niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_edu_01_scale.py

@@ -0,0 +1,216 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_EDU_01_SCALE_METADATA = Metadata(
+    id="421ae3b97be6019b8194c6bf2db5b0b7024dbd25.boutiques",
+    name="3dEdu_01_scale",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dEdu01ScaleParameters = typing.TypedDict('V3dEdu01ScaleParameters', {
+    "__STYX_TYPE__": typing.Literal["3dEdu_01_scale"],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mult_factors": typing.NotRequired[list[float] | None],
+    "option_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dEdu_01_scale": v_3d_edu_01_scale_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 {
+        "3dEdu_01_scale": v_3d_edu_01_scale_outputs,
+    }.get(t)
+
+
+class V3dEdu01ScaleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_edu_01_scale(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output scaled and/or masked copy of the [0]th volume of the input
+    dataset"""
+
+
+def v_3d_edu_01_scale_params(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    mult_factors: list[float] | None = None,
+    option_flag: bool = False,
+) -> V3dEdu01ScaleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input dataset.
+        mask: Mask dataset on same grid/data structure as the input dataset.
+        mult_factors: Numerical factors for multiplying each voxel; each voxel\
+            is multiplied by both A and B.
+        option_flag: Option flag to do something.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dEdu_01_scale",
+        "input": input_,
+        "option_flag": option_flag,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if mult_factors is not None:
+        params["mult_factors"] = mult_factors
+    return params
+
+
+def v_3d_edu_01_scale_cargs(
+    params: V3dEdu01ScaleParameters,
+    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("3dEdu_01_scale")
+    cargs.append(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("mult_factors") is not None:
+        cargs.extend([
+            "-mult_facs",
+            *map(str, params.get("mult_factors"))
+        ])
+    if params.get("option_flag"):
+        cargs.append("-some_opt")
+    return cargs
+
+
+def v_3d_edu_01_scale_outputs(
+    params: V3dEdu01ScaleParameters,
+    execution: Execution,
+) -> V3dEdu01ScaleOutputs:
+    """
+    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 = V3dEdu01ScaleOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("OUT_edu_[1-9]*"),
+    )
+    return ret
+
+
+def v_3d_edu_01_scale_execute(
+    params: V3dEdu01ScaleParameters,
+    execution: Execution,
+) -> V3dEdu01ScaleOutputs:
+    """
+    Educational program to create a new AFNI program. Scales and masks dataset
+    volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dEdu01ScaleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_edu_01_scale_cargs(params, execution)
+    ret = v_3d_edu_01_scale_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_edu_01_scale(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    mult_factors: list[float] | None = None,
+    option_flag: bool = False,
+    runner: Runner | None = None,
+) -> V3dEdu01ScaleOutputs:
+    """
+    Educational program to create a new AFNI program. Scales and masks dataset
+    volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input dataset.
+        mask: Mask dataset on same grid/data structure as the input dataset.
+        mult_factors: Numerical factors for multiplying each voxel; each voxel\
+            is multiplied by both A and B.
+        option_flag: Option flag to do something.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dEdu01ScaleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EDU_01_SCALE_METADATA)
+    params = v_3d_edu_01_scale_params(
+        input_=input_,
+        mask=mask,
+        mult_factors=mult_factors,
+        option_flag=option_flag,
+    )
+    return v_3d_edu_01_scale_execute(params, execution)
+
+
+__all__ = [
+    "V3dEdu01ScaleOutputs",
+    "V3dEdu01ScaleParameters",
+    "V_3D_EDU_01_SCALE_METADATA",
+    "v_3d_edu_01_scale",
+    "v_3d_edu_01_scale_params",
+]

