niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tnorm.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TNORM_METADATA = Metadata(
+    id="2f017fb0846acaa4d9cf83666f160e4cc99d7998.boutiques",
+    name="3dTnorm",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTnormParameters = typing.TypedDict('V3dTnormParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTnorm"],
+    "prefix": typing.NotRequired[str | None],
+    "norm2": bool,
+    "normR": bool,
+    "norm1": bool,
+    "normx": bool,
+    "polort": typing.NotRequired[float | None],
+    "L1fit": 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 {
+        "3dTnorm": v_3d_tnorm_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 {
+        "3dTnorm": v_3d_tnorm_outputs,
+    }.get(t)
+
+
+class V3dTnormOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tnorm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Normalized output dataset"""
+
+
+def v_3d_tnorm_params(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    norm2: bool = False,
+    norm_r: bool = False,
+    norm1: bool = False,
+    normx: bool = False,
+    polort: float | None = None,
+    l1fit: bool = False,
+) -> V3dTnormParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g. data.nii).
+        prefix: Prefix for the output dataset.
+        norm2: L2 normalize (sum of squares = 1).
+        norm_r: Normalize so sum of squares = number of time points.
+        norm1: L1 normalize (sum of absolute values = 1).
+        normx: Scale so max absolute value = 1 (L_infinity norm).
+        polort: Detrend with polynomials of order p before normalizing.
+        l1fit: Detrend with L1 regression (L2 is default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTnorm",
+        "norm2": norm2,
+        "normR": norm_r,
+        "norm1": norm1,
+        "normx": normx,
+        "L1fit": l1fit,
+        "input_dataset": input_dataset,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if polort is not None:
+        params["polort"] = polort
+    return params
+
+
+def v_3d_tnorm_cargs(
+    params: V3dTnormParameters,
+    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("3dTnorm")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("norm2"):
+        cargs.append("-norm2")
+    if params.get("normR"):
+        cargs.append("-normR")
+    if params.get("norm1"):
+        cargs.append("-norm1")
+    if params.get("normx"):
+        cargs.append("-normx")
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("L1fit"):
+        cargs.append("-L1fit")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    return cargs
+
+
+def v_3d_tnorm_outputs(
+    params: V3dTnormParameters,
+    execution: Execution,
+) -> V3dTnormOutputs:
+    """
+    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 = V3dTnormOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + ".nii") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_tnorm_execute(
+    params: V3dTnormParameters,
+    execution: Execution,
+) -> V3dTnormOutputs:
+    """
+    Normalizes each voxel time series by multiplicative scaling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTnormOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tnorm_cargs(params, execution)
+    ret = v_3d_tnorm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tnorm(
+    input_dataset: InputPathType,
+    prefix: str | None = None,
+    norm2: bool = False,
+    norm_r: bool = False,
+    norm1: bool = False,
+    normx: bool = False,
+    polort: float | None = None,
+    l1fit: bool = False,
+    runner: Runner | None = None,
+) -> V3dTnormOutputs:
+    """
+    Normalizes each voxel time series by multiplicative scaling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g. data.nii).
+        prefix: Prefix for the output dataset.
+        norm2: L2 normalize (sum of squares = 1).
+        norm_r: Normalize so sum of squares = number of time points.
+        norm1: L1 normalize (sum of absolute values = 1).
+        normx: Scale so max absolute value = 1 (L_infinity norm).
+        polort: Detrend with polynomials of order p before normalizing.
+        l1fit: Detrend with L1 regression (L2 is default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTnormOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TNORM_METADATA)
+    params = v_3d_tnorm_params(
+        prefix=prefix,
+        norm2=norm2,
+        norm_r=norm_r,
+        norm1=norm1,
+        normx=normx,
+        polort=polort,
+        l1fit=l1fit,
+        input_dataset=input_dataset,
+    )
+    return v_3d_tnorm_execute(params, execution)
+
+
+__all__ = [
+    "V3dTnormOutputs",
+    "V3dTnormParameters",
+    "V_3D_TNORM_METADATA",
+    "v_3d_tnorm",
+    "v_3d_tnorm_params",
+]

niwrap_afni/afni/v_3d_tortoiseto_here.py

@@ -0,0 +1,239 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TORTOISETO_HERE_METADATA = Metadata(
+    id="daf64b9d38f580b031c7bf8ec8344f0a10916677.boutiques",
+    name="3dTORTOISEtoHere",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTortoisetoHereParameters = typing.TypedDict('V3dTortoisetoHereParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTORTOISEtoHere"],
+    "dt_tort": InputPathType,
+    "prefix": str,
+    "scale_factor": typing.NotRequired[float | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTORTOISEtoHere": v_3d_tortoiseto_here_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 {
+        "3dTORTOISEtoHere": v_3d_tortoiseto_here_outputs,
+    }.get(t)
+
+
+class V3dTortoisetoHereOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tortoiseto_here(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dt_file: OutputPathType
+    """Output AFNI-style DT file with the following ordering of the 6 bricks:
+    Dxx, Dxy, Dyy, Dxz, Dyz, Dzz."""
