niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/map_track_id.py

@@ -0,0 +1,254 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MAP_TRACK_ID_METADATA = Metadata(
+    id="8a4654eaf53cc77b2cf484e321c0f2ad7ebde3ea.boutiques",
+    name="map_TrackID",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MapTrackIdParameters = typing.TypedDict('MapTrackIdParameters', {
+    "__STYX_TYPE__": typing.Literal["map_TrackID"],
+    "prefix": str,
+    "in_trk": InputPathType,
+    "in_map": InputPathType,
+    "reference": InputPathType,
+    "verbose": bool,
+    "orig_zero": bool,
+    "line_only_num": bool,
+    "already_inv": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "map_TrackID": map_track_id_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 {
+        "map_TrackID": map_track_id_outputs,
+    }.get(t)
+
+
+class MapTrackIdOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `map_track_id(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_trk_file: OutputPathType
+    """Mapped track file to new space"""
+
+
+def map_track_id_params(
+    prefix: str,
+    in_trk: InputPathType,
+    in_map: InputPathType,
+    reference: InputPathType,
+    verbose: bool = False,
+    orig_zero: bool = False,
+    line_only_num: bool = False,
+    already_inv: bool = False,
+) -> MapTrackIdParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for the output track file.
+        in_trk: The name of the *.trk file to be mapped.
+        in_map: Single line of matrix values for the transformation.
+        reference: 3D data set in the space to which the TRK file is being\
+            mapped.
+        verbose: Verbose output.
+        orig_zero: Put (0,0,0) as the origin in the output *.trk file.
+        line_only_num: If your 1D_MATR file is just 12 numbers in a row.
+        already_inv: If you have inverted the mapping or use another program\
+            than 3dAllineate.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "map_TrackID",
+        "prefix": prefix,
+        "in_trk": in_trk,
+        "in_map": in_map,
+        "reference": reference,
+        "verbose": verbose,
+        "orig_zero": orig_zero,
+        "line_only_num": line_only_num,
+        "already_inv": already_inv,
+    }
+    return params
+
+
+def map_track_id_cargs(
+    params: MapTrackIdParameters,
+    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("map_TrackID")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-in_trk",
+        execution.input_file(params.get("in_trk"))
+    ])
+    cargs.extend([
+        "-in_map",
+        execution.input_file(params.get("in_map"))
+    ])
+    cargs.extend([
+        "-ref",
+        execution.input_file(params.get("reference"))
+    ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("orig_zero"):
+        cargs.append("-orig_zero")
+    if params.get("line_only_num"):
+        cargs.append("-line_only_num")
+    if params.get("already_inv"):
+        cargs.append("-already_inv")
+    return cargs
+
+
+def map_track_id_outputs(
+    params: MapTrackIdParameters,
+    execution: Execution,
+) -> MapTrackIdOutputs:
+    """
+    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 = MapTrackIdOutputs(
+        root=execution.output_file("."),
+        output_trk_file=execution.output_file(params.get("prefix") + ".trk"),
+    )
+    return ret
+
+
+def map_track_id_execute(
+    params: MapTrackIdParameters,
+    execution: Execution,
+) -> MapTrackIdOutputs:
+    """
+    Maps the track file (*.trk) output of 3dTrackID to another space using the
+    1Dmatrix_save info of 3dAllineate.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MapTrackIdOutputs`).
+    """
+    params = execution.params(params)
+    cargs = map_track_id_cargs(params, execution)
+    ret = map_track_id_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def map_track_id(
+    prefix: str,
+    in_trk: InputPathType,
+    in_map: InputPathType,
+    reference: InputPathType,
+    verbose: bool = False,
+    orig_zero: bool = False,
+    line_only_num: bool = False,
+    already_inv: bool = False,
+    runner: Runner | None = None,
+) -> MapTrackIdOutputs:
+    """
+    Maps the track file (*.trk) output of 3dTrackID to another space using the
+    1Dmatrix_save info of 3dAllineate.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for the output track file.
+        in_trk: The name of the *.trk file to be mapped.
+        in_map: Single line of matrix values for the transformation.
+        reference: 3D data set in the space to which the TRK file is being\
+            mapped.
+        verbose: Verbose output.
+        orig_zero: Put (0,0,0) as the origin in the output *.trk file.
+        line_only_num: If your 1D_MATR file is just 12 numbers in a row.
