niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_mat_tableize.py

@@ -0,0 +1,292 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_MAT_TABLEIZE_METADATA = Metadata(
+    id="5ba44998c47e95e162b9d566a509d5fcbb197e51.boutiques",
+    name="fat_mat_tableize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatMatTableizeParameters = typing.TypedDict('FatMatTableizeParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_mat_tableize"],
+    "input_matrices": list[str],
+    "input_csv": typing.NotRequired[InputPathType | None],
+    "input_list": typing.NotRequired[InputPathType | None],
+    "output_prefix": str,
+    "parameters": typing.NotRequired[list[str] | None],
+    "version": bool,
+    "date": bool,
+    "help": bool,
+    "help_short": bool,
+    "help_view": 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_mat_tableize": fat_mat_tableize_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_mat_tableize": fat_mat_tableize_outputs,
+    }.get(t)
+
+
+class FatMatTableizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_mat_tableize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_table: OutputPathType
+    """Table file usable in AFNI group analysis programs."""
+    output_log: OutputPathType
+    """Log file reporting inputs, matching, and aspects of creating the table
+    file."""
+
+
+def fat_mat_tableize_params(
+    input_matrices: list[str],
+    output_prefix: str,
+    input_csv: InputPathType | None = None,
+    input_list: InputPathType | None = None,
+    parameters: list[str] | None = None,
+    version: bool = False,
+    date: bool = False,
+    help_: bool = False,
+    help_short: bool = False,
+    help_view: bool = False,
+) -> FatMatTableizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_matrices: Names of *.netcc or *.grid files with matrices to be\
+            used to make table; can be provided using wildcard chars.
+        output_prefix: Output basename for the table and log files. Suffix and\
+            file extensions will be added for the outputs.
+        input_csv: Name of a CSV file to include in the table. The first column\
+            must have subject ID labels that match with the input matrix files.
+        input_list: File containing paths to subject matrices and optionally\
+            CSV IDs for matching.
+        parameters: List of matrices to be included in the table, identified by\
+            their parameter name.
+        version: Display current version.
+        date: Display release/editing date of current version.
+        help_: Display help in terminal.
+        help_short: Display help in terminal (short flag).
+        help_view: Display help in a separate text editor.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_mat_tableize",
+        "input_matrices": input_matrices,
+        "output_prefix": output_prefix,
+        "version": version,
+        "date": date,
+        "help": help_,
+        "help_short": help_short,
+        "help_view": help_view,
+    }
+    if input_csv is not None:
+        params["input_csv"] = input_csv
+    if input_list is not None:
+        params["input_list"] = input_list
+    if parameters is not None:
+        params["parameters"] = parameters
+    return params
+
+
+def fat_mat_tableize_cargs(
+    params: FatMatTableizeParameters,
+    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_mat_tableize.py")
+    cargs.extend([
+        "-in_mat",
+        *params.get("input_matrices")
+    ])
+    if params.get("input_csv") is not None:
+        cargs.extend([
+            "-in_csv",
+            execution.input_file(params.get("input_csv"))
+        ])
+    if params.get("input_list") is not None:
+        cargs.extend([
+            "-in_listfile",
+            execution.input_file(params.get("input_list"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("parameters") is not None:
+        cargs.extend([
+            "-pars",
+            *params.get("parameters")
+        ])
+    if params.get("version"):
+        cargs.append("-ver")
+    if params.get("date"):
+        cargs.append("-date")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("help_short"):
+        cargs.append("-h")
+    if params.get("help_view"):
+        cargs.append("-hview")
+    return cargs
+
+
+def fat_mat_tableize_outputs(
+    params: FatMatTableizeParameters,
+    execution: Execution,
+) -> FatMatTableizeOutputs:
+    """
+    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 = FatMatTableizeOutputs(
+        root=execution.output_file("."),
+        output_table=execution.output_file(params.get("output_prefix") + "_tbl.txt"),
+        output_log=execution.output_file(params.get("output_prefix") + "_prep.log"),
+    )
+    return ret
+
+
+def fat_mat_tableize_execute(
+    params: FatMatTableizeParameters,
+    execution: Execution,
+) -> FatMatTableizeOutputs:
+    """
+    Make tables for AFNI group analysis programs from 3dNetCorr (*.netcc) and
+    3dTrackID (*.grid) outputs, with optional additional subject information from
+    CSV files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatMatTableizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_mat_tableize_cargs(params, execution)
+    ret = fat_mat_tableize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_mat_tableize(
+    input_matrices: list[str],
+    output_prefix: str,
+    input_csv: InputPathType | None = None,
+    input_list: InputPathType | None = None,
+    parameters: list[str] | None = None,
+    version: bool = False,
+    date: bool = False,
+    help_: bool = False,
+    help_short: bool = False,
+    help_view: bool = False,
+    runner: Runner | None = None,
+) -> FatMatTableizeOutputs:
+    """
+    Make tables for AFNI group analysis programs from 3dNetCorr (*.netcc) and
+    3dTrackID (*.grid) outputs, with optional additional subject information from
+    CSV files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_matrices: Names of *.netcc or *.grid files with matrices to be\
+            used to make table; can be provided using wildcard chars.
+        output_prefix: Output basename for the table and log files. Suffix and\
+            file extensions will be added for the outputs.
+        input_csv: Name of a CSV file to include in the table. The first column\
+            must have subject ID labels that match with the input matrix files.
+        input_list: File containing paths to subject matrices and optionally\
+            CSV IDs for matching.
+        parameters: List of matrices to be included in the table, identified by\
+            their parameter name.
+        version: Display current version.
+        date: Display release/editing date of current version.
+        help_: Display help in terminal.
+        help_short: Display help in terminal (short flag).
+        help_view: Display help in a separate text editor.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatMatTableizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MAT_TABLEIZE_METADATA)
+    params = fat_mat_tableize_params(
+        input_matrices=input_matrices,
+        input_csv=input_csv,
+        input_list=input_list,
+        output_prefix=output_prefix,
+        parameters=parameters,
+        version=version,
+        date=date,
+        help_=help_,
+        help_short=help_short,
+        help_view=help_view,
+    )
+    return fat_mat_tableize_execute(params, execution)
+
+
+__all__ = [
+    "FAT_MAT_TABLEIZE_METADATA",
+    "FatMatTableizeOutputs",
+    "FatMatTableizeParameters",
+    "fat_mat_tableize",
+    "fat_mat_tableize_params",
+]

