niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/imcat.py

@@ -0,0 +1,498 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+IMCAT_METADATA = Metadata(
+    id="aaf3852ed2e5487ca6e742c661a53a14976a9a76.boutiques",
+    name="imcat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ImcatParameters = typing.TypedDict('ImcatParameters', {
+    "__STYX_TYPE__": typing.Literal["imcat"],
+    "input_files": list[InputPathType],
+    "scale_image": typing.NotRequired[InputPathType | None],
+    "scale_pixels": typing.NotRequired[InputPathType | None],
+    "scale_intensity": bool,
+    "gscale": typing.NotRequired[float | None],
+    "rgb_out": bool,
+    "res_in": typing.NotRequired[list[float] | None],
+    "respad_in": typing.NotRequired[list[float] | None],
+    "pad_val": typing.NotRequired[float | None],
+    "crop": typing.NotRequired[list[float] | None],
+    "autocrop_ctol": typing.NotRequired[float | None],
+    "autocrop_atol": typing.NotRequired[float | None],
+    "autocrop": bool,
+    "zero_wrap": bool,
+    "white_wrap": bool,
+    "gray_wrap": typing.NotRequired[float | None],
+    "image_wrap": bool,
+    "rand_wrap": bool,
+    "prefix": typing.NotRequired[str | None],
+    "matrix": typing.NotRequired[list[float] | None],
+    "nx": typing.NotRequired[float | None],
+    "ny": typing.NotRequired[float | None],
+    "matrix_from_scale": bool,
+    "gap": typing.NotRequired[float | None],
+    "gap_col": 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 {
+        "imcat": imcat_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 {
+        "imcat": imcat_outputs,
+    }.get(t)
+
+
+class ImcatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `imcat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_image_file: OutputPathType | None
+    """Output image file"""
+
+
+def imcat_params(
+    input_files: list[InputPathType],
+    scale_image: InputPathType | None = None,
+    scale_pixels: InputPathType | None = None,
+    scale_intensity: bool = False,
+    gscale: float | None = None,
+    rgb_out: bool = False,
+    res_in: list[float] | None = None,
+    respad_in: list[float] | None = None,
+    pad_val: float | None = None,
+    crop: list[float] | None = None,
+    autocrop_ctol: float | None = None,
+    autocrop_atol: float | None = None,
+    autocrop: bool = False,
+    zero_wrap: bool = False,
+    white_wrap: bool = False,
+    gray_wrap: float | None = None,
+    image_wrap: bool = False,
+    rand_wrap: bool = False,
+    prefix: str | None = None,
+    matrix: list[float] | None = None,
+    nx: float | None = None,
+    ny: float | None = None,
+    matrix_from_scale: bool = False,
+    gap: float | None = None,
+    gap_col: list[float] | None = None,
+) -> ImcatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input image files.
+        scale_image: Multiply each image IM(i,j) in output image matrix IM by\
+            the color or intensity of the pixel (i,j) in SCALE_IMG.
+        scale_pixels: Multiply each pixel (i,j) in output image by the color or\
+            intensity of the pixel (i,j) in SCALE_IMG. SCALE_IMG is automatically\
+            resized to the resolution of the output image.
+        scale_intensity: Instead of multiplying by the color of pixel (i,j),\
+            use its intensity (average color).
+        gscale: Apply FAC in addition to scaling of -scale_* options.
+        rgb_out: Force output to be in RGB, even if input is bytes. This option\
+            is turned on automatically in certain cases.
+        res_in: Set resolution of all input images to RX by RY pixels. Default\
+            is to make all input have the same resolution as the first image.
+        respad_in: Like -res_in, but resample to the max while respecting the\
+            aspect ratio, and then pad to achieve desired pixel count.
+        pad_val: Set the padding value, should it be needed by -respad_in to\
+            VAL. VAL is typecast to byte, default is 0, max is 255.
+        crop: Crop images by L (Left), R (Right), T (Top), B (Bottom) pixels.\
+            Cutting is performed after any resolution change, if any, is to be\
+            done.
+        autocrop_ctol: A line is eliminated if none of its R G B values differ\
+            by more than CTOL% from those of the corner pixel.
+        autocrop_atol: A line is eliminated if none of its R G B values differ\
+            by more than ATOL% from those of line average.
+        autocrop: This option is the same as using both of -autocrop_atol 20\
+            and -autocrop_ctol 20.
+        zero_wrap: If number of images is not enough to fill matrix solid black\
+            images are used.
+        white_wrap: If number of images is not enough to fill matrix solid\
+            white images are used.
+        gray_wrap: If number of images is not enough to fill matrix, solid gray\
+            images are used. GRAY must be between 0 and 1.0.
+        image_wrap: If number of images is not enough to fill matrix, images on\
+            command line are reused (default).
+        rand_wrap: When reusing images to fill matrix, randomize the order in\
+            refill section only.
+        prefix: Prefix the output files with string 'ppp'.
+        matrix: Specify number of images in each row and column of IM at the\
+            same time.
+        nx: Number of images in each row.
+        ny: Number of images in each column.
