Update to include new hole7 features

AreaPlot.py

@@ -81,6 +81,9 @@ def ReadAreaFile(filename, nx, ny):
 
 #****************MAIN PROGRAM*****************
 
+data = [0.77, 0.91, 0.005451, 0.01382, -1.284, [0.001796, 0.003346, 0.001127, 0.001273, 0.000985, 0.000571]]
+dataij = [0, 0, 1, 1, 0, [4,2,5,4,5,8]]
+
 # First, read the .cfg file
 run = 0
 
@@ -107,6 +110,7 @@ def ReadAreaFile(filename, nx, ny):
 yfit = []
 xneg = []
 yneg = []
+fullfile = open(outputfiledir+"/full_corr.txt","w")
 for i in range(Nx):
     for j in range(Ny):
         rsquared = float((i - NxCenter)**2 + (j - NyCenter)**2)
@@ -119,18 +123,35 @@ def ReadAreaFile(filename, nx, ny):
         else:
             x.append(rsquared)
             y.append(yvalue)
-        if rsquared > 1.1 and rsquared < 10.1 and yvalue > 0:
+        if rsquared > 1.1 and abs(i - NxCenter) < 3 and abs(j - NyCenter) < 3 and yvalue > 0:
+            fullfile.write("i = %d, j = %d, C = %.6f\n"%(i-NxCenter,j-NxCenter,yvalue))
             xfit.append(rsquared)
             yfit.append(yvalue)
 
+xdata = []
+ydata = []
+for i,dat in enumerate(data):
+    if i != 5:
+        if dataij[i] == 0:
+            continue
+        else:
+            xdata.append(dataij[i])
+            ydata.append(data[i])
+    else:
+        for j,d in enumerate(dat):
+            xdata.append(dataij[i][j])
+            ydata.append(data[i][j])
+
 figure()
 title("Covariance vs Distance: %d e-"%NumElec)
 xscale('log')
 yscale('log')
 xlim(0.8, 100.0)
 ylim(1E-5, 1E-1)
-scatter(array(x), array(y))
-scatter(xneg, yneg, color = 'magenta', label = 'Negative Values')
+scatter(xdata, ydata, marker = 'x', s = 50, color = 'green', label = 'Data')
+scatter(array(x), array(y), color = 'blue', label = 'Sim')
+#scatter(xfit, yfit, marker="x", color = 'black')
+#scatter(xneg, yneg, color = 'magenta', label = 'Negative Values')
 
 from scipy import stats
 slope, intercept, r_value, p_value, std_err = stats.linregress(log10(xfit),log10(yfit))
@@ -142,16 +163,20 @@ def ReadAreaFile(filename, nx, ny):
 text(10.0, 0.002, "C01 = %.5g"%((area[NxCenter,NyCenter+1] - Area_0) / Area_0))
 xlabel("$i^2 + j^2$")
 ylabel("$\delta$ Area / Area")
+xlim(0.8,100)
 legend()
-#savefig(outputfiledir+"/plots/Area_%d_%d.pdf"%(run, step))
-savefig("Area_%d_%d.pdf"%(run, step))
+savefig(outputfiledir+"/plots/Area_UnBiased_%d_%d.pdf"%(run, step))
+#savefig("Area_%d_%d.pdf"%(run, step))
 
-file = open("corr.txt","w")
+file = open(outputfiledir+"/corr.txt","w")
 file.write("Slope = %.3f\n"%slope)
 file.write("C10 = %.5g\n"%((area[NxCenter+1,NyCenter] - Area_0) / Area_0))
 file.write("C01 = %.5g\n"%((area[NxCenter,NyCenter+1] - Area_0) / Area_0))
+fullfile.write("Slope = %.3f\n"%slope)
+fullfile.write("C10 = %.5g\n"%((area[NxCenter+1,NyCenter] - Area_0) / Area_0))
+fullfile.write("C01 = %.5g\n"%((area[NxCenter,NyCenter+1] - Area_0) / Area_0))
 file.close()
-
+fullfile.close()
 figure()
 title("Pixel Area: %d e-"%NumElec)
 
