Merge branch 'master' of https://github.com/cidarlab/pyparchmint

Author: rkrishnasanka

parchmint/benchmarking.py

@@ -34,7 +34,9 @@ def characterize_devices(devices: List[Device]) -> npt.NDArray[Any]:
 
         # Save yes if the device has a layer of type CONTROL
         file_info[index, 5] = (
-            "YES" if "CONTROL" in [layer.type for layer in device.layers] else "NO"
+            "YES"
+            if "CONTROL" in [layer.layer_type for layer in device.layers]
+            else "NO"
         )
 
         # Save the max connectiveity of the connection in the device

parchmint/component.py

@@ -147,9 +147,9 @@ def rotation(self) -> float:
         """
         try:
             return self.params.get_param("rotation")
-        except Exception:
-            print("Could not find rotation for component")
-            raise KeyError
+        except Exception as error:
+            print("Could not find rotation for component", error)
+            raise Exception("Could not find rotation for component") from error
 
     @rotation.setter
     def rotation(self, value):
@@ -258,15 +258,16 @@ def rotate_point(
         Returns:
             Tuple[float, float]: A tuple containing the rotated coordinates
         """
+        # pylint: disable=invalid-name, too-many-locals
         # Setup the center to be used the translation matrices
         center_x = self.xspan / 2
         center_y = self.yspan / 2
 
         # Setup all the corner points
-        old_topLeft = np.array((0, 0, 1)).transpose()
-        old_topRight = np.array((self.xspan, 0, 1)).transpose()
-        old_bottomLeft = np.array((0, self.yspan, 1)).transpose()
-        old_bottomRight = np.array((self.xspan, self.yspan, 1)).transpose()
+        old_topleft = np.array((0, 0, 1)).transpose()
+        old_topright = np.array((self.xspan, 0, 1)).transpose()
+        old_bottomleft = np.array((0, self.yspan, 1)).transpose()
+        old_bottomright = np.array((self.xspan, self.yspan, 1)).transpose()
 
         pos = np.array(((xpos), (ypos), (1)))
 
@@ -278,23 +279,23 @@ def rotate_point(
         T2 = np.array(((1, 0, center_x), (0, 1, center_y), (0, 0, 1)))
 
         # Rotate the topRight corner and the bottomLeft corner about the center
-        rotated_topLeft = T2.dot(R.dot(T1.dot(old_bottomLeft)))
-        rotated_topRight = T2.dot(R.dot(T1.dot(old_topLeft)))
-        rotated_bottomRight = T2.dot(R.dot(T1.dot(old_topRight)))
-        rotated_bottomLeft = T2.dot(R.dot(T1.dot(old_bottomRight)))
+        rotated_topleft = T2.dot(R.dot(T1.dot(old_bottomleft)))
+        rotated_topright = T2.dot(R.dot(T1.dot(old_topleft)))
+        rotated_bottomright = T2.dot(R.dot(T1.dot(old_topright)))
+        rotated_bottomleft = T2.dot(R.dot(T1.dot(old_bottomright)))
 
         # Find the new position of the topleft corner by finding the min of all the corner points
         xmin = min(
-            rotated_topLeft[0],
-            rotated_topRight[0],
-            rotated_bottomLeft[0],
-            rotated_bottomRight[0],
+            rotated_topleft[0],
+            rotated_topright[0],
+            rotated_bottomleft[0],
+            rotated_bottomright[0],
         )
         ymin = min(
-            rotated_topLeft[1],
-            rotated_topRight[1],
-            rotated_bottomLeft[1],
-            rotated_bottomRight[1],
+            rotated_topleft[1],
+            rotated_topright[1],
+            rotated_bottomleft[1],
+            rotated_bottomright[1],
         )
 
