niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_dtto_noisy_dwi.py

@@ -0,0 +1,275 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DTTO_NOISY_DWI_METADATA = Metadata(
+    id="0ef5fe03a8b952b27e737adb59a395ac94790601.boutiques",
+    name="3dDTtoNoisyDWI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDttoNoisyDwiParameters = typing.TypedDict('V3dDttoNoisyDwiParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDTtoNoisyDWI"],
+    "dt_file": InputPathType,
+    "grad_file": InputPathType,
+    "noise_dwi": float,
+    "noise_b0": typing.NotRequired[float | None],
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "bval": typing.NotRequired[float | None],
+    "s0": 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 {
+        "3dDTtoNoisyDWI": v_3d_dtto_noisy_dwi_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 {
+        "3dDTtoNoisyDWI": v_3d_dtto_noisy_dwi_outputs,
+    }.get(t)
+
+
+class V3dDttoNoisyDwiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_dtto_noisy_dwi(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dwi: OutputPathType
+    """Synthetic set of DWI measures with noise. Contains N+1 bricks mimicking
+    B0+DWI data."""
+
+
+def v_3d_dtto_noisy_dwi_params(
+    dt_file: InputPathType,
+    grad_file: InputPathType,
+    noise_dwi: float,
+    prefix: str,
+    noise_b0: float | None = None,
+    mask: InputPathType | None = None,
+    bval: float | None = None,
+    s0: float | None = None,
+) -> V3dDttoNoisyDwiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dt_file: Diffusion tensor file with six bricks of DT components ordered\
+            in the AFNI manner: Dxx,Dxy,Dyy,Dxz,Dyz,Dzz.
+        grad_file: Text file of gradients arranged in three columns. There\
+            should be no row of all zeros representing the b=0 line.
+        noise_dwi: Fractional value of noise in DWIs. FF = sigma/S0 = 1/SNR0.\
+            For example, FF=0.05 corresponds to SNR0=20.
+        prefix: Output file name prefix. Will have N+1 bricks when GRADFILE has\
+            N rows of gradients.
+        noise_b0: Optional fraction of Rician noise in the b=0 reference image.\
+            If not provided, FF2=FF.
+        mask: Optional mask within which to calculate uncertainty. Data should\
+            be masked already otherwise.
+        bval: Optional DW factor to use if DT values are scaled to something\
+            physical. Default is BB=1.
+        s0: Optional reference b=0 signal strength. Default value is SS=1000.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDTtoNoisyDWI",
+        "dt_file": dt_file,
+        "grad_file": grad_file,
+        "noise_dwi": noise_dwi,
+        "prefix": prefix,
+    }
+    if noise_b0 is not None:
+        params["noise_b0"] = noise_b0
+    if mask is not None:
+        params["mask"] = mask
+    if bval is not None:
+        params["bval"] = bval
+    if s0 is not None:
+        params["s0"] = s0
+    return params
+
+
+def v_3d_dtto_noisy_dwi_cargs(
+    params: V3dDttoNoisyDwiParameters,
+    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("3dDTtoNoisyDWI")
+    cargs.append(execution.input_file(params.get("dt_file")))
+    cargs.append(execution.input_file(params.get("grad_file")))
+    cargs.extend([
+        "-noise_DWI",
+        str(params.get("noise_dwi"))
+    ])
+    if params.get("noise_b0") is not None:
+        cargs.extend([
+            "-noise_B0",
+            str(params.get("noise_b0"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("bval") is not None:
+        cargs.extend([
+            "-bval",
+            str(params.get("bval"))
+        ])
+    if params.get("s0") is not None:
+        cargs.extend([
+            "-S0",
+            str(params.get("s0"))
+        ])
+    return cargs
+
+
+def v_3d_dtto_noisy_dwi_outputs(
+    params: V3dDttoNoisyDwiParameters,
+    execution: Execution,
+) -> V3dDttoNoisyDwiOutputs:
+    """
+    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 = V3dDttoNoisyDwiOutputs(
+        root=execution.output_file("."),
+        output_dwi=execution.output_file(params.get("prefix") + "+orig"),
+    )
+    return ret
+
+
+def v_3d_dtto_noisy_dwi_execute(
+    params: V3dDttoNoisyDwiParameters,
+    execution: Execution,
+) -> V3dDttoNoisyDwiOutputs:
+    """
+    Generate a synthetic set of DWI measures with a given SNR from an AFNI-style DT
+    file and a set of gradients. This can be useful for simulations and testing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDttoNoisyDwiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_dtto_noisy_dwi_cargs(params, execution)
+    ret = v_3d_dtto_noisy_dwi_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_dtto_noisy_dwi(
+    dt_file: InputPathType,
+    grad_file: InputPathType,
+    noise_dwi: float,
+    prefix: str,
+    noise_b0: float | None = None,
+    mask: InputPathType | None = None,
+    bval: float | None = None,
+    s0: float | None = None,
+    runner: Runner | None = None,
+) -> V3dDttoNoisyDwiOutputs:
+    """
+    Generate a synthetic set of DWI measures with a given SNR from an AFNI-style DT
+    file and a set of gradients. This can be useful for simulations and testing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dt_file: Diffusion tensor file with six bricks of DT components ordered\
+            in the AFNI manner: Dxx,Dxy,Dyy,Dxz,Dyz,Dzz.
+        grad_file: Text file of gradients arranged in three columns. There\
+            should be no row of all zeros representing the b=0 line.
+        noise_dwi: Fractional value of noise in DWIs. FF = sigma/S0 = 1/SNR0.\
+            For example, FF=0.05 corresponds to SNR0=20.
+        prefix: Output file name prefix. Will have N+1 bricks when GRADFILE has\
+            N rows of gradients.
+        noise_b0: Optional fraction of Rician noise in the b=0 reference image.\
+            If not provided, FF2=FF.
+        mask: Optional mask within which to calculate uncertainty. Data should\
+            be masked already otherwise.
+        bval: Optional DW factor to use if DT values are scaled to something\
+            physical. Default is BB=1.
+        s0: Optional reference b=0 signal strength. Default value is SS=1000.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDttoNoisyDwiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DTTO_NOISY_DWI_METADATA)
+    params = v_3d_dtto_noisy_dwi_params(
+        dt_file=dt_file,
+        grad_file=grad_file,
+        noise_dwi=noise_dwi,
+        noise_b0=noise_b0,
+        prefix=prefix,
+        mask=mask,
+        bval=bval,
+        s0=s0,
+    )
+    return v_3d_dtto_noisy_dwi_execute(params, execution)
+
+
+__all__ = [
+    "V3dDttoNoisyDwiOutputs",
+    "V3dDttoNoisyDwiParameters",
+    "V_3D_DTTO_NOISY_DWI_METADATA",
+    "v_3d_dtto_noisy_dwi",
+    "v_3d_dtto_noisy_dwi_params",
+]

