Startup

devices/CurrentCamera.properties

@@ -1,4 +1,4 @@
-#Thu May 11 11:21:30 CEST 2017
+#Wed May 17 08:34:25 CEST 2017
 colormap=Flame
 colormapAutomatic=true
 colormapMax=0.0
@@ -6,11 +6,11 @@ colormapMin=0.0
 flipHorizontally=false
 flipVertically=false
 grayscale=false
-imageHeight=-1
-imageWidth=-1
+imageHeight=2160
+imageWidth=2560
 invert=false
-regionStartX=0
-regionStartY=0
+regionStartX=1
+regionStartY=1
 rescaleFactor=1.0
 rescaleOffset=0.0
 roiHeight=-1
@@ -21,9 +21,9 @@ rotation=0.0
 rotationCrop=false
 scale=1.0
 serverURL=localhost\:10000
-spatialCalOffsetX=NaN
-spatialCalOffsetY=NaN
-spatialCalScaleX=NaN
-spatialCalScaleY=NaN
+spatialCalOffsetX=-1057.4895329398094
+spatialCalOffsetY=-1420.5549062527236
+spatialCalScaleX=-8.510638153514359
+spatialCalScaleY=-8.235817137431614
 spatialCalUnits=mm
 transpose=false

devices/cam1.properties

@@ -1,4 +1,4 @@
-#Thu May 11 13:01:43 CEST 2017
+#Thu May 11 14:22:56 CEST 2017
 colormap=Temperature
 colormapAutomatic=true
 colormapMax=30000.0
@@ -6,8 +6,8 @@ colormapMin=0.0
 flipHorizontally=false
 flipVertically=false
 grayscale=false
-imageHeight=0
-imageWidth=0
+imageHeight=1628
+imageWidth=1280
 invert=false
 offsetX=0.0
 offsetY=0.0

devices/cam2.properties

@@ -1,4 +1,4 @@
-#Thu May 11 13:01:43 CEST 2017
+#Thu May 11 14:22:56 CEST 2017
 colormap=Grayscale
 colormapAutomatic=true
 colormapMax=255.0
@@ -6,8 +6,8 @@ colormapMin=0.0
 flipHorizontally=false
 flipVertically=false
 grayscale=false
-imageHeight=0
-imageWidth=0
+imageHeight=1680
+imageWidth=1744
 invert=false
 offsetX=0.0
 offsetY=0.0

plugins/GunScan.java

@@ -22,7 +22,7 @@ import javax.swing.JSpinner;
 public class GunScan extends Panel {
 
     LinePlotErrorSeries seriesEnergy = new LinePlotErrorSeries("Energy");
-    LinePlotErrorSeries seriesEnergySpread = new LinePlotErrorSeries("Energy Spread");
+    LinePlotErrorSeries seriesEnergySpread = new LinePlotErrorSeries("Energy Spread", null, 2);
     double dispersion;
     double energy0;
 
@@ -30,7 +30,7 @@ public class GunScan extends Panel {
         initComponents();
         plot.setStyle(LinePlotJFree.Style.ErrorY);
         plot.addSeries(seriesEnergy);
-        plot.addSeries(seriesEnergySpread);
+        plot.addSeries(seriesEnergySpread);        
         plot.getAxis(Plot.AxisId.X).setLabel("Gun Phase");
         plot.getAxis(Plot.AxisId.Y).setLabel("Energy (MeV)");
         plot.getAxis(Plot.AxisId.Y2).setLabel("Energy Spread (MeV)");

script/CPython/gfitoff.py

@@ -0,0 +1,30 @@
+import numpy as np
+import scipy.optimize
+
+
+def gfitoff(x, y, off=None, amp=None, com=None, sigma=None):
+    if off is None:
+        off = y.min()  # good enough starting point for offset
+
+    if com is None:
+        com = x[y.argmax()]
+
+    if amp is None:
+        amp = y.max() - off
+
+    # For normalised gauss curve sigma=1/(amp*sqrt(2*pi))
+    if sigma is None:
+        surface = np.trapz((y-off), x=x)
+        sigma = surface / (amp * np.sqrt(2 * np.pi))
+    try:
+        popt, pcov = scipy.optimize.curve_fit(gauss_fn, x, y, p0=[off, amp, com, sigma], method='lm')
+        popt[3] = abs(popt[3])  # sigma should be returned as positive
+    except Exception as e:
+        print("Gauss fitting not successful.\n" + str(e))
+        popt = [off, amp, com, abs(sigma)]
+
+    return popt
+
+
+def gauss_fn(x, a, b, c, d):
+    return a + b * np.exp(-(np.power((x - c), 2) / (2 * np.power(d, 2))))

