niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__clust_exp_cat_lab.py

@@ -0,0 +1,201 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__CLUST_EXP_CAT_LAB_METADATA = Metadata(
+    id="e3acc2b13b06a35c413b7c5aede3d8651316dbe3.boutiques",
+    name="@ClustExp_CatLab",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VClustExpCatLabParameters = typing.TypedDict('VClustExpCatLabParameters', {
+    "__STYX_TYPE__": typing.Literal["@ClustExp_CatLab"],
+    "prefix": str,
+    "input_file": InputPathType,
+    "help": 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_CatLab": v__clust_exp_cat_lab_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_CatLab": v__clust_exp_cat_lab_outputs,
+    }.get(t)
+
+
+class VClustExpCatLabOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__clust_exp_cat_lab(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output data set concatenating labeled subbriks"""
+
+
+def v__clust_exp_cat_lab_params(
+    prefix: str,
+    input_file: InputPathType,
+    help_: bool = False,
+) -> VClustExpCatLabParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output file name.
+        input_file: Name of file containing the labels and data sets table\
+            (e.g. subjects.csv).
+        help_: Show help information.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ClustExp_CatLab",
+        "prefix": prefix,
+        "input_file": input_file,
+        "help": help_,
+    }
+    return params
+
+
+def v__clust_exp_cat_lab_cargs(
+    params: VClustExpCatLabParameters,
+    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_CatLab")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v__clust_exp_cat_lab_outputs(
+    params: VClustExpCatLabParameters,
+    execution: Execution,
+) -> VClustExpCatLabOutputs:
+    """
+    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 = VClustExpCatLabOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v__clust_exp_cat_lab_execute(
+    params: VClustExpCatLabParameters,
+    execution: Execution,
+) -> VClustExpCatLabOutputs:
+    """
+    Helper script to concatenate and label a group of data sets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VClustExpCatLabOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__clust_exp_cat_lab_cargs(params, execution)
+    ret = v__clust_exp_cat_lab_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__clust_exp_cat_lab(
+    prefix: str,
+    input_file: InputPathType,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VClustExpCatLabOutputs:
+    """
+    Helper script to concatenate and label a group of data sets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output file name.
+        input_file: Name of file containing the labels and data sets table\
+            (e.g. subjects.csv).
+        help_: Show help information.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VClustExpCatLabOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CLUST_EXP_CAT_LAB_METADATA)
+    params = v__clust_exp_cat_lab_params(
+        prefix=prefix,
+        input_file=input_file,
+        help_=help_,
+    )
+    return v__clust_exp_cat_lab_execute(params, execution)
+
+
+__all__ = [
+    "VClustExpCatLabOutputs",
+    "VClustExpCatLabParameters",
+    "V__CLUST_EXP_CAT_LAB_METADATA",
+    "v__clust_exp_cat_lab",
+    "v__clust_exp_cat_lab_params",
+]

niwrap_afni/afni/v__clust_exp_run_shiny.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 *
+
+V__CLUST_EXP_RUN_SHINY_METADATA = Metadata(
+    id="fda3a7d2925f29a17f3a4aecaecf82a67d6aa1fc.boutiques",
+    name="@ClustExp_run_shiny",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VClustExpRunShinyParameters = typing.TypedDict('VClustExpRunShinyParameters', {
+    "__STYX_TYPE__": typing.Literal["@ClustExp_run_shiny"],
+    "directory": str,
+    "help": 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_run_shiny": v__clust_exp_run_shiny_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 VClustExpRunShinyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__clust_exp_run_shiny(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__clust_exp_run_shiny_params(
+    directory: str,
+    help_: bool = False,
+) -> VClustExpRunShinyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        directory: Folder created by ClustExp_StatParse.py.
+        help_: Show help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ClustExp_run_shiny",
+        "directory": directory,
+        "help": help_,
+    }
+    return params
+
+
+def v__clust_exp_run_shiny_cargs(
+    params: VClustExpRunShinyParameters,
+    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_run_shiny")
+    cargs.append(params.get("directory"))
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v__clust_exp_run_shiny_outputs(
+    params: VClustExpRunShinyParameters,
+    execution: Execution,
+) -> VClustExpRunShinyOutputs:
+    """
+    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 = VClustExpRunShinyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__clust_exp_run_shiny_execute(
+    params: VClustExpRunShinyParameters,
+    execution: Execution,
+) -> VClustExpRunShinyOutputs:
+    """
+    Launch a shiny app that was created by ClustExp_StatParse.py.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VClustExpRunShinyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__clust_exp_run_shiny_cargs(params, execution)
+    ret = v__clust_exp_run_shiny_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__clust_exp_run_shiny(
+    directory: str,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VClustExpRunShinyOutputs:
+    """
+    Launch a shiny app that was created by ClustExp_StatParse.py.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        directory: Folder created by ClustExp_StatParse.py.
+        help_: Show help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VClustExpRunShinyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__CLUST_EXP_RUN_SHINY_METADATA)
+    params = v__clust_exp_run_shiny_params(
+        directory=directory,
+        help_=help_,
+    )
+    return v__clust_exp_run_shiny_execute(params, execution)
+
+
+__all__ = [
+    "VClustExpRunShinyOutputs",
+    "VClustExpRunShinyParameters",
+    "V__CLUST_EXP_RUN_SHINY_METADATA",
+    "v__clust_exp_run_shiny",
+    "v__clust_exp_run_shiny_params",
+]

