#255 Support for cellsVisualizationSpacingMultiplier

* Removal of old attributes

Author: Lucas Rebscher

netpyne_ui/netpyne_geppetto.py

@@ -41,33 +41,6 @@ def __init__(self):
         jupyter_geppetto.context = {'netpyne_geppetto': self}
 
     def getData(self):
-        # TODO: this needs to be moved into the metadata.py of netpyne repository.
-        metadata['netParams']['children']['cellsVisualizationSpacingMultiplierX'] = {
-            "label": "Cells visualization spacing multiplier X",
-            "help": "Multiplier for spacing in X axis in 3d visualization of cells (default: 1)",
-            "suggestions": "",
-            "hintText": "",
-            "type": "float"
-        }
-        metadata['netParams']['children']['cellsVisualizationSpacingMultiplierY'] = {
-            "label": "Cells visualization spacing multiplier Y",
-            "help": "Multiplier for spacing in Y axis in 3d visualization of cells (default: 1)",
-            "suggestions": "",
-            "hintText": "",
-            "type": "float"
-        }
-        metadata['netParams']['children']['cellsVisualizationSpacingMultiplierZ'] = {
-            "label": "Cells visualization spacing multiplier Z",
-            "help": "Multiplier for spacing in Z axis in 3d visualization of cells (default: 1)",
-            "suggestions": "",
-            "hintText": "",
-            "type": "float"
-        }
-
-        self.netParams.cellsVisualizationSpacingMultiplierX = 1
-        self.netParams.cellsVisualizationSpacingMultiplierY = 1
-        self.netParams.cellsVisualizationSpacingMultiplierZ = 1
-
         return {
             "metadata": metadata,
             "netParams": self.netParams.todict(),

netpyne_ui/netpyne_model_interpreter.py

@@ -75,7 +75,7 @@ def extractPopulations(self, netpyne_model, netpyne_geppetto_library, geppetto_m
                         if 'pt3d' in sec['geom']:
                             points = sec['geom']['pt3d']
                             for i in range(len(points) - 1):
-                                # draw soma as a cylinder, not as a sphere (more accurate representation of 3d pts)  
+                                # draw soma as a cylinder, not as a sphere (more accurate representation of 3d pts)
                                 visualType.variables.append(self.factory.createCylinder(str(sec_name),
                                                                                         bottomRadius=float(
                                                                                             points[i][3] / 2),
@@ -93,20 +93,17 @@ def extractPopulations(self, netpyne_model, netpyne_geppetto_library, geppetto_m
             # Save the cell position and update elements in defaultValue and size
             populations[cell['tags']['pop']].size = populations[cell['tags']['pop']].size + 1
             populations[cell['tags']['pop']].defaultValue.elements.append(
-                ArrayElement(index=len(populations[cell['tags']['pop']].defaultValue.elements),
-                             position=Point(
-                                 x=float(cell['tags']['x'] * getattr(netpyne_model.net.params,
-                                                                     "cellsVisualizationSpacingMultiplierX", 1.0)),
-                                 y=-float(cell['tags']['y'] * getattr(netpyne_model.net.params,
-                                                                      "cellsVisualizationSpacingMultiplierY", 1.0)),
-                                 z=float(cell['tags']['z'] * getattr(netpyne_model.net.params,
-                                                                     "cellsVisualizationSpacingMultiplierZ", 1.0))
-                             )
-                             )
+                ArrayElement(
+                    index=len(populations[cell['tags']['pop']].defaultValue.elements),
+                    position=Point(
+                        x=float(cell['tags']['x'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[0]),
+                        y=-float(cell['tags']['y'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[1]),
+                        z=float(cell['tags']['z'] * netpyne_model.net.params.cellsVisualizationSpacingMultiplier[2])
+                    )
+                )
             )
 
     def extractInstances(self, netpyne_model, netpyne_geppetto_library, geppetto_model):
         instance = pygeppetto.Variable(id='network')
         instance.types.append(netpyne_geppetto_library.types[0])
         geppetto_model.variables.append(instance)
-        pass

webapp/components/definition/configuration/NetPyNESimConfig.js

@@ -410,28 +410,6 @@ class NetPyNESimConfig extends React.Component {
               model="netParams.rotateCellsRandomly"
             />
           </NetPyNEField>
-
-          <NetPyNEField id="netParams.cellsVisualizationSpacingMultiplierX">
-            <NetPyNETextField
-              fullWidth
-              variant="filled"
-              model="netParams.cellsVisualizationSpacingMultiplierX"
-            />
-          </NetPyNEField>
-          <NetPyNEField id="netParams.cellsVisualizationSpacingMultiplierY">
-            <NetPyNETextField
-              fullWidth
-              variant="filled"
-              model="netParams.cellsVisualizationSpacingMultiplierY"
-            />
-          </NetPyNEField>
-          <NetPyNEField id="netParams.cellsVisualizationSpacingMultiplierZ">
-            <NetPyNETextField
-              fullWidth
-              variant="filled"
-              model="netParams.cellsVisualizationSpacingMultiplierZ"
-            />
-          </NetPyNEField>
         </div>
       );
     }