niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_diff.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 *
+
+V_3D_DIFF_METADATA = Metadata(
+    id="310e8ce2db4e828d08b7d1bb6c0af6eff1fa85cd.boutiques",
+    name="3dDiff",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDiffParameters = typing.TypedDict('V3dDiffParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDiff"],
+    "dataset_a": InputPathType,
+    "dataset_b": InputPathType,
+    "tolerance": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "quiet_mode": bool,
+    "tabular_mode": bool,
+    "brutalist_mode": bool,
+    "long_report_mode": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dDiff": v_3d_diff_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 {
+        "3dDiff": v_3d_diff_outputs,
+    }.get(t)
+
+
+class V3dDiffOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_diff(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_log: OutputPathType
+    """Log file containing the element-wise differences."""
+
+
+def v_3d_diff_params(
+    dataset_a: InputPathType,
+    dataset_b: InputPathType,
+    tolerance: float | None = None,
+    mask: InputPathType | None = None,
+    quiet_mode: bool = False,
+    tabular_mode: bool = False,
+    brutalist_mode: bool = False,
+    long_report_mode: bool = False,
+) -> V3dDiffParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset_a: First input dataset for comparison.
+        dataset_b: Second input dataset for comparison.
+        tolerance: Floating-point tolerance/epsilon for the comparison.
+        mask: Mask to use when comparing the datasets.
+        quiet_mode: Quiet mode: 0 for no differences, 1 for differences, -1 for\
+            error.
+        tabular_mode: Display a table of differences, mainly for 4D data.
+        brutalist_mode: Display one-liner with summary of differences.
+        long_report_mode: Print a detailed report with more information.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDiff",
+        "dataset_a": dataset_a,
+        "dataset_b": dataset_b,
+        "quiet_mode": quiet_mode,
+        "tabular_mode": tabular_mode,
+        "brutalist_mode": brutalist_mode,
+        "long_report_mode": long_report_mode,
+    }
+    if tolerance is not None:
+        params["tolerance"] = tolerance
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_diff_cargs(
+    params: V3dDiffParameters,
+    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("3dDiff")
+    cargs.extend([
+        "-a",
+        execution.input_file(params.get("dataset_a"))
+    ])
+    cargs.extend([
+        "-b",
+        execution.input_file(params.get("dataset_b"))
+    ])
+    if params.get("tolerance") is not None:
+        cargs.extend([
+            "-tol",
+            str(params.get("tolerance"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("quiet_mode"):
+        cargs.append("-q")
+    if params.get("tabular_mode"):
+        cargs.append("-tabular")
+    if params.get("brutalist_mode"):
+        cargs.append("-brutalist")
+    if params.get("long_report_mode"):
+        cargs.append("-long_report")
+    return cargs
+
+
+def v_3d_diff_outputs(
+    params: V3dDiffParameters,
+    execution: Execution,
+) -> V3dDiffOutputs:
+    """
+    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 = V3dDiffOutputs(
+        root=execution.output_file("."),
+        output_log=execution.output_file(pathlib.Path(params.get("dataset_a")).name + "_vs_" + pathlib.Path(params.get("dataset_b")).name + ".log"),
+    )
+    return ret
+
+
+def v_3d_diff_execute(
+    params: V3dDiffParameters,
+    execution: Execution,
+) -> V3dDiffOutputs:
+    """
+    A program to examine element-wise differences between two images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDiffOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_diff_cargs(params, execution)
+    ret = v_3d_diff_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_diff(
+    dataset_a: InputPathType,
+    dataset_b: InputPathType,
+    tolerance: float | None = None,
+    mask: InputPathType | None = None,
+    quiet_mode: bool = False,
+    tabular_mode: bool = False,
+    brutalist_mode: bool = False,
+    long_report_mode: bool = False,
+    runner: Runner | None = None,
+) -> V3dDiffOutputs:
+    """
+    A program to examine element-wise differences between two images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset_a: First input dataset for comparison.
+        dataset_b: Second input dataset for comparison.
+        tolerance: Floating-point tolerance/epsilon for the comparison.
+        mask: Mask to use when comparing the datasets.
+        quiet_mode: Quiet mode: 0 for no differences, 1 for differences, -1 for\
+            error.
+        tabular_mode: Display a table of differences, mainly for 4D data.
+        brutalist_mode: Display one-liner with summary of differences.
