niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_entropy.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_3D_ENTROPY_METADATA = Metadata(
+    id="65268d877950e23f9bd06dfb7ede10b57050e1e9.boutiques",
+    name="3dEntropy",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dEntropyParameters = typing.TypedDict('V3dEntropyParameters', {
+    "__STYX_TYPE__": typing.Literal["3dEntropy"],
+    "zskip": bool,
+    "input_dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dEntropy": v_3d_entropy_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 V3dEntropyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_entropy(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_entropy_params(
+    input_dataset: InputPathType,
+    zskip: bool = False,
+) -> V3dEntropyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (stored as 16 bit shorts).
+        zskip: Skip 0 values in the entropy computation.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dEntropy",
+        "zskip": zskip,
+        "input_dataset": input_dataset,
+    }
+    return params
+
+
+def v_3d_entropy_cargs(
+    params: V3dEntropyParameters,
+    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("3dEntropy")
+    if params.get("zskip"):
+        cargs.append("-zskip")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    return cargs
+
+
+def v_3d_entropy_outputs(
+    params: V3dEntropyParameters,
+    execution: Execution,
+) -> V3dEntropyOutputs:
+    """
+    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 = V3dEntropyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_entropy_execute(
+    params: V3dEntropyParameters,
+    execution: Execution,
+) -> V3dEntropyOutputs:
+    """
+    Computes entropy for a 3D dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dEntropyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_entropy_cargs(params, execution)
+    ret = v_3d_entropy_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_entropy(
+    input_dataset: InputPathType,
+    zskip: bool = False,
+    runner: Runner | None = None,
+) -> V3dEntropyOutputs:
+    """
+    Computes entropy for a 3D dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (stored as 16 bit shorts).
+        zskip: Skip 0 values in the entropy computation.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dEntropyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ENTROPY_METADATA)
+    params = v_3d_entropy_params(
+        zskip=zskip,
+        input_dataset=input_dataset,
+    )
+    return v_3d_entropy_execute(params, execution)
+
+
+__all__ = [
+    "V3dEntropyOutputs",
+    "V3dEntropyParameters",
+    "V_3D_ENTROPY_METADATA",
+    "v_3d_entropy",
+    "v_3d_entropy_params",
+]

niwrap_afni/afni/v_3d_errts_cormat.py

@@ -0,0 +1,243 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ERRTS_CORMAT_METADATA = Metadata(
+    id="2f4cd813e00c21c8ed95885addacf3502e722a23.boutiques",
+    name="3dErrtsCormat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dErrtsCormatParameters = typing.TypedDict('V3dErrtsCormatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dErrtsCormat"],
+    "dset": InputPathType,
+    "concat": typing.NotRequired[str | None],
+    "input": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "maxlag": typing.NotRequired[float | None],
+    "polort": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dErrtsCormat": v_3d_errts_cormat_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 {
+        "3dErrtsCormat": v_3d_errts_cormat_outputs,
+    }.get(t)
+
+
+class V3dErrtsCormatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_errts_cormat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """1D file of the Toeplitz entries."""
+
+
+def v_3d_errts_cormat_params(
+    dset: InputPathType,
+    concat: str | None = None,
+    input_: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    maxlag: float | None = None,
+    polort: float | None = None,
+) -> V3dErrtsCormatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Dataset to read, usually the '-errts' output from 3dDeconvolve.
+        concat: As used in 3dDeconvolve.
+        input_: Alternate way of specifying the dataset to read.
+        mask: Mask dataset to apply.
+        maxlag: Set maximum lag.
+        polort: Set polort level. Default is 0.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dErrtsCormat",
+        "dset": dset,
+    }
+    if concat is not None:
+        params["concat"] = concat
+    if input_ is not None:
+        params["input"] = input_
+    if mask is not None:
+        params["mask"] = mask
+    if maxlag is not None:
+        params["maxlag"] = maxlag
+    if polort is not None:
+        params["polort"] = polort
+    return params
+
+
+def v_3d_errts_cormat_cargs(
+    params: V3dErrtsCormatParameters,
+    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("3dErrtsCormat")
+    cargs.append(execution.input_file(params.get("dset")))
+    if params.get("concat") is not None:
+        cargs.extend([
+            "-concat",
+            params.get("concat")
+        ])
+    if params.get("input") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("maxlag") is not None:
+        cargs.extend([
+            "-maxlag",
+            str(params.get("maxlag"))
+        ])
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    return cargs
+
+
+def v_3d_errts_cormat_outputs(
+    params: V3dErrtsCormatParameters,
+    execution: Execution,
+) -> V3dErrtsCormatOutputs:
+    """
+    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 = V3dErrtsCormatOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_3d_errts_cormat_execute(
+    params: V3dErrtsCormatParameters,
+    execution: Execution,
+) -> V3dErrtsCormatOutputs:
+    """
+    Computes the correlation matrix corresponding to the residual (or error) time
+    series in 'dset'.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dErrtsCormatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_errts_cormat_cargs(params, execution)
+    ret = v_3d_errts_cormat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_errts_cormat(
+    dset: InputPathType,
+    concat: str | None = None,
+    input_: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    maxlag: float | None = None,
+    polort: float | None = None,
+    runner: Runner | None = None,
+) -> V3dErrtsCormatOutputs:
+    """
+    Computes the correlation matrix corresponding to the residual (or error) time
+    series in 'dset'.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Dataset to read, usually the '-errts' output from 3dDeconvolve.
+        concat: As used in 3dDeconvolve.
+        input_: Alternate way of specifying the dataset to read.
+        mask: Mask dataset to apply.
+        maxlag: Set maximum lag.
+        polort: Set polort level. Default is 0.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dErrtsCormatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ERRTS_CORMAT_METADATA)
+    params = v_3d_errts_cormat_params(
+        dset=dset,
+        concat=concat,
+        input_=input_,
+        mask=mask,
+        maxlag=maxlag,
+        polort=polort,
+    )
+    return v_3d_errts_cormat_execute(params, execution)
+
+
+__all__ = [
+    "V3dErrtsCormatOutputs",
+    "V3dErrtsCormatParameters",
+    "V_3D_ERRTS_CORMAT_METADATA",
+    "v_3d_errts_cormat",
+    "v_3d_errts_cormat_params",
+]

