def test2():
start = time.time()
swc_tree = SwcTree()
swc_tree.load("D:\gitProject\mine\PyNeval\\test\data_example\gold\ExampleGoldStandard.swc")
bin_tree = convert_to_binarytree(swc_tree)
test_print_bin_tree(bin_tree)
print(time.time() - start)
def read_swc_trees(swc_file_paths):
swc_tree_list = []
if os.path.isfile(swc_file_paths):
if not (swc_file_paths[-4:] == ".swc" or swc_file_paths[-4:] == ".SWC"):
print(swc_file_paths + "is not a tif file")
return None
swc_tree = SwcTree()
swc_tree.load(swc_file_paths)
swc_tree_list.append(swc_tree)
elif os.path.isdir(swc_file_paths):
for file in os.listdir(swc_file_paths):
swc_tree_list += read_swc_trees(swc_file_paths=os.path.join(swc_file_paths, file))
return swc_tree_list
def test_len_1(self):
goldtree = SwcTree()
testTree = SwcTree()
goldtree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\\2_18_gold.swc"
)
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\2_18_test.swc"
)
recall1, precision1, vertical_tree = length_metric(
gold_swc_tree=goldtree,
test_swc_tree=testTree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
recall2, precision2, vertical_tree = length_metric(
gold_swc_tree=testTree,
test_swc_tree=goldtree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
self.assertEqual(recall1, 0.7030284661586385)
self.assertEqual(recall2, 0.8685749970409651)
self.assertEqual(precision1, 0.7174338664651955)
self.assertEqual(precision2, 0.8511348243456205)
def test_len_4(self):
goldtree = SwcTree()
testTree = SwcTree()
goldtree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\\conner.swc")
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\conner.swc")
recall1, precision1, vertical_tree = length_metric(
gold_swc_tree=goldtree,
test_swc_tree=testTree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
recall2, precision2, vertical_tree = length_metric(
gold_swc_tree=testTree,
test_swc_tree=goldtree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
self.assertEqual(recall1, 1.0)
self.assertEqual(recall2, 0.0)
self.assertEqual(precision1, 0.9385873563259137)
self.assertEqual(precision2, 0.0)
def web_length_metric(gold_swc, test_swc, method, rad_threshold, len_threshold):
gold_tree = SwcTree()
test_tree = SwcTree()
gold_tree.load_list(adjust_swcfile(gold_swc))
test_tree.load_list(adjust_swcfile(test_swc))
config = {
'method': method,
'len_threshold': len_threshold,
'rad_threshold': rad_threshold
}
recall, precision, vertical_tree = length_metric(gold_swc_tree=gold_tree,
test_swc_tree=test_tree,
abs_dir="",
config=config)
# gold_tree.radius_limit(10)
# test_tree.radius_limit(10)
result = {
'recall': recall,
'precision': precision,
'gold_swc': swc_to_list(gold_tree),
'test_swc': swc_to_list(test_tree),
'vertical_swc': vertical_tree
}
return result
def test_len_3(self):
goldtree = SwcTree()
testTree = SwcTree()
goldtree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\\34_23_10_gold.swc"
)
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\34_23_10_test.swc"
)
recall1, precision1, vertical_tree = length_metric(
gold_swc_tree=goldtree,
test_swc_tree=testTree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
recall2, precision2, vertical_tree = length_metric(
gold_swc_tree=testTree,
test_swc_tree=goldtree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
self.assertEqual(recall1, 0.6092362772577844)