         T3 = np.array(((1, 0, -xmin), (0, 1, -ymin), (0, 0, 1)))
@@ -315,6 +316,8 @@ def rotate_point_around_center(
         Returns:
             Tuple[float, float]: A tuple containing the rotated coordinates
         """
+        # pylint: disable=invalid-name,too-many-locals
+
         # Setup the center to be used the translation matrices
         center_x = self.xpos + self.xspan / 2
         center_y = self.ypos + self.yspan / 2
@@ -340,23 +343,23 @@ def get_rotated_component_definition(self, angle: int) -> Component:
         Returns:
             Component: [description]
         """
-        new_topLeft = self.rotate_point(0, 0, angle)
-        new_topRight = self.rotate_point(self.xspan, 0, angle)
-        new_bottomLeft = self.rotate_point(0, self.yspan, angle)
-        new_bottomRight = self.rotate_point(self.xspan, self.yspan, angle)
+        new_topleft = self.rotate_point(0, 0, angle)
+        new_topright = self.rotate_point(self.xspan, 0, angle)
+        new_bottomleft = self.rotate_point(0, self.yspan, angle)
+        new_bottomright = self.rotate_point(self.xspan, self.yspan, angle)
 
         # Find xmin, ymin, xmax, ymax for all the corner points
         xmin = min(
-            new_topLeft[0], new_topRight[0], new_bottomLeft[0], new_bottomRight[0]
+            new_topleft[0], new_topright[0], new_bottomleft[0], new_bottomright[0]
         )
         ymin = min(
-            new_topLeft[1], new_topRight[1], new_bottomLeft[1], new_bottomRight[1]
+            new_topleft[1], new_topright[1], new_bottomleft[1], new_bottomright[1]
         )
         xmax = max(
-            new_topLeft[0], new_topRight[0], new_bottomLeft[0], new_bottomRight[0]
+            new_topleft[0], new_topright[0], new_bottomleft[0], new_bottomright[0]
         )
         ymax = max(
-            new_topLeft[1], new_topRight[1], new_bottomLeft[1], new_bottomRight[1]
+            new_topleft[1], new_topright[1], new_bottomleft[1], new_bottomright[1]
         )
 
         # Find the new xspan and yspan
@@ -408,31 +411,31 @@ def rotate_component(self) -> None:
             port.x = new_location[0]
             port.y = new_location[1]
 
-        new_topLeft = self.rotate_point_around_center(
+        new_topleft = self.rotate_point_around_center(
             self.xpos + 0, self.ypos + 0, self.rotation
         )
-        new_topRight = self.rotate_point_around_center(
+        new_topright = self.rotate_point_around_center(
             self.xpos + self.xspan, self.ypos + 0, self.rotation
         )
-        new_bottomLeft = self.rotate_point_around_center(
+        new_bottomleft = self.rotate_point_around_center(
             self.xpos + 0, self.ypos + self.yspan, self.rotation
         )
-        new_bottomRight = self.rotate_point_around_center(
+        new_bottomright = self.rotate_point_around_center(
             self.xpos + self.xspan, self.ypos + self.yspan, self.rotation
         )
 
         # Find xmin, ymin, xmax, ymax for all the corner points
         xmin = min(
-            new_topLeft[0], new_topRight[0], new_bottomLeft[0], new_bottomRight[0]
+            new_topleft[0], new_topright[0], new_bottomleft[0], new_bottomright[0]
         )
         ymin = min(
-            new_topLeft[1], new_topRight[1], new_bottomLeft[1], new_bottomRight[1]
+            new_topleft[1], new_topright[1], new_bottomleft[1], new_bottomright[1]
         )
         xmax = max(
-            new_topLeft[0], new_topRight[0], new_bottomLeft[0], new_bottomRight[0]
+            new_topleft[0], new_topright[0], new_bottomleft[0], new_bottomright[0]
         )
         ymax = max(
-            new_topLeft[1], new_topRight[1], new_bottomLeft[1], new_bottomRight[1]
+            new_topleft[1], new_topright[1], new_bottomleft[1], new_bottomright[1]
         )
 
         # Find the new xspan and yspan

parchmint/device.py

@@ -201,17 +201,17 @@ def remove_valve(self, valve_id) -> None:
 
         self.remove_component(valve_id)
 
-    def compare(self, device: Device, ignore_parameter_diffs: bool = True) -> bool:
+    def compare(self, device: Device, compare_params: bool = False) -> bool:
         """compare against the input device. Return true if they are semnatcally feasible.
 