script/CPython/hfitoff.py

@@ -0,0 +1,23 @@
+import numpy as np
+from scipy.optimize import leastsq
+
+
+def hfitoff(data, xdeg):
+    """
+    Harmonic fit with offset
+    """
+    start, end = min(xdeg), max(xdeg)
+    guess_amplitude = 2 ** 0.5 * np.std(data)
+    guess_phase = 0
+    guess_offset = np.mean(data)
+    xrad = xdeg / 180 * np.pi
+    optimize_func = lambda x: x[0] * np.sin(xrad + x[1]) + x[2] - data
+    fit_amplitude, fit_phase, fit_offset = leastsq(optimize_func, [guess_amplitude, guess_phase, guess_offset])[0]
+    fit_xdeg = np.linspace(start, end, 100)
+    fit_data = fit_amplitude * np.sin(fit_xdeg / 180 * np.pi + fit_phase) + fit_offset
+    ph_crest = 90 - fit_phase / np.pi * 180
+    xdeg_max = xdeg[np.argmax(data)]
+    if start <= ph_crest <= end:
+        return (fit_amplitude, fit_phase, fit_offset, True, ph_crest, fit_xdeg, fit_data)
+    else:
+        return (fit_amplitude, fit_phase, fit_offset, False, xdeg_max, fit_xdeg, fit_data)

script/CPython/wrapper.py

@@ -0,0 +1,10 @@
+from jeputils import *
+
+def hfitoff(data, xdeg):
+    ret =  call_jep("CPython/hfitoff", "hfitoff", [to_npa(data),to_npa(xdeg)])
+    print ret
+    return (ret[0], ret[1], ret[2],ret[3], ret[4],  ret[5].data,ret[6].data)
+
+def gfitoff(x, y, off=None, amp=None, com=None, sigma=None):
+    ret = call_jep("CPython/gfitoff", "gfitoff", [to_npa(x), to_npa(y), off, amp, com, sigma])
+    return ret if ret is None or is_list(ret) else ret.data    

script/RFscan/GunScan.py

@@ -18,7 +18,8 @@ else:
     disp    = args[5]
     energy0 = args[6]
 
-phase = ControlledVariable("Phase", "SINEG01-RSYS:SET-VSUM-PHASE", "SINEG01-RSYS:GET-VSUM-PHASE")
+#phase = ControlledVariable("Phase", "SINEG01-RSYS:SET-VSUM-PHASE", "SINEG01-RSYS:GET-VSUM-PHASE")
+phase = ControlledVariable("Phase", "STEST01-RSYS:SET-VSUM-PHASE", "STEST01-RSYS:GET-VSUM-PHASE")
 phase.config.minValue   =-180.0
 phase.config.maxValue   = 360.0
 phase.config.precision  = 3
@@ -28,7 +29,7 @@ phase.initialize()
 
 phase0 = phase.read()
 
-kill_camtool()
+#kill_camtool()
 check_camtool()
 camtool.start("SINBD01-DSCR010")
 wait_camtool_message()