niwrap_afni/afni/fat_mvm_gridconv_py.py

@@ -0,0 +1,207 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_MVM_GRIDCONV_PY_METADATA = Metadata(
+    id="8ae9f4629987e35362a12cb081ce643576e4a5c4.boutiques",
+    name="fat_mvm_gridconv.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatMvmGridconvPyParameters = typing.TypedDict('FatMvmGridconvPyParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_mvm_gridconv.py"],
+    "matrix_files": typing.NotRequired[str | None],
+    "list_file": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "fat_mvm_gridconv.py": fat_mvm_gridconv_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 {
+        "fat_mvm_gridconv.py": fat_mvm_gridconv_py_outputs,
+    }.get(t)
+
+
+class FatMvmGridconvPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_mvm_gridconv_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    converted_grid_files: OutputPathType
+    """Output converted grid files, with '_MOD.grid' postfix or custom output
+    name provided in the list file."""
+
+
+def fat_mvm_gridconv_py_params(
+    matrix_files: str | None = None,
+    list_file: InputPathType | None = None,
+) -> FatMvmGridconvPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        matrix_files: Provide the set of matrix (*.grid) files as a searchable\
+            path. This can be a globbable entry in quotes containing wildcard\
+            characters.
+        list_file: Provide the matrix (*.grid) files by explicit path in a text\
+            file. The LIST text file must contain at least one column (path to\
+            subject matrix file) with an optional second column (output file\
+            names). If no second column is given, the default '_MOD.grid' postfix\
+            is applied.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_mvm_gridconv.py",
+    }
+    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_mvm_gridconv_py_cargs(
+    params: FatMvmGridconvPyParameters,
+    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_mvm_gridconv.py")
+    if params.get("matrix_files") is not None:
+        cargs.extend([
+            "-m",
+            params.get("matrix_files")
+        ])
+    if params.get("list_file") is not None:
+        cargs.extend([
+            "-l",
+            execution.input_file(params.get("list_file"))
+        ])
+    return cargs
+
+
+def fat_mvm_gridconv_py_outputs(
+    params: FatMvmGridconvPyParameters,
+    execution: Execution,
+) -> FatMvmGridconvPyOutputs:
+    """
+    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 = FatMvmGridconvPyOutputs(
+        root=execution.output_file("."),
+        converted_grid_files=execution.output_file("*_MOD.grid"),
+    )
+    return ret
+
+
+def fat_mvm_gridconv_py_execute(
+    params: FatMvmGridconvPyParameters,
+    execution: Execution,
+) -> FatMvmGridconvPyOutputs:
+    """
+    Preprocess 'old school' *.grid files for statistical modeling using 3dMVM.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatMvmGridconvPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_mvm_gridconv_py_cargs(params, execution)
+    ret = fat_mvm_gridconv_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_mvm_gridconv_py(
+    matrix_files: str | None = None,
+    list_file: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> FatMvmGridconvPyOutputs:
+    """
+    Preprocess 'old school' *.grid files for statistical modeling using 3dMVM.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        matrix_files: Provide the set of matrix (*.grid) files as a searchable\
+            path. This can be a globbable entry in quotes containing wildcard\
+            characters.
+        list_file: Provide the matrix (*.grid) files by explicit path in a text\
+            file. The LIST text file must contain at least one column (path to\
+            subject matrix file) with an optional second column (output file\
+            names). If no second column is given, the default '_MOD.grid' postfix\
+            is applied.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatMvmGridconvPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MVM_GRIDCONV_PY_METADATA)
+    params = fat_mvm_gridconv_py_params(
+        matrix_files=matrix_files,
+        list_file=list_file,
+    )
+    return fat_mvm_gridconv_py_execute(params, execution)
+
+
+__all__ = [
+    "FAT_MVM_GRIDCONV_PY_METADATA",
+    "FatMvmGridconvPyOutputs",
+    "FatMvmGridconvPyParameters",
+    "fat_mvm_gridconv_py",
+    "fat_mvm_gridconv_py_params",
+]