niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fat_mvm_prep.py

@@ -0,0 +1,256 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_MVM_PREP_METADATA = Metadata(
+    id="90f6bc657de16af423e425320b0789c1d1f1d2eb.boutiques",
+    name="fat_mvm_prep",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatMvmPrepParameters = typing.TypedDict('FatMvmPrepParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_mvm_prep"],
+    "prefix": str,
+    "csv_file": InputPathType,
+    "matrix_files": typing.NotRequired[str | None],
+    "list_match": typing.NotRequired[InputPathType | None],
+    "unionize_rois": bool,
+    "na_warn_off": bool,
+    "extern_labels_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_mvm_prep": fat_mvm_prep_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_prep": fat_mvm_prep_outputs,
+    }.get(t)
+
+
+class FatMvmPrepOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_mvm_prep(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    mvmtbl: OutputPathType
+    """Output tabular text file for 3dMVM."""
+    mvmprep_log: OutputPathType
+    """Log file detailing subject matching and ROI list."""
+
+
+def fat_mvm_prep_params(
+    prefix: str,
+    csv_file: InputPathType,
+    matrix_files: str | None = None,
+    list_match: InputPathType | None = None,
+    unionize_rois: bool = False,
+    na_warn_off: bool = False,
+    extern_labels_no: bool = False,
+) -> FatMvmPrepParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for output files.
+        csv_file: Comma-separated variable (CSV) file for input.
+        matrix_files: Set of matrix (*.grid or *.netcc) files by searchable\
+            path.
+        list_match: Text file containing two columns: path to subject matrix\
+            file and CSV IDs.
+        unionize_rois: Make the ROI list as the union of elements across the\
+            group.
+        na_warn_off: Turn off the automatic warnings as the data table is\
+            created.
+        extern_labels_no: Turn off the writing/usage of user-defined labels in\
+            the *.grid/*.netcc files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_mvm_prep",
+        "prefix": prefix,
+        "csv_file": csv_file,
+        "unionize_rois": unionize_rois,
+        "na_warn_off": na_warn_off,
+        "extern_labels_no": extern_labels_no,
+    }
+    if matrix_files is not None:
+        params["matrix_files"] = matrix_files
+    if list_match is not None:
+        params["list_match"] = list_match
+    return params
+
+
+def fat_mvm_prep_cargs(
+    params: FatMvmPrepParameters,
+    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_prep.py")
+    cargs.extend([
+        "-p",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-c",
+        execution.input_file(params.get("csv_file"))
+    ])
+    if params.get("matrix_files") is not None:
+        cargs.extend([
+            "-m",
+            params.get("matrix_files")
+        ])
+    if params.get("list_match") is not None:
+        cargs.extend([
+            "-l",
+            execution.input_file(params.get("list_match"))
+        ])
+    if params.get("unionize_rois"):
+        cargs.append("-u")
+    if params.get("na_warn_off"):
+        cargs.append("-N")
+    if params.get("extern_labels_no"):
+        cargs.append("-E")
+    return cargs
+
+
+def fat_mvm_prep_outputs(
+    params: FatMvmPrepParameters,
+    execution: Execution,
+) -> FatMvmPrepOutputs:
+    """
+    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 = FatMvmPrepOutputs(
+        root=execution.output_file("."),
+        mvmtbl=execution.output_file(params.get("prefix") + "_MVMtbl.txt"),
+        mvmprep_log=execution.output_file(params.get("prefix") + "_MVMprep.log"),
+    )
+    return ret
+
+
+def fat_mvm_prep_execute(
+    params: FatMvmPrepParameters,
+    execution: Execution,
+) -> FatMvmPrepOutputs:
+    """
+    Combine FATCAT output with CSV data for statistical modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatMvmPrepOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_mvm_prep_cargs(params, execution)
+    ret = fat_mvm_prep_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_mvm_prep(
+    prefix: str,
+    csv_file: InputPathType,
+    matrix_files: str | None = None,
+    list_match: InputPathType | None = None,
+    unionize_rois: bool = False,
+    na_warn_off: bool = False,
+    extern_labels_no: bool = False,
+    runner: Runner | None = None,
+) -> FatMvmPrepOutputs:
+    """
+    Combine FATCAT output with CSV data for statistical modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for output files.
