def _run(self, *args, **kwargs):
ncyc, nz, nch = self.config.n_cycles, self.config.n_z_planes, self.config.n_channels_per_cycle
_validate_mode(self.mode)
# If in "raw" mode, load a tile by accumlating individual grayscale images
if self.mode == 'raw':
# Tile should have shape (cycles, z, channel, height, width)
img_cyc = []
for icyc in range(ncyc):
img_ch = []
for ich in range(nch):
img_z = []
for iz in range(nz):
img_path = cytokit_io.get_raw_img_path(self.region_index, self.tile_index, icyc, ich, iz)
img_path = osp.join(self.data_dir, img_path)
img = cytokit_io.read_raw_microscope_image(img_path, self.raw_file_type)
if img.ndim != 2:
raise ValueError(
'Expecting raw image at path "{}" to have 2 dims but found shape {}'
.format(img_path, img.shape)
)
img_z.append(img)
img_ch.append(np.stack(img_z, 0))
img_cyc.append(np.stack(img_ch, 1))
tile = np.stack(img_cyc, 0)
# Otherwise assume that the tile has already been assembled and just read it in instead
else:
tx, ty = self.config.get_tile_coordinates(self.tile_index)
img_path = cytokit_io.get_img_path(self.path_fmt_name, self.region_index, tx, ty)
tile = cytokit_io.read_tile(osp.join(self.data_dir, img_path))
return tile
def test_raw_img_paths(self):
cytokit.set_path_formats(cytokit.FF_DEFAULT)
# Test raw image path generation with default settings
path = cytokit_io.get_raw_img_path(ireg=0,
itile=0,
icyc=0,
ich=0,
iz=0)
self.assertEqual('Cyc1_reg1/1_00001_Z001_CH1.tif', path)
# Test raw image path generation with explicit overrides on index mappings
cytokit.set_raw_index_symlinks(
dict(region={1: 2}, cycle={1: 5}, z={1: 3}, channel={1: 9}))
path = cytokit_io.get_raw_img_path(ireg=0,
itile=0,
icyc=0,
ich=0,
iz=0)
self.assertEqual('Cyc5_reg2/2_00001_Z003_CH9.tif', path)
cytokit.set_raw_index_symlinks({})
def get_tile_montage(config, image_dir, hyperstack, icyc=0, iz=0, ich=0, ireg=0, bw=0, bv_fn=None, allow_missing=False,
imread_fn=None):
"""Generate a montage image for a specific cycle, z-plane, channel, and region
This function supports both raw, flattened 2D images as well as consolidated, 5D
hyperstacks (as determined by `hyperstack` argument)
Args:
config: Experiment configuration
image_dir: Location of tiled images; These should include all z-planes, cycles, and channels in
individual tif files (e.g. the output of the pre-processing or segmentation pipelines)
hyperstack: Flag indicating whether or not images are 5D hyperstacks or flattened 2D images:
- Hyperstacks are typically results from any sort of processing or segmentation step
- Flattened 2D images are typically raw files generated directly from a microscope
icyc: 0-based cycle index
iz: 0-based z-plane index
ich: 0-based channel index
ireg: 0-based region index
bw: Border width (in pixels) to add to each tile in the montage image, which useful for determining
tile location within the montage; If <= 0, this parameter will do nothing
bv_fn: Border value function with signature `fn(tile_x, tile_y) --> float`; if not given all
border values are assigned a value of 0
allow_missing: Flag indicating whether or not to allow missing tiles into the montage; defaults
to false and is generally only useful when debugging missing data
imread_fn: When not using 5D hyperstacks (i.e. reading raw image files) this can be useful for cases when,
for example, raw, single-channel files are actually 3 channel files with the first two channels blank
(this happens w/ Keyence somehow). This function will take an image path and must return a single 2D
image with shape (rows, cols)
Returns:
A (usually very large) 2D array containing all tiles stitched together
"""
tile_indexes = list(range(config.n_tiles_per_region))
tw, th = config.tile_width, config.tile_height
tiles = []
for itile in tile_indexes:
tx, ty = config.get_tile_coordinates(itile)
# If operating on a hyperstack, extract the appropriate slice to add to the montage
if hyperstack:
path = cytokit_io.get_processor_img_path(ireg, tx, ty)
path = osp.join(image_dir, path)
if not osp.exists(path) and allow_missing:
tile = np.zeros((th, tw))
else:
tile = cytokit_io.read_tile(path)
tile = tile[icyc, iz, ich, :, :]
# Otherwise, assume raw acquisition files are to be loaded and then cropped before being added
else:
path = cytokit_io.get_raw_img_path(ireg, itile, icyc, ich, iz)
path = osp.join(image_dir, path)
if not osp.exists(path) and allow_missing:
tile = np.zeros((th, tw))
else:
tile = cytokit_io.read_image(path) if imread_fn is None else imread_fn(path)
if tile.ndim != 2:
raise ValueError(
'Expecting 2D image at path "{}" but shape found is {}. Consider using the '
'`imread_fn` argument to specify a custom function to open files or if already using it, '
'make sure that results are 2D'
.format(path, tile.shape)
)
tile = tile_crop.apply_slice(tile, tile_crop.get_slice(config))
# Highlight borders, if configured to do so
if bw > 0:
bv = 0 if bv_fn is None else bv_fn(tx, ty)
tile[0:bw, :] = bv
tile[-bw:, :] = bv
tile[:, 0:bw] = bv
tile[:, -bw:] = bv
# Add to montage
tiles.append(tile)
return core.montage(tiles, config)