def grid_view(files, bounds, padding=40): from lasagna.io import b_idx, compose_stacks, get_mapped_tif arr = [] for filename, bounds_ in zip(files, bounds): I = get_mapped_tif(filename) I_cell = I[b_idx(None, bounds=bounds_, padding=((padding,padding), I.shape))] arr.append(I_cell.copy()) return compose_stacks(arr)
def test_nuclei_stitch(well=(('A2',),0)):
io.initialize_paths('20150716', subset='stitched/',
lasagna_dir='/Volumes/blainey_lab/David/lasagna/')
dict_20X = defaultdict(list)
[dict_20X[io.get_well_site(f)].append(f) for f in io.DIR['stacks'] if '20X' in f]
test_files = dict_20X[well]
print '(well, site) found', dict_20X.keys()
print 'from', well, 'loading', test_files
data = {f: io.read_stack(f, memmap=False) for f in test_files}
offsets = process.register_images(data.values())
C = io.compose_stacks([io.offset_stack(d, offset)
for d, offset in zip(data.values(), offsets)])
return data, offsets, C
def test_nuclei_stitch(well=(('A2', ), 0)):
io.initialize_paths('20150716',
subset='stitched/',
lasagna_dir='/Volumes/blainey_lab/David/lasagna/')
dict_20X = defaultdict(list)
[
dict_20X[io.get_well_site(f)].append(f) for f in io.DIR['stacks']
if '20X' in f
]
test_files = dict_20X[well]
print '(well, site) found', dict_20X.keys()
print 'from', well, 'loading', test_files
data = {f: io.read_stack(f, memmap=False) for f in test_files}
offsets = process.register_images(data.values())
C = io.compose_stacks(
[io.offset(d, offset) for d, offset in zip(data.values(), offsets)])
return data, offsets, C
