def test_write(setup_folder):
"""
Test the write function of the writer
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test',
hcs=True,
hcs_meta=hcs_meta,
verbose=False)
writer.create_zarr_root('test_zarr_root')
data = np.random.randint(1,
60000,
size=(3, 3, 11, 128, 128),
dtype='uint16')
data_shape = data.shape
chunk_size = (1, 1, 1, 128, 128)
chan_names = ['State0', 'State1', 'State3']
clims = [(-0.5, 0.5), (0, 25), (0, 10000)]
dtype = 'uint16'
writer.init_array(0,
data_shape,
chunk_size,
chan_names,
dtype,
clims,
position_name=None,
overwrite=True)
# Write single index for each channel
writer.write(data[0, 0, 0], p=0, t=0, c=0, z=0)
assert (np.array_equal(
writer.sub_writer.store['A']['1']['FOV1']['arr_0'][0, 0, 0], data[0, 0,
0]))
# Write full data
writer.write(data, p=0)
assert (np.array_equal(
writer.sub_writer.store['A']['1']['FOV1']['arr_0'][:, :, :, :, :],
data))
# Write full data with alt method
writer.write(data, p=0, t=slice(0, 3), c=slice(0, 3), z=slice(0, 11))
assert (np.array_equal(
writer.sub_writer.store['A']['1']['FOV1']['arr_0'][:, :, :, :, :],
data))
row_list = (ns // N_space).astype('int')
column_list = (ms // M_space).astype('int')
uPTI_file = zarr.open(os.path.join(output_path, uPTI_file_name), mode='a')
uPTI_file.create_dataset('row_list', data=row_list)
uPTI_file.create_dataset('column_list', data=column_list)
uPTI_file.create_dataset('overlap', data=N_edge)
# ### Patch-wise processing
t0 = time.time()
for ll in range(len(ns)):
position = ll
writer.init_array(position,
data_shape,
chunk_size,
chan_names,
position_name=None,
overwrite=True)
n_start = [int(ns[ll]), int(ms[ll])]
# Compute background-removed Stokes vectors
S_image_recon = setup.Stokes_recon(
I_meas_full[:, :, n_start[0]:n_start[0] + Ns,
n_start[1]:n_start[1] + Ms, ::-1])
S_bg_recon = setup.Stokes_recon(I_bg_full[:, :, n_start[0]:n_start[0] + Ns,
n_start[1]:n_start[1] + Ms])
S_image_tm = np.zeros_like(S_image_recon)
S_image_tm[0] = S_image_recon[0] / S_bg_recon[0, :, :, :, np.newaxis] - 1
S_image_tm[1] = S_image_recon[1] / S_bg_recon[
0, :, :, :, np.newaxis] - S_bg_recon[
def test_init_array(setup_folder):
"""
Test the correct initialization of desired array and the associated
metadata
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test',
hcs=True,
hcs_meta=hcs_meta,
verbose=False)
writer.create_zarr_root('test_zarr_root')
data_shape = (3, 3, 21, 128, 128) # T, C, Z, Y, X
chunk_size = (1, 1, 1, 128, 128)
chan_names = ['State0', 'State1', 'State3']
clims = [(-0.5, 0.5), (0, 25), (0, 10000)]
dtype = 'uint16'
writer.init_array(0,
data_shape,
chunk_size,
chan_names,
dtype,
clims,
position_name=None,
overwrite=False)
writer.init_array(11,
data_shape,
chunk_size,
chan_names,
dtype,
clims,
position_name='Test',
overwrite=False)
assert (isinstance(writer.sub_writer.store['A']['1']['FOV1'], zarr.Group))
meta_folder = writer.store['A']['1']['FOV1']
meta = meta_folder.attrs.asdict()
array = meta_folder['arr_0']
assert (meta_folder is not None)
assert (array is not None)
assert (array.shape == data_shape)
assert (array.chunks == chunk_size)
assert (array.dtype == dtype)
assert (meta is not None)
assert ('multiscales' in meta)
assert ('omero' in meta)
assert ('rdefs' in meta['omero'])
# Test Chan Names and clims
for i in range(len(meta['omero']['channels'])):
assert (meta['omero']['channels'][i]['label'] == chan_names[i])
assert (meta['omero']['channels'][i]['window']['start'] == clims[i][0])
assert (meta['omero']['channels'][i]['window']['end'] == clims[i][1])
assert (isinstance(writer.sub_writer.store['B']['2']['FOV2'], zarr.Group))
meta_folder = writer.store['B']['2']['FOV2']
meta = meta_folder.attrs.asdict()
array = meta_folder['arr_0']
assert (meta_folder is not None)
assert (array is not None)
assert (array.shape == data_shape)
assert (array.chunks == chunk_size)
assert (array.dtype == dtype)
assert (meta is not None)
assert ('multiscales' in meta)
assert ('omero' in meta)
assert ('rdefs' in meta['omero'])
# Test Chan Names and clims
for i in range(len(meta['omero']['channels'])):
assert (meta['omero']['channels'][i]['label'] == chan_names[i])
assert (meta['omero']['channels'][i]['window']['start'] == clims[i][0])
assert (meta['omero']['channels'][i]['window']['end'] == clims[i][1])