niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__djunct_dwi_selector.py

@@ -0,0 +1,192 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DJUNCT_DWI_SELECTOR_METADATA = Metadata(
+    id="322cd55e91869cfd3befcc11394010a6d10dddc6.boutiques",
+    name="@djunct_dwi_selector",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDjunctDwiSelectorParameters = typing.TypedDict('VDjunctDwiSelectorParameters', {
+    "__STYX_TYPE__": typing.Literal["@djunct_dwi_selector"],
+    "dwi": InputPathType,
+    "png": InputPathType,
+    "outfile": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@djunct_dwi_selector": v__djunct_dwi_selector_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 {
+        "@djunct_dwi_selector": v__djunct_dwi_selector_outputs,
+    }.get(t)
+
+
+class VDjunctDwiSelectorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__djunct_dwi_selector(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """The main output file"""
+
+
+def v__djunct_dwi_selector_params(
+    dwi: InputPathType,
+    png: InputPathType,
+    outfile: str,
+) -> VDjunctDwiSelectorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dwi: Input DWI file.
+        png: Output PNG image.
+        outfile: Path to the output file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@djunct_dwi_selector",
+        "dwi": dwi,
+        "png": png,
+        "outfile": outfile,
+    }
+    return params
+
+
+def v__djunct_dwi_selector_cargs(
+    params: VDjunctDwiSelectorParameters,
+    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("@djunct_dwi_selector.tcsh")
+    cargs.append(execution.input_file(params.get("dwi")))
+    cargs.append(execution.input_file(params.get("png")))
+    cargs.append(params.get("outfile"))
+    return cargs
+
+
+def v__djunct_dwi_selector_outputs(
+    params: VDjunctDwiSelectorParameters,
+    execution: Execution,
+) -> VDjunctDwiSelectorOutputs:
+    """
+    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 = VDjunctDwiSelectorOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("outfile")),
+    )
+    return ret
+
+
+def v__djunct_dwi_selector_execute(
+    params: VDjunctDwiSelectorParameters,
+    execution: Execution,
+) -> VDjunctDwiSelectorOutputs:
+    """
+    Selects DWI data and creates a representative image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctDwiSelectorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__djunct_dwi_selector_cargs(params, execution)
+    ret = v__djunct_dwi_selector_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__djunct_dwi_selector(
+    dwi: InputPathType,
+    png: InputPathType,
+    outfile: str,
+    runner: Runner | None = None,
+) -> VDjunctDwiSelectorOutputs:
+    """
+    Selects DWI data and creates a representative image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dwi: Input DWI file.
+        png: Output PNG image.
+        outfile: Path to the output file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctDwiSelectorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DJUNCT_DWI_SELECTOR_METADATA)
+    params = v__djunct_dwi_selector_params(
+        dwi=dwi,
+        png=png,
+        outfile=outfile,
+    )
+    return v__djunct_dwi_selector_execute(params, execution)
+
+
+__all__ = [
+    "VDjunctDwiSelectorOutputs",
+    "VDjunctDwiSelectorParameters",
+    "V__DJUNCT_DWI_SELECTOR_METADATA",
+    "v__djunct_dwi_selector",
+    "v__djunct_dwi_selector_params",
+]

niwrap_afni/afni/v__djunct_edgy_align_check.py

@@ -0,0 +1,339 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__DJUNCT_EDGY_ALIGN_CHECK_METADATA = Metadata(
+    id="b256b5bb4b47e9c6b85c30cb947f43710826ac49.boutiques",
+    name="@djunct_edgy_align_check",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VDjunctEdgyAlignCheckParameters = typing.TypedDict('VDjunctEdgyAlignCheckParameters', {
+    "__STYX_TYPE__": typing.Literal["@djunct_edgy_align_check"],
+    "ULAY": str,
+    "OLAY": str,
+    "PREFIX": str,
+    "set_dicom_xyz": typing.NotRequired[list[float] | None],
+    "box_focus_slices": typing.NotRequired[str | None],
+    "montgap": typing.NotRequired[float | None],
+    "montcolor": typing.NotRequired[str | None],
+    "cbar": typing.NotRequired[str | None],
+    "save_ftype": typing.NotRequired[str | None],
+    "umin_fac": typing.NotRequired[float | None],
+    "montx": typing.NotRequired[float | None],
+    "monty": typing.NotRequired[float | None],
+    "use_olay_grid": typing.NotRequired[str | None],
+    "label_mode": typing.NotRequired[str | None],
+    "ulay_range": typing.NotRequired[list[float] | None],
+    "ulay_range_nz": typing.NotRequired[list[float] | None],
+    "ulay_range_am": typing.NotRequired[list[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 {
+        "@djunct_edgy_align_check": v__djunct_edgy_align_check_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 VDjunctEdgyAlignCheckOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__djunct_edgy_align_check(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__djunct_edgy_align_check_params(
+    ulay: str,
+    olay: str,
+    prefix: str,
+    set_dicom_xyz: list[float] | None = None,
+    box_focus_slices: str | None = None,
+    montgap: float | None = None,
+    montcolor: str | None = None,
+    cbar: str | None = None,
+    save_ftype: str | None = None,
+    umin_fac: float | None = None,
+    montx: float | None = None,
+    monty: float | None = None,
+    use_olay_grid: str | None = None,
+    label_mode: str | None = None,
+    ulay_range: list[float] | None = None,
+    ulay_range_nz: list[float] | None = None,
+    ulay_range_am: list[float] | None = None,
+) -> VDjunctEdgyAlignCheckParameters:
+    """
+    Build parameters.