self.assertEqual(recall2, 0.5585330586568052)
self.assertEqual(precision1, 0.5318779478680355)
self.assertEqual(precision2, 0.6397682076225172)
def test_len_2(self):
goldtree = SwcTree()
testTree = SwcTree()
goldtree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\\30_18_10_gold.swc"
)
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\30_18_10_test.swc"
)
recall1, precision1, vertical_tree = length_metric(
gold_swc_tree=goldtree,
test_swc_tree=testTree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
recall2, precision2, vertical_tree = length_metric(
gold_swc_tree=testTree,
test_swc_tree=goldtree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
self.assertEqual(recall1, 0.6818040837428125)
self.assertEqual(recall2, 0.6971179817818407)
self.assertEqual(precision1, 0.6327624077188985)
self.assertEqual(precision2, 0.7511474781551107)
def test_rtree(self):
swctree = SwcTree()
swctree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\30_18_10_test.swc"
)
rtree = get_edge_rtree(swctree)
id_edge_dict = get_idedge_dict(swctree)
point = SwcNode(center=[22.5822, 172.856, 300.413])
(line_tuple, dis) = get_nearby_edges(rtree, point, id_edge_dict,
point.radius())[0]
print(
point.distance(
Line(coords=[[15.3249, 130.821, 327.012],
[19.8495, 132.384, 323.395]])))
print("dis = {}, line:{}, {}".format(dis, line_tuple[0]._pos,
line_tuple[1]._pos))
def reconstruct_tree(swc_tree, is_activate, down_pa):
new_swc_tree = SwcTree()
node_list = [node for node in PreOrderIter(swc_tree.root())]
id_node_map = {-1: new_swc_tree.root()}
for node in node_list:
if node.is_virtual():
continue
if is_activate[node.get_id()]:
tmp_node = SwcNode()
tmp_node._id = node.get_id()
tmp_node._type = node._type
tmp_node._pos = copy.copy(node._pos)
tmp_node._radius = node._radius
pa = id_node_map[down_pa[node].get_id()]
tmp_node.parent = pa
id_node_map[node.get_id()] = tmp_node
return new_swc_tree
def test_5(self):
testTree = SwcTree()
goldTree = SwcTree()
goldTree.load("D:\gitProject\mine\PyNeval\\test\data_example\gold\diadem\diadem7.swc")
testTree.load("D:\gitProject\mine\PyNeval\\test\data_example\\test\diadem\diadem7.swc")
get_default_threshold(goldTree)
score = diadem_metric(swc_test_tree=testTree,
swc_gold_tree=goldTree,
config=read_json("D:\gitProject\mine\PyNeval\config\diadem_metric.json"))
print(score)
self.assertEqual(score, 0.5)
class TestGetLcaLength(unittest.TestCase):
test_swc_tree = SwcTree()
test_rtree = None
id_edge_dict = None
def init(self):
self.test_swc_tree.load(
"../../data_example/unit_test/get_nearby_edges_tree1.swc")
self.test_rtree = get_edge_rtree(self.test_swc_tree)
self.id_edge_dict = get_idedge_dict(self.test_swc_tree)
self.test_swc_tree.get_lca_preprocess()
def test_1(self):
self.init()
line_tuple_a = tuple([
self.test_swc_tree.node_from_id(8),
self.test_swc_tree.node_from_id(7)
])
line_tuple_b = tuple([
self.test_swc_tree.node_from_id(7),
self.test_swc_tree.node_from_id(6)
])
e_node1 = EuclideanPoint(center=[1.03, -2.1, 6.31])
e_node2 = EuclideanPoint(center=[3.87, 0.98, 1.17])
test_length = get_lca_length(self.test_swc_tree, \
line_tuple_a, \
line_tuple_b, \
Line(e_node_1=e_node1,
e_node_2=e_node2))
self.assertEqual(test_length, 9.589854552695694)
def test_2(self):
self.init()
line_tuple_a = tuple([
self.test_swc_tree.node_from_id(4),
self.test_swc_tree.node_from_id(3)
])
line_tuple_b = tuple([