@@ -170,5 +195,5 @@ def ReadAreaFile(filename, nx, ny):
 ylim(10.0, 100.0)
 xlabel("X(microns)")
 ylabel("Y(microns)")
-#savefig(outputfiledir+"/plots/PixelAreas_%d_%d.pdf"%(run, step))
-savefig("PixelAreas_%d_%d.pdf"%(run, step))
+savefig(outputfiledir+"/plots/PixelAreas_UnBiased_%d_%d.pdf"%(run, step))
+#savefig("PixelAreas_%d_%d.pdf"%(run, step))

AreaPlot_Corr.py

@@ -0,0 +1,199 @@
+#!/usr/bin/env python
+
+#Author: Craig Lage, NYU; 
+#Date: 16-Nov-15
+
+#This program plots the pixel area plots from the Poisson CCD solver
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+import sys, time, h5py
+
+#****************SUBROUTINES*****************
+
+def ReadConfigFile(filename):
+    # This reads the config file for the necessary settings
+    # and returns a dictionary with the values
+    file = open(filename,'r')
+    lines=file.readlines()
+    file.close()
+    ConfigData = {}
+    try:
+        for line in lines:
+            ThisLine=line.strip().split()
+            ThisLineLength=len(ThisLine)
+            if ThisLineLength < 3:
+                continue
+            if list(ThisLine[0])[0]=='#' or ThisLine[0]=='\n':
+                continue
+            try:
+                ParamName = ThisLine[0]
+                ThisLine.remove(ThisLine[0])
+                for counter,item in enumerate(ThisLine):
+                    if list(item)[0] == '#':
+                        del ThisLine[counter:] # Strip the rest of the line as a comment
+                        continue
+                    if item == '=':
+                        ThisLine.remove(item)
+                        continue
+                if len(ThisLine) == 0:
+                    continue
+                elif len(ThisLine) == 1:
+                    ThisParam = ThisLine[0]
+                    try: ConfigData[ParamName] = int(ThisParam)
+                    except ValueError:
+                        try: ConfigData[ParamName] = float(ThisParam)
+                        except ValueError:
+                            try:
+                                ConfigData[ParamName] = ThisParam
+                            except ValueError:
+                                print "Error reading .cfg file"
+                else:
+                    ThisParam = []
+                    for item in ThisLine:
+                        try: ThisParam.append(int(item))
+                        except ValueError:
+                            try: ThisParam.append(float(item))
+                            except ValueError:
+                                ThisParam.append(item)
+                    ConfigData[ParamName] = ThisParam
+            except:
+                continue
+    except:
+        print "Error reading .cfg file"
+
+    return ConfigData
+
+def ReadAreaFile(filename, nx, ny):
+    area = zeros([nx, ny])
+    file = open(filename, 'r')
+    lines = file.readlines()
+    file.close()
+    for line in lines:
+        items = line.split()
+        if items[0] == "Nx":
+            continue
+        i = int(items[0])
+        j = int(items[1])
+        area[i,j] = float(items[2])
+    return area
+
+
+#****************MAIN PROGRAM*****************
+
+data = [0.77, 0.91, 0.005943, 0.01227, -1.275, [0.001591, 0.002966, 0.000994, 0.000882, 0.000862, 0.000501]]
+dataij = [0, 0, 1, 1, 0, [4,2,5,4,5,8]]
+
+# First, read the .cfg file
+run = 0
+
+configfile = sys.argv[1]
+step = int(sys.argv[2])
+ConfigData = ReadConfigFile(configfile)
+outputfilebase = ConfigData["outputfilebase"]
+outputfiledir = ConfigData["outputfiledir"]
+Nx = ConfigData["PixelBoundaryNx"]