         Args:
             device (Device): expected device
-            ignore_parameter_diffs (bool): ignore parameter differences. Defaults to True.
+            compare_params (bool): comparision includes parameter differences. Defaults to False.
 
         Returns:
             bool: If semntically feasible, return true. Else false.
         """
-        matcher = SimilarityMatcher(self, device)
+        matcher = SimilarityMatcher(self, device, compare_params=compare_params)
 
         is_same = matcher.is_isomorphic()
         matcher.print_params_diff()
@@ -384,7 +384,7 @@ def remove_layer(self, layer_id: str) -> None:
 
         # Remove all the components and connections associated with the layer
         for component in self.components:
-            if set([layer.ID for layer in component.layers]) == set(layer_to_delete.ID):
+            if {[layer.ID for layer in component.layers]} == set(layer_to_delete.ID):
                 self.remove_component(component.ID)
             else:
                 warn(
@@ -429,7 +429,8 @@ def merge_netlist(self, netlist: Device) -> None:
                 self.add_layer(layer)
                 layer_mapping[layer] = layer
             else:
-                assert layer.ID is not None
+                if layer.ID is None:
+                    raise Exception("Layer ID is None, cannot merge the layers")
                 layer_mapping[layer] = self.get_layer(layer.ID)
 
         for component in netlist.components:
@@ -634,14 +635,16 @@ def to_parchmint_v1_2(self) -> Dict:
         ret["version"] = "1.2"
 
         # Add the valvemap information
-        valve_map = {}
-        valve_type_map = {}
+        valve_objects = []
         for valve, connection in self._valve_map.items():
-            valve_map[valve.ID] = connection.ID
-        ret["valveMap"] = valve_map
-        for valve, valve_type in self._valve_type_map.items():
-            valve_type_map[valve.ID] = str(valve_type)
-        ret["valveTypeMap"] = valve_type_map
+            valve_object = {
+                "componentid": valve.ID,
+                "connectionid": connection.ID,
+                "type": str(self._valve_type_map[valve]),
+            }
+            valve_objects.append(valve_object)
+        ret["valves"] = valve_objects
+
         return ret
 
     @staticmethod
@@ -727,7 +730,7 @@ def from_parchmint_v1(json_data: Dict) -> Device:
         # First always add the layers
         if "layers" in json_data.keys():
             for layer in json_data["layers"]:
-                device_ref.add_layer(Layer(layer))
+                device_ref.add_layer(Layer(json_data=layer))
         else:
             print("no layers found")
 
@@ -799,10 +802,16 @@ def from_parchmint_v1_2(json_data: Dict) -> Device:
         # First always add the layers
         if "layers" in json_data.keys():
             for layer in json_data["layers"]:
-                device_ref.add_layer(Layer(layer))
+                device_ref.add_layer(Layer(json_data=layer))
         else:
             print("no layers found")
 
+        # Second add all the features
+        if "features" in json_data.keys():
+            for feature_json in json_data["features"]:
+                feature = Feature.from_parchmint_v1_2(feature_json, device_ref)
+                device_ref.add_feature(feature)
+
         # Loop through the components
         if "components" in json_data.keys():
             for component_json in json_data["components"]:
@@ -829,23 +838,28 @@ def from_parchmint_v1_2(json_data: Dict) -> Device:
         else:
             print("no params found")
 
-        def get_valve_type(value: str):
-            if value is ValveType.NORMALLY_OPEN:
+        def get_valve_type(value: str) -> ValveType:
+            if value == ValveType.NORMALLY_OPEN:
                 return ValveType.NORMALLY_OPEN
-            elif value is ValveType.NORMALLY_CLOSED:
+            elif value == ValveType.NORMALLY_CLOSED:
                 return ValveType.NORMALLY_CLOSED
             else:
                 raise Exception("Unknown valve type {}".format(value))
 
