Merge pull request #52 from CSDLLab/2021_6_5_rewrite_detail_save

rewrite detail save

Author: HanZhaang

config/diadem_metric.json

@@ -3,9 +3,9 @@
   "remove_spur": false,
   "count_excess_nodes": true,
   "align_tree_by_root": false,
-  "list_miss": false,
-  "list_distant_matches": false,
-  "list_continuations": false,
+  "list_miss": true,
+  "list_distant_matches": true,
+  "list_continuations": true,
   "find_proper_root": true,
   "z_scale": 1,
   "TRAJECTORY_NONE": -1.0,

config/ssd_metric.json

@@ -1,6 +1,6 @@
 {
   "threshold_mode": 1,
-  "ssd_threshold": 2,
+  "ssd_threshold": 1,
   "up_sample_threshold": 1.0,
   "z_scale": 1,
   "debug": false

pyneval/cli/pyneval.py

@@ -185,16 +185,6 @@ def set_configs(abs_dir, args):
     # info: how many trees read
     print("There are {} test image(s)".format(len(test_swc_trees)))
 
-    # argument: output
-    output_dir = None
-    if args.output:
-        output_dir = os.path.join(abs_dir, args.output)
-
-    # argument: detail
-    detail_dir = None
-    if args.detail:
-        detail_dir = os.path.join(abs_dir, args.detail)
-
     # argument: config
     config_path = args.config
     if config_path is None:
@@ -208,36 +198,46 @@ def set_configs(abs_dir, args):
     except Exception:
         raise Exception("[Error: ]Error in analyzing config json file")
 
+    # argument: output
+    output_dir = None
+    if args.output:
+        output_dir = os.path.join(abs_dir, args.output)
+
+    # argument: detail
+    detail_dir = None
+    if args.detail:
+        detail_dir = os.path.join(abs_dir, args.detail)
+        config["detail"] = True
+
     # argument: debug
     is_debug = args.debug
 
     return gold_swc_tree, test_swc_trees, metric, output_dir, detail_dir, config, is_debug
 
 
-def excute_metric(metric, gold_swc_tree, test_swc_tree, config, detail_dir, output_dir, file_name_extra=""):
+def excute_metric(metric, gold_swc_tree, test_swc_tree, config, detail_dir, output_dir):
     metric_method = get_metric_method(metric)
     test_swc_name = test_swc_tree.get_name()
-    gold_swc_name = gold_swc_tree.get_name()
 
-    result = metric_method(gold_swc_tree=gold_swc_tree, test_swc_tree=test_swc_tree, config=config)
+    result, res_gold_swc_tree, res_test_swc_tree = metric_method(gold_swc_tree=gold_swc_tree,
+                                                                 test_swc_tree=test_swc_tree, config=config)
 
     print("---------------Result---------------")
     for key in result:
         print("{} = {}".format(key.ljust(15, ' '), result[key]))
     print("----------------End-----------------\n")
 
-    if file_name_extra == "reverse":
-        file_name = gold_swc_name[:-4] + "_" + metric + "_" + file_name_extra + ".swc"
-    else:
-        file_name = test_swc_name[:-4] + "_" + metric + "_" + file_name_extra + ".swc"
+    file_name = test_swc_name[:-4] + "_" + metric + "_"
 
     if detail_dir:
-        swc_save(swc_tree=gold_swc_tree,
-                 out_path=os.path.join(detail_dir, file_name))
+        swc_save(swc_tree=res_gold_swc_tree,
+                 out_path=os.path.join(detail_dir, file_name + "recall.swc"))
+        swc_save(swc_tree=res_test_swc_tree,
+                 out_path=os.path.join(detail_dir, file_name + "precision.swc"))
 
     if output_dir:
         read_json.save_json(data=result,
-                            json_file_path=os.path.join(output_dir, file_name))
+                            json_file_path=os.path.join(output_dir, file_name + ".json"))
 
 
 # command program
@@ -254,9 +254,6 @@ def run():
     for test_swc_tree in test_swc_trees:
         excute_metric(metric=metric, gold_swc_tree=gold_swc_tree, test_swc_tree=test_swc_tree,
                       config=config, detail_dir=detail_dir, output_dir=output_dir)
-        if metric in ["length_metric", "diadem_metric"]:
-            excute_metric(metric=metric, gold_swc_tree=test_swc_tree, test_swc_tree=gold_swc_tree,
-                          config=config, detail_dir=detail_dir, output_dir=output_dir, file_name_extra="reverse")
 
 
 if __name__ == "__main__":
@@ -278,4 +275,4 @@ def run():
 
 # pyneval --gold .\\data\test_data\geo_metric_data\gold_34_23_10.swc --test .\data\test_data\geo_metric_data\test_34_23_10.swc --metric branch_metric
 
