage of user-defined\
+            labels in the *.grid/*.netcc files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_roi_row",
+        "roi": roi,
+        "extern_labs_no": extern_labs_no,
+    }
+    if matrix_files is not None:
+        params["matrix_files"] = matrix_files
+    if list_file is not None:
+        params["list_file"] = list_file
+    return params
+
+
+def fat_roi_row_cargs(
+    params: FatRoiRowParameters,
+    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("fat_roi_row.py")
+    cargs.extend([
+        "-r",
+        params.get("roi")
+    ])
+    cargs.append("{")
+    if params.get("matrix_files") is not None:
+        cargs.extend([
+            "-m",
+            params.get("matrix_files")
+        ])
+    cargs.append("|")
+    if params.get("list_file") is not None:
+        cargs.extend([
+            "-l",
+            execution.input_file(params.get("list_file"))
+        ])
+    cargs.append("}")
+    if params.get("extern_labs_no"):
+        cargs.append("-E")
+    return cargs
+
+
+def fat_roi_row_outputs(
+    params: FatRoiRowParameters,
+    execution: Execution,
+) -> FatRoiRowOutputs:
+    """
+    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 = FatRoiRowOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("roi") + "_selected.row"),
+    )
+    return ret
+
+
+def fat_roi_row_execute(
+    params: FatRoiRowParameters,
+    execution: Execution,
+) -> FatRoiRowOutputs:
+    """
+    Select a single ROI's row out of a connectivity matrix file (*.grid or *.netcc)
+    for viewing and/or 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 `FatRoiRowOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_roi_row_cargs(params, execution)
+    ret = fat_roi_row_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_roi_row(
+    roi: str,
+    matrix_files: str | None = None,
+    list_file: InputPathType | None = None,
+    extern_labs_no: bool = False,
+    runner: Runner | None = None,
+) -> FatRoiRowOutputs:
+    """
+    Select a single ROI's row out of a connectivity matrix file (*.grid or *.netcc)
+    for viewing and/or further analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        roi: Specify which ROI's row of connectivity you want to select out. If\
+            labeltables were used, you may select the ROI by either the string\
+            label or the ROI mask number.
+        matrix_files: Provide the set of matrix (*.grid or *.netcc) files by\
+            searchable path. This can be a globbable entry in quotes containing\
+            wildcard characters.
+        list_file: Provide the set of matrix (*.grid or *.netcc) files by\
+            explicit path in a text file. The LIST text file must contain at least\
+            one column with the path to subject matrix file.
+        extern_labs_no: Switch to turn off the writing/usage of user-defined\
+            labels in the *.grid/*.netcc files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatRoiRowOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_ROI_ROW_METADATA)
+    params = fat_roi_row_params(
+        roi=roi,
+        matrix_files=matrix_files,
+        list_file=list_file,
+        extern_labs_no=extern_labs_no,
+    )
+    return fat_roi_row_execute(params, execution)
+
+
+__all__ = [
+    "FAT_ROI_ROW_METADATA",
+    "FatRoiRowOutputs",
+    "FatRoiRowParameters",
+    "fat_roi_row",
+    "fat_roi_row_params",
+]

niwrap_afni/afni/fatcat_matplot.py

@@ -0,0 +1,181 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FATCAT_MATPLOT_METADATA = Metadata(
+    id="f644c652339bbfb3aa84d71606689abe580b8c2b.boutiques",
+    name="FATCAT_matplot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatcatMatplotParameters = typing.TypedDict('FatcatMatplotParameters', {
+    "__STYX_TYPE__": typing.Literal["FATCAT_matplot"],
+    "directory": str,
+    "shiny_folder": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "FATCAT_matplot": fatcat_matplot_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 FatcatMatplotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fatcat_matplot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def fatcat_matplot_params(
+    directory: str,
+    shiny_folder: bool = False,
+) -> FatcatMatplotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        directory: Path to a folder containing .netcc and/or .grid files.
+        shiny_folder: Use a custom shiny folder (for testing purposes).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "FATCAT_matplot",
+        "directory": directory,
+        "shiny_folder": shiny_folder,
+    }
+    return params
+
+
+def fatcat_matplot_cargs(
+    params: FatcatMatplotParameters,
+    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("FATCAT_matplot")
+    cargs.append(params.get("directory"))
+    if params.get("shiny_folder"):
+        cargs.append("-ShinyFolder")
+    return cargs
+
+
+def fatcat_matplot_outputs(
+    params: FatcatMatplotParameters,
+    execution: Execution,
+) -> FatcatMatplotOutputs:
+    """
+    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 = FatcatMatplotOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def fatcat_matplot_execute(
+    params: FatcatMatplotParameters,
+    execution: Execution,
+) -> FatcatMatplotOutputs:
+    """
+    Launch a shiny app to visualize .netcc and/or .grid files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatcatMatplotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fatcat_matplot_cargs(params, execution)
+    ret = fatcat_matplot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fatcat_matplot(
+    directory: str,
+    shiny_folder: bool = False,
+    runner: Runner | None = None,
+) -> FatcatMatplotOutputs:
+    """
+    Launch a shiny app to visualize .netcc and/or .grid files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        directory: Path to a folder containing .netcc and/or .grid files.
+        shiny_folder: Use a custom shiny folder (for testing purposes).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatcatMatplotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FATCAT_MATPLOT_METADATA)
+    params = fatcat_matplot_params(
+        directory=directory,
+        shiny_folder=shiny_folder,
+    )
+    return fatcat_matplot_execute(params, execution)
+
+
+__all__ = [
+    "FATCAT_MATPLOT_METADATA",
+    "FatcatMatplotOutputs",
+    "FatcatMatplotParameters",
+    "fatcat_matplot",
+    "fatcat_matplot_params",
+]

