Updated the look and feel of Cartograms. Added warping to Polygons.

bin/release_notes.html

@@ -10,6 +10,17 @@
         <h3>New Features</h3>
 		<p>See <b>kiwi.cs.dal.ca/GenGIS/Revision_History</b> for all bug fixes.</p>
 
+		<h4>Version 2.5.3 (April 22, 2017)</h4>
+		<ul>
+			<li> Added the ability to warp pre-existing polygons with cartograms.<\li>
+			<li> Updated the UI to display the UTM grid shift for the Location Multiplier.<\li>
+		</ul>
+
+		<h4>Version 2.5.2 (Aug 07, 2016)</h4>
+		<ul>
+			<li> Fixed read/write bug in Cartogram creation that stopped in on some machines.<\li>
+		</ul>
+
 		<h4>Version 2.5.1 (May 15, 2016)</h4>
 		<ul>
 			<li> Renamed Phylogenetic Distance Plugin to GCPD.<\li>

plugins/PhylogeneticDistance/PhylogeneticDistance.py

@@ -0,0 +1,245 @@
+# execfile("C:\Users\Admin\Documents\PEscript.py")
+from PhylogeneticDistanceLayout import PhylogeneticDistanceLayout
+import GenGIS
+import wx
+from scipy.spatial import Delaunay
+import dendropy
+
+
+class PhylogeneticDistance( PhylogeneticDistanceLayout ):
+
+	combinationMethods = {"Average(Local)": "AVGLOCAL", "Average(Global)": "AVGGLOBAL", "Sum": "SUM"}
+
+	def __init__(self, parent=None):
+		PhylogeneticDistanceLayout.__init__( self, parent )
+		self.SetIcon(wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico", wx.BITMAP_TYPE_ICO))
+
+		if GenGIS.layerTree.GetNumMapLayers() == 0 or GenGIS.layerTree.GetNumLocationSetLayers() == 0 or GenGIS.layerTree.GetNumTreeLayers() == 0:
+			wx.MessageBox("This plugin requires map, location, and tree data to be loaded.", "Additional data required.")
+			self.Close()
+			return
+		# load up measure options
+		for keys in self.combinationMethods.keys():
+			self.m_cboMeasure.Append(keys)
+		self.m_cboMeasure.SetSelection(0)
+		# load up location layers
+		for locLayer in GenGIS.layerTree.GetLocationSetLayers():
+			self.m_cboLocationLayerField.Append(locLayer.GetName())
+		self.m_cboLocationLayerField.SetSelection(0)
+		# load up tree layers
+		for treeIndex in range(0,GenGIS.layerTree.GetNumTreeLayers()):
+			tree = GenGIS.layerTree.GetTreeLayer(treeIndex)
+			self.m_cboTreeLayerField.Append(tree.GetName())
+		self.m_cboTreeLayerField.SetSelection(0)
+		self.OnMeasureChanged("fake")
+
+	def OnOK(self, event):
+		self.Close()
+
+	def OnMeasureChanged(self, event):
+		if self.m_cboMeasure.GetStringSelection() == "Average(Local)":
+			self.txtFullName.SetValue("Average(Local)")
+			self.txtFormula.SetValue("(a + b)/count(a,b)")
+			self.txtDescription.SetValue("This option combines edge weights by averaging every edge associated with a location. The sum of all associated weights is divided by the number of branches associated with that location. This accounts more strongly for differing edge counts between nodes.")
+
+		elif self.m_cboMeasure.GetStringSelection() == "Average(Global)":
+			self.txtFullName.SetValue("Average(Global)")
+			self.txtFormula.SetValue("(a + b)/ (Number of Locations)")
+			self.txtDescription.SetValue("This option combines edge weights by averaging every edge associated with a location. The sum of all associated weights is divided by the number of locations. This more strongly preserves network like signal")
+
+		elif self.m_cboMeasure.GetStringSelection() == "Sum":
+			self.txtFullName.SetValue("Sum")
+			self.txtFormula.SetValue(" a + b ")
+			self.txtDescription.SetValue("This option combines edge weights by summing every edge associated with a location.")
+
+	def OnCalculate(self, event):
+		# get selected location layer
+		self.locSetIndex = self.m_cboLocationLayerField.GetSelection()
+		# get selected tree layer
+		self.treeIndex = self.m_cboTreeLayerField.GetSelection()
+		# get selected combination method
+		selectedMethod = self.m_cboMeasure.GetStringSelection()
+
+		self.locWeights = self.Main( self.locSetIndex, self.treeIndex, self.combinationMethods[selectedMethod] )
+		self.PrintWeights(self.locSetIndex, self.locWeights)
+
+	def PrintWeights(self, locSetIndex, locWeights):
+		locSet = GenGIS.layerTree.GetLocationSetLayer(locSetIndex)
+		for i in range(0, locSet.GetNumLocationLayers() ):
+			loc = locSet.GetLocationLayer(i)
+			if i in locWeights.keys():
+				value = locWeights[i]
+			else:
+				continue
+
+			printStr = "%s: %s\n" %(loc.GetName(), value)
+			self.txtLog.AppendText(printStr)
+		self.txtLog.AppendText("\n\n")
+
+
+	def OnAddToGenGIS(self, event):
+		self.AddDataToLocationLayer()
+
+	def CombineWeights(self, phyloWeights, comb):
+		final = {}
+		if comb == "SUM":
+			for key in phyloWeights.keys():
+				val = sum(phyloWeights[key])
+				final[key] = val
+
+		elif comb == "AVGLOCAL":
