def make_skel_from_json(json_path: str):
"""
Creates a skeleton object from the binary targets of the data sources in json
Args:
json_path: the path of the data source json file
Returns:
skel: the skeleton object
"""
data_sources_dict = WkwData.convert_ds_to_dict(
WkwData.read_short_ds_json(json_path=json_path))
# Init with empty skeleton
empty_skel_name = os.path.join(get_data_dir(), 'NML', 'empty_skel.nml')
skel = wkskel.Skeleton(nml_path=empty_skel_name)
# Loop over each bbox
keys = list(data_sources_dict.keys())
num_nodes_perTree = 5
for idx, key in tqdm(enumerate(keys),
desc='Making bbox nml',
total=len(keys)):
# Get minimum and maximum node id
min_id = (num_nodes_perTree * idx) + 1
max_id = num_nodes_perTree * (idx + 1)
# Encode the target in the tree name
cur_target = data_sources_dict[key]['target_class']
cur_name = f'{key}, Debris: {cur_target[0]}, Myelin: {cur_target[1]}'
# add current tree
add_bbox_tree(skel=skel,
bbox=data_sources_dict[key]['input_bbox'],
tree_name=cur_name,
node_id_min_max=[min_id, max_id])
return skel
import os
from genEM3.data.wkwdata import WkwData
from genEM3.util.path import get_data_dir
# Read Json file
json_names = ['dense_3X_10_10_2_um/original_merged_double_binary_v01.json',
'10x_test_bboxes/10X_9_9_1_um_double_binary_v01.json']
ds_names = [os.path.join(get_data_dir(), j_name) for j_name in json_names]
data_sources = []
dataset_path = '/tmpscratch/webknossos/Connectomics_Department/2018-11-13_scMS109_1to7199_v01_l4_06_24_fixed_mag8_artifact_pred/color/1'
for ds in ds_names:
cur_ds = WkwData.datasources_from_json(json_path=ds)
cur_ds_dict = WkwData.convert_ds_to_dict(cur_ds)
# all pathes use the artifact_pred dataset
for s in cur_ds_dict:
cur_source = cur_ds_dict[s]
cur_source['input_path'] = dataset_path
cur_source['target_path'] = dataset_path
cur_ds_dict[s] = cur_source
# Write out the jsons
cur_ds_corrected_list = WkwData.convert_ds_to_list(datasources_dict=cur_ds_dict)
WkwData.datasources_to_json(datasources=cur_ds_corrected_list, json_path=ds)
import os
from genEM3.data.wkwdata import WkwData
from genEM3.util.path import get_data_dir
# Read the two jsons
target_names = ['Debris', 'Myelin']
json_names = ['combined_20K_patches.json', 'combined_20K_patches_v2.json']
full_names = [
os.path.join(get_data_dir(), 'combined', f_name) for f_name in json_names
]
ds_list = [WkwData.read_short_ds_json(name) for name in full_names]
ds_dict = [WkwData.convert_ds_to_dict(ds) for ds in ds_list]
# Get the difference between the two data sources from jsons
diff_sources = WkwData.compare_ds_targets(two_datasources=ds_dict,
source_names=json_names,
target_names=target_names)
print(diff_sources)