+        long_report_mode: Print a detailed report with more information.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDiffOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DIFF_METADATA)
+    params = v_3d_diff_params(
+        dataset_a=dataset_a,
+        dataset_b=dataset_b,
+        tolerance=tolerance,
+        mask=mask,
+        quiet_mode=quiet_mode,
+        tabular_mode=tabular_mode,
+        brutalist_mode=brutalist_mode,
+        long_report_mode=long_report_mode,
+    )
+    return v_3d_diff_execute(params, execution)
+
+
+__all__ = [
+    "V3dDiffOutputs",
+    "V3dDiffParameters",
+    "V_3D_DIFF_METADATA",
+    "v_3d_diff",
+    "v_3d_diff_params",
+]

niwrap_afni/afni/v_3d_dteig.py

@@ -0,0 +1,236 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DTEIG_METADATA = Metadata(
+    id="5c446bf21775547faf60f0fa1576969e859e8381.boutiques",
+    name="3dDTeig",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDteigParameters = typing.TypedDict('V3dDteigParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDTeig"],
+    "input_dataset": str,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
+    "sep_dsets": bool,
+    "uddata": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dDTeig": v_3d_dteig_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 {
+        "3dDTeig": v_3d_dteig_outputs,
+    }.get(t)
+
+
+class V3dDteigOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_dteig(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Output dataset with computed eigenvalues, eigenvectors, FA, and MD"""
+    output_lambda: OutputPathType | None
+    """Output dataset for eigenvalues"""
+    output_eigvec: OutputPathType | None
+    """Output dataset for eigenvectors"""
+    output_fa: OutputPathType | None
+    """Output dataset for fractional anisotropy"""
+    output_md: OutputPathType | None
+    """Output dataset for mean diffusivity"""
+
+
+def v_3d_dteig_params(
+    input_dataset: str,
+    prefix: str | None = None,
+    datum: typing.Literal["byte", "short", "float"] | None = None,
+    sep_dsets: bool = False,
+    uddata: bool = False,
+) -> V3dDteigParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset of Dxx, Dxy, Dyy, Dxz, Dyz, Dzz sub-bricks.
+        prefix: Use the given prefix for the output dataset.
+        datum: Coerce the output data to be stored as the given type (byte,\
+            short, or float).
+        sep_dsets: Save eigenvalues, vectors, FA, and MD in separate datasets.
+        uddata: Tensor data is stored as upper diagonal instead of lower\
+            diagonal.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDTeig",
+        "input_dataset": input_dataset,
+        "sep_dsets": sep_dsets,
+        "uddata": uddata,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum is not None:
+        params["datum"] = datum
+    return params
+
+
+def v_3d_dteig_cargs(
+    params: V3dDteigParameters,
+    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("3dDTeig")
+    cargs.append(params.get("input_dataset"))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("sep_dsets"):
+        cargs.append("-sep_dsets")
+    if params.get("uddata"):
+        cargs.append("-uddata")
+    return cargs
+
+
+def v_3d_dteig_outputs(
+    params: V3dDteigParameters,
+    execution: Execution,
+) -> V3dDteigOutputs:
+    """
+    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 = V3dDteigOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_lambda=execution.output_file(params.get("prefix") + "_lambda.nii.gz") if (params.get("prefix") is not None) else None,
+        output_eigvec=execution.output_file(params.get("prefix") + "_eigvec.nii.gz") if (params.get("prefix") is not None) else None,
+        output_fa=execution.output_file(params.get("prefix") + "_FA.nii.gz") if (params.get("prefix") is not None) else None,
+        output_md=execution.output_file(params.get("prefix") + "_MD.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_dteig_execute(
+    params: V3dDteigParameters,
+    execution: Execution,
+) -> V3dDteigOutputs:
+    """
+    Computes eigenvalues and eigenvectors for an input dataset of tensors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDteigOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_dteig_cargs(params, execution)
+    ret = v_3d_dteig_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_dteig(
+    input_dataset: str,
+    prefix: str | None = None,
+    datum: typing.Literal["byte", "short", "float"] | None = None,
+    sep_dsets: bool = False,
+    uddata: bool = False,
+    runner: Runner | None = None,
+) -> V3dDteigOutputs:
+    """
+    Computes eigenvalues and eigenvectors for an input dataset of tensors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset of Dxx, Dxy, Dyy, Dxz, Dyz, Dzz sub-bricks.
+        prefix: Use the given prefix for the output dataset.
+        datum: Coerce the output data to be stored as the given type (byte,\
+            short, or float).
+        sep_dsets: Save eigenvalues, vectors, FA, and MD in separate datasets.