+			for key in phyloWeights.keys():
+				sm = sum(phyloWeights[key])
+			#	leng = len(phyloWeights[key])
+				leng = len(phyloWeights[key]) if len(phyloWeights[key])!=0 else 1
+				val = sm/leng
+				final[key]= val
+
+		elif comb == "AVGGLOBAL":
+			leng = 0
+			for key in phyloWeights.keys():
+				sm = sum(phyloWeights[key])
+				leng = leng + len(phyloWeights[key])
+				final[key] = sm
+			for key,val in final.items():
+				final[key] = val/leng
+		return final
+
+	# distribute all the edge weights to locations
+	def WeightsToLocations(self, phyloWeights ):
+		locations={}	
+		for key,value in phyloWeights.items():
+			loc1 = key[0]
+			loc2 = key[1]
+			if loc1 in locations.keys():
+				locations[loc1] += value * .5
+			else:
+				locations[loc1] = value *.5
+
+			if loc2 in locations.keys():
+				locations[loc2] += value * .5
+			else:
+				locations[loc2] = value *.5
+		return locations
+
+	def AddDataToLocationLayer(self):
+		# ADD DATA BACK TO LOCATIONS METADATA
+
+		val = []
+		name = "PhylogeneticDistance"
+		for i in range(0,GenGIS.layerTree.GetNumLocationLayers()):
+			if i in self.locWeights.keys():
+				if isinstance(self.locWeights[i],float):
+					val.append("%0.15f" %self.locWeights[i])
+				else:
+					val.append(str(self.locWeights[i]))
+			#	val.append(""self.locWeights[i])
+			else:
+				val.append("0")
+		GenGIS.layerTree.GetLocationSetLayer(self.locSetIndex).GetController().AddMetadata( name , val )
+
+	def Main(self,locationLayer, treeLayer, combinationMethod):	
+		#need at least location, and tree layers.
+		# check required data has been loaded		
+	#	treeLayer = 0
+	#	locationLayer = 0
+	#	combinationMethod = "AVG"
+
+		# weights of every leaf node against every other
+		newick = GenGIS.layerTree.GetTreeLayer(treeLayer).GetGeoTreeView().GetNewickString()
+		leafNames = GenGIS.layerTree.GetTreeLayer(0).GetGeoTreeView().GetLeafNames()
+		tree = dendropy.Tree.get_from_string(newick,schema="newick")
+		pdm = dendropy.treecalc.PatristicDistanceMatrix(tree)
+
+		# make array of points
+		points = []
+		treeLocationMap = {}
+		PhyloDistance = {}
+		activeLocations = GenGIS.layerTree.GetLocationSetLayer(locationLayer).GetAllActiveLocationLayers()
+		i=0
+
+		# map leaf names to nodes for easy use
+		leafMap = {}
+		for taxon in tree.taxon_set:
+			for leaf in leafNames:
+				if leaf == taxon.label:
+					leafMap[leaf] = taxon
+					continue
+
+		for loc in activeLocations:
+			taxonObjects = []
+
+			east = loc.GetController().GetEasting()
+			north = loc.GetController().GetNorthing()
+			points.append([east,north])
+
+			if loc.GetName() in leafNames:
+				taxonObjects.append( leafMap[ loc.GetName() ] )
+			# translate sequence ID to taxon objects
+			if loc.GetNumSequenceLayers() > 0:
+				for seq in loc.GetAllActiveSequenceLayers():
+					if seq.GetName() in leafNames:
+						taxonObjects.append( leafMap[ seq.GetName() ] )
+						continue
+
+			treeLocationMap[i] = taxonObjects	
+			i += 1
+
+		tri = Delaunay(points)
+		# indices are in the same order as stored by GenGIS in the Active Location Layer Set
+
+		indices = tri.simplices
+		pairs = []
+		for line in indices:
+			pairs.append((line[0],line[1]))
+			pairs.append((line[0],line[2]))
+			pairs.append((line[1],line[2]))
+
+		# total weight to divide pairwise weights by (0-1 metric)
+		totalWeight = tree.length()
+
+		max = 0
+		for pair in pairs:
+			a = pair[0]
+			b = pair[1]
+			dist = 0
+			'''
+			if (a,b) in PhyloDistance.keys():
+				weights = []
+				for t1 in treeLocationMap[a]:
+					for t2 in treeLocationMap[b]:
+						weights.append(1-pdm(t1, t2))
+				PhyloDistance[a,b].extend(weights)
+			else:
+				weights = []
+				for t1 in treeLocationMap[a]:
+					for t2 in treeLocationMap[b]:
+						weights.append(1-pdm(t1, t2))
+				if len(weights) > 0:
+					PhyloDistance[a,b] = weights
+			'''
+			weights = []
+			for t1 in treeLocationMap[a]:
+				for t2 in treeLocationMap[b]:
+					dist = pdm(t1,t2)
+					weights.append(dist)
+					if dist > max:
+						max = dist
+			if (a,b) in PhyloDistance.keys():
+				PhyloDistance[a,b].extend(weights)
+			else:
+				PhyloDistance[a,b] = weights
+		flipWeights = True
+		if flipWeights:
+			# flip PD so that closely related things have the largest values
+			for key, val in PhyloDistance.iteritems():
+				weights = []
+				for wght in val:
+					wght = max - wght
+					weights.append(wght)
+
+				PhyloDistance[key] = weights
+		phyloDistComb = self.CombineWeights(PhyloDistance, combinationMethod)
+	#	print phyloDistComb
+		locationWeights = self.WeightsToLocations(phyloDistComb)
+		return locationWeights