+    
+    Args:
+        ulay: ULAY dataset.
+        olay: OLAY dataset.
+        prefix: Prefix for output files.
+        set_dicom_xyz: DICOM coordinates {XX YY ZZ}.
+        box_focus_slices: Dataset to focus slices.
+        montgap: Gap between slices in montage.
+        montcolor: Color for montage.
+        cbar: Color bar for overlay.
+        save_ftype: File type to save.
+        umin_fac: Scaling factor for underlay minimum.
+        montx: Number of slices in X-direction for montage.
+        monty: Number of slices in Y-direction for montage.
+        use_olay_grid: Grid interpolation method for overlay.
+        label_mode: Mode for labeling.
+        ulay_range: Range for underlay {umin umax}.
+        ulay_range_nz: Range for non-zero underlay {umin umax}.
+        ulay_range_am: Range for auto-mask underlay {umin umax}.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@djunct_edgy_align_check",
+        "ULAY": ulay,
+        "OLAY": olay,
+        "PREFIX": prefix,
+    }
+    if set_dicom_xyz is not None:
+        params["set_dicom_xyz"] = set_dicom_xyz
+    if box_focus_slices is not None:
+        params["box_focus_slices"] = box_focus_slices
+    if montgap is not None:
+        params["montgap"] = montgap
+    if montcolor is not None:
+        params["montcolor"] = montcolor
+    if cbar is not None:
+        params["cbar"] = cbar
+    if save_ftype is not None:
+        params["save_ftype"] = save_ftype
+    if umin_fac is not None:
+        params["umin_fac"] = umin_fac
+    if montx is not None:
+        params["montx"] = montx
+    if monty is not None:
+        params["monty"] = monty
+    if use_olay_grid is not None:
+        params["use_olay_grid"] = use_olay_grid
+    if label_mode is not None:
+        params["label_mode"] = label_mode
+    if ulay_range is not None:
+        params["ulay_range"] = ulay_range
+    if ulay_range_nz is not None:
+        params["ulay_range_nz"] = ulay_range_nz
+    if ulay_range_am is not None:
+        params["ulay_range_am"] = ulay_range_am
+    return params
+
+
+def v__djunct_edgy_align_check_cargs(
+    params: VDjunctEdgyAlignCheckParameters,
+    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("@djunct_edgy_align_check")
+    cargs.append(params.get("ULAY"))
+    cargs.append(params.get("OLAY"))
+    cargs.append(params.get("PREFIX"))
+    if params.get("set_dicom_xyz") is not None:
+        cargs.extend(map(str, params.get("set_dicom_xyz")))
+    if params.get("box_focus_slices") is not None:
+        cargs.append(params.get("box_focus_slices"))
+    if params.get("montgap") is not None:
+        cargs.append(str(params.get("montgap")))
+    if params.get("montcolor") is not None:
+        cargs.append(params.get("montcolor"))
+    if params.get("cbar") is not None:
+        cargs.append(params.get("cbar"))
+    if params.get("save_ftype") is not None:
+        cargs.append(params.get("save_ftype"))
+    if params.get("umin_fac") is not None:
+        cargs.append(str(params.get("umin_fac")))
+    if params.get("montx") is not None:
+        cargs.append(str(params.get("montx")))
+    if params.get("monty") is not None:
+        cargs.append(str(params.get("monty")))
+    if params.get("use_olay_grid") is not None:
+        cargs.append(params.get("use_olay_grid"))
+    if params.get("label_mode") is not None:
+        cargs.append(params.get("label_mode"))
+    cargs.append("[help_flag]")
+    cargs.append("[ver_flag]")
+    cargs.append("[echo_flag]")
+    cargs.append("[sharpen_ulay_off_flag]")
+    cargs.append("[mask_olay_edges_flag]")
+    cargs.append("[no_cor_flag]")
+    cargs.append("[no_sag_flag]")
+    cargs.append("[no_axi_flag]")
+    cargs.append("[no_clean_flag]")
+    if params.get("ulay_range") is not None:
