Fix gradient inversion (#196)

* update weights instead of distances while inverting gradient

* add credential file to gitignore

* add info in default values

* Log location of pack

* fix linting

* add invert options based on weight or distance

* * invert distances after checking for outliers
* check for outliers in weights

* updating tests

.gitignore

@@ -120,3 +120,6 @@ cellpack/tests/outputs/
 # data
 data/
 **/converted/*
+
+# credentials
+.creds

cellpack/autopack/Gradient.py

@@ -207,12 +207,15 @@ def set_weights_by_mode(self):
 
         self.scaled_distances = self.get_normalized_values(self.distances)
 
-        if (max(self.scaled_distances) > 1.0) or (min(self.scaled_distances) < 0.0):
+        if (numpy.nanmax(self.scaled_distances) > 1.0) or (
+            numpy.nanmin(self.scaled_distances) < 0.0
+        ):
             raise ValueError(
                 "CHECK CALCULATED DISTANCES",
                 f"Max: {max(self.scaled_distances)}, Min: {min(self.scaled_distances)}",
             )
-        if self.invert:
+
+        if self.invert == "distance":
             self.scaled_distances = 1.0 - self.scaled_distances
         if self.weight_mode == "linear":
             self.weight = 1.0 - self.scaled_distances
@@ -231,8 +234,17 @@ def set_weights_by_mode(self):
         # normalize the weight
         self.weight = self.get_normalized_values(self.weight)
 
+        if (numpy.nanmax(self.weight) > 1.0) or (numpy.nanmin(self.weight) < 0.0):
+            raise ValueError(
+                "CHECK CALCULATED WEIGHTS",
+                f"Max: {max(self.weight)}, Min: {min(self.weight)}",
+            )
+
         self.weight[numpy.isnan(self.weight)] = 0
 
+        if self.invert == "weight":
+            self.weight = 1.0 - self.weight
+
         # TODO: talk to Ludo about calculating gaussian weights
 
     def getMaxWeight(self, listPts):

cellpack/autopack/interface_objects/default_values.py

@@ -8,8 +8,8 @@
     "weight_mode": "linear",
     "pick_mode": "linear",
     "description": "Linear gradient in the X direction",
-    "reversed": False,
-    "invert": False,
+    "reversed": False,  # is the direction of the vector reversed?
+    "invert": None,  # options: "weight", "distance"
     "mode_settings": {},
     "weight_mode_settings": {},
 }

cellpack/autopack/interface_objects/gradient_data.py

@@ -60,6 +60,15 @@ class ModeOptions(MetaEnum):
     scale_distance_between = "scale_distance_between"
 
 
+class InvertOptions(MetaEnum):
+    """
+    All available options for individual invert modes
+    """
+
+    weight = "weight"
+    distance = "distance"
+
+
 class WeightModeOptions(MetaEnum):
     """
     All available options for individual weight modes
@@ -118,6 +127,7 @@ def validate_gradient_data(self, gradient_data):
         self.validate_weight_mode_settings(
             gradient_data["weight_mode"], gradient_data.get("weight_mode_settings")
         )
+        self.validate_invert_settings(gradient_data["invert"])
 
     def validate_mode_settings(self, mode_name, mode_settings_dict):
         required_options = REQUIRED_MODE_OPTIONS.get(mode_name)
@@ -151,6 +161,16 @@ def validate_weight_mode_settings(
                     f"Missing required weight mode setting {option} for {weight_mode_name}"
                 )
 
+    def validate_invert_settings(
+        self,
+        invert_option,
+    ):
+        if not invert_option:
+            return
+
+        if not InvertOptions.is_member(invert_option):
+            raise ValueError(f"Invalid gradient invert option: {invert_option}")
+
     def set_mode_properties(self, gradient_data):
         if not gradient_data.get("mode_settings"):
             gradient_data["mode_settings"] = {}

cellpack/bin/pack.py

@@ -29,6 +29,8 @@ def pack(recipe, config_path=None, analysis_config_path=None):
 
     :return: void
     """
+    log.info(f"Running in {__file__}")
+
     packing_config_data = ConfigLoader(config_path).config
     recipe_data = RecipeLoader(
         recipe, packing_config_data["save_converted_recipe"]

cellpack/tests/recipes/v2/test_mesh_image_gradient.json

@@ -20,7 +20,7 @@
             "weight_mode": "exponential",
             "pick_mode": "rnd",
             "mode": "vector",
-            "invert": true,
+            "invert": "weight",
             "mode_settings": {
                 "direction": [
                     0.707,
@@ -34,7 +34,7 @@
                 ]
             },
             "weight_mode_settings": {
-                "decay_length": 0.05
+                "decay_length": 0.3
             }
         }
     },    
@@ -61,7 +61,7 @@
                 1,
                 1
             ],
-            "radius": 0.1,
+            "radius": 1,
             "packing_mode": "gradient",
             "gradient": "planar_gradient"
         }

cellpack/tests/test_gradient_data.py

@@ -22,7 +22,7 @@
                 "pick_mode": "linear",
                 "description": "Linear gradient in the X direction",
                 "reversed": False,
-                "invert": False,
+                "invert": None,
                 "name": "gradient_name",
                 "mode_settings": {
                     "direction": [1, 0, 0],
@@ -49,7 +49,7 @@
                 "pick_mode": "linear",
                 "description": "Square gradient in the radial direction",
                 "reversed": False,
-                "invert": False,
+                "invert": None,
                 "name": "gradient_name",
                 "mode_settings": {
                     "center": [0, 0, 0],
@@ -74,7 +74,7 @@
                 "pick_mode": "linear",
                 "description": "Cubic gradient in the Y direction",
                 "reversed": True,
-                "invert": False,
+                "invert": None,
                 "name": "gradient_name",
                 "mode_settings": {"direction": [0, -1, 0]},
                 "weight_mode_settings": {},
@@ -101,7 +101,7 @@
                 "description": "power law gradient from surface",
                 "pick_mode": "linear",
                 "reversed": False,
-                "invert": False,
+                "invert": None,
                 "mode_settings": {
                     "object": "object_name",
                 },