+        already_inv: If you have inverted the mapping or use another program\
+            than 3dAllineate.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MapTrackIdOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAP_TRACK_ID_METADATA)
+    params = map_track_id_params(
+        prefix=prefix,
+        in_trk=in_trk,
+        in_map=in_map,
+        reference=reference,
+        verbose=verbose,
+        orig_zero=orig_zero,
+        line_only_num=line_only_num,
+        already_inv=already_inv,
+    )
+    return map_track_id_execute(params, execution)
+
+
+__all__ = [
+    "MAP_TRACK_ID_METADATA",
+    "MapTrackIdOutputs",
+    "MapTrackIdParameters",
+    "map_track_id",
+    "map_track_id_params",
+]

niwrap_afni/afni/mba.py

@@ -0,0 +1,360 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MBA_METADATA = Metadata(
+    id="eb3770a45e9a9a1d951dda7cc20331a2afd73cf7.boutiques",
+    name="MBA",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+MbaParameters = typing.TypedDict('MbaParameters', {
+    "__STYX_TYPE__": typing.Literal["MBA"],
+    "prefix": str,
+    "chains": typing.NotRequired[int | None],
+    "iterations": typing.NotRequired[int | None],
+    "model": typing.NotRequired[str | None],
+    "eoi": typing.NotRequired[str | None],
+    "data_table": InputPathType,
+    "cvars": typing.NotRequired[str | None],
+    "qvars": typing.NotRequired[str | None],
+    "qcvar": typing.NotRequired[str | None],
+    "stdz": typing.NotRequired[str | None],
+    "wcp": typing.NotRequired[int | None],
+    "disty": typing.NotRequired[str | None],
+    "se": typing.NotRequired[str | None],
+    "dbgArgs": bool,
+    "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 {
+        "MBA": mba_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 {
+        "MBA": mba_outputs,
+    }.get(t)
+
+
+class MbaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mba(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_txt: OutputPathType
+    """Main output text file storing inference information"""
+    output_rdata: OutputPathType
+    """R data file for post hoc processing and plotting"""
+    matrix_plot: OutputPathType
+    """Matrix plot visualization of analysis"""
+
+
+def mba_params(
+    prefix: str,
+    data_table: InputPathType,
+    chains: int | None = None,
+    iterations: int | None = None,
+    model: str | None = None,
+    eoi: str | None = None,
+    cvars: str | None = None,
+    qvars: str | None = None,
+    qcvar: str | None = None,
+    stdz: str | None = None,
+    wcp: int | None = None,
+    disty: str | None = None,
+    se: str | None = None,
+    dbg_args: bool = False,
+    help_: bool = False,
+) -> MbaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for output file names.
+        data_table: Specify the data structure in a table of long format.
+        chains: Specify the number of Markov chains.
+        iterations: Specify the number of iterations per Markov chain.
+        model: Specify the effects associated with explanatory variables.
+        eoi: Identify effects of interest in the output.
+        cvars: Identify categorical (qualitative) variables.
+        qvars: Identify quantitative variables (or covariates).
+        qcvar: Identify comparisons of interest between quantitative variables.
+        stdz: Identify quantitative variables (or covariates) to be\
+            standardized.
+        wcp: Invoke within-chain parallelization to speed up runtime.
+        disty: Specify the distribution for the response variable.
+        se: Specify the column name that designates the standard error for the\
+            response variable.
+        dbg_args: Enable R to save the parameters in a file called\
+            .MBA.dbg.AFNI.args for debugging purposes.