niwrap_afni/afni/v_3d_eigs_to_dt.py

@@ -0,0 +1,271 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_EIGS_TO_DT_METADATA = Metadata(
+    id="28fad7eb2ac634dd2431ef9451ad93178516ba6f.boutiques",
+    name="3dEigsToDT",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dEigsToDtParameters = typing.TypedDict('V3dEigsToDtParameters', {
+    "__STYX_TYPE__": typing.Literal["3dEigsToDT"],
+    "eig_vals": str,
+    "eig_vecs": str,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "scale_eigs": 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 {
+        "3dEigsToDT": v_3d_eigs_to_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 {
+        "3dEigsToDT": v_3d_eigs_to_dt_outputs,
+    }.get(t)
+
+
+class V3dEigsToDtOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_eigs_to_dt(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    dt_brik_output: OutputPathType
+    """Output diffusion tensor (DT) file in AFNI format (BRIK)"""
+    dt_head_output: OutputPathType
+    """Output diffusion tensor (DT) file in AFNI format (HEAD)"""
+
+
+def v_3d_eigs_to_dt_params(
+    eig_vals: str,
+    eig_vecs: str,
+    prefix: str,
+    mask: InputPathType | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    scale_eigs: float | None = None,
+) -> V3dEigsToDtParameters:
+    """
+    Build parameters.
+    
+    Args:
+        eig_vals: Searchable descriptor for finding all three required\
+            eigenvalue files. It should list all three eigenvalue files in\
+            descending order of magnitude.
+        eig_vecs: Searchable descriptor for finding all three required\
+            eigenvector files. It should list all three eigenvector files in order\
+            matching the eigenvalue files.
+        prefix: Prefix for the output file name. It is recommended to include a\
+            'DT' label in it.
+        mask: Optional mask within which to calculate uncertainty. If not\
+            provided, the data should be masked already.
+        flip_x: Change sign of the first element of eigenvectors.
+        flip_y: Change sign of the second element of eigenvectors.
+        flip_z: Change sign of the third element of eigenvectors.
+        scale_eigs: Rescale the eigenvalues by dividing by a number X > 0.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dEigsToDT",
+        "eig_vals": eig_vals,
+        "eig_vecs": eig_vecs,
+        "prefix": prefix,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
+        "flip_z": flip_z,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if scale_eigs is not None:
+        params["scale_eigs"] = scale_eigs
+    return params
+
+
+def v_3d_eigs_to_dt_cargs(
+    params: V3dEigsToDtParameters,
+    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("3dEigsToDT")
+    cargs.extend([
+        "-eig_vals",
+        params.get("eig_vals")
+    ])
+    cargs.extend([
+        "-eig_vecs",
+        params.get("eig_vecs")
+    ])
+    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("flip_x"):
+        cargs.append("-flip_x")
+    if params.get("flip_y"):
+        cargs.append("-flip_y")
+    if params.get("flip_z"):
+        cargs.append("-flip_z")
+    if params.get("scale_eigs") is not None:
+        cargs.extend([
+            "-scale_eigs",
+            str(params.get("scale_eigs"))
+        ])
+    return cargs
+
+
+def v_3d_eigs_to_dt_outputs(
+    params: V3dEigsToDtParameters,
+    execution: Execution,
+) -> V3dEigsToDtOutputs:
+    """
+    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 = V3dEigsToDtOutputs(
+        root=execution.output_file("."),
+        dt_brik_output=execution.output_file(params.get("prefix") + "_DT+orig.BRIK"),
+        dt_head_output=execution.output_file(params.get("prefix") + "_DT+orig.HEAD"),
+    )
+    return ret
+
+
+def v_3d_eigs_to_dt_execute(
+    params: V3dEigsToDtParameters,
+    execution: Execution,
+) -> V3dEigsToDtOutputs:
+    """
+    Convert set of DTI eigenvectors and eigenvalues to a diffusion tensor, with
+    optional value-scaling and vector-flipping.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dEigsToDtOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_eigs_to_dt_cargs(params, execution)
+    ret = v_3d_eigs_to_dt_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_eigs_to_dt(
+    eig_vals: str,
+    eig_vecs: str,
+    prefix: str,
+    mask: InputPathType | None = None,
+    flip_x: bool = False,
+    flip_y: bool = False,
+    flip_z: bool = False,
+    scale_eigs: float | None = None,
+    runner: Runner | None = None,
+) -> V3dEigsToDtOutputs:
+    """
+    Convert set of DTI eigenvectors and eigenvalues to a diffusion tensor, with
+    optional value-scaling and vector-flipping.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        eig_vals: Searchable descriptor for finding all three required\
+            eigenvalue files. It should list all three eigenvalue files in\
+            descending order of magnitude.
+        eig_vecs: Searchable descriptor for finding all three required\
+            eigenvector files. It should list all three eigenvector files in order\
+            matching the eigenvalue files.
+        prefix: Prefix for the output file name. It is recommended to include a\
+            'DT' label in it.
+        mask: Optional mask within which to calculate uncertainty. If not\
+            provided, the data should be masked already.
+        flip_x: Change sign of the first element of eigenvectors.
+        flip_y: Change sign of the second element of eigenvectors.
+        flip_z: Change sign of the third element of eigenvectors.
+        scale_eigs: Rescale the eigenvalues by dividing by a number X > 0.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dEigsToDtOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EIGS_TO_DT_METADATA)
+    params = v_3d_eigs_to_dt_params(
+        eig_vals=eig_vals,
+        eig_vecs=eig_vecs,
+        prefix=prefix,
+        mask=mask,
+        flip_x=flip_x,
+        flip_y=flip_y,
+        flip_z=flip_z,
+        scale_eigs=scale_eigs,
+    )
+    return v_3d_eigs_to_dt_execute(params, execution)
+
+
+__all__ = [
+    "V3dEigsToDtOutputs",
+    "V3dEigsToDtParameters",
+    "V_3D_EIGS_TO_DT_METADATA",
+    "v_3d_eigs_to_dt",
+    "v_3d_eigs_to_dt_params",
+]

