Time optimizations

config/settings.properties

@@ -1,12 +1,12 @@
-#Wed Feb 05 13:59:28 CET 2020
+#Sun Feb 09 15:51:55 CET 2020
 HARMONIC_ID_1=1
 ALPHA_ID_2=0.0
-ENERGY=800.0
+ENERGY=708.5
 ALPHA_ID_1=0.0
-POL_ID_2=Lin_Hor
-POL_ID_1=Lin_Hor
-OFFSET_ID_1=0.0
-NORM_FILE=/sls/X11MA/data/X11MA/Data1/public/PEEM/2020_02/20200205/Take_Image_350/0/i350_1_0.tif
-ID=ID2
-OFFSET_ID_2=0.0
+POL_ID_2=Circ_Minus
+POL_ID_1=Circ_Plus
+OFFSET_ID_1=-2.5
+NORM_FILE=/sls/X11MA/data/X11MA/Data1/public/PEEM/2020_02/20200206/Take_Image_402/0/i402_1_0.tif
+ID=ID1_ID2
+OFFSET_ID_2=-2.5
 HARMONIC_ID_2=1

config/variables.properties

@@ -1,2 +1,2 @@
-#Wed Feb 05 14:20:03 CET 2020
-FileSequentialNumber=381
+#Tue Feb 11 15:43:01 CET 2020
+FileSequentialNumber=568

devices/image.properties

@@ -1,4 +1,4 @@
-#Wed Feb 05 10:26:08 CET 2020
+#Sat Feb 08 23:55:14 CET 2020
 spatialCalOffsetY=NaN
 spatialCalOffsetX=NaN
 colormapLogarithmic=false
@@ -6,10 +6,10 @@ scale=1.0
 grayscale=false
 spatialCalScaleX=NaN
 spatialCalScaleY=NaN
-colormapMax=1000.0
+colormapMax=200.0
 rescaleOffset=0.0
 roiWidth=-1
-colormap=Flame
+colormap=Grayscale
 invert=false
 colormapMin=0.0
 rotationCrop=false

devices/norm.properties

@@ -1,4 +1,4 @@
-#Wed Feb 05 13:41:09 CET 2020
+#Mon Feb 10 22:27:33 CET 2020
 spatialCalOffsetY=NaN
 spatialCalOffsetX=NaN
 colormapLogarithmic=false
@@ -6,7 +6,7 @@ scale=1.0
 grayscale=false
 spatialCalScaleX=NaN
 spatialCalScaleY=NaN
-colormapMax=2.0
+colormapMax=1.5
 rescaleOffset=0.0
 roiWidth=-1
 colormap=Grayscale
@@ -19,7 +19,7 @@ spatialCalUnits=null
 flipVertically=false
 roiHeight=-1
 flipHorizontally=false
-colormapAutomatic=true
+colormapAutomatic=false
 roiY=0
 roiX=0
 transpose=false

script/devices/eiger.py

@@ -90,10 +90,10 @@ def grab_frame(source, roi=None, wait_next=False, rmv_outliers=True):
     if wait_next:
         if str(eiger.grabMode)=="Single":
             eiger.start()
-            #eigar.waitCacheChange(20000)
+        #eiger.getDataArray().waitCacheChange(2000)
         source.waitNext(20000)
     #ret = load_image(Utils.grayscale(source.output, Rectangle(roi[0], roi[1], roi[2], roi[3]) if (roi is not None) else None))
-    time.sleep(1.0)
+    time.sleep(0.01)
     data=source.data
     if roi is not None:
         data = data.getRoi(Rectangle(roi[0], roi[1], roi[2], roi[3]))
@@ -141,15 +141,13 @@ def remove_outliers(imgdata, threshold = 1e9, replace_value=None):
     return data
 """
 
-def save_as_tiff(data, filename, check=False, show = False):
+def _save_as_tiff(data, filename, check=False, show = False):
     if type(data) == Data:
         ip = load_array(data.matrix)
     else:
         ip = data
         
     data = get_ip_array(ip)
-    #ip.show()
-    #plot(data)
     if not os.path.exists(os.path.dirname(filename)):
         os.makedirs(os.path.dirname(filename))    
     save_image(ip, filename,"tiff")    
@@ -157,10 +155,16 @@ def save_as_tiff(data, filename, check=False, show = False):
     if check:
         import java.util.Arrays  as Arrays
         ip=open_image(filename)
-        read = get_ip_array(ip)
-        if not Arrays.deepEquals(read, data):
-            raise Exception("Error reading array")
-        #plot(read)
+        read = get_ip_array(ip)        
+        print (" ------> Error reading array: " + str(filename))
+
+    
+def save_as_tiff(data, filename, check=False, show = False, parallel=True):
+    if parallel:
+        fork((_save_as_tiff,(filename, check, show)),)
+    else:
+        _save_as_tiff(data, filename, check, show)
+
 