script/test/TestGaussFitOffset.py

@@ -0,0 +1,15 @@
+run("CPython/wrapper")
+
+x=[-200.30429237268825, -200.2650700434188, -200.22115208318002, -199.9457671375377, -199.86345548879072, -199.85213073174933, -199.35687977133284, -199.13811861090275, -197.97304970346386, -197.2952215624348, -195.09076092936948, -192.92276048970703, -191.96871876227698, -189.49577852322938, -187.9652790409825, -183.63756456925222, -180.04899765472996, -178.43839623242422, -174.07311671294445, -172.0410133577918, -165.90824309893102, -160.99771795989466, -159.30176653939253, -154.27688897558514, -152.0854103810786, -145.75652847587313, -140.80843828908465, -139.23982133191495, -134.27073891256106, -132.12649284133064, -125.95947209775511, -121.00309550337462, -119.26736932643232, -114.2706655484383, -112.07393889578914, -105.72295990367157, -100.8088439880125, -99.2034906238494, -94.30042325164636, -92.15010048151461, -85.92203653534293, -81.03913275494665, -79.27412793784428, -74.33487658582118, -72.06274362408762, -65.76562628131825, -60.91255356825276, -59.20334389560392, -54.33286972659312, -52.19387171350535, -45.94978737932291, -41.03014719193582, -39.301602568238906, -34.35572209014114, -32.04464301272608, -25.8221033382824, -20.922074315528747, -19.21590299233186, -14.31090212502093, -12.217203140101386, -5.9283722049240435, -0.9863587170369246, 0.7408048387279834, 5.71126832601389, 7.972628957879352, 14.204559894256546, 19.11839959633025, 20.8218087836657, 25.678748486941828, 27.822718344586864, 34.062659474970715, 38.9745656819391, 40.77409719734158, 45.72080631619803, 47.974156754056835, 54.23453768983539, 59.12020360609568, 60.77306570712026, 65.70734521458867, 67.8344660434617, 74.03187028154134, 78.96532114824849, 80.76070945985495, 85.74802197591286, 87.9140889204674, 94.18082276873524, 99.25790470037091, 100.68454787413205, 105.7213026221542, 107.79483801526698, 113.99555681638138, 119.0707052529143, 120.72715813056156, 125.77551384921307, 127.91257836719551, 134.2011330887875, 139.23043006997628, 140.71673537840158, 145.76288138835983, 147.80216629676042, 154.06420451405637, 159.0846626604798, 160.76183155710717, 165.73699067536242, 167.9265357747636, 173.96705069576544, 178.2522282751915, 179.9042617354548, 183.54586165856657, 185.23269803071796, 189.41678143751972, 191.87149157986588, 192.8741468985015, 195.0241934550453, 195.966634211846, 197.9821647518146, 198.99006812859284, 199.33202054855676, 199.91897441965887, 200.11536227958896, 200.22280936469997, 200.25181179127208]
+y=[11.0, 6.0, 8.0, 5.0, 11.0, 7.0, 18.0, 11.0, 12.0, 10.0, 8.0, 6.0, 16.0, 4.0, 12.0, 9.0, 15.0, 14.0, 8.0, 20.0, 15.0, 8.0, 9.0, 11.0, 13.0, 12.0, 13.0, 15.0, 13.0, 20.0, 10.0, 7.0, 17.0, 11.0, 20.0, 13.0, 13.0, 23.0, 14.0, 10.0, 17.0, 15.0, 20.0, 16.0, 14.0, 13.0, 18.0, 22.0, 9.0, 20.0, 12.0, 14.0, 17.0, 19.0, 14.0, 14.0, 23.0, 19.0, 15.0, 20.0, 20.0, 21.0, 20.0, 23.0, 22.0, 15.0, 10.0, 17.0, 21.0, 15.0, 23.0, 23.0, 25.0, 18.0, 16.0, 21.0, 22.0, 16.0, 16.0, 14.0, 19.0, 20.0, 18.0, 20.0, 23.0, 13.0, 16.0, 20.0, 25.0, 15.0, 15.0, 17.0, 22.0, 26.0, 19.0, 30.0, 25.0, 17.0, 17.0, 23.0, 16.0, 27.0, 21.0, 21.0, 26.0, 27.0, 21.0, 17.0, 20.0, 20.0, 21.0, 19.0, 25.0, 19.0, 13.0, 23.0, 20.0, 20.0, 18.0, 20.0, 19.0, 25.0]
+
+[off, amp, com, sigma] = gfitoff(x, y, off=None, amp=None, com=None, sigma=None)
+print "Fit: ", [off, amp, com, sigma]
+from mathutils import Gaussian
+
+#Plotting results
+from mathutils import Gaussian
+g = Gaussian(amp, com, sigma)
+fit = [g.value(i)+off for i in x]
+
+plot([y, fit], ["data", "fit"], xdata = x)       

script/test/TestHarmonicFitOffset.py

@@ -0,0 +1,9 @@
+run("CPython/wrapper")
+
+y = [0,2,5,8,15,25, 20, 16,4,-2,-5]
+x = [0,10,20,30,40,50, 60, 70, 80, 90, 100]
+
+r = hfitoff(y, x)
+print r
+
+plot([y,r[6]], ["data", "fit"], [x, r[5]])

script/tmp.py

@@ -0,0 +1,5 @@
+run("hfitoff_wrapper")
+y = [0,2,5,8,15,25, 20, 16,4,-2,-5]
+x = [0,10,20,30,40,50, 60, 70, 80, 90, 100]
+r = hfitoff(y, x)
+plot([y,r[6]], ["data", "fit"], [x, r[5]])