Merge pull request #55 from CSDLLab/2021_0607_add_config_help

HanZhaang · web-flow · commit 72d107487f8d · 2021-06-12T15:23:53.000+08:00
change z scale in to scale including z,y scale. Show schema error
diff --git a/config/branch_metric.json b/config/branch_metric.json
@@ -1,7 +1,7 @@
 {
   "threshold_dis": 2,
   "threshold_mode": 1,
-  "z_scale": 1,
+  "scale": [1, 1, 1],
   "true_positive": 3,
   "missed": 4,
   "excess": 5
diff --git a/config/diadem_metric.json b/config/diadem_metric.json
@@ -7,8 +7,7 @@
   "list_distant_matches": true,
   "list_continuations": true,
   "find_proper_root": true,
-  "z_scale": 1,
-  "TRAJECTORY_NONE": -1.0,
+  "scale": [1, 1, 1],
   "xy_threshold": 1.2,
   "z_threshold": 0.0,
   "default_xy_path_error_threshold": 0.05,
diff --git a/config/length_metric.json b/config/length_metric.json
@@ -2,6 +2,6 @@
   "rad_mode": 1,
   "rad_threshold": 1,
   "len_threshold": 0.2,
-  "z_scale": 1,
+  "scale": [1,1,1],
   "debug": false
 }
diff --git a/config/link_metric.json b/config/link_metric.json
@@ -1,3 +1,3 @@
 {
-  "z_scale": 1
+  "scale": [1, 1, 1]
 }
diff --git a/config/schemas/branch_metric_schema.json b/config/schemas/branch_metric_schema.json
@@ -4,15 +4,19 @@
   "required": [
       "threshold_dis",
       "threshold_mode",
-      "z_scale",
+      "scale",
       "true_positive",
       "missed",
       "excess"
   ],
   "properties": {
-    "threshold_dis": {"type": "number", "exclusiveMinimum": 0},
+    "threshold_dis": {"type": "number", "minimum": 0},
     "threshold_mode": {"type": "number", "enum": [1, 2]},
-    "z_scale": {"type": "number","minimum": 0},
+    "scale": {"type":"array",
+              "additionalItems": {"type": "number", "minimum": 0},
+              "minItems": 3,
+              "maxItems": 3
+    },
     "true_positive": {"type": "integer", "exclusiveMinimum": 0},
     "missed": {"type": "integer", "exclusiveMinimum": 0},
     "excess": {"type": "integer", "exclusiveMinimum": 0}
diff --git a/config/schemas/diadem_metric_schema.json b/config/schemas/diadem_metric_schema.json
@@ -13,8 +13,11 @@
     "list_distant_matches": {"type": "boolean", "default": "false"},
     "list_continuations": {"type": "boolean", "default": "false"},
     "find_proper_root": {"type": "boolean", "default": "true"},
-    "z_scale": {"type": "number", "minimum": 0},
-    "TRAJECTORY_NONE": {"type": "number"},
+    "scale": {"type":"array",
+              "additionalItems": {"type": "number", "minimum": 0},
+              "minItems": 3,
+              "maxItems": 3
+    },
     "xy_threshold": {"type": "number", "minimum": 0},
     "z_threshold": {"type": "number", "minimum": 0},
     "default_xy_path_error_threshold": {"type": "number", "minimum": 0},
diff --git a/config/schemas/length_metric_schema.json b/config/schemas/length_metric_schema.json
@@ -5,14 +5,18 @@
       "rad_mode",
       "rad_threshold",
       "len_threshold",
-      "z_scale",
+      "scale",
       "debug"
   ],
   "properties": {
     "rad_mode": {"type": "number", "enum": [1,2]},
-    "rad_threshold": {"type": "number", "exclusiveMinimum": 0},
-    "len_threshold": {"type": "number", "exclusiveMinimum": 0},
-    "z_scale": {"type": "number", "minimum": 0},
+    "rad_threshold": {"type": "number", "minimum": 0},
+    "len_threshold": {"type": "number", "minimum": 0},
+    "scale": {"type":"array",
+              "additionalItems": {"type": "number", "minimum": 0},
+              "minItems": 3,
+              "maxItems": 3
+    },
     "debug": {"type": "boolean"}
   }
 }
diff --git a/config/schemas/link_metric_schema.json b/config/schemas/link_metric_schema.json
@@ -2,9 +2,13 @@
   "title": "link metric schema",
   "type": "object",
   "required": [
-      "z_scale"
+      "scale"
   ],
   "properties": {
-    "z_scale": {"type": "number", "minimum": 0}
+    "scale": {"type":"array",
+              "additionalItems": {"type": "number", "minimum": 0},
+              "minItems": 3,
+              "maxItems": 3
+    }
   }
 }
diff --git a/config/schemas/overlap_clean_schema.json b/config/schemas/overlap_clean_schema.json
diff --git a/config/schemas/ssd_metric_schema.json b/config/schemas/ssd_metric_schema.json
@@ -5,14 +5,18 @@
       "threshold_mode",
       "ssd_threshold",
       "up_sample_threshold",
-      "z_scale",
+      "scale",
       "debug"
   ],
   "properties": {
     "threshold_mode": {"type": "integer", "enum": [1,2]},
-    "ssd_threshold": {"type": "number", "exclusiveMinimum": 0},
-    "up_sample_threshold": {"type": "number", "exclusiveMinimum": 0},
-    "z_scale": {"type":"number", "minimum": 0},
+    "ssd_threshold": {"type": "number", "minimum": 0},
+    "up_sample_threshold": {"type": "number", "minimum": 0},
+    "scale": {"type":"array",
+              "additionalItems": {"type": "number", "minimum": 0},
+              "minItems": 3,
+              "maxItems": 3
+    },
     "debug": {"type": "boolean"}
   }
 }
diff --git a/config/schemas/up_sample_schema.json b/config/schemas/up_sample_schema.json
diff --git a/config/schemas/volume_metric_schema.json b/config/schemas/volume_metric_schema.json
@@ -7,8 +7,8 @@
       "debug"
   ],
   "properties": {
-    "length_threshold": {"type": "number", "exclusiveMinimum": 0},
-    "intensity_threshold": {"type": "number", "exclusiveMinimum": 0},
+    "length_threshold": {"type": "number", "minimum": 0},
+    "intensity_threshold": {"type": "number", "minimum": 0},
     "debug": {"type": "boolean"}
   }
 }
diff --git a/config/ssd_metric.json b/config/ssd_metric.json
@@ -1,7 +1,7 @@
 {
   "threshold_mode": 1,
-  "ssd_threshold": 1,
-  "up_sample_threshold": 1.0,
-  "z_scale": 1,
+  "ssd_threshold": 2,
+  "up_sample_threshold": 1,
+  "scale": [1,1,1],
   "debug": false
 }
diff --git a/pyneval/cli/pyneval.py b/pyneval/cli/pyneval.py
@@ -240,7 +240,6 @@ def excute_metric(metric, gold_swc_tree, test_swc_tree, config, detail_dir, outp
                      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,
                             json_file_path=os.path.join(output_dir, file_name + ".json"))
diff --git a/pyneval/metric/branch_leaf_metric.py b/pyneval/metric/branch_leaf_metric.py
@@ -148,10 +148,10 @@ def branch_leaf_metric(gold_swc_tree, test_swc_tree, config):
     # read configs
     threshold_dis = config["threshold_dis"]
     threshold_mode = config["threshold_mode"]
-    z_scale = config["z_scale"]
+    scale = config["scale"]
 