niwrap_afni/afni/fdrval.py

@@ -0,0 +1,241 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FDRVAL_METADATA = Metadata(
+    id="f92df9dc9c7bd351f5f06439c97a5434e22b31b8.boutiques",
+    name="fdrval",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FdrvalParameters = typing.TypedDict('FdrvalParameters', {
+    "__STYX_TYPE__": typing.Literal["fdrval"],
+    "dset": InputPathType,
+    "sub": float,
+    "val_list": list[float],
+    "pval": bool,
+    "ponly": bool,
+    "qonly": bool,
+    "qinput": bool,
+    "inverse": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fdrval": fdrval_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 {
+        "fdrval": fdrval_outputs,
+    }.get(t)
+
+
+class FdrvalOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fdrval(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """Computed q-values or p-values for the given thresholds"""
+
+
+def fdrval_params(
+    dset: InputPathType,
+    sub: float,
+    val_list: list[float],
+    pval: bool = False,
+    ponly: bool = False,
+    qonly: bool = False,
+    qinput: bool = False,
+    inverse: bool = False,
+) -> FdrvalParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Input dataset.
+        sub: Sub-brick number.
+        val_list: List of threshold values.
+        pval: Output the p-value (on the same line, after q).
+        ponly: Don't output q-values, just p-values.
+        qonly: Don't output p-values, just q-values.
+        qinput: The 'val' inputs are taken to be q-values and then the outputs\
+            are the corresponding statistical thresholds.
+        inverse: Inverse of the usual operation. 'Val' inputs must be between 0\
+            and 1 (exclusive). Cannot be used with '-ponly' or '-pval'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fdrval",
+        "dset": dset,
+        "sub": sub,
+        "val_list": val_list,
+        "pval": pval,
+        "ponly": ponly,
+        "qonly": qonly,
+        "qinput": qinput,
+        "inverse": inverse,
+    }
+    return params
+
+
+def fdrval_cargs(
+    params: FdrvalParameters,
+    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("fdrval")
+    cargs.append(execution.input_file(params.get("dset")))
+    cargs.append(str(params.get("sub")))
+    cargs.extend(map(str, params.get("val_list")))
+    if params.get("pval"):
+        cargs.append("-pval")
+    if params.get("ponly"):
+        cargs.append("-ponly")
+    if params.get("qonly"):
+        cargs.append("-qonly")
+    if params.get("qinput"):
+        cargs.append("-qinput")
+    if params.get("inverse"):
+        cargs.append("-inverse")
+    return cargs
+
+
+def fdrval_outputs(
+    params: FdrvalParameters,
+    execution: Execution,
+) -> FdrvalOutputs:
+    """
+    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 = FdrvalOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file("stdout.txt"),
+    )
+    return ret
+
+
+def fdrval_execute(
+    params: FdrvalParameters,
+    execution: Execution,
+) -> FdrvalOutputs:
+    """
+    Computes q-values from FDR curve data stored in dataset headers.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FdrvalOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fdrval_cargs(params, execution)
+    ret = fdrval_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fdrval(
+    dset: InputPathType,
+    sub: float,
+    val_list: list[float],
+    pval: bool = False,
+    ponly: bool = False,
+    qonly: bool = False,
+    qinput: bool = False,
+    inverse: bool = False,
+    runner: Runner | None = None,
+) -> FdrvalOutputs:
+    """
+    Computes q-values from FDR curve data stored in dataset headers.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Input dataset.
+        sub: Sub-brick number.
+        val_list: List of threshold values.
+        pval: Output the p-value (on the same line, after q).
+        ponly: Don't output q-values, just p-values.
+        qonly: Don't output p-values, just q-values.
+        qinput: The 'val' inputs are taken to be q-values and then the outputs\
+            are the corresponding statistical thresholds.
+        inverse: Inverse of the usual operation. 'Val' inputs must be between 0\
+            and 1 (exclusive). Cannot be used with '-ponly' or '-pval'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FdrvalOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FDRVAL_METADATA)
+    params = fdrval_params(
+        dset=dset,
+        sub=sub,
+        val_list=val_list,
+        pval=pval,
+        ponly=ponly,
+        qonly=qonly,
+        qinput=qinput,
+        inverse=inverse,
+    )
+    return fdrval_execute(params, execution)
+
+
+__all__ = [
+    "FDRVAL_METADATA",
+    "FdrvalOutputs",
+    "FdrvalParameters",
+    "fdrval",
+    "fdrval_params",
+]