Merge pull request #69 from MetaCell/changePlotMethod

use only one function for plotting

Author: adrianq

netpyne_ui/netpyne_geppetto.py

@@ -211,151 +211,24 @@ def getDirList(self, dir=None, onlyDirs = False):
            elif not onlyDirs:
                dir_list.append({'title': f, 'path': ff})
         return dir_list
-            
-    def getNetPyNE2DNetPlot(self):
-        args = self.getPlotSettings('plot2Dnet')
-        fig = analysis.plot2Dnet(showFig=False, **args)
-        if fig==-1:
-            return fig
-        svgs=[]
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
-    
-    def getNetPyNEShapePlot(self):
-        args = self.getPlotSettings('plotShape')
-        fig = analysis.plotShape(showFig=False, **args)
-        if fig==-1:
-            return fig
-        svgs = []
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
-
-    def getNetPyNEConnectionsPlot(self):
-        args = self.getPlotSettings('plotConn')
-        fig = analysis.plotConn(showFig=False, **args)
-        if fig==-1:
-            return fig
-        svgs=[]
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
-
-    def getNetPyNERasterPlot(self):
-        args = self.getPlotSettings('plotRaster')
-        fig = analysis.plotRaster(showFig=False, **args)
-        if fig==-1:
-            return fig
-        svgs=[]
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
-
-    def getNetPyNETracesPlot(self):
-        args = self.getPlotSettings('plotTraces')
-        figs = analysis.plotTraces(showFig=False, **args)
-        if figs==-1:
-            return figs
-        svgs = []
-        for key, value in figs.iteritems():
-            logging.debug("Found plot for "+ key)
-            svgs.append(ui.getSVG(value))
-        return svgs.__str__()
 
-    def getNetPyNESpikeHistPlot(self):
-        args = self.getPlotSettings('plotSpikeHist')    
-        fig = analysis.plotSpikeHist(showFig=False, **args)
-        if fig==-1:
-            return fig
-        else:
-            svgs=[]
-            svgs.append(ui.getSVG(fig[0]))
-        return svgs.__str__()
-
-    def getNetPyNESpikeStatsPlot(self):
-        args = self.getPlotSettings('plotSpikeStats')
-        fig = analysis.plotSpikeStats(showFig=False, **args)
-        if fig==-1:
-            return fig
-        else:
-            svgs=[]
-            svgs.append(ui.getSVG(fig[0]))
-        return svgs.__str__()
-
-    def getNetPyNEGrangerPlot(self):
-        args = self.getPlotSettings('granger')
-        fig = analysis.granger(plotFig=True, showFig=False, **args)
-        if fig==-1:
-            return fig
-        else:
-            fig=fig[-1]
-        svgs=[]
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
-
-    def getNetPyNERatePSDPlot(self):
-        args = self.getPlotSettings('plotRatePSD')
-        fig = analysis.plotRatePSD(showFig=False, **args)
+    def getPlot(self, plotName, LFPflavour):
+        args = self.getPlotSettings(plotName)
+        if LFPflavour:
+            args['plots'] = [LFPflavour]
+        fig = getattr(analysis, plotName)(showFig=False, **args)[0]
         if fig==-1:
             return fig
-        else:
-            fig=fig[0]
-        svgs = []
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
-        
-    def getNetPyNELFPTimeSeriesPlot(self):
-       args = self.getPlotSettings('plotLFP')
-       args['plots'] = ['timeSeries']
-       fig = analysis.plotLFP(showFig=False, **args)
-       if fig==-1:
-           return fig
-       else:
-            svgs = []
-            svgs.append(ui.getSVG(fig[0][0]))
-       return svgs.__str__()
-
-    def getNetPyNELFPPSDPlot(self):
-        args = self.getPlotSettings('plotLFP')
-        args['plots'] = ['PSD']
-        fig = analysis.plotLFP(showFig=False, **args)
-        if fig==-1:
-            return fig
-        else:
-            svgs = []
-            svgs.append(ui.getSVG(fig[0][0]))
-        
-        return svgs.__str__()
-
-    def getNetPyNELFPSpectrogramPlot(self):
-        args = self.getPlotSettings('plotLFP')
-        args['plots'] = ['spectrogram']
-        fig = analysis.plotLFP(showFig=False, **args)
-        if fig==-1:
-            return fig
-        else:
+        elif isinstance(fig, list):
+            return [ui.getSVG(fig[0])].__str__()
+        elif isinstance(fig, dict):
             svgs = []
-            svgs.append(ui.getSVG(fig[0][0]))
-        
-        return svgs.__str__()
-
-    def getNetPyNELFPLocationsPlot(self):
-        args = self.getPlotSettings('plotLFP')
-        args['plots'] = ['locations']
-        fig = analysis.plotLFP(showFig=False, **args)
-        if fig==-1:
-            return fig
+            for key, value in fig.iteritems():
+                logging.debug("Found plot for "+ key)
+                svgs.append(ui.getSVG(value))
+            return svgs.__str__()
         else:
-            svgs = []
-            svgs.append(ui.getSVG(fig[0][0]))
-        
-        return svgs.__str__()
-
-    def getNetPyNERxDConcentrationPlot(self):
-        args = self.getPlotSettings('plotRxDConcentration')
-        fig = analysis.plotRxDConcentration(showFig=False, **args)
-        if fig==-1:
-            return fig
-        svgs=[]
-        svgs.append(ui.getSVG(fig))
-        return svgs.__str__()
+            return [ui.getSVG(fig)].__str__()
 
     def getAvailablePops(self):
         return netParams.popParams.keys()

utilities/install.py

@@ -46,7 +46,7 @@ def main(argv):
 clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.1-M1')
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')
 
-clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','0.7.9')
+clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.7.9')
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
 
 clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.1-M2','', True )