def test_nuclei():
io.initialize_paths('20150717', subset='20X_hyb_and_washes/',
lasagna_dir='/Volumes/blainey_lab/David/lasagna/')
master = io.DIR['stacks'][0]
test_file = io.DIR['stacks'][3]
data = io.read_stack(test_file, master=master, memmap=False)
process.DOWNSAMPLE = 2
n = process.get_nuclei(data[0, 0, :, :])
return n
def test_nuclei():
io.initialize_paths('20150717',
subset='20X_hyb_and_washes/',
lasagna_dir='/Volumes/blainey_lab/David/lasagna/')
master = io.DIR['stacks'][0]
test_file = io.DIR['stacks'][3]
data = io.read_stack(test_file, master=master, memmap=False)
process.DOWNSAMPLE = 2
n = process.get_nuclei(data[0, 0, :, :])
return n
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
def test_nuclei_to_table():
io.initialize_paths(dataset='20150629/40X_scan',
lasagna_dir='/Volumes/blainey_lab/David/lasagna')
df = process.table_from_nuclei(io.DIR['stacks'][0])
return df
def test_nuclei_to_table():
io.initialize_paths(dataset='20150629/40X_scan',
lasagna_dir='/Volumes/blainey_lab/David/lasagna')
df = process.table_from_nuclei(io.DIR['stacks'][0])
return df