niwrap_afni/afni/v_3d_empty.py

@@ -0,0 +1,224 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_EMPTY_METADATA = Metadata(
+    id="458e0d6419fbf58fb595b4f42ae970422fb2886a.boutiques",
+    name="3dEmpty",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dEmptyParameters = typing.TypedDict('V3dEmptyParameters', {
+    "__STYX_TYPE__": typing.Literal["3dEmpty"],
+    "prefix": typing.NotRequired[str | None],
+    "geometry": typing.NotRequired[str | None],
+    "nxyz": typing.NotRequired[list[float] | None],
+    "nt": 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 {
+        "3dEmpty": v_3d_empty_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 {
+        "3dEmpty": v_3d_empty_outputs,
+    }.get(t)
+
+
+class V3dEmptyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_empty(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """Output empty dataset header file"""
+
+
+def v_3d_empty_params(
+    prefix: str | None = None,
+    geometry: str | None = None,
+    nxyz: list[float] | None = None,
+    nt_: float | None = None,
+) -> V3dEmptyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix name for output file (default = 'Empty').
+        geometry: Set the 3D geometry of the grid using a string of the form\
+            'MATRIX(a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34):nx,ny,nz'.
+        nxyz: Set number of voxels to 'x', 'y', and 'z' along the 3 axes\
+            [defaults=64].
+        nt_: Number of time points [default=1].
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dEmpty",
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if geometry is not None:
+        params["geometry"] = geometry
+    if nxyz is not None:
+        params["nxyz"] = nxyz
+    if nt_ is not None:
+        params["nt"] = nt_
+    return params
+
+
+def v_3d_empty_cargs(
+    params: V3dEmptyParameters,
+    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("3dEmpty")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("geometry") is not None:
+        cargs.extend([
+            "-geometry",
+            params.get("geometry")
+        ])
+    if params.get("nxyz") is not None:
+        cargs.extend([
+            "-nxyz",
+            *map(str, params.get("nxyz"))
+        ])
+    if params.get("nt") is not None:
+        cargs.extend([
+            "-nt",
+            str(params.get("nt"))
+        ])
+    return cargs
+
+
+def v_3d_empty_outputs(
+    params: V3dEmptyParameters,
+    execution: Execution,
+) -> V3dEmptyOutputs:
+    """
+    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 = V3dEmptyOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_empty_execute(
+    params: V3dEmptyParameters,
+    execution: Execution,
+) -> V3dEmptyOutputs:
+    """
+    Tool to create an 'empty' dataset .HEAD file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dEmptyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_empty_cargs(params, execution)
+    ret = v_3d_empty_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_empty(
+    prefix: str | None = None,
+    geometry: str | None = None,
+    nxyz: list[float] | None = None,
+    nt_: float | None = None,
+    runner: Runner | None = None,
+) -> V3dEmptyOutputs:
+    """
+    Tool to create an 'empty' dataset .HEAD file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix name for output file (default = 'Empty').
+        geometry: Set the 3D geometry of the grid using a string of the form\
+            'MATRIX(a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34):nx,ny,nz'.
+        nxyz: Set number of voxels to 'x', 'y', and 'z' along the 3 axes\
+            [defaults=64].
+        nt_: Number of time points [default=1].
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dEmptyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EMPTY_METADATA)
+    params = v_3d_empty_params(
+        prefix=prefix,
+        geometry=geometry,
+        nxyz=nxyz,
+        nt_=nt_,
+    )
+    return v_3d_empty_execute(params, execution)
+
+
+__all__ = [
+    "V3dEmptyOutputs",
+    "V3dEmptyParameters",
+    "V_3D_EMPTY_METADATA",
+    "v_3d_empty",
+    "v_3d_empty_params",
+]