Merge branch 'master' of https://bitbucket.org/cosmicvoids/vide_public

python_tools/void_python_tools/voidUtil/catalogUtil.py

@@ -368,7 +368,8 @@ def loadVoidCatalog(sampleDir, dataPortion="central", loadParticles=True,
                                eigenVecs = np.zeros((3,3)),
                                ))
 
-  print "Read %d voids" % len(catalog.voids)
+  catalog.numVoids = len(catalog.voids)
+  print "Read %d voids" % catalog.numVoids  
 
   print "Loading barycenters..."
   iLine = 0
@@ -565,10 +566,10 @@ def stackVoids(catalog, stackMode = "ball"):
       localPart = catalog.partPos[ getBall(partTree, center, rMax) ]
     else:
       voidPart = getVoidPart(catalog, void.voidID)
-      localPart = np.zeros((3,len(voidPart)))
-      localPart[0,:] = getArray(voidPart, 'x')
-      localPart[1,:] = getArray(voidPart, 'y')
-      localPart[2,:] = getArray(voidPart, 'z')
+      localPart = np.zeros((len(voidPart),3))
+      localPart[:,0] = getArray(voidPart, 'x')
+      localPart[:,1] = getArray(voidPart, 'y')
+      localPart[:,2] = getArray(voidPart, 'z')
 
     shiftedPart = shiftPart(localPart, center, periodicLine, catalog.ranges)
 

python_tools/void_python_tools/voidUtil/matchUtil.py

@@ -71,7 +71,7 @@ def compareCatalogs(baseCatalogDir, compareCatalogDir,
   launchVoidOverlap(baseSample, sample, baseCatalogDir, 
                     compareCatalogDir, binPath, 
                     thisDataPortion=dataPortion, logFile=logFile,
-                    continueRun=False, workDir=workDir,
+                    continueRun=False, 
                     outputFile=stepOutputFileName,
                     matchMethod=matchMethod,
                     strictMatch=strictMatch)

python_tools/void_python_tools/voidUtil/plotUtil.py

@@ -58,6 +58,8 @@ def plotNumberFunction(catalogList,
 
   print "Plotting number function"
   
+  catalogList = np.atleast_1d(catalogList)
+
   plt.clf()
   plt.xlabel("$R_{eff}$ [$h^{-1}Mpc$]", fontsize=14)
   
@@ -160,6 +162,8 @@ def plotEllipDist(catalogList,
   
   ellipDistList = [] 
 
+  catalogList = np.atleast_1d(catalogList)
+
   for (iSample,catalog) in enumerate(catalogList):
     sample = catalog.sampleInfo
     data = getArray(catalog.voids, 'ellipticity')
@@ -167,8 +171,9 @@ def plotEllipDist(catalogList,
     dataWeights = np.ones_like(data)/len(data)
     dataHist, dataBins = np.histogram(data, bins=10, weights=dataWeights,
                                          range=(0.0,0.35)) 
+    binCenters = 0.5*(dataBins[1:] + dataBins[:-1])
   
-    plt.plot(dataBins, dataHist, label=sample.fullName, 
+    plt.plot(binCenters, dataHist, label=sample.fullName, 
              color=colorList[iSample])
   
     ellipDistList.append((dataBins, dataHist,))
@@ -252,13 +257,13 @@ def plotVoidCells(catalog,
 
   voidPart = getVoidPart(catalog, voidID)
 
-  newpart = np.zeros((3,len(voidPart)))
+  newpart = np.zeros((len(voidPart),3))
   volume=np.zeros(len(voidPart))
   radius=np.zeros(len(voidPart))
 
-  newpart[0,:] = getArray(voidPart, 'x')
-  newpart[1,:] = getArray(voidPart, 'y')
-  newpart[2,:] = getArray(voidPart, 'z')
+  newpart[:,0] = getArray(voidPart, 'x')
+  newpart[:,1] = getArray(voidPart, 'y')
+  newpart[:,2] = getArray(voidPart, 'z')
 
   volume = getArray(voidPart, 'volume')
   radius = (3.*volume/(4.*np.pi))**(1./3.)

python_tools/void_python_tools/voidUtil/xcorUtil.py

@@ -119,7 +119,9 @@ def computeXcor(catalog,
   plt.xlim(rmin,rmax)
   plt.ylim(min(10**np.floor(np.log10(abs(Xvm).min())),10**np.floor(np.log10(abs(Xmm).min())))/margin, max(10**np.ceil(np.log10(Xmm.max())),10**np.ceil(np.log10(Xvv.max())))*margin)
   plt.legend([pa, pb, pc],['tt', 'vt', 'vv'],'best',prop={'size':12})
-  plt.savefig(figDir+'/correlation.eps', format='eps', bbox_inches="tight") 
+  plt.savefig(figDir+'/correlation.eps', bbox_inches="tight") 
+  plt.savefig(figDir+'/correlation.pdf', bbox_inches="tight")
+  plt.savefig(figDir+'/correlation.png', bbox_inches="tight")
   plt.clf()