+        uddata: Tensor data is stored as upper diagonal instead of lower\
+            diagonal.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDteigOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DTEIG_METADATA)
+    params = v_3d_dteig_params(
+        input_dataset=input_dataset,
+        prefix=prefix,
+        datum=datum,
+        sep_dsets=sep_dsets,
+        uddata=uddata,
+    )
+    return v_3d_dteig_execute(params, execution)
+
+
+__all__ = [
+    "V3dDteigOutputs",
+    "V3dDteigParameters",
+    "V_3D_DTEIG_METADATA",
+    "v_3d_dteig",
+    "v_3d_dteig_params",
+]

niwrap_afni/afni/v_3d_dtto_dwi.py

@@ -0,0 +1,199 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DTTO_DWI_METADATA = Metadata(
+    id="0f0fbb0dc2b7d522416ef673b66be8d6a5895cef.boutiques",
+    name="3dDTtoDWI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDttoDwiParameters = typing.TypedDict('V3dDttoDwiParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDTtoDWI"],
+    "gradient_file": InputPathType,
+    "i0_dataset": InputPathType,
+    "dt_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 {
+        "3dDTtoDWI": v_3d_dtto_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 {
+        "3dDTtoDWI": v_3d_dtto_dwi_outputs,
+    }.get(t)
+
+
+class V3dDttoDwiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_dtto_dwi(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dwi: OutputPathType
+    """Computed DWI images including sub-brick for each gradient vector."""
+
+
+def v_3d_dtto_dwi_params(
+    gradient_file: InputPathType,
+    i0_dataset: InputPathType,
+    dt_dataset: InputPathType,
+) -> V3dDttoDwiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        gradient_file: 1D file containing the gradient vectors (ASCII floats)\
+            for non-zero gradients.
+        i0_dataset: Volume without any gradient applied.
+        dt_dataset: 6-sub-brick dataset containing the diffusion tensor data\
+            (Dxx, Dxy, Dyy, Dxz, Dyz, Dzz).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDTtoDWI",
+        "gradient_file": gradient_file,
+        "i0_dataset": i0_dataset,
+        "dt_dataset": dt_dataset,
+    }
+    return params
+
+
+def v_3d_dtto_dwi_cargs(
+    params: V3dDttoDwiParameters,
+    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("3dDTtoDWI")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("gradient_file")))
+    cargs.append(execution.input_file(params.get("i0_dataset")))
+    cargs.append(execution.input_file(params.get("dt_dataset")))
+    return cargs
+
+
+def v_3d_dtto_dwi_outputs(
+    params: V3dDttoDwiParameters,
+    execution: Execution,
+) -> V3dDttoDwiOutputs:
+    """
+    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 = V3dDttoDwiOutputs(
+        root=execution.output_file("."),
+        output_dwi=execution.output_file("[PREFIX]*.HEAD"),
+    )
+    return ret
+
+
+def v_3d_dtto_dwi_execute(
+    params: V3dDttoDwiParameters,
+    execution: Execution,
+) -> V3dDttoDwiOutputs:
+    """
+    Tool to compute multiple gradient images from tensors and gradient vector
+    coordinates applied to the I0-dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDttoDwiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_dtto_dwi_cargs(params, execution)
+    ret = v_3d_dtto_dwi_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_dtto_dwi(
+    gradient_file: InputPathType,
+    i0_dataset: InputPathType,
+    dt_dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dDttoDwiOutputs:
+    """
+    Tool to compute multiple gradient images from tensors and gradient vector
+    coordinates applied to the I0-dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        gradient_file: 1D file containing the gradient vectors (ASCII floats)\
+            for non-zero gradients.
+        i0_dataset: Volume without any gradient applied.
+        dt_dataset: 6-sub-brick dataset containing the diffusion tensor data\
+            (Dxx, Dxy, Dyy, Dxz, Dyz, Dzz).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDttoDwiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DTTO_DWI_METADATA)
+    params = v_3d_dtto_dwi_params(
+        gradient_file=gradient_file,
+        i0_dataset=i0_dataset,
+        dt_dataset=dt_dataset,
+    )
+    return v_3d_dtto_dwi_execute(params, execution)
+
+
+__all__ = [
+    "V3dDttoDwiOutputs",
+    "V3dDttoDwiParameters",
+    "V_3D_DTTO_DWI_METADATA",
+    "v_3d_dtto_dwi",
+    "v_3d_dtto_dwi_params",
+]