-# pyneval --gold ./data/test_data/geo_metric_data/gold_fake_data1.swc --test ./data/test_data/geo_test/ --metric branch_metric --detail ./output
+# pyneval --gold ./data/test_data/geo_metric_data/gold_fake_data1.swc --test ./data/test_data/geo_test/test_fake_data1.swc --metric branch_metric --detail ./output/detail --output ./output/output

pyneval/io/read_json.py

@@ -26,7 +26,7 @@ def save_json(json_file_path, data, DEBUG=False):
         raise Exception("[Error: ] \" {} \"  is not a json file. Wrong format".format(json_file_path))
     try:
         with open(json_file_path, 'w') as f:
-            json.dump(data, f)
+            json.dump(data, f, indent=4)
             if DEBUG:
                 print(type(data))
     except:

pyneval/metric/branch_leaf_metric.py

@@ -188,7 +188,7 @@ def branch_leaf_metric(gold_swc_tree, test_swc_tree, config):
         "pt_cost": branch_result_tuple[7],
         "iso_node_num": branch_result_tuple[8]
     }
-    return branch_result
+    return branch_result, gold_swc_tree, test_swc_tree
 
 
 if __name__ == "__main__":

pyneval/metric/diadem_metric.py

@@ -780,24 +780,24 @@ def color_tree_only():
     if g_list_miss:
         if len(g_miss) > 0:
             for node in g_miss:
-                # 3 means this node is missed
-                node.data._type = 2
+                # 9 means this node is missed
+                node.data._type = 9
         if len(g_excess_nodes) > 0:
             for node in g_excess_nodes.keys():
-                # 4 means this node is excessive
-                node.data._type = 3
+                # 10 means this node is excessive
+                node.data._type = 10
 
     if g_list_continuations:
         if len(g_continuation) > 0:
             for node in g_continuation:
-                # 5 means this node is a continuation
-                node.data._type = 4
+                # 11 means this node is a continuation
+                node.data._type = 11
 
     if g_list_distant_matches:
         if len(g_distance_match) > 0:
             for node in g_distance_match:
-                # 6 means this node is a distant match
-                node.data._type = 5
+                # 12 means this node is a distant match
+                node.data._type = 12
 
 
 def print_result():
@@ -821,8 +821,8 @@ def print_result():
                 print("node_ID = {} poi = {} weight = {}".format(
                     node.data.get_id(), node.data._pos, g_weight_dict[node]
                 ))
-                # 3 means this node is missed
-                node.data._type = 2
+                # 9 means this node is missed
+                node.data._type = 9
             print("--END--")
         else:
             print("---Nodes that are missed:None---")
@@ -835,8 +835,8 @@ def print_result():
                 print("node_ID = {} poi = {} weight = {}".format(
                     node.data.get_id(), node.data._pos, g_excess_nodes[node]
                 ))
-                # 4 means this node is excessive
-                node.data._type = 3
+                # 10 means this node is excessive
+                node.data._type = 10
         else:
             print("---extra Nodes in test reconstruction: None---")
 
@@ -848,8 +848,8 @@ def print_result():
                 print("node_ID = {} poi = {} weight = {}".format(
                     node.data.get_id(), node.data._pos, g_weight_dict[node]
                 ))
-                # 5 means this node is a continuation
-                node.data._type = 4
+                # 11 means this node is a continuation
+                node.data._type = 11
         else:
             print("---continuation Nodes None---")
 
@@ -861,8 +861,8 @@ def print_result():
                 print("node_ID = {} poi = {} weight = {}".format(
                     node.data.get_id(), node.data._pos, g_weight_dict[node]
                 ))
-                # 6 means this node is a distant match
-                node.data._type = 5
+                # 12 means this node is a distant match
+                node.data._type = 12
         else:
             print("Distant Matches: none")
 
@@ -935,8 +935,8 @@ def diadem_metric(gold_swc_tree, test_swc_tree, config):
     """
     global g_spur_set
     global g_weight_dict
-    gold_swc_tree.type_clear(0)
-    test_swc_tree.type_clear(1)
+    gold_swc_tree.set_node_type_by_topo(root_id=1)
+    test_swc_tree.set_node_type_by_topo(root_id=5)
     diadem_init()
     config_init(config)
     diadam_match_utils.diadem_utils_init(config)
@@ -979,6 +979,7 @@ def diadem_metric(gold_swc_tree, test_swc_tree, config):
                 print('match1 = {}, match2 = {}'.format(
                     key.data.get_id(), g_matches[key].data.get_id()
                 ))
+    color_tree_only()
     if debug:
         for k in g_weight_dict:
             print("id = {} wt = {}".format(k.data.get_id(), g_weight_dict[k]))
@@ -991,7 +992,7 @@ def diadem_metric(gold_swc_tree, test_swc_tree, config):
         "score_sum": g_score_sum,
         "final_score": g_final_score
     }
-    return res
+    return res, gold_swc_tree, test_swc_tree
 
 
 def pyneval_diadem_metric(gold_swc, test_swc, config):
@@ -1010,7 +1011,7 @@ def pyneval_diadem_metric(gold_swc, test_swc, config):
     gold_tree.load_list(read_swc.adjust_swcfile(gold_swc))
     test_tree.load_list(read_swc.adjust_swcfile(test_swc))
 