niwrap_afni/afni/v_3d_exchange.py

@@ -0,0 +1,226 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_EXCHANGE_METADATA = Metadata(
+    id="5e04c8d2b1860f0ec51964e8b982b73eaddf8469.boutiques",
+    name="3dExchange",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dExchangeParameters = typing.TypedDict('V3dExchangeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dExchange"],
+    "prefix": str,
+    "infile": InputPathType,
+    "mapfile": InputPathType,
+    "version": 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 {
+        "3dExchange": v_3d_exchange_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 {
+        "3dExchange": v_3d_exchange_outputs,
+    }.get(t)
+
+
+class V3dExchangeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_exchange(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head: OutputPathType
+    """Output HEAD file"""
+    output_brik: OutputPathType
+    """Output BRIK file"""
+
+
+def v_3d_exchange_params(
+    prefix: str,
+    infile: InputPathType,
+    mapfile: InputPathType,
+    version: bool = False,
+    help_: bool = False,
+) -> V3dExchangeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output prefix.
+        infile: Input dataset. Acceptable data types are byte, short, and\
+            floats.
+        mapfile: Mapping columns. Input values in the first column, output\
+            values in the second column.
+        version: Print author and version info.
+        help_: Print this help screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dExchange",
+        "prefix": prefix,
+        "infile": infile,
+        "mapfile": mapfile,
+        "version": version,
+        "help": help_,
+    }
+    return params
+
+
+def v_3d_exchange_cargs(
+    params: V3dExchangeParameters,
+    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("3dExchange")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("infile"))
+    ])
+    cargs.extend([
+        "-map",
+        execution.input_file(params.get("mapfile"))
+    ])
+    if params.get("version"):
+        cargs.append("-ver")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v_3d_exchange_outputs(
+    params: V3dExchangeParameters,
+    execution: Execution,
+) -> V3dExchangeOutputs:
+    """
+    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 = V3dExchangeOutputs(
+        root=execution.output_file("."),
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+    )
+    return ret
+
+
+def v_3d_exchange_execute(
+    params: V3dExchangeParameters,
+    execution: Execution,
+) -> V3dExchangeOutputs:
+    """
+    Replaces voxel values using a mapping file with specified columns.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dExchangeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_exchange_cargs(params, execution)
+    ret = v_3d_exchange_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_exchange(
+    prefix: str,
+    infile: InputPathType,
+    mapfile: InputPathType,
+    version: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> V3dExchangeOutputs:
+    """
+    Replaces voxel values using a mapping file with specified columns.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output prefix.
+        infile: Input dataset. Acceptable data types are byte, short, and\
+            floats.
+        mapfile: Mapping columns. Input values in the first column, output\
+            values in the second column.
+        version: Print author and version info.
+        help_: Print this help screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dExchangeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EXCHANGE_METADATA)
+    params = v_3d_exchange_params(
+        prefix=prefix,
+        infile=infile,
+        mapfile=mapfile,
+        version=version,
+        help_=help_,
+    )
+    return v_3d_exchange_execute(params, execution)
+
+
+__all__ = [
+    "V3dExchangeOutputs",
+    "V3dExchangeParameters",
+    "V_3D_EXCHANGE_METADATA",
+    "v_3d_exchange",
+    "v_3d_exchange_params",
+]