+        csv_file: Comma-separated variable (CSV) file for input.
+        matrix_files: Set of matrix (*.grid or *.netcc) files by searchable\
+            path.
+        list_match: Text file containing two columns: path to subject matrix\
+            file and CSV IDs.
+        unionize_rois: Make the ROI list as the union of elements across the\
+            group.
+        na_warn_off: Turn off the automatic warnings as the data table is\
+            created.
+        extern_labels_no: Turn off the writing/usage of user-defined labels in\
+            the *.grid/*.netcc files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatMvmPrepOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MVM_PREP_METADATA)
+    params = fat_mvm_prep_params(
+        prefix=prefix,
+        csv_file=csv_file,
+        matrix_files=matrix_files,
+        list_match=list_match,
+        unionize_rois=unionize_rois,
+        na_warn_off=na_warn_off,
+        extern_labels_no=extern_labels_no,
+    )
+    return fat_mvm_prep_execute(params, execution)
+
+
+__all__ = [
+    "FAT_MVM_PREP_METADATA",
+    "FatMvmPrepOutputs",
+    "FatMvmPrepParameters",
+    "fat_mvm_prep",
+    "fat_mvm_prep_params",
+]

niwrap_afni/afni/fat_mvm_scripter_py.py

@@ -0,0 +1,353 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FAT_MVM_SCRIPTER_PY_METADATA = Metadata(
+    id="2b93a491c79b77f3d34fa9c5577a2b3807db847a.boutiques",
+    name="fat_mvm_scripter.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FatMvmScripterPyParameters = typing.TypedDict('FatMvmScripterPyParameters', {
+    "__STYX_TYPE__": typing.Literal["fat_mvm_scripter.py"],
+    "prefix": str,
+    "table": InputPathType,
+    "log": InputPathType,
+    "vars": typing.NotRequired[str | None],
+    "file_vars": typing.NotRequired[InputPathType | None],
+    "Pars": typing.NotRequired[str | None],
+    "file_Pars": typing.NotRequired[InputPathType | None],
+    "rois": typing.NotRequired[str | None],
+    "file_rois": typing.NotRequired[InputPathType | None],
+    "no_posthoc": bool,
+    "NA_warn_off": bool,
+    "subnet_pref": typing.NotRequired[str | None],
+    "cat_pair_off": 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_mvm_scripter.py": fat_mvm_scripter_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_scripter.py": fat_mvm_scripter_py_outputs,
+    }.get(t)
+
+
+class FatMvmScripterPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fat_mvm_scripter_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    generated_script: OutputPathType
+    """Script for running 3dMVM, using the prescribed variables along with each
+    individual parameter."""
+    results_file: OutputPathType
+    """Text file of the test results."""
+
+
+def fat_mvm_scripter_py_params(
+    prefix: str,
+    table: InputPathType,
+    log: InputPathType,
+    vars_: str | None = None,
+    file_vars: InputPathType | None = None,
+    pars: str | None = None,
+    file_pars: InputPathType | None = None,
+    rois: str | None = None,
+    file_rois: InputPathType | None = None,
+    no_posthoc: bool = False,
+    na_warn_off: bool = False,
+    subnet_pref: str | None = None,
+    cat_pair_off: bool = False,
+) -> FatMvmScripterPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output prefix for the script file, which will ultimately create\
+            a PREFIX_MVM.txt file of statistical results from 3dMVM.
+        table: Text file containing columns of subject data, one subject per\
+            row, formatted as a *_MVMtbl.txt output by fat_mvm_prep.py.
+        log: File formatted according to fat_mvm_prep.py containing commented\
+            headings and lists of cross-group ROIs and parameters.