-    gold_swc_tree.z_rescale(z_scale)
-    test_swc_tree.z_rescale(z_scale)
+    gold_swc_tree.rescale(scale)
+    test_swc_tree.rescale(scale)
     # in threshold mode 2, threshold is a multiple of the average length of edges
     if threshold_mode == 2:
         # length of the entire gold swc forest
diff --git a/pyneval/metric/diadem_metric.py b/pyneval/metric/diadem_metric.py
@@ -940,9 +940,9 @@ def diadem_metric(gold_swc_tree, test_swc_tree, config):
     diadem_init()
     config_init(config)
     diadam_match_utils.diadem_utils_init(config)
-    z_scale = config["z_scale"]
-    gold_swc_tree.z_rescale(z_scale)
-    test_swc_tree.z_rescale(z_scale)
+    scale = config["scale"]
+    gold_swc_tree.rescale(scale)
+    test_swc_tree.rescale(scale)
     test_kdtree, test_pos_node_dict = point_match_utils.create_kdtree(test_swc_tree.get_node_list())
 
     t_matches = {}
diff --git a/pyneval/metric/length_metric.py b/pyneval/metric/length_metric.py
@@ -88,11 +88,11 @@ def length_metric(gold_swc_tree, test_swc_tree, config):
     rad_mode = config["rad_mode"]
     rad_threshold = config["rad_threshold"]
     len_threshold = config["len_threshold"]
-    z_scale = config["z_scale"]
+    scale = config["scale"]
     debug = config["debug"]
 
