From 85f3b58123e7c9a5cba87555fb361c65a066b05e Mon Sep 17 00:00:00 2001
From: gac-x03da <gac-x03da@x03da-cons-1.psi.ch>
Date: Tue, 19 Feb 2019 11:51:30 +0100
Subject: [PATCH] Closedown

---
 script/HoloScan.py    |  3 ++-
 script/XPSSpectrum.py | 41 +++++++++++++++++++++++++++++++++--------
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/script/HoloScan.py b/script/HoloScan.py
index 45fc9da6..f3520d74 100644
--- a/script/HoloScan.py
+++ b/script/HoloScan.py
@@ -18,7 +18,8 @@ set_adc_averaging()
 set_preference(Preference.PLOT_TYPES, {'Scienta spectrum':1})
 
 try:
-    ascan((ManipulatorPhi, ManipulatorTheta), SENSORS, (PHI_RANGE[0], THETA_RANGE[0]), (PHI_RANGE[1], THETA_RANGE[1]), STEPS, LATENCY, RELATIVE, zigzag = ZIGZAG, before_read=before_readout, after_read = after_readout)
+    ascan((ManipulatorPhi, ManipulatorTheta), SENSORS, (PHI_RANGE[0], THETA_RANGE[0]), (PHI_RANGE[1], THETA_RANGE[1]), STEPS, LATENCY, RELATIVE, zigzag = ZIGZAG, \
+          before_read=before_readout, after_read = after_readout, compression = True)
 finally:
     if ENDSCAN:
         after_scan()   
\ No newline at end of file
diff --git a/script/XPSSpectrum.py b/script/XPSSpectrum.py
index 515efb37..b8bd3978 100644
--- a/script/XPSSpectrum.py
+++ b/script/XPSSpectrum.py
@@ -31,7 +31,7 @@ for i in range(len(ranges)):
     names.append(str(ranges[i]))
 plots = plot(None, names)
 
-for p in plots:
+for p in plots[1:]:
     p.getAxis(p.AxisId.X).label = "kinetic energy"
     eb_axis = NumberAxis("binding energy")
     eb_axis.inverted = True
@@ -45,10 +45,15 @@ for p in plots:
 
 # online spectrum
 
-p = plots[0]
-spectrum_series = p.getSeries(0)
-spectrum_eb_axis = p.chart.plot.getDomainAxis(1)
-def plot_cur_spectrum():
+# p = plots[0]
+# spectrum_series = p.getSeries(0)
+# spectrum_eb_axis = p.chart.plot.getDomainAxis(1)
+def plot_cur_spectrum_eb():
+    """
+    plot online spectrum function for forked task.
+    with binding energy scale.
+    issue: this should not set the axis while the plot is zoomed!
+    """
     global spectrum_series
     global spectrum_eb_axis
     try:
@@ -72,6 +77,18 @@ def plot_cur_spectrum():
         time.sleep(1.0)
     finally:
         print "Stopping spectrum plotting"
+
+def plot_cur_spectrum():
+    try:
+      while get_context().state.running:
+        y = Scienta.spectrum.take(100)
+        x = Scienta.spectrumX
+        spectrum_series.setData(x, y)
+
+        time.sleep(1.0)
+    finally:
+        print "Stopping spectrum plotting"
+
 task = None
 
 
@@ -96,7 +113,7 @@ try:
         xdata = None
         ydata = None
         image_data = None
-        task = fork(plot_cur_spectrum)
+        task = fork(plot_cur_spectrum)        
 
         path="scan" + str(cur_range+1) + "/"
         for cur_iteration in range(vars[2]):   
@@ -107,6 +124,8 @@ try:
                 trig_scienta()
                 spectrum_array = Scienta.spectrum.read()                
                 if beam_ok:
+                    if image_data is None:
+                        (_width, _height) = Scienta.getImageSize()
                     break
             if ydata is None:
                 ydata = spectrum_array
@@ -129,9 +148,15 @@ try:
             eb1 = ephot - elo - workfunc
             eb2 = ephot - ehi - workfunc
             eb_axis.setRange(eb2, eb1)
-
+    
             if save_scienta_image:
                 image_array = Scienta.dataMatrix.read()
+                if _width !=  len(image_array[0]) or _height !=  len(image_array):
+                    err = "Scienta image size changed during the acquisition: " + str((len(image_array[0]), len(image_array))) + " - original: " + str((_width, _height))
+                    print err
+                    log(err)
+                    raise Exception(err)
+                
                 if image_data is None:
                     image_data = image_array
                 else:
@@ -143,7 +168,7 @@ try:
             save_dataset(path + "ScientaSpectrum", ydata)            
             set_attribute(path, "Iterations",cur_iteration+1)
             if save_scienta_image:
-                save_dataset(path + "ScientaImage", image_data)
+                save_dataset(path + "ScientaImage", image_data, features = {"compression":True})
             if cur_iteration==0:
                 save_dataset(path + "ScientaChannels", xdata)
                 set_attribute(path + "ScientaChannels", ATTR_WRITABLE_DIMENSION, 1)