+        vars_: List of variables for the 3dMVM model. Names must be separated\
+            with whitespace. Categorical variables will be detected automatically\
+            by the presence of nonnumeric characters in their columns.
+        file_vars: Second method for supplying a list of variables for 3dMVM.\
+            VAR_FILE is a text file with a single column of variable names.
+        pars: List of parameters (names of matrices) to run in distinct 3dMVM\
+            models. Names must be separated with whitespace.
+        file_pars: Second method for supplying a list of parameters for 3dMVM\
+            runs. PAR_FILE is a text file with a single column of parameter names.
+        rois: Optional command to select a subset of available network ROIs.\
+            Names must be separated with whitespace.
+        file_rois: Second method for supplying a subset of ROIs for 3dMVM runs.\
+            ROI_FILE is a text file with a single column of variable names.
+        no_posthoc: Switch to turn off the automatic generation of per-ROI post\
+            hoc tests.
+        na_warn_off: Switch to turn off the automatic warnings as the data\
+            table is created. 3dMVM will excise subjects with NA values, so there\
+            shouldn't be NA values in columns you want to model.
+        subnet_pref: Name SUBPR for the new table file that is created when a\
+            subnetwork list of ROIs is used.
+        cat_pair_off: Switch to turn off the test for categorical variables\
+            undergoing posthoc testing.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fat_mvm_scripter.py",
+        "prefix": prefix,
+        "table": table,
+        "log": log,
+        "no_posthoc": no_posthoc,
+        "NA_warn_off": na_warn_off,
+        "cat_pair_off": cat_pair_off,
+    }
+    if vars_ is not None:
+        params["vars"] = vars_
+    if file_vars is not None:
+        params["file_vars"] = file_vars
+    if pars is not None:
+        params["Pars"] = pars
+    if file_pars is not None:
+        params["file_Pars"] = file_pars
+    if rois is not None:
+        params["rois"] = rois
+    if file_rois is not None:
+        params["file_rois"] = file_rois
+    if subnet_pref is not None:
+        params["subnet_pref"] = subnet_pref
+    return params
+
+
+def fat_mvm_scripter_py_cargs(
+    params: FatMvmScripterPyParameters,
+    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_scripter.py")
+    cargs.extend([
+        "--prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "--table",
+        execution.input_file(params.get("table"))
+    ])
+    cargs.extend([
+        "--log",
+        execution.input_file(params.get("log"))
+    ])
+    if params.get("vars") is not None:
+        cargs.extend([
+            "--vars",
+            params.get("vars")
+        ])
+    if params.get("file_vars") is not None:
+        cargs.extend([
+            "--file_vars",
+            execution.input_file(params.get("file_vars"))
+        ])
+    if params.get("Pars") is not None:
+        cargs.extend([
+            "--Pars",
+            params.get("Pars")
+        ])
+    if params.get("file_Pars") is not None:
+        cargs.extend([
+            "--File_Pars",
+            execution.input_file(params.get("file_Pars"))
+        ])
+    if params.get("rois") is not None:
+        cargs.extend([
+            "--rois",
+            params.get("rois")
+        ])
+    if params.get("file_rois") is not None:
+        cargs.extend([
+            "--file_rois",
+            execution.input_file(params.get("file_rois"))
+        ])
+    if params.get("no_posthoc"):
+        cargs.append("--no_posthoc")
+    if params.get("NA_warn_off"):
+        cargs.append("--NA_warn_off")
+    if params.get("subnet_pref") is not None:
+        cargs.extend([
+            "--subnet_pref",
+            params.get("subnet_pref")
+        ])
+    if params.get("cat_pair_off"):
+        cargs.append("--cat_pair_off")
+    return cargs
+
+
+def fat_mvm_scripter_py_outputs(
+    params: FatMvmScripterPyParameters,
+    execution: Execution,
+) -> FatMvmScripterPyOutputs:
+    """
