ngio.core
ngio.core
Core classes for the ngio library.
NGFFImage
ngio.core.NgffImage
A class to handle OME-NGFF images.
Source code in ngio/core/ngff_image.py
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 |
|
group: zarr.Group
property
Get the group of the image.
group_path: str
property
Get the path of the group.
image_meta: ImageMeta
property
Get the image metadata.
levels_paths: list[str]
property
Get the paths of the levels in the image.
num_levels: int
property
Get the number of levels in the image.
root_path: str
property
Get the root path of the image.
__init__(store: StoreLike, cache: bool = False, mode: AccessModeLiteral = 'r+') -> None
Initialize the NGFFImage in read mode.
Source code in ngio/core/ngff_image.py
22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 |
|
__repr__() -> str
Get the string representation of the image.
Source code in ngio/core/ngff_image.py
45 46 47 48 49 50 51 52 53 54 55 56 |
|
derive_new_image(store: StoreLike, name: str, overwrite: bool = True, **kwargs: dict) -> NgffImage
Derive a new image from the current image.
Parameters:
-
store
(StoreLike
) –The store to create the new image in.
-
name
(str
) –The name of the new image.
-
overwrite
(bool
, default:True
) –Whether to overwrite the image if it exists
-
**kwargs
(dict
, default:{}
) –Additional keyword arguments. Follow the same signature as
create_empty_ome_zarr_image
.
Returns:
-
NgffImage
(NgffImage
) –The new image.
Source code in ngio/core/ngff_image.py
298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 |
|
get_image(*, path: str | None = None, pixel_size: PixelSize | None = None, highest_resolution: bool = True) -> Image
Get an image handler for the given level.
Parameters:
-
path
(str | None
, default:None
) –The path to the level.
-
pixel_size
(tuple[float, ...] | list[float] | None
, default:None
) –The pixel size of the level.
-
highest_resolution
(bool
, default:True
) –Whether to get the highest resolution level
Returns:
-
ImageHandler
(Image
) –The image handler.
Source code in ngio/core/ngff_image.py
93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 |
|
lazy_init_omero(labels: list[str] | int | None = None, wavelength_ids: list[str] | None = None, colors: list[str] | None = None, active: list[bool] | None = None, start_percentile: float | None = 1, end_percentile: float | None = 99, data_type: Any = np.uint16, consolidate: bool = True) -> None
Set the OMERO metadata for the image.
Parameters:
-
labels
(list[str] | int | None
, default:None
) –The labels of the channels.
-
wavelength_ids
(list[str] | None
, default:None
) –The wavelengths of the channels.
-
colors
(list[str] | None
, default:None
) –The colors of the channels.
-
active
(list[bool] | None
, default:None
) –Whether the channels are active.
-
start_percentile
(float | None
, default:1
) –The start percentile for computing the data range. If None, the start is the same as the min value of the data type.
-
end_percentile
(float | None
, default:99
) –The end percentile for for computing the data range. If None, the start is the same as the max value of the data type.
-
data_type
(Any
, default:uint16
) –The data type of the image.
-
consolidate
(bool
, default:True
) –Whether to consolidate the metadata.
Source code in ngio/core/ngff_image.py
174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 |
|
update_omero_window(start_percentile: int = 1, end_percentile: int = 99, min_value: int | float | None = None, max_value: int | float | None = None) -> None
Update the OMERO window.
This will setup percentiles based values for the window of each channel.
Parameters:
-
start_percentile
(int
, default:1
) –The start percentile.
-
end_percentile
(int
, default:99
) –The end percentile
-
min_value
(int | float | None
, default:None
) –The minimum value of the window.
-
max_value
(int | float | None
, default:None
) –The maximum value of the window.
Source code in ngio/core/ngff_image.py
229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 |
|