wsipipe.load.slides package
Slide loaders wrap different WSI image formats into generic slide loader
slide module
SlideBase is a parent class that contains functionality for reading slides. This is used to render different types of slides into a common format
- class SlideBase[source]
Bases:
objectGeneric base class for slide loaders.
- path()
returns the filepath to the slide
- dimensions()
returns a list of the slide dimensions in pixels
- for each level present in the WSI pyramid
- read_region()[source]
returns a specified region of the slide as a PIL image
- Parameters
region (Region) –
- Return type
Image
- read_regions()[source]
returns multiple regions as a list of PIL images
- Parameters
regions (List[Region]) –
- Return type
List[Image]
- get_thumbnail()[source]
returns the whole of the slide at a given level
- Parameters
level (int) –
- Return type
numpy.array
- in the WSI pyramid as numpy array. This can run out of memory if
- too low a level in the pyramid is selected
- abstract property dimensions: List[Size]
Gets slide dimensions in pixels for all levels in pyramid :returns: A list of sizes :rtype: (List[Size])
- get_thumbnail(level)[source]
Get thumbnail of whole slide downsized to a level in the pyramid
- Parameters
level (int) – Level at which to return thumbnail
- Returns
thumbnail as an RGB numpy array
- Return type
im (np.array)
- abstract property path: Path
openslide module
- class OSSlide(path)[source]
Bases:
SlideBaseRead slides to generic format using the openslide package. For example, to open OMETiff WSIs.
- Parameters
path (Path) –
- check_level(region)[source]
Checks if level specified in region exists in pyramid :param region: A Region to check :type region: Region
- Returns
True if level in region exists in pyramid
- Return type
(bool)
- Parameters
region (Region) –
- convert_region(region)[source]
Creates a PIL image of a region by downsampling from lower level :param region: A Region to create :type region: Region
- Returns
A downsampled PIL Image
- Return type
image (Image)
- Parameters
region (Region) –
- property dimensions: List[Size]
Gets slide dimensions in pixels for all levels in pyramid
If fewer than 10 levels exist in the pyramid it calculates the extra sizes and adds them to the list
- Returns
A list of sizes
- Return type
sizelist (List[Size])
- property path: Path
- read_region(region)[source]
Read a region from a WSI
Checks if the specified level for the region exists in the pyramid. If not reads the region from the highest level that exists and downscales it
- Parameters
region (Region) – A region of the image
- Returns
A PIL Image of the specified region
- Return type
image (Image)
region module
- class Region(level, location, size)[source]
Bases:
tupleClass for a Region of a whole slide image :param level: Level to extract the region :type level: int :param location: x y tuple giving location of top left of region at that level :type location: Point :param size: width and height tuple giving size of region at that level :type size: Size
- as_values()[source]
Splits out location and size into separate values
- Return type
Tuple[int, int, int, int, int]
- property level
Alias for field number 0
- property location
Alias for field number 1
- classmethod make(x, y, size, level)[source]
An alternate construction method for square region
Assumes a square region of width and height equal to size
- Parameters
x (int) – the pixel location of left of image at level
y (int) – the pixel location of top of image at level
size (int) – size of square region
level (int) – Level to extract the region
- property size
Alias for field number 2