+Ny = ConfigData["PixelBoundaryNy"]
+NxCenter = 4
+NyCenter = 4
+Area_0 = 100.0
+
+filename = outputfiledir + '/' + outputfilebase +'_%d_Area'%step
+
+area = ReadAreaFile(filename, Nx, Ny)
+
+NumElec = step * 1000
+
+x = []
+y = []
+xfit = []
+yfit = []
+xneg = []
+yneg = []
+fullfile = open(outputfiledir+"/full_corr.txt","w")
+for i in range(Nx):
+    for j in range(Ny):
+        rsquared = float((i - NxCenter)**2 + (j - NyCenter)**2)
+        yvalue = (area[i,j] - Area_0) / Area_0
+        if (i == NxCenter and j == NyCenter) or rsquared > 18.0:
+            continue
+        if yvalue < 0:
+            xneg.append(rsquared)
+            yneg.append(-yvalue)
+        else:
+            x.append(rsquared)
+            y.append(yvalue)
+        if rsquared > 1.1 and abs(i - NxCenter) < 3 and abs(j - NyCenter) < 3 and yvalue > 0:
+            fullfile.write("i = %d, j = %d, C = %.6f\n"%(i-NxCenter,j-NxCenter,yvalue))
+            xfit.append(rsquared)
+            yfit.append(yvalue)
+
+xdata = []
+ydata = []
+for i,dat in enumerate(data):
+    if i != 5:
+        if dataij[i] == 0:
+            continue
+        else:
+            xdata.append(dataij[i])
+            ydata.append(data[i])
+    else:
+        for j,d in enumerate(dat):
+            xdata.append(dataij[i][j])
+            ydata.append(data[i][j])
+
+figure()
+title("Covariance vs Distance: %d e-"%NumElec)
+xscale('log')
+yscale('log')
+xlim(0.8, 100.0)
+ylim(1E-5, 1E-1)
+scatter(xdata, ydata, marker = 'x', s = 50, color = 'green', label = 'Data')
+scatter(array(x), array(y), color = 'blue', label = 'Sim')
+#scatter(xfit, yfit, marker="x", color = 'black')
+#scatter(xneg, yneg, color = 'magenta', label = 'Negative Values')
+
+from scipy import stats
+slope, intercept, r_value, p_value, std_err = stats.linregress(log10(xfit),log10(yfit))
+xplot=linspace(0.0, 2.0, 100)
+yplot = slope * xplot + intercept
+plot(10**xplot, 10**yplot, color='red', lw = 2, ls = '--')
+text(10.0, 0.005, "Slope = %.3f"%slope)
+text(10.0, 0.00316, "C10 = %.5g"%((area[NxCenter+1,NyCenter] - Area_0) / Area_0))
+text(10.0, 0.002, "C01 = %.5g"%((area[NxCenter,NyCenter+1] - Area_0) / Area_0))
+xlabel("$i^2 + j^2$")
+ylabel("$\delta$ Area / Area")
+xlim(0.8,100)
+legend()
+savefig(outputfiledir+"/plots/Area_UnBiased_Corr_%d_%d.pdf"%(run, step))
+#savefig("Area_%d_%d.pdf"%(run, step))
+
+file = open(outputfiledir+"/corr.txt","w")
+file.write("Slope = %.3f\n"%slope)
+file.write("C10 = %.5g\n"%((area[NxCenter+1,NyCenter] - Area_0) / Area_0))
+file.write("C01 = %.5g\n"%((area[NxCenter,NyCenter+1] - Area_0) / Area_0))
+fullfile.write("Slope = %.3f\n"%slope)
+fullfile.write("C10 = %.5g\n"%((area[NxCenter+1,NyCenter] - Area_0) / Area_0))
+fullfile.write("C01 = %.5g\n"%((area[NxCenter,NyCenter+1] - Area_0) / Area_0))
+file.close()
+fullfile.close()
+figure()
+title("Pixel Area: %d e-"%NumElec)
+
+for i in range(Nx+1):
+    plot([10.0 + 10.0 * i, 10.0 + 10.0 * i], [10.0, 100.0], color = 'black')
+for j in range(Ny+1):
+    plot([10.0, 100.0], [10.0 + 10.0 * j, 10.0 + 10.0 * j], color = 'black') 
+for i in range(Nx):
+    for j in range(Ny):
+        if i == NxCenter and j == NyCenter:
+            textcolor = 'red'
+        else:
+            textcolor = 'black'
+        text(11.0 + 10.0 * i, 14.0 + 10.0 * j, str(area[i,j]), color = textcolor, fontsize = 8, fontweight = 'bold')
+xlim(10.0, 100.0)
+ylim(10.0, 100.0)
+xlabel("X(microns)")
+ylabel("Y(microns)")
+savefig(outputfiledir+"/plots/PixelAreas_UnBiased_Corr_%d_%d.pdf"%(run, step))
+#savefig("PixelAreas_%d_%d.pdf"%(run, step))