+        help_: Show help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "MBA",
+        "prefix": prefix,
+        "data_table": data_table,
+        "dbgArgs": dbg_args,
+        "help": help_,
+    }
+    if chains is not None:
+        params["chains"] = chains
+    if iterations is not None:
+        params["iterations"] = iterations
+    if model is not None:
+        params["model"] = model
+    if eoi is not None:
+        params["eoi"] = eoi
+    if cvars is not None:
+        params["cvars"] = cvars
+    if qvars is not None:
+        params["qvars"] = qvars
+    if qcvar is not None:
+        params["qcvar"] = qcvar
+    if stdz is not None:
+        params["stdz"] = stdz
+    if wcp is not None:
+        params["wcp"] = wcp
+    if disty is not None:
+        params["disty"] = disty
+    if se is not None:
+        params["se"] = se
+    return params
+
+
+def mba_cargs(
+    params: MbaParameters,
+    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("MBA")
+    cargs.append(params.get("prefix"))
+    if params.get("chains") is not None:
+        cargs.extend([
+            "-chains",
+            str(params.get("chains"))
+        ])
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "-iterations",
+            str(params.get("iterations"))
+        ])
+    if params.get("model") is not None:
+        cargs.extend([
+            "-model",
+            params.get("model")
+        ])
+    if params.get("eoi") is not None:
+        cargs.extend([
+            "-EOI",
+            params.get("eoi")
+        ])
+    cargs.extend([
+        "-dataTable",
+        execution.input_file(params.get("data_table"))
+    ])
+    if params.get("cvars") is not None:
+        cargs.extend([
+            "-cVars",
+            params.get("cvars")
+        ])
+    if params.get("qvars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("qvars")
+        ])
+    if params.get("qcvar") is not None:
+        cargs.extend([
+            "-qContr",
+            params.get("qcvar")
+        ])
+    if params.get("stdz") is not None:
+        cargs.extend([
+            "-stdz",
+            params.get("stdz")
+        ])
+    if params.get("wcp") is not None:
+        cargs.extend([
+            "-WCP",
+            str(params.get("wcp"))
+        ])
+    if params.get("disty") is not None:
+        cargs.extend([
+            "-distY",
+            params.get("disty")
+        ])
+    if params.get("se") is not None:
+        cargs.extend([
+            "-se",
+            params.get("se")
+        ])
+    if params.get("dbgArgs"):
+        cargs.append("-dbgArgs")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def mba_outputs(
+    params: MbaParameters,
+    execution: Execution,
+) -> MbaOutputs:
+    """
+    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 = MbaOutputs(
+        root=execution.output_file("."),
+        output_txt=execution.output_file(params.get("prefix") + ".txt"),
+        output_rdata=execution.output_file(params.get("prefix") + ".RData"),
+        matrix_plot=execution.output_file(params.get("prefix") + "_matrixplot.png"),
+    )
+    return ret
+
+
+def mba_execute(
+    params: MbaParameters,
+    execution: Execution,
+) -> MbaOutputs:
+    """
+    Matrix-Based Analysis Program through Bayesian Multilevel Modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MbaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mba_cargs(params, execution)
+    ret = mba_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mba(
+    prefix: str,
+    data_table: InputPathType,
+    chains: int | None = None,
+    iterations: int | None = None,
+    model: str | None = None,
+    eoi: str | None = None,
+    cvars: str | None = None,
+    qvars: str | None = None,
+    qcvar: str | None = None,
+    stdz: str | None = None,
+    wcp: int | None = None,
+    disty: str | None = None,
+    se: str | None = None,
+    dbg_args: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> MbaOutputs:
+    """
+    Matrix-Based Analysis Program through Bayesian Multilevel Modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for output file names.
+        data_table: Specify the data structure in a table of long format.
+        chains: Specify the number of Markov chains.
+        iterations: Specify the number of iterations per Markov chain.
+        model: Specify the effects associated with explanatory variables.
+        eoi: Identify effects of interest in the output.
+        cvars: Identify categorical (qualitative) variables.
+        qvars: Identify quantitative variables (or covariates).
+        qcvar: Identify comparisons of interest between quantitative variables.
+        stdz: Identify quantitative variables (or covariates) to be\
+            standardized.
+        wcp: Invoke within-chain parallelization to speed up runtime.
+        disty: Specify the distribution for the response variable.
+        se: Specify the column name that designates the standard error for the\
+            response variable.
+        dbg_args: Enable R to save the parameters in a file called\
+            .MBA.dbg.AFNI.args for debugging purposes.
+        help_: Show help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MbaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MBA_METADATA)
+    params = mba_params(
+        prefix=prefix,
+        chains=chains,
+        iterations=iterations,
+        model=model,
+        eoi=eoi,
+        data_table=data_table,
+        cvars=cvars,
+        qvars=qvars,
+        qcvar=qcvar,
+        stdz=stdz,
+        wcp=wcp,
+        disty=disty,
+        se=se,
+        dbg_args=dbg_args,
+        help_=help_,
+    )
+    return mba_execute(params, execution)
+
+
+__all__ = [
+    "MBA_METADATA",
+    "MbaOutputs",
+    "MbaParameters",
+    "mba",
+    "mba_params",
+]