self.test_swc_tree.node_from_id(15),
self.test_swc_tree.node_from_id(9)
])
e_node1 = EuclideanPoint(center=[-1.89657, 6.51822, -1.40403])
e_node2 = EuclideanPoint(center=[-2.02446, 0.54277, 7.48183])
test_length = get_lca_length(self.test_swc_tree, \
line_tuple_a, \
line_tuple_b, \
Line(e_node_1=e_node1,
e_node_2=e_node2))
self.assertEqual(test_length, 34.372721303735716)
def test_3(self):
testTree = SwcTree()
goldTree = SwcTree()
goldTree.load("D:\gitProject\mine\PyNeval\\test\data_example\gold\ExampleGoldStandard.swc")
testTree.load("D:\gitProject\mine\PyNeval\\test\data_example\\test\ExampleTest.swc")
# goldtree.load("D:\gitProject\mine\PyNeval\\test\data_example\\gold\\ExampleGoldStandard.swc")
# testTree.load("D:\gitProject\mine\PyNeval\\test\data_example\\test\\ExampleTest.swc")
get_default_threshold(goldTree)
score = diadem_metric(swc_test_tree=testTree,
swc_gold_tree=goldTree,
config=read_json("D:\gitProject\mine\PyNeval\config\diadem_metric.json"))
print(score)
self.assertEqual(score, 0.9564541213063764)
def web_diadem_metric(gold_swc, test_swc, config):
gold_tree = SwcTree()
test_tree = SwcTree()
gold_tree.load_list(adjust_swcfile(gold_swc))
test_tree.load_list(adjust_swcfile(test_swc))
diadem_metric(swc_gold_tree=gold_tree,
swc_test_tree=test_tree,
config=config)
# gold_tree.radius_limit(10)
# test_tree.radius_limit(10)
print(swc_to_list(test_tree))
result = {
'gold_swc': swc_to_list(gold_tree),
'test_swc': swc_to_list(test_tree),
'weight_sum': g_weight_sum,
'score_sum': g_score_sum,
'final_score': g_final_score
}
return result
class TestGetLcaLength(unittest.TestCase):
test_swc_tree = SwcTree()
test_rtree = None
id_edge_dict = None
def init(self):
self.test_swc_tree.load(
"../../data_example/unit_test/get_nearby_edges_tree1.swc")
self.test_rtree = get_edge_rtree(self.test_swc_tree)
self.id_edge_dict = get_idedge_dict(self.test_swc_tree)
self.test_swc_tree.get_lca_preprocess()
def test_1(self):
line_tuple_a = tuple([
self.test_swc_tree.node_from_id(8),
self.test_swc_tree.node_from_id(7)
])
line_tuple_b = tuple([
self.test_swc_tree.node_from_id(7),
self.test_swc_tree.node_from_id(6)
])
e_node1 = EuclideanPoint(center=[1.03, -2.1, 6.31])
e_node2 = EuclideanPoint(center=[3.87, 0.98, 1.17])
get_self_match_edges_e_fast(swc_tree=new_swc_tree,
rad_threshold=dis_threshold,
len_threshold=length_threshold,
list_size=swc_tree.node_count(),
mode="not_self",
DEBUG=False)
color_origin_tree(new_swc_tree, swc_tree)
delete_overlap_node(new_swc_tree)
swc_save(new_swc_tree, out_path)
if __name__ == '__main__':
file_path = "D:\gitProject\mine\PyNeval\\test\data_example\gold\swc_data_2"
out_path = "D:\gitProject\mine\PyNeval\output\swc_data_2"
files = os.listdir(file_path)
for file in files:
tree = SwcTree()
tree.clear()
tree.load(os.path.join(file_path, file))
config = read_json(
"D:\gitProject\mine\PyNeval\config\overlap_detect.json")
overlap_clean(tree, os.path.join(out_path, "clean_" + file), config)
# node = SwcNode(center=[101, 100.1, 100], radius=0.6)
# son = SwcNode(center=[100, 100, 100], radius=0.5)
# pa = SwcNode(center=[102, 100, 100], radius=0.5)
# print(itp_ok(node=node, son=son, pa=pa))
if gold_node.distance(get_kdtree_data(node)) > dis_threshold:
gold_node_knn.remove(node)
if DEBUG:
print("knn of gold = {}".format(gold_node_knn))
for son in gold_node.children:
son_node_knn = test_kdtree.search_knn(son._pos, knn)
if DEBUG:
print("son of gold = {}".format(son_node_knn))
match = check_match(gold_node_knn, son_node_knn, edge_set,
id_center_dict)
if match is not None:
match_edge[tuple([gold_node, son])] = match
if DEBUG:
print(len(match_edge))
return match_edge
# for diadem metric
# def find
if __name__ == "__main__":
goldtree = SwcTree()
goldtree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\\ExampleGoldStandard.swc"
)
get_default_threshold(goldtree)
testTree = SwcTree()
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\ExampleTest.swc")
get_match_edges_p(goldtree, testTree, 3, True)
config=config)
# gold_tree.radius_limit(10)
# test_tree.radius_limit(10)
result = {
'recall': recall,
'precision': precision,
'gold_swc': swc_to_list(gold_tree),
'test_swc': swc_to_list(test_tree),
'vertical_swc': vertical_tree
}
return result
if __name__ == "__main__":
goldtree = SwcTree()
testTree = SwcTree()
goldtree.load("D:\gitProject\mine\PyNeval\\test\data_example\\test\multy_useage\push.swc")
testTree.load("D:\gitProject\mine\PyNeval\\test\data_example\gold\multy_useage\push.swc")
recall1, precision1, vertical_tree = length_metric(gold_swc_tree=goldtree,
test_swc_tree=testTree,
abs_dir="D:\gitProject\mine\PyNeval",
config=read_json(
"D:\gitProject\mine\PyNeval\config\length_metric.json"))
# recall2, precision2, vertical_tree = length_metric(gold_swc_tree=testTree,
# test_swc_tree=goldtree,
# abs_dir="D:\gitProject\mine\PyNeval",
# config=read_json(
def read_from_str(swc_str):
swc_tree = SwcTree()
swc_list = adjust_swcfile(swc_str)
swc_tree.load_list(swc_list)
return swc_tree
# gold_tree.radius_limit(10)
# test_tree.radius_limit(10)
print(swc_to_list(test_tree))
result = {
'gold_swc': swc_to_list(gold_tree),
'test_swc': swc_to_list(test_tree),
'weight_sum': g_weight_sum,
'score_sum': g_score_sum,
'final_score': g_final_score
}
return result
if __name__ == "__main__":
testTree = SwcTree()
goldTree = SwcTree()
goldTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\diadem\diadem11.swc"
)
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\diadem\diadem11.swc"
)
# goldTree.load("D:\gitProject\mine\PyNeval\\test\data_example\\gold\\ExampleGoldStandard.swc")
# testTree.load("D:\gitProject\mine\PyNeval\\test\data_example\\test\\ExampleTest.swc")
get_default_threshold(goldTree)
diadem_metric(swc_test_tree=testTree,
swc_gold_tree=goldTree,
config=read_json(
def test_get_bintree():
goldtree = SwcTree()
goldtree.load("D:\gitProject\mine\PyNeval\\test\data_example\\test\\ExampleTest.swc")
bintree = convert_to_binarytree(goldtree)
return bintree
test_swc_tree,
dis_threshold,
DEBUG=True)
match_length = 0.0
for line_tuple in match_edges:
match_length += line_tuple[0].parent_distance()
gold_total_length = round(gold_swc_tree.length(), 8)
match_length = round(match_length, 8)
if DEBUG:
print("match_length b = {}, gold_total_length = {}".format(
match_length, gold_total_length))
return match_length / gold_total_length
if __name__ == "__main__":
goldtree = SwcTree()
goldtree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\gold\\30_18_10_gold.swc"
)
testTree = SwcTree()
testTree.load(
"D:\gitProject\mine\PyNeval\\test\data_example\\test\\30_18_10_test.swc"
)
start = time.time()
print(length_metric_2_2(gold_swc_tree=goldtree, test_swc_tree=testTree))
print(time.time() - start)