+
+
+def v_3d_tortoiseto_here_params(
+    dt_tort: InputPathType,
+    prefix: str,
+    scale_factor: float | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+) -> V3dTortoisetoHereParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dt_tort: Diffusion tensor file with six bricks of DT components ordered\
+            in the TORTOISE manner (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
+        prefix: Output file name prefix. Will have N+1 bricks when GRADFILE has\
+            N rows of gradients.
+        scale_factor: Optional switch to rescale the DT elements, dividing by a\
+            number X>0.
+        flip_x: Change sign of the first element of (inner) eigenvectors.
+        flip_y: Change sign of the second element of (inner) eigenvectors.
+        flip_z: Change sign of the third element of (inner) eigenvectors.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTORTOISEtoHere",
+        "dt_tort": dt_tort,
+        "prefix": prefix,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
+        "flip_z": flip_z,
+    }
+    if scale_factor is not None:
+        params["scale_factor"] = scale_factor
+    return params
+
+
+def v_3d_tortoiseto_here_cargs(
+    params: V3dTortoisetoHereParameters,
+    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("3dTORTOISEtoHere")
+    cargs.extend([
+        "-dt_tort",
+        execution.input_file(params.get("dt_tort"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("scale_factor") is not None:
+        cargs.extend([
+            "-scale_fac",
+            str(params.get("scale_factor"))
+        ])
+    if params.get("flip_x"):
+        cargs.append("-flip_x")
+    if params.get("flip_y"):
+        cargs.append("-flip_y")
+    if params.get("flip_z"):
+        cargs.append("-flip_z")
+    return cargs
+
+
+def v_3d_tortoiseto_here_outputs(
+    params: V3dTortoisetoHereParameters,
+    execution: Execution,
+) -> V3dTortoisetoHereOutputs:
+    """
+    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 = V3dTortoisetoHereOutputs(
+        root=execution.output_file("."),
+        output_dt_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v_3d_tortoiseto_here_execute(
+    params: V3dTortoisetoHereParameters,
+    execution: Execution,
+) -> V3dTortoisetoHereOutputs:
+    """
+    Convert standard TORTOISE DTs (diagonal-first format) to standard AFNI (lower
+    triangular, row-wise) format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTortoisetoHereOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tortoiseto_here_cargs(params, execution)
+    ret = v_3d_tortoiseto_here_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tortoiseto_here(
+    dt_tort: InputPathType,
+    prefix: str,
+    scale_factor: float | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    runner: Runner | None = None,
+) -> V3dTortoisetoHereOutputs:
+    """
+    Convert standard TORTOISE DTs (diagonal-first format) to standard AFNI (lower
+    triangular, row-wise) format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dt_tort: Diffusion tensor file with six bricks of DT components ordered\
+            in the TORTOISE manner (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
+        prefix: Output file name prefix. Will have N+1 bricks when GRADFILE has\
+            N rows of gradients.
+        scale_factor: Optional switch to rescale the DT elements, dividing by a\
+            number X>0.
+        flip_x: Change sign of the first element of (inner) eigenvectors.
+        flip_y: Change sign of the second element of (inner) eigenvectors.
+        flip_z: Change sign of the third element of (inner) eigenvectors.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTortoisetoHereOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TORTOISETO_HERE_METADATA)
+    params = v_3d_tortoiseto_here_params(
+        dt_tort=dt_tort,
+        prefix=prefix,
+        scale_factor=scale_factor,
+        flip_x=flip_x,
+        flip_y=flip_y,
+        flip_z=flip_z,
+    )
+    return v_3d_tortoiseto_here_execute(params, execution)
+
+
+__all__ = [
+    "V3dTortoisetoHereOutputs",
+    "V3dTortoisetoHereParameters",
+    "V_3D_TORTOISETO_HERE_METADATA",
+    "v_3d_tortoiseto_here",
+    "v_3d_tortoiseto_here_params",
+]