-    gold_swc_tree.z_rescale(z_scale)
-    test_swc_tree.z_rescale(z_scale)
+    gold_swc_tree.rescale(scale)
+    test_swc_tree.rescale(scale)
     gold_swc_tree.set_node_type_by_topo(root_id=1)
     test_swc_tree.set_node_type_by_topo(root_id=5)
 
diff --git a/pyneval/metric/link_metric.py b/pyneval/metric/link_metric.py
@@ -39,9 +39,9 @@ def get_extra_pos_nodes(big_set, subset):
 
 
 def link_metric(gold_swc_tree, test_swc_tree, config):
-    z_scale = config['z_scale']
-    gold_swc_tree.z_rescale(z_scale)
-    test_swc_tree.z_rescale(z_scale)
+    scale = config['scale']
+    gold_swc_tree.rescale(scale)
+    test_swc_tree.rescale(scale)
 
     gold_list = gold_swc_tree.get_node_list()
     test_list = test_swc_tree.get_node_list()
diff --git a/pyneval/metric/ssd_metric.py b/pyneval/metric/ssd_metric.py
@@ -103,10 +103,10 @@ def ssd_metric(gold_swc_tree: swc_node.SwcTree, test_swc_tree: swc_node.SwcTree,
     threshold_mode = config["threshold_mode"]
     ssd_threshold = config["ssd_threshold"]
     up_sample_threshold = config["up_sample_threshold"]
-    z_scale = config["z_scale"]
+    scale = config["scale"]
 
-    gold_swc_tree.z_rescale(z_scale)
-    test_swc_tree.z_rescale(z_scale)
+    gold_swc_tree.rescale(scale)
+    test_swc_tree.rescale(scale)
     u_gold_swc_tree = re_sample.up_sample_swc_tree(swc_tree=gold_swc_tree,
                                                    length_threshold=up_sample_threshold)
     u_test_swc_tree = re_sample.up_sample_swc_tree(swc_tree=test_swc_tree,
diff --git a/pyneval/metric/utils/diadam_match_utils.py b/pyneval/metric/utils/diadam_match_utils.py
@@ -8,7 +8,7 @@
 
 _2D = "2d"
 
-global TRAJECTORY_NONE
+TRAJECTORY_NONE = -1.0
 global g_xy_threshold
 global g_z_threshold
 global g_default_xy_path_error_threshold
@@ -24,7 +24,6 @@ def diadem_utils_init(config):
     global g_default_z_path_error_threshold
     global g_local_path_error_threshold
 
-    TRAJECTORY_NONE = config["TRAJECTORY_NONE"]
     g_xy_threshold = config["xy_threshold"]
     g_z_threshold = config["z_threshold"]
     g_default_xy_path_error_threshold = config["default_xy_path_error_threshold"]
diff --git a/pyneval/model/swc_node.py b/pyneval/model/swc_node.py
@@ -469,9 +469,11 @@ def scale(self, sx, sy, sz, adjusting_radius=True):
         for tn in niter:
             tn.scale(sx, sy, sz, adjusting_radius)
 
-    def z_rescale(self, z_scale):
+    def rescale(self, scale):
         for node in self.get_node_list():
-            node.set_z(node.get_z() * z_scale)
+            node.set_z(node.get_z() * scale[2])
+            node.set_y(node.get_y() * scale[1])
+            node.set_x(node.get_x() * scale[0])
 
     def length(self, force_update=False):
         if self._total_length is not None and force_update == False:
diff --git a/setup.py b/setup.py
@@ -9,10 +9,12 @@
       url='https://github.com/bennieHan/PyNeval.git',
       packages=['pyneval', 'pyneval.cli', 'test', 'test.test_model',
                 'test.test_model.diadem_metric', 'test.test_model.length_metric',
-                'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model', 'pyneval.tools', 'pyneval.tools.optimize'],
+                'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model',
+                'pyneval.tools', 'pyneval.tools.optimize'],
       py_modules=['pyneval', 'pyneval.cli', 'test', 'test.test_model',
                 'test.test_model.diadem_metric', 'test.test_model.length_metric',
-                'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model', 'pyneval.tools', 'pyneval.tools.optimize'],
+                'pyneval.io', 'pyneval.metric', 'pyneval.metric.utils', 'pyneval.metric.utils.klib', 'pyneval.model',
+                'pyneval.tools', 'pyneval.tools.optimize'],
       data_files=[('config', glob.glob('config/*.json')),
                   ("config/schemas", glob.glob('config/schemas/*.json'))],
       install_requires=[

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"threshold_dis": 2,`
`3`	`3`	`"threshold_mode": 1,`
`4`		`- "z_scale": 1,`
	`4`	`+ "scale": [1, 1, 1],`
`5`	`5`	`"true_positive": 3,`
`6`	`6`	`"missed": 4,`
`7`	`7`	`"excess": 5`
Original file line number	Diff line number	Diff line change
`@@ -2,6 +2,6 @@`
`2`	`2`	`"rad_mode": 1,`
`3`	`3`	`"rad_threshold": 1,`
`4`	`4`	`"len_threshold": 0.2,`
`5`		`- "z_scale": 1,`
	`5`	`+ "scale": [1,1,1],`
`6`	`6`	`"debug": false`
`7`	`7`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`{`
`2`		`- "z_scale": 1`
	`2`	`+ "scale": [1, 1, 1]`
`3`	`3`	`}`