+    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 = FatMvmScripterPyOutputs(
+        root=execution.output_file("."),
+        generated_script=execution.output_file(params.get("prefix") + "_scri.tcsh"),
+        results_file=execution.output_file(params.get("prefix") + "_MVM.txt"),
+    )
+    return ret
+
+
+def fat_mvm_scripter_py_execute(
+    params: FatMvmScripterPyParameters,
+    execution: Execution,
+) -> FatMvmScripterPyOutputs:
+    """
+    Automated tool to create command scripts for 3dMVM statistical modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FatMvmScripterPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = fat_mvm_scripter_py_cargs(params, execution)
+    ret = fat_mvm_scripter_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fat_mvm_scripter_py(
+    prefix: str,
+    table: InputPathType,
+    log: InputPathType,
+    vars_: str | None = None,
+    file_vars: InputPathType | None = None,
+    pars: str | None = None,
+    file_pars: InputPathType | None = None,
+    rois: str | None = None,
+    file_rois: InputPathType | None = None,
+    no_posthoc: bool = False,
+    na_warn_off: bool = False,
+    subnet_pref: str | None = None,
+    cat_pair_off: bool = False,
+    runner: Runner | None = None,
+) -> FatMvmScripterPyOutputs:
+    """
+    Automated tool to create command scripts for 3dMVM statistical modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output prefix for the script file, which will ultimately create\
+            a PREFIX_MVM.txt file of statistical results from 3dMVM.
+        table: Text file containing columns of subject data, one subject per\
+            row, formatted as a *_MVMtbl.txt output by fat_mvm_prep.py.
+        log: File formatted according to fat_mvm_prep.py containing commented\
+            headings and lists of cross-group ROIs and parameters.
+        vars_: List of variables for the 3dMVM model. Names must be separated\
+            with whitespace. Categorical variables will be detected automatically\
+            by the presence of nonnumeric characters in their columns.
+        file_vars: Second method for supplying a list of variables for 3dMVM.\
+            VAR_FILE is a text file with a single column of variable names.
+        pars: List of parameters (names of matrices) to run in distinct 3dMVM\
+            models. Names must be separated with whitespace.
+        file_pars: Second method for supplying a list of parameters for 3dMVM\
+            runs. PAR_FILE is a text file with a single column of parameter names.
+        rois: Optional command to select a subset of available network ROIs.\
+            Names must be separated with whitespace.
+        file_rois: Second method for supplying a subset of ROIs for 3dMVM runs.\
+            ROI_FILE is a text file with a single column of variable names.
+        no_posthoc: Switch to turn off the automatic generation of per-ROI post\
+            hoc tests.
+        na_warn_off: Switch to turn off the automatic warnings as the data\
+            table is created. 3dMVM will excise subjects with NA values, so there\
+            shouldn't be NA values in columns you want to model.
+        subnet_pref: Name SUBPR for the new table file that is created when a\
+            subnetwork list of ROIs is used.
+        cat_pair_off: Switch to turn off the test for categorical variables\
+            undergoing posthoc testing.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FatMvmScripterPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MVM_SCRIPTER_PY_METADATA)
+    params = fat_mvm_scripter_py_params(
+        prefix=prefix,
+        table=table,
+        log=log,
+        vars_=vars_,
+        file_vars=file_vars,
+        pars=pars,
+        file_pars=file_pars,
+        rois=rois,
+        file_rois=file_rois,
+        no_posthoc=no_posthoc,
+        na_warn_off=na_warn_off,
+        subnet_pref=subnet_pref,
+        cat_pair_off=cat_pair_off,
+    )
+    return fat_mvm_scripter_py_execute(params, execution)
+
+
+__all__ = [
+    "FAT_MVM_SCRIPTER_PY_METADATA",
+    "FatMvmScripterPyOutputs",
+    "FatMvmScripterPyParameters",
+    "fat_mvm_scripter_py",
+    "fat_mvm_scripter_py_params",
+]