-    diadem_res= diadem_metric(gold_swc_tree=gold_tree,
+    diadem_res = diadem_metric(gold_swc_tree=gold_tree,
                               test_swc_tree=test_tree,
                               config=config)
 
@@ -1030,8 +1031,8 @@ def pyneval_diadem_metric(gold_swc, test_swc, config):
     testTree = swc_node.SwcTree()
     goldTree = swc_node.SwcTree()
 
-    goldTree.load("../../data/test_data/topo_metric_data/ExampleGoldStandard.swc")
-    testTree.load("../../data/test_data/topo_metric_data/ExampleTest.swc")
+    goldTree.load("../../data/test_data/topo_metric_data/gold_fake_data3.swc")
+    testTree.load("../../data/test_data/topo_metric_data/test_fake_data3.swc")
     config_utils.get_default_threshold(goldTree)
     config = read_json.read_json("../../config/diadem_metric.json")
     config_schema = read_json.read_json("../../config/schemas/diadem_metric_schema.json")
@@ -1041,9 +1042,9 @@ def pyneval_diadem_metric(gold_swc, test_swc, config):
     except Exception as e:
         raise Exception("[Error: ]Error in analyzing config json file")
 
-    diadem_result = diadem_metric(test_swc_tree=testTree,
-                                  gold_swc_tree=goldTree,
-                                  config=config)
+    diadem_result, tmp1, tmp2 = diadem_metric(test_swc_tree=testTree,
+                                              gold_swc_tree=goldTree,
+                                              config=config)
     print("matched weight = {}\n"
           "total weight   = {}\n"
           "diadem score   = {}\n".

pyneval/metric/length_metric.py

@@ -93,6 +93,8 @@ def length_metric(gold_swc_tree, test_swc_tree, config):
 
     gold_swc_tree.z_rescale(z_scale)
     test_swc_tree.z_rescale(z_scale)
+    gold_swc_tree.set_node_type_by_topo(root_id=1)
+    test_swc_tree.set_node_type_by_topo(root_id=5)
 
     if rad_mode == 1:
         rad_threshold *= -1
@@ -113,7 +115,7 @@ def length_metric(gold_swc_tree, test_swc_tree, config):
         "recall": recall,
         "precision": precision
     }
-    return res
+    return res, gold_swc_tree, test_swc_tree
 
 
 def web_length_metric(gold_swc, test_swc, mode, rad_threshold, len_threshold):

pyneval/metric/link_metric.py

@@ -88,7 +88,7 @@ def link_metric(gold_swc_tree, test_swc_tree, config):
         "edge_loss": edge_loss,
         "tree_dis_loss": tree_dis_loss
     }
-    return res
+    return res, None, None
 
 
 if __name__ == "__main__":

pyneval/metric/ssd_metric.py

@@ -119,10 +119,6 @@ def ssd_metric(gold_swc_tree: swc_node.SwcTree, test_swc_tree: swc_node.SwcTree,
     t2g_score, t2g_num = get_mse(src_tree=u_test_swc_tree, tar_tree=u_gold_swc_tree,
                                  ssd_threshold=ssd_threshold, mode=threshold_mode)
 
-    if "detail_path" in config:
-        swc_writer.swc_save(u_gold_swc_tree, config["detail_path"][:-4] + "_gold_upsampled.swc")
-        swc_writer.swc_save(u_test_swc_tree, config["detail_path"][:-4] + "_test_upsampled.swc")
-
     if debug:
         print("recall_num = {}, pre_num = {}, gold_tot_num = {}, test_tot_num = {} {} {}".format(
             g2t_num, t2g_num, u_gold_swc_tree.size(), u_test_swc_tree.size(), gold_swc_tree.length(), test_swc_tree.length()
@@ -133,6 +129,9 @@ def ssd_metric(gold_swc_tree: swc_node.SwcTree, test_swc_tree: swc_node.SwcTree,
         "recall": 1 - g2t_num/u_gold_swc_tree.size(),
         "precision": 1 - t2g_num/u_test_swc_tree.size()
     }
+
+    if "detail" in config:
+        return res, u_gold_swc_tree, u_test_swc_tree
     return res
 
 

pyneval/metric/volume_metric.py

@@ -104,7 +104,7 @@ def volume_metric(gold_swc_tree, test_swc_tree, config=None):
     res = {
         "recall": recall
     }
-    return res
+    return res, None, None
 
 
 if __name__ == "__main__":