+        matrix_from_scale: Set NX and NY to be the same as the SCALE_IMG's\
+            dimensions. (needs -scale_image).
+        gap: Put a line G pixels wide between images.
+        gap_col: Set color of line to R G B values. Values range between 0 and\
+            255.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "imcat",
+        "input_files": input_files,
+        "scale_intensity": scale_intensity,
+        "rgb_out": rgb_out,
+        "autocrop": autocrop,
+        "zero_wrap": zero_wrap,
+        "white_wrap": white_wrap,
+        "image_wrap": image_wrap,
+        "rand_wrap": rand_wrap,
+        "matrix_from_scale": matrix_from_scale,
+    }
+    if scale_image is not None:
+        params["scale_image"] = scale_image
+    if scale_pixels is not None:
+        params["scale_pixels"] = scale_pixels
+    if gscale is not None:
+        params["gscale"] = gscale
+    if res_in is not None:
+        params["res_in"] = res_in
+    if respad_in is not None:
+        params["respad_in"] = respad_in
+    if pad_val is not None:
+        params["pad_val"] = pad_val
+    if crop is not None:
+        params["crop"] = crop
+    if autocrop_ctol is not None:
+        params["autocrop_ctol"] = autocrop_ctol
+    if autocrop_atol is not None:
+        params["autocrop_atol"] = autocrop_atol
+    if gray_wrap is not None:
+        params["gray_wrap"] = gray_wrap
+    if prefix is not None:
+        params["prefix"] = prefix
+    if matrix is not None:
+        params["matrix"] = matrix
+    if nx is not None:
+        params["nx"] = nx
+    if ny is not None:
+        params["ny"] = ny
+    if gap is not None:
+        params["gap"] = gap
+    if gap_col is not None:
+        params["gap_col"] = gap_col
+    return params
+
+
+def imcat_cargs(
+    params: ImcatParameters,
+    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("imcat")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("scale_image") is not None:
+        cargs.extend([
+            "-scale_image",
+            execution.input_file(params.get("scale_image"))
+        ])
+    if params.get("scale_pixels") is not None:
+        cargs.extend([
+            "-scale_pixels",
+            execution.input_file(params.get("scale_pixels"))
+        ])
+    if params.get("scale_intensity"):
+        cargs.append("-scale_intensity")
+    if params.get("gscale") is not None:
+        cargs.extend([
+            "-gscale",
+            str(params.get("gscale"))
+        ])
+    if params.get("rgb_out"):
+        cargs.append("-rgb_out")
+    if params.get("res_in") is not None:
+        cargs.extend([
+            "-res_in",
+            *map(str, params.get("res_in"))
+        ])
+    if params.get("respad_in") is not None:
+        cargs.extend([
+            "-respad_in",
+            *map(str, params.get("respad_in"))
+        ])
+    if params.get("pad_val") is not None:
+        cargs.extend([
+            "-pad_val",
+            str(params.get("pad_val"))
+        ])
+    if params.get("crop") is not None:
+        cargs.extend([
+            "-crop",
+            *map(str, params.get("crop"))
+        ])
+    if params.get("autocrop_ctol") is not None:
+        cargs.extend([
+            "-autocrop_ctol",
+            str(params.get("autocrop_ctol"))
+        ])
+    if params.get("autocrop_atol") is not None:
+        cargs.extend([
+            "-autocrop_atol",
+            str(params.get("autocrop_atol"))
+        ])
+    if params.get("autocrop"):
+        cargs.append("-autocrop")
+    if params.get("zero_wrap"):
+        cargs.append("-zero_wrap")
+    if params.get("white_wrap"):
+        cargs.append("-white_wrap")
+    if params.get("gray_wrap") is not None:
+        cargs.extend([
+            "-gray_wrap",
+            str(params.get("gray_wrap"))
+        ])
+    if params.get("image_wrap"):
+        cargs.append("-image_wrap")
+    if params.get("rand_wrap"):
+        cargs.append("-rand_wrap")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("matrix") is not None:
+        cargs.extend([
+            "-matrix",
+            *map(str, params.get("matrix"))
+        ])
+    if params.get("nx") is not None:
+        cargs.extend([
+            "-nx",
+            str(params.get("nx"))
+        ])
+    if params.get("ny") is not None:
+        cargs.extend([
+            "-ny",
+            str(params.get("ny"))
+        ])
+    if params.get("matrix_from_scale"):
+        cargs.append("-matrix_from_scale")
+    if params.get("gap") is not None:
+        cargs.extend([
+            "-gap",
+            str(params.get("gap"))
+        ])
+    if params.get("gap_col") is not None:
+        cargs.extend([
+            "-gap_col",
+            *map(str, params.get("gap_col"))
+        ])
+    return cargs
+
+
+def imcat_outputs(
+    params: ImcatParameters,
+    execution: Execution,
+) -> ImcatOutputs:
+    """
+    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 = ImcatOutputs(
+        root=execution.output_file("."),
+        output_image_file=execution.output_file(params.get("prefix") + "output_image.[EXT]") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def imcat_execute(
+    params: ImcatParameters,
+    execution: Execution,
+) -> ImcatOutputs:
+    """
+    Assembles a set of images into an image matrix (IM) montage of NX by NY images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ImcatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = imcat_cargs(params, execution)
+    ret = imcat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def imcat(
+    input_files: list[InputPathType],
+    scale_image: InputPathType | None = None,
+    scale_pixels: InputPathType | None = None,
+    scale_intensity: bool = False,
+    gscale: float | None = None,
+    rgb_out: bool = False,
+    res_in: list[float] | None = None,
+    respad_in: list[float] | None = None,
+    pad_val: float | None = None,
+    crop: list[float] | None = None,
+    autocrop_ctol: float | None = None,
+    autocrop_atol: float | None = None,
+    autocrop: bool = False,
+    zero_wrap: bool = False,
+    white_wrap: bool = False,
+    gray_wrap: float | None = None,
+    image_wrap: bool = False,
+    rand_wrap: bool = False,
+    prefix: str | None = None,
+    matrix: list[float] | None = None,
+    nx: float | None = None,
+    ny: float | None = None,
+    matrix_from_scale: bool = False,
+    gap: float | None = None,
+    gap_col: list[float] | None = None,
+    runner: Runner | None = None,
+) -> ImcatOutputs:
+    """
+    Assembles a set of images into an image matrix (IM) montage of NX by NY images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input image files.
