add explaination on the detail type

config/branch_metric.json

@@ -2,7 +2,7 @@
   "threshold_dis": 2,
   "threshold_mode": 1,
   "z_scale": 1,
-  "true_positive_type": 3,
-  "false_negative_type": 4,
-  "false_positive_type": 5
+  "true_positive": 3,
+  "missed": 4,
+  "excess": 5
 }

config/schemas/branch_metric_schema.json

@@ -5,16 +5,16 @@
       "threshold_dis",
       "threshold_mode",
       "z_scale",
-      "true_positive_type",
-      "false_negative_type",
-      "false_positive_type"
+      "true_positive",
+      "missed",
+      "excess"
   ],
   "properties": {
     "threshold_dis": {"type": "number", "exclusiveMinimum": 0},
     "threshold_mode": {"type": "number", "enum": [1, 2]},
     "z_scale": {"type": "number","minimum": 0},
-    "true_positive_type": {"type": "integer", "exclusiveMinimum": 0},
-    "false_negative_type": {"type": "integer", "exclusiveMinimum": 0},
-    "false_positive_type": {"type": "integer", "exclusiveMinimum": 0}
+    "true_positive": {"type": "integer", "exclusiveMinimum": 0},
+    "missed": {"type": "integer", "exclusiveMinimum": 0},
+    "excess": {"type": "integer", "exclusiveMinimum": 0}
   }
 }

pyneval/cli/pyneval.py

@@ -13,6 +13,8 @@
 from pyneval.metric import branch_leaf_metric
 from pyneval.metric import link_metric
 from pyneval.metric import ssd_metric
+from pyneval.metric.utils import anno_utils
+
 
 METRICS = {
     'diadem_metric': {
@@ -193,10 +195,9 @@ def set_configs(abs_dir, args):
 
     config = read_json.read_json(config_path)
     config_schema = read_json.read_json(config_schema_path)
-    try:
-        jsonschema.validate(config, config_schema)
-    except Exception:
-        raise Exception("[Error: ]Error in analyzing config json file")
+
+    jsonschema.validate(config, config_schema)
+
 
     # argument: output
     output_dir = None
@@ -230,10 +231,15 @@ def excute_metric(metric, gold_swc_tree, test_swc_tree, config, detail_dir, outp
     file_name = test_swc_name[:-4] + "_" + metric + "_"
 
     if detail_dir:
-        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 res_gold_swc_tree is not None:
+            swc_save(swc_tree=res_gold_swc_tree,
+                     out_path=os.path.join(detail_dir, file_name + "recall.swc"),
+                     extra=anno_utils.get_detail_type(metric))
+        if res_test_swc_tree is not None:
+            swc_save(swc_tree=res_test_swc_tree,
+                     out_path=os.path.join(detail_dir, file_name + "precision.swc"),
+                     extra=anno_utils.get_detail_type(metric))
+
 
     if output_dir:
         read_json.save_json(data=result,

pyneval/io/swc_writer.py

@@ -46,13 +46,15 @@ def print_swc(object):
         print_line_tuple_swc(object)
 
 
-def swc_save(swc_tree, out_path):
+def swc_save(swc_tree, out_path, extra=None):
     if not is_path_valid(out_path):
         return False
     swc_node_list = swc_tree.get_node_list()
     swc_tree.sort_node_list(key="id")
     with open(out_path, 'w') as f:
         f.truncate()
+        if extra is not None:
+            f.write(extra)
         for node in swc_node_list:
             if node.is_virtual():
                 continue

pyneval/metric/branch_leaf_metric.py

@@ -161,9 +161,9 @@ def branch_leaf_metric(gold_swc_tree, test_swc_tree, config):
         threshold_dis = threshold_dis * tot_dis / edge_num
     # denote the color id of different type of nodes.
     color = [
-        config["true_positive_type"],
-        config["false_negative_type"],
-        config["false_positive_type"]
+        config["true_positive"],
+        config["missed"],
+        config["excess"]
     ]
     gold_swc_tree.type_clear(0, 0)
     test_swc_tree.type_clear(0, 0)

pyneval/metric/utils/anno_utils.py

@@ -0,0 +1,48 @@
+from pyneval.io.read_json import read_json
+
+
+def get_detail_type(metric_name):
+    detail_type_annotation = dict()
+    detail_type_annotation["ssd_metric"] = "# 1: gold standard root\n" \
+                                           "# 2: gold standard branch(degree >= 3)\n" \
+                                           "# 3: gold standard continuation(degree == 2)\n" \
+                                           "# 4: gold standard leaf(degree == 1)\n" \
+                                           "# 5: reconstruction root\n" \
+                                           "# 6: reconstruction branch(degree >= 3)\n" \
+                                           "# 7: reconstruction continuation(degree == 2)\n" \
+                                           "# 8: reconstruction leaf(degree == 1)\n" \
+                                           "# 9: mismatched node(regardless rules above)\n\n"
+    detail_type_annotation["length_metric"] = "# 1: gold standard root\n" \
+                                              "# 2: gold standard branch(degree >= 3)\n" \
+                                              "# 3: gold standard continuation(degree == 2)\n" \
+                                              "# 4: gold standard leaf(degree == 1)\n" \
+                                              "# 5: reconstruction root\n" \
+                                              "# 6: reconstruction branch(degree >= 3)\n" \
+                                              "# 7: reconstruction continuation(degree == 2)\n" \
+                                              "# 8: reconstruction leaf(degree == 1)\n" \
+                                              "# 9: edge between this node and its parent is mismatched" \
+                                              "(regardless rules above)\n\n"
+    detail_type_annotation["branch_metric"] = "# type of nodes in this metric detail could be change in configs\n" \
+                                              "# true_positive_type: successfully reconstructed nodes, " \
+                                              "exists in both GS and R\n" \
+                                              "# missed: wrongly reconstructed as negative. " \
+                                              "exist in GS but not in R\n" \
+                                              "# excess: wrongly reconstructed as positive. " \
+                                              "exist in R but not in GS.\n\n"
+    detail_type_annotation["diadem_metric"] = "# 1: gold standard root\n" \
+                                              "# 2: gold standard branch(degree >= 3)\n" \
+                                              "# 3: gold standard continuation(degree == 2)\n" \
+                                              "# 4: gold standard leaf(degree == 1)\n" \
+                                              "# 5: reconstruction root\n" \
+                                              "# 6: reconstruction branch(degree >= 3)\n" \
+                                              "# 7: reconstruction continuation(degree == 2)\n" \
+                                              "# 8: reconstruction leaf(degree == 1)\n" \
+                                              "# 9: missed: exist in GS but not in R\n" \
+                                              "# 10 excess: exist in R but not in GS\n\n"
+    if metric_name not in detail_type_annotation:
+        return None
+    return detail_type_annotation[metric_name]
+
+
+if __name__ == "__main__":
+    print(get_detail_type("branch_metric"))