niwrap.ants.smooth_image

  1# This file was auto generated by Styx.
  2# Do not edit this file directly.
  3
  4import typing
  5import pathlib
  6from styxdefs import *
  7
  8SMOOTH_IMAGE_METADATA = Metadata(
  9    id="c743ecca2407454064c39d3994944e2822b5560a.boutiques",
 10    name="SmoothImage",
 11    package="ants",
 12    container_image_tag="antsx/ants:v2.5.3",
 13)
 14
 15
 16SmoothImageParameters = typing.TypedDict('SmoothImageParameters', {
 17    "__STYX_TYPE__": typing.Literal["SmoothImage"],
 18    "image_dimension": int,
 19    "image_ext": InputPathType,
 20    "smoothing_sigma": str,
 21    "out_image_ext": str,
 22    "sigma_units": typing.NotRequired[typing.Literal[0, 1] | None],
 23    "median_filter": typing.NotRequired[typing.Literal[0, 1] | None],
 24})
 25
 26
 27def dyn_cargs(
 28    t: str,
 29) -> typing.Any:
 30    """
 31    Get build cargs function by command type.
 32    
 33    Args:
 34        t: Command type.
 35    Returns:
 36        Build cargs function.
 37    """
 38    return {
 39        "SmoothImage": smooth_image_cargs,
 40    }.get(t)
 41
 42
 43def dyn_outputs(
 44    t: str,
 45) -> typing.Any:
 46    """
 47    Get build outputs function by command type.
 48    
 49    Args:
 50        t: Command type.
 51    Returns:
 52        Build outputs function.
 53    """
 54    return {
 55        "SmoothImage": smooth_image_outputs,
 56    }.get(t)
 57
 58
 59class SmoothImageOutputs(typing.NamedTuple):
 60    """
 61    Output object returned when calling `smooth_image(...)`.
 62    """
 63    root: OutputPathType
 64    """Output root folder. This is the root folder for all outputs."""
 65    smoothed_image: OutputPathType
 66    """The output smoothed image file."""
 67
 68
 69def smooth_image_params(
 70    image_dimension: int,
 71    image_ext: InputPathType,
 72    smoothing_sigma: str,
 73    out_image_ext: str,
 74    sigma_units: typing.Literal[0, 1] | None = None,
 75    median_filter: typing.Literal[0, 1] | None = None,
 76) -> SmoothImageParameters:
 77    """
 78    Build parameters.
 79    
 80    Args:
 81        image_dimension: Specifies the dimensionality of the image.
 82        image_ext: The input image file to be smoothed.
 83        smoothing_sigma: The sigma value for smoothing. A separate sigma may be\
 84            specified for each dimension, e.g., '1.5x1x2'.
 85        out_image_ext: The output smoothed image file.
 86        sigma_units: Determines if sigma is in spacing units (1) or not (0).\
 87            Default is 0.
 88        median_filter: Whether to use median filter. Default is 0. If using\
 89            median filter, sigma represents the radius in voxels.
 90    Returns:
 91        Parameter dictionary
 92    """
 93    params = {
 94        "__STYXTYPE__": "SmoothImage",
 95        "image_dimension": image_dimension,
 96        "image_ext": image_ext,
 97        "smoothing_sigma": smoothing_sigma,
 98        "out_image_ext": out_image_ext,
 99    }
100    if sigma_units is not None:
101        params["sigma_units"] = sigma_units
102    if median_filter is not None:
103        params["median_filter"] = median_filter
104    return params
105
106
107def smooth_image_cargs(
108    params: SmoothImageParameters,
109    execution: Execution,
110) -> list[str]:
111    """
112    Build command-line arguments from parameters.
113    
114    Args:
115        params: The parameters.
116        execution: The execution object for resolving input paths.
117    Returns:
118        Command-line arguments.
119    """
120    cargs = []
121    cargs.append("SmoothImage")
122    cargs.append(str(params.get("image_dimension")))
123    cargs.append(execution.input_file(params.get("image_ext")))
124    cargs.append(params.get("smoothing_sigma"))
125    cargs.append(params.get("out_image_ext"))
126    if params.get("sigma_units") is not None:
127        cargs.append(str(params.get("sigma_units")))
128    if params.get("median_filter") is not None:
129        cargs.append(str(params.get("median_filter")))
130    return cargs
131
132
133def smooth_image_outputs(
134    params: SmoothImageParameters,
135    execution: Execution,
136) -> SmoothImageOutputs:
137    """
138    Build outputs object containing output file paths and possibly stdout/stderr.
139    
140    Args:
141        params: The parameters.
142        execution: The execution object for resolving input paths.
143    Returns:
144        Outputs object.
145    """
146    ret = SmoothImageOutputs(
147        root=execution.output_file("."),
148        smoothed_image=execution.output_file(params.get("out_image_ext")),
149    )
150    return ret
151
152
153def smooth_image_execute(
154    params: SmoothImageParameters,
155    execution: Execution,
156) -> SmoothImageOutputs:
157    """
158    SmoothImage allows smoothing of images with adjustable sigma values, offering
159    optional median filtering functionality.
160    
161    Author: ANTs Developers
162    
163    URL: https://github.com/ANTsX/ANTs
164    
165    Args:
166        params: The parameters.
167        execution: The execution object.
168    Returns:
169        NamedTuple of outputs (described in `SmoothImageOutputs`).
170    """
171    params = execution.params(params)
172    cargs = smooth_image_cargs(params, execution)
173    ret = smooth_image_outputs(params, execution)
174    execution.run(cargs)
175    return ret
176
177
178def smooth_image(
179    image_dimension: int,
180    image_ext: InputPathType,
181    smoothing_sigma: str,
182    out_image_ext: str,
183    sigma_units: typing.Literal[0, 1] | None = None,
184    median_filter: typing.Literal[0, 1] | None = None,
185    runner: Runner | None = None,
186) -> SmoothImageOutputs:
187    """
188    SmoothImage allows smoothing of images with adjustable sigma values, offering
189    optional median filtering functionality.
190    
191    Author: ANTs Developers
192    
193    URL: https://github.com/ANTsX/ANTs
194    
195    Args:
196        image_dimension: Specifies the dimensionality of the image.
197        image_ext: The input image file to be smoothed.
198        smoothing_sigma: The sigma value for smoothing. A separate sigma may be\
199            specified for each dimension, e.g., '1.5x1x2'.
200        out_image_ext: The output smoothed image file.
201        sigma_units: Determines if sigma is in spacing units (1) or not (0).\
202            Default is 0.
203        median_filter: Whether to use median filter. Default is 0. If using\
204            median filter, sigma represents the radius in voxels.
205        runner: Command runner.
206    Returns:
207        NamedTuple of outputs (described in `SmoothImageOutputs`).
208    """
209    runner = runner or get_global_runner()
210    execution = runner.start_execution(SMOOTH_IMAGE_METADATA)
211    params = smooth_image_params(
212        image_dimension=image_dimension,
213        image_ext=image_ext,
214        smoothing_sigma=smoothing_sigma,
215        out_image_ext=out_image_ext,
216        sigma_units=sigma_units,
217        median_filter=median_filter,
218    )
219    return smooth_image_execute(params, execution)
220
221
222__all__ = [
223    "SMOOTH_IMAGE_METADATA",
224    "SmoothImageOutputs",
225    "SmoothImageParameters",
226    "smooth_image",
227    "smooth_image_params",
228]