+        scale_image: Multiply each image IM(i,j) in output image matrix IM by\
+            the color or intensity of the pixel (i,j) in SCALE_IMG.
+        scale_pixels: Multiply each pixel (i,j) in output image by the color or\
+            intensity of the pixel (i,j) in SCALE_IMG. SCALE_IMG is automatically\
+            resized to the resolution of the output image.
+        scale_intensity: Instead of multiplying by the color of pixel (i,j),\
+            use its intensity (average color).
+        gscale: Apply FAC in addition to scaling of -scale_* options.
+        rgb_out: Force output to be in RGB, even if input is bytes. This option\
+            is turned on automatically in certain cases.
+        res_in: Set resolution of all input images to RX by RY pixels. Default\
+            is to make all input have the same resolution as the first image.
+        respad_in: Like -res_in, but resample to the max while respecting the\
+            aspect ratio, and then pad to achieve desired pixel count.
+        pad_val: Set the padding value, should it be needed by -respad_in to\
+            VAL. VAL is typecast to byte, default is 0, max is 255.
+        crop: Crop images by L (Left), R (Right), T (Top), B (Bottom) pixels.\
+            Cutting is performed after any resolution change, if any, is to be\
+            done.
+        autocrop_ctol: A line is eliminated if none of its R G B values differ\
+            by more than CTOL% from those of the corner pixel.
+        autocrop_atol: A line is eliminated if none of its R G B values differ\
+            by more than ATOL% from those of line average.
+        autocrop: This option is the same as using both of -autocrop_atol 20\
+            and -autocrop_ctol 20.
+        zero_wrap: If number of images is not enough to fill matrix solid black\
+            images are used.
+        white_wrap: If number of images is not enough to fill matrix solid\
+            white images are used.
+        gray_wrap: If number of images is not enough to fill matrix, solid gray\
+            images are used. GRAY must be between 0 and 1.0.
+        image_wrap: If number of images is not enough to fill matrix, images on\
+            command line are reused (default).
+        rand_wrap: When reusing images to fill matrix, randomize the order in\
+            refill section only.
+        prefix: Prefix the output files with string 'ppp'.
+        matrix: Specify number of images in each row and column of IM at the\
+            same time.
+        nx: Number of images in each row.
+        ny: Number of images in each column.
+        matrix_from_scale: Set NX and NY to be the same as the SCALE_IMG's\
+            dimensions. (needs -scale_image).
+        gap: Put a line G pixels wide between images.
+        gap_col: Set color of line to R G B values. Values range between 0 and\
+            255.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ImcatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMCAT_METADATA)
+    params = imcat_params(
+        input_files=input_files,
+        scale_image=scale_image,
+        scale_pixels=scale_pixels,
+        scale_intensity=scale_intensity,
+        gscale=gscale,
+        rgb_out=rgb_out,
+        res_in=res_in,
+        respad_in=respad_in,
+        pad_val=pad_val,
+        crop=crop,
+        autocrop_ctol=autocrop_ctol,
+        autocrop_atol=autocrop_atol,
+        autocrop=autocrop,
+        zero_wrap=zero_wrap,
+        white_wrap=white_wrap,
+        gray_wrap=gray_wrap,
+        image_wrap=image_wrap,
+        rand_wrap=rand_wrap,
+        prefix=prefix,
+        matrix=matrix,
+        nx=nx,
+        ny=ny,
+        matrix_from_scale=matrix_from_scale,
+        gap=gap,
+        gap_col=gap_col,
+    )
+    return imcat_execute(params, execution)
+
+
+__all__ = [
+    "IMCAT_METADATA",
+    "ImcatOutputs",
+    "ImcatParameters",
+    "imcat",
+    "imcat_params",
+]