+        cargs.extend(map(str, params.get("ulay_range")))
+    if params.get("ulay_range_nz") is not None:
+        cargs.extend(map(str, params.get("ulay_range_nz")))
+    if params.get("ulay_range_am") is not None:
+        cargs.extend(map(str, params.get("ulay_range_am")))
+    return cargs
+
+
+def v__djunct_edgy_align_check_outputs(
+    params: VDjunctEdgyAlignCheckParameters,
+    execution: Execution,
+) -> VDjunctEdgyAlignCheckOutputs:
+    """
+    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 = VDjunctEdgyAlignCheckOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__djunct_edgy_align_check_execute(
+    params: VDjunctEdgyAlignCheckParameters,
+    execution: Execution,
+) -> VDjunctEdgyAlignCheckOutputs:
+    """
+    Helper script for various tasks, heavily modeled on RW Cox's '@snapshot_volreg'
+    script.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctEdgyAlignCheckOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__djunct_edgy_align_check_cargs(params, execution)
+    ret = v__djunct_edgy_align_check_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__djunct_edgy_align_check(
+    ulay: str,
+    olay: str,
+    prefix: str,
+    set_dicom_xyz: list[float] | None = None,
+    box_focus_slices: str | None = None,
+    montgap: float | None = None,
+    montcolor: str | None = None,
+    cbar: str | None = None,
+    save_ftype: str | None = None,
+    umin_fac: float | None = None,
+    montx: float | None = None,
+    monty: float | None = None,
+    use_olay_grid: str | None = None,
+    label_mode: str | None = None,
+    ulay_range: list[float] | None = None,
+    ulay_range_nz: list[float] | None = None,
+    ulay_range_am: list[float] | None = None,
+    runner: Runner | None = None,
+) -> VDjunctEdgyAlignCheckOutputs:
+    """
+    Helper script for various tasks, heavily modeled on RW Cox's '@snapshot_volreg'
+    script.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        ulay: ULAY dataset.
+        olay: OLAY dataset.
+        prefix: Prefix for output files.
+        set_dicom_xyz: DICOM coordinates {XX YY ZZ}.
+        box_focus_slices: Dataset to focus slices.
+        montgap: Gap between slices in montage.
+        montcolor: Color for montage.
+        cbar: Color bar for overlay.
+        save_ftype: File type to save.
+        umin_fac: Scaling factor for underlay minimum.
+        montx: Number of slices in X-direction for montage.
+        monty: Number of slices in Y-direction for montage.
+        use_olay_grid: Grid interpolation method for overlay.
+        label_mode: Mode for labeling.
+        ulay_range: Range for underlay {umin umax}.
+        ulay_range_nz: Range for non-zero underlay {umin umax}.
+        ulay_range_am: Range for auto-mask underlay {umin umax}.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VDjunctEdgyAlignCheckOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__DJUNCT_EDGY_ALIGN_CHECK_METADATA)
+    params = v__djunct_edgy_align_check_params(
+        ulay=ulay,
+        olay=olay,
+        prefix=prefix,
+        set_dicom_xyz=set_dicom_xyz,
+        box_focus_slices=box_focus_slices,
+        montgap=montgap,
+        montcolor=montcolor,
+        cbar=cbar,
+        save_ftype=save_ftype,
+        umin_fac=umin_fac,
+        montx=montx,
+        monty=monty,
+        use_olay_grid=use_olay_grid,
+        label_mode=label_mode,
+        ulay_range=ulay_range,
+        ulay_range_nz=ulay_range_nz,
+        ulay_range_am=ulay_range_am,
+    )
+    return v__djunct_edgy_align_check_execute(params, execution)
+
+
+__all__ = [
+    "VDjunctEdgyAlignCheckOutputs",
+    "VDjunctEdgyAlignCheckParameters",
+    "V__DJUNCT_EDGY_ALIGN_CHECK_METADATA",
+    "v__djunct_edgy_align_check",
+    "v__djunct_edgy_align_check_params",
+]