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 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_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_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)
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)
'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(
"D:\gitProject\mine\PyNeval\config\diadem_metric.json"),
DEBUG=True)
swc_save(goldTree, "D:\gitProject\mine\PyNeval\output\gold_tree_out.swc")
def pyneval(DEBUG=True):
# init path parameter
abs_dir = os.path.abspath("")
sys.path.append(abs_dir)
sys.path.append(os.path.join(abs_dir, "src"))
sys.path.append(os.path.join(abs_dir, "test"))
# read parameter
args = read_parameters()
# set config
# gold/test files
if args.test is None:
test_swc_files = []
else:
test_swc_files = [os.path.join(abs_dir, path) for path in args.test]
gold_swc_file = os.path.join(abs_dir, args.gold)
# reverse
reverse = args.reverse
if reverse is None:
reverse = False
# metric
metric = args.metric
if metric not in metric_list:
raise Exception("[Error: ] Unknown metric method {}".format(
metric
))
# output path
output_dest = args.output
if output_dest is not None:
output_dest = os.path.join(abs_dir, output_dest)
# config
config = args.config
if config is None:
if platform.system() == "Windows":
if metric == "diadem_metric" or metric == "DM":
config = os.path.join(abs_dir, "config\\diadem_metric.json")
if metric in ["overall_length", "matched_length", "OL", "ML"]:
config = os.path.join(abs_dir, "config\\length_metric.json")
if metric in ["overlap_clean", "OD"]:
config = os.path.join(abs_dir, "config\\overlap_clean.json")
elif platform.system() == "Linux":
if metric == "diadem_metric" or metric == "DM":
config = os.path.join(abs_dir, "config/diadem_metric.json")
if metric in ["overall_length", "matched_length", "OL", "ML"]:
config = os.path.join(abs_dir, "config/length_metric.json")
if metric in ["overlap_clean", "OD"]:
config = os.path.join(abs_dir, "config/overlap_clean.json")
if DEBUG:
print("Config = {}".format(config))
# read test trees, gold trees and configs
test_swc_trees = []
for test_swc_file in test_swc_files:
test_swc_trees += read_swc_trees(test_swc_file)
gold_swc_trees = read_swc_trees(gold_swc_file)
config = read_json(config)
# info: how many trees read
print("There are {} test image(s) and {} gold image(s)".format(len(test_swc_trees), len(gold_swc_trees)))
if len(gold_swc_trees) == 0:
raise Exception("[Error: ] No gold image detected")
if len(gold_swc_trees) > 1:
print("[Warning: ] More than one gold image detected, only the first one will be used")
# entries to different metrics
gold_swc_treeroot = gold_swc_trees[0]
for test_swc_treeroot in test_swc_trees:
if metric == "diadem_metric" or metric == "DM":
diadem_metric(swc_test_tree=test_swc_treeroot,
swc_gold_tree=gold_swc_treeroot,
config=read_json("D:\gitProject\mine\PyNeval\config\diadem_metric.json"))
if reverse:
diadem_metric(gold_swc_treeroot, test_swc_treeroot)
if metric == "overall_length" or metric == "OL":
config["method"] = 1
length_metric(gold_swc_treeroot, test_swc_treeroot,
abs_dir, config)
if reverse:
length_metric(test_swc_treeroot, gold_swc_treeroot,
abs_dir, config)
if metric == "matched_length" or metric == "ML":
config["method"] = 2
length_metric(gold_swc_treeroot, test_swc_treeroot,
abs_dir, config)
if reverse:
config["detail"] = config["detail"][:-4] + "_reverse.swc"
length_metric(test_swc_treeroot, gold_swc_treeroot,
abs_dir, config)
if metric == "overlap_clean" or metric == "OC":
# debug
print("entry")
print(config["radius_threshold"])
print(config["length_threshold"])
print(output_dest)
overlap_clean(gold_swc_treeroot, output_dest, 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(
# "D:\gitProject\mine\PyNeval\config\length_metric.json"))
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))