def run(self, target_ids, u_info):
###
###
print('Simple merger runs.')
## Load DB
db = DB(u_info)
## Clear undo buffer
u_info.ids_files_undo = []
## Target id
flatten_target_ids = set(chain.from_iterable(target_ids))
for iw in range(db.num_tiles_w):
for iz, iy, ix in product(range(db.num_tiles_z), range(db.num_tiles_y_at_w[iw]), range(db.num_tiles_x_at_w[iw])):
### Load tile file
### tile_ids( ( tile_num_pixels_y, tile_num_pixels_x ), np.uint32 )
tile_ids_filename = u_info.tile_ids_path + u_info.tile_ids_filename_wzyx.format( iw, iz, iy, ix )
tile_ids = m.load_hdf5( tile_ids_filename, u_info.tile_var_name )
## Check whether ids should be updated.
unique_tile_ids = np.unique(tile_ids)
if bool(flatten_target_ids.intersection( set(unique_tile_ids) ) ):
# Backup for undo
m.save_hdf5(tile_ids_filename+'_', u_info.tile_var_name, tile_ids)
u_info.ids_files_undo.append(tile_ids_filename)
# Merge target ids
for ids in target_ids:
for i in ids:
tile_ids[ tile_ids == i ] = ids[0]
# Save changes
m.save_hdf5( tile_ids_filename, u_info.tile_var_name, tile_ids )
print('Save: ', tile_ids_filename)
## For Undo
db.Backup( u_info.segment_info_db_undo_file )
u_info.flag_undo = 1
u_info.flag_redo = 0
## Update
db.Update()
def Redo(u_info):
if u_info.flag_redo < 1:
print('No redo buffer.')
return False
u_info.flag_redo = 0
## Load DB
db = DB(u_info)
##
print('Redo: Database updated.')
db.Backup(u_info.segment_info_db_undo_file)
db.restore(u_info.segment_info_db_redo_file)
print('Redo: Id panels updated.')
u_info.ids_files_undo = u_info.ids_files_redo
u_info.ids_files_redo = []
for filename in u_info.ids_files_redo:
shutil.move(filename, filename + '_') ## Backup for undo
shutil.move(filename + '~', filename) ## Copy from redo backup
u_info.flag_undo = 1
print('Redo: Completed.')
def __init__(self, disconnect_id, u_info):
## Nortification
print('3D disconnector runs.')
## Load DB
db = DB(u_info)
## Clear undo buffer
u_info.ids_files_undo = []
## Obtain a target region as a bool 3d array
mask = np.zeros((db.canvas_size_y, db.canvas_size_x, db.num_tiles_z),
dtype=bool)
for iz in range(db.num_tiles_z):
full_map = m.ObtainFullSizeIdsPanel(u_info, db, iz)
mask[:, :, iz] = (full_map == disconnect_id)
## Obtain disconnect regions by use of "measure.label"
labels, num_labels = measure.label(
mask, neighbors=4,
return_num=True) # "labels" will require large memory.
print('Number of disconnected components: ', num_labels)
## Assign new ids
assigned_id, maxid = db.ObtainUnusedIdsFromDB(u_info, num_labels - 1)
## Make changes on files
## Original images
for iz in range(db.num_tiles_z):
# Resize ids
for iw in range(db.num_tiles_w):
current_num_voxels_y = db.num_tiles_y_at_w[
iw] * db.num_voxels_per_tile_y
current_num_voxels_x = db.num_tiles_x_at_w[
iw] * db.num_voxels_per_tile_x
targ = labels[::(2**iw), ::(2**iw), iz]
current_labels = zeros(
(current_num_voxels_y, current_num_voxels_x), targ.dtype)
current_labels[0:targ.shape[0], 0:targ.shape[1]] = targ
for iy, ix in itertools.product(range(db.num_tiles_y_at_w[iw]),
range(
db.num_tiles_x_at_w[iw])):
## Obtain a target id panel
yid_start = iy * db.num_voxels_per_tile_y
xid_start = ix * db.num_voxels_per_tile_x
yid_goal = iy * db.num_voxels_per_tile_y + db.num_voxels_per_tile_y
xid_goal = ix * db.num_voxels_per_tile_x + db.num_voxels_per_tile_x
tmp_labels = current_labels[yid_start:yid_goal,
xid_start:xid_goal, iz]
if np.max(tmp_labels) > 0:
## Obtain the target tile
tile_ids_filename = u_info.mojo_tile_ids_path \
+ u_info.tile_ids_filename_wzyx.format(iw, iz, iy, ix)
tile_ids = m.load_hdf5(tile_ids_filename,
u_info.tile_var_name)
# Backup undo
m.save_hdf5(tile_ids_filename + '_',
u_info.tile_var_name, tile_ids)
ids_files_undo.append(
tile_ids_filename) ## Filename for undo
# Make changes
for i in range(num_labels):
tile_ids[tmp_labels == i + 1] = assigned_id[i]
m.save_hdf5(tile_ids_filename, u_info.tile_var_name,
tile_ids)
##
## Update database
##
## For Undo
db.Backup(u_info.segment_info_db_undo_file)
u_info.flag_undo = 1
u_info.flag_redo = 0
## Update
db.Update(u_info)