-        if "valveMap" in json_data.keys():
-            valve_map = json_data["valveMap"]
-            valve_type_map = json_data["valveTypeMap"]
+        if "valves" in json_data.keys():
+            valve_objects = json_data["valves"]
 
-            for key, value in valve_map.items():
+            for valve_object in valve_objects:
+                componentid = valve_object["componentid"]
+                connectionid = valve_object["connectionid"]
+                # Note - Sets it to default normally open if nothign is specified
+                valve_type = valve_object["type"] if "type" in valve_object else None
                 device_ref.map_valve(
-                    device_ref.get_component(key),
-                    device_ref.get_connection(value),
-                    get_valve_type(valve_type_map[key]),
+                    device_ref.get_component(componentid),
+                    device_ref.get_connection(connectionid),
+                    get_valve_type(valve_type)
+                    if valve_type is not None
+                    else ValveType.NORMALLY_OPEN,
                 )
 
         return device_ref

parchmint/layer.py

@@ -1,4 +1,4 @@
-from typing import Optional
+from typing import Dict, Optional
 
 from parchmint.params import Params
 
@@ -9,17 +9,25 @@ class Layer:
     Used to define a layer object that can be used in the device model.
     """
 
-    def __init__(self, json_data=None) -> None:
+    def __init__(
+        self,
+        layer_id: Optional[str] = None,
+        name: Optional[str] = None,
+        layer_type: Optional[str] = None,
+        group: Optional[str] = None,
+        params: Optional[Params] = None,
+        json_data: Optional[Dict] = None,
+    ) -> None:
         """Creates a new instance Layer
 
         Args:
             json (dict, optional): json dict after json.loads(). Defaults to None.
         """
-        self._id: str = ""
-        self.name: str = ""
-        self.type: str = ""
-        self.group: str = ""
-        self.params: Params = Params()
+        self._id: str = "" if layer_id is None else layer_id
+        self.name: str = "" if name is None else name
+        self.layertype: str = "" if layer_type is None else layer_type
+        self.group: str = "" if group is None else group
+        self.params: Params = Params() if params is None else params
 
         if json_data:
             self.parse_from_json(json_data)
@@ -45,6 +53,24 @@ def ID(self, value: str) -> None:
         """
         self._id = value
 
+    @property
+    def layer_type(self) -> str:
+        """Returns the layer type
+
+        Returns:
+            str: layer type
+        """
+        return self.layertype
+
+    @layer_type.setter
+    def layer_type(self, value: str) -> None:
+        """Sets the layer type
+
+        Args:
+            value (str): layer type
+        """
+        self.layertype = value
+
     def parse_from_json(self, json_data):
         """Loads instance data json dict from json.loads()
 
@@ -53,7 +79,7 @@ def parse_from_json(self, json_data):
         """
         self.name = json_data["name"]
         self.ID = json_data["id"]
-        self.type = json_data["type"]
+        self.layertype = json_data["type"]
         self.group = json_data["group"]
         self.params = Params(json_data["params"])
 
@@ -66,7 +92,7 @@ def to_parchmint_v1(self):
         return {
             "name": self.name,
             "id": self.ID,
-            "type": self.type,
+            "type": self.layertype,
             "params": self.params.to_parchmint_v1(),
             "group": self.group,
         }

parchmint/port.py

@@ -10,7 +10,7 @@ def __init__(
         layer: Optional[str] = None,
         x: float = -1,
         y: float = -1,
-        json_data: Dict = {},
+        json_data: Optional[Dict] = None,
     ):
         """Creates a ComponentPort which is used to represent the points
         where a connection connects on the component

parchmint/target.py

@@ -8,7 +8,7 @@ def __init__(
         self,
         component_id: Optional[str] = None,
         port: Optional[str] = None,
-        json_data: Dict = {},
+        json_data: Optional[Dict] = None,
     ):
         """Creates a Target object that describes where the connection will connect to