niwrap_afni/afni/v__command_globb.py

@@ -0,0 +1,220 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__COMMAND_GLOBB_METADATA = Metadata(
+    id="c2faf81a08e05a3e16060acc326e418fbdfeaad0.boutiques",
+    name="@CommandGlobb",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VCommandGlobbParameters = typing.TypedDict('VCommandGlobbParameters', {
+    "__STYX_TYPE__": typing.Literal["@CommandGlobb"],
+    "program_command": str,
+    "output_dir": str,
+    "extension": typing.NotRequired[str | None],
+    "brick_list": 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 {
+        "@CommandGlobb": v__command_globb_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 {
+        "@CommandGlobb": v__command_globb_outputs,
+    }.get(t)
+
+
+class VCommandGlobbOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__command_globb(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """Output files generated by the specified program command line."""
+
+
+def v__command_globb_params(
+    program_command: str,
+    output_dir: str,
+    brick_list: list[str],
+    extension: str | None = None,
+) -> VCommandGlobbParameters:
+    """
+    Build parameters.
+    
+    Args:
+        program_command: The entire command line for the program desired. The\
+            command is best put between single quotes, do not use the \\ to break a\
+            long line within the quotes.
+        output_dir: The output directory where the results will be saved.
+        brick_list: A list of bricks (or anything) on which the program command\
+            will be executed.
+        extension: If the program requires a -prefix option, then you can\
+            specify the extension which will get appended to the Brick names before\
+            +orig.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@CommandGlobb",
+        "program_command": program_command,
+        "output_dir": output_dir,
+        "brick_list": brick_list,
+    }
+    if extension is not None:
+        params["extension"] = extension
+    return params
+
+
+def v__command_globb_cargs(
+    params: VCommandGlobbParameters,
+    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("@CommandGlobb")
+    cargs.append("-com")
+    cargs.append(params.get("program_command"))
+    cargs.append("-session")
+    cargs.append(params.get("output_dir"))
+    cargs.append("-newxt")
+    if params.get("extension") is not None:
+        cargs.append(params.get("extension"))
+    cargs.extend([
+        "-list",
+        *params.get("brick_list")
+    ])
+    return cargs
+
+
+def v__command_globb_outputs(
+    params: VCommandGlobbParameters,
+    execution: Execution,
+) -> VCommandGlobbOutputs:
+    """
+    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 = VCommandGlobbOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("output_dir") + "/*"),
+    )
+    return ret
+
+
+def v__command_globb_execute(
+    params: VCommandGlobbParameters,
+    execution: Execution,
+) -> VCommandGlobbOutputs:
+    """
+    A command-line tool to execute a specified program command line on a list of
+    input bricks.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VCommandGlobbOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__command_globb_cargs(params, execution)
+    ret = v__command_globb_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__command_globb(
+    program_command: str,
+    output_dir: str,
+    brick_list: list[str],
+    extension: str | None = None,
+    runner: Runner | None = None,
+) -> VCommandGlobbOutputs:
+    """
+    A command-line tool to execute a specified program command line on a list of
+    input bricks.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        program_command: The entire command line for the program desired. The\
+            command is best put between single quotes, do not use the \\ to break a\
+            long line within the quotes.
+        output_dir: The output directory where the results will be saved.
+        brick_list: A list of bricks (or anything) on which the program command\
+            will be executed.
+        extension: If the program requires a -prefix option, then you can\
+            specify the extension which will get appended to the Brick names before\
+            +orig.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VCommandGlobbOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__COMMAND_GLOBB_METADATA)
+    params = v__command_globb_params(
+        program_command=program_command,
+        output_dir=output_dir,
+        extension=extension,
+        brick_list=brick_list,
+    )
+    return v__command_globb_execute(params, execution)
+
+
+__all__ = [
+    "VCommandGlobbOutputs",
+    "VCommandGlobbParameters",
+    "V__COMMAND_GLOBB_METADATA",
+    "v__command_globb",
+    "v__command_globb_params",
+]