large_image_source_vips package

Submodules

large_image_source_vips.girder_source module

class large_image_source_vips.girder_source.VipsGirderTileSource(*args, **kwargs)[source]

Bases: VipsFileTileSource, GirderTileSource

Vips large_image tile source for Girder.

Initialize the tile class. See the base class for other available parameters.

Parameters

path – a filesystem path for the tile source.

cacheName = 'tilesource'
name = 'vips'

Name of the tile source

Module contents

class large_image_source_vips.VipsFileTileSource(*args, **kwargs)[source]

Bases: FileTileSource

Provides tile access to any libvips compatible file.

Initialize the tile class. See the base class for other available parameters.

Parameters

path – a filesystem path for the tile source.

addTile(tile, x=0, y=0, mask=None, interpretation=None)[source]

Add a numpy or image tile to the image, expanding the image as needed to accommodate it.

Parameters
  • tile – a numpy array, PIL Image, vips image, or a binary string with an image. The numpy array can have 2 or 3 dimensions.

  • x – location in destination for upper-left corner.

  • y – location in destination for upper-left corner.

  • mask – a 2-d numpy array (or 3-d if the last dimension is 1). If specified, areas where the mask is false will not be altered.

  • interpretation – one of the pyvips.enums.Interpretation or ‘L’, ‘LA’, ‘RGB’, “RGBA’. This defaults to RGB/RGBA for 3/4 channel images and L/LA for 1/2 channels. The special value ‘pixelmap’ will convert a 1 channel integer to a 3 channel RGB map. For images which are not 1 or 3 bands with an optional alpha, specify MULTIBAND. In this case, the mask option cannot be used.

property bandFormat
property bandRanges
cacheName = 'tilesource'
property crop

Crop only applies to the output file, not the internal data access.

It consists of x, y, w, h in pixels.

extensions = {None: 5}

A dictionary of known file extensions and the SourcePriority given to each. It must contain a None key with a priority for the tile source when the extension does not match.

getInternalMetadata(**kwargs)[source]

Return additional known metadata about the tile source. Data returned from this method is not guaranteed to be in any particular format or have specific values.

Returns

a dictionary of data or None.

getMetadata()[source]

Return a dictionary of metadata containing levels, sizeX, sizeY, tileWidth, tileHeight, magnification, mm_x, mm_y, and frames.

Returns

metadata dictionary.

getNativeMagnification()[source]

Get the magnification at a particular level.

Returns

magnification, width of a pixel in mm, height of a pixel in mm.

getState()[source]

Return a string reflecting the state of the tile source. This is used as part of a cache key when hashing function return values.

Returns

a string hash value of the source state.

getTile(x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs)[source]

Get a tile from a tile source, returning it as an binary image, a PIL image, or a numpy array.

Parameters
  • x – the 0-based x position of the tile on the specified z level. 0 is left.

  • y – the 0-based y position of the tile on the specified z level. 0 is top.

  • z – the z level of the tile. May range from [0, self.levels], where 0 is the lowest resolution, single tile for the whole source.

  • pilImageAllowed – True if a PIL image may be returned.

  • numpyAllowed – True if a numpy image may be returned. ‘always’ to return a numpy array.

  • sparseFallback – if False and a tile doesn’t exist, raise an error. If True, check if a lower resolution tile exists, and, if so, interpolate the needed data for this tile.

  • frame – the frame number within the tile source. None is the same as 0 for multi-frame sources.

Returns

either a numpy array, a PIL image, or a memory object with an image file.

mimeTypes = {None: 8}

A dictionary of common mime-types handled by the source and the SourcePriority given to each. This are used in place of or in additional to extensions.

property minHeight
property minWidth
property mm_x
property mm_y
name = 'vips'

Name of the tile source

write(path, lossy=True, alpha=True, overwriteAllowed=True, vips_kwargs=None)[source]

Output the current image to a file.

Parameters
  • path – output path.

  • lossy – if false, emit a lossless file.

  • alpha – True if an alpha channel is allowed.

  • overwriteAllowed – if False, raise an exception if the output path exists.

  • vips_kwargs – if not None, save the image using these kwargs to the write_to_file function instead of the automatically chosen ones. In this case, lossy is ignored and all vips options must be manually specified.

large_image_source_vips.canRead(*args, **kwargs)[source]

Check if an input can be read by the module class.

large_image_source_vips.new(*args, **kwargs)[source]

Create a new image, collecting the results from patches of numpy arrays or smaller images.

large_image_source_vips.open(*args, **kwargs)[source]

Create an instance of the module class.