niwrap_afni/afni/v_3d_dwito_dt.py

@@ -0,0 +1,191 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DWITO_DT_METADATA = Metadata(
+    id="edef0edb2012159a76d51a09912a5bd6c5660ab2.boutiques",
+    name="3dDWItoDT",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDwitoDtParameters = typing.TypedDict('V3dDwitoDtParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDWItoDT"],
+    "gradient_file": InputPathType,
+    "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 {
+        "3dDWItoDT": v_3d_dwito_dt_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 {
+        "3dDWItoDT": v_3d_dwito_dt_outputs,
+    }.get(t)
+
+
+class V3dDwitoDtOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_dwito_dt(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Output dataset"""
+
+
+def v_3d_dwito_dt_params(
+    gradient_file: InputPathType,
+    dataset: InputPathType,
+) -> V3dDwitoDtParameters:
+    """
+    Build parameters.
+    
+    Args:
+        gradient_file: A 1D file of the gradient vectors with lines of ASCII\
+            floats (Gxi, Gyi, Gzi) or a 1D file of b-matrix elements.
+        dataset: A 3D bucket dataset with Np+1 sub-briks where the first\
+            sub-brik is the volume acquired with no diffusion weighting.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDWItoDT",
+        "gradient_file": gradient_file,
+        "dataset": dataset,
+    }
+    return params
+
+
+def v_3d_dwito_dt_cargs(
+    params: V3dDwitoDtParameters,
+    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("3dDWItoDT")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("gradient_file")))
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_dwito_dt_outputs(
+    params: V3dDwitoDtParameters,
+    execution: Execution,
+) -> V3dDwitoDtOutputs:
+    """
+    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 = V3dDwitoDtOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file("<PREFIX>.*"),
+    )
+    return ret
+
+
+def v_3d_dwito_dt_execute(
+    params: V3dDwitoDtParameters,
+    execution: Execution,
+) -> V3dDwitoDtOutputs:
+    """
+    Computes 6 principal direction tensors from multiple gradient vectors and
+    corresponding DTI image volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDwitoDtOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_dwito_dt_cargs(params, execution)
+    ret = v_3d_dwito_dt_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_dwito_dt(
+    gradient_file: InputPathType,
+    dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dDwitoDtOutputs:
+    """
+    Computes 6 principal direction tensors from multiple gradient vectors and
+    corresponding DTI image volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        gradient_file: A 1D file of the gradient vectors with lines of ASCII\
+            floats (Gxi, Gyi, Gzi) or a 1D file of b-matrix elements.
+        dataset: A 3D bucket dataset with Np+1 sub-briks where the first\
+            sub-brik is the volume acquired with no diffusion weighting.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDwitoDtOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DWITO_DT_METADATA)
+    params = v_3d_dwito_dt_params(
+        gradient_file=gradient_file,
+        dataset=dataset,
+    )
+    return v_3d_dwito_dt_execute(params, execution)
+
+
+__all__ = [
+    "V3dDwitoDtOutputs",
+    "V3dDwitoDtParameters",
+    "V_3D_DWITO_DT_METADATA",
+    "v_3d_dwito_dt",
+    "v_3d_dwito_dt_params",
+]