 def trigger_eiger(wait=False):
     eiger.start()

script/local.py

@@ -288,6 +288,7 @@ def assert_machine_ok(wait = True):
     ID1status=get_id_control(1)
     ID2status=get_id_control(2)
     Ringstatus=get_ring_status()	
+ 
     oldRingstatus=Ringstatus
     checkRing=0    
 

script/templates/Eiger2Img.py

@@ -25,12 +25,13 @@ AVERAGE = [int(AVERAGE_1), int(AVERAGE_2)]
 AVERAGE = [int(AVERAGE_1), int(AVERAGE_2)]
 ENERGY = [ENERGY_1, ENERGY_2]
 POLARIZATION = [POLARIZATION_1, POLARIZATION_2]
-
 
 if METHOD == "Two_Energies":
     for en in [ENERGY_1, ENERGY_2]:
         if en < 89.9 or en > 2000:
             raise Exception("Bad energy argument")
+
+start = time.time()
 
 path = "{data}/{year}_{month}/{date}" + "/" + METHOD + "_{seq}%03d"
 set_exec_pars(path= path, format="txt", layout="table", open=True)
@@ -155,14 +156,13 @@ def save_image_file(frame, cycle=-1, frame_index=0):
     if SHOW_IMAGES:    
         plot(frame.matrix if (type(frame) == Data) else get_ip_array(frame), name = get_image_file_name(cycle, frame_index, True))
     if AUTO_SAVE and (frame is not None):        
-        filename = get_image_file_name(cycle, frame_index)
+        filename = get_image_file_name(cycle, frame_index)
         save_as_tiff(frame, filename, check=False)
         log(filename)
         print filename
         # log("SV:"+Format(startvoltage,"0.000")+" OB:"+Format(objective,"0.00")+" ST:"+Format(LEEMtemp,"0.0"))		
 
 eiger.stop()
-eiger.grabMode=eiger.GrabMode.Single
 eiger.grabMode=eiger.GrabMode.Single
 try:
     #Do the measurement loop
@@ -175,12 +175,13 @@ try:
         if METHOD == "Two_Energies":        
             change_energy(ENERGY_1)
     
-        ###??? SETAR POLARIZATION?     
+        ###??? SETAR POLARIZATION?     
         #time.sleep(1)
     
-        for i in range(2):
-            assert_status_ok()
-            eiger.setExposure(EXPOSURE[i])
+        for i in range(2):
+            if (cycle == 1) or  (METHOD != "Take_Image"):
+                assert_status_ok()
+                eiger.setExposure(EXPOSURE[i])
             print "--- Grabing " + str(AVERAGE[i])+ " frames - cycle: " + str(cycle) + " step: " + str(i)
             ret = grab_frames(image, AVERAGE[i], roi=None, wait_next=True)
             frames.append(average_frames(ret) if AVERAGE[i] > 1 else ret[0])
@@ -196,7 +197,7 @@ try:
                 switch_pol()
             if METHOD == "Two_Energies":            
                 print "--- Switching energy..."
-                change_energy(ENERGY_2)
+                change_energy(ENERGY_2)
             #time.sleep(1)
     
         if (METHOD == "Two_Pol") or (METHOD == "Two_Energies"):        
@@ -213,7 +214,7 @@ try:
         # temp = getLEEMtemp()
         # log(0 , "Temp : " + Format(temp,"0.00") + " OB : " + Format(objective,"0.00") + " StigmaA : " + " StigmaB : " )
         # Auto average and save
-    
+    
     if (METHOD != "Take_Image") and (MEASUREMENTS > 1) and (AUTO_SAVE == 1):
         print "--- Averaging..."
         for i in range(len(frames)):
@@ -225,8 +226,9 @@ try:
                 measures.append(ip)
             #av = average_frames(measures) #Result is transposed???
             av=average_ips (measures, roi=None, as_float=True)                  
-            save_image_file(av, -1, i)        
+            save_image_file(av, -1, i)        
 finally:     
     if not DRY_RUN:   
         close_vg10()   
-    eiger.grabMode=eiger.GrabMode.Continuous
+    eiger.grabMode=eiger.GrabMode.Continuous
+    eiger.start()

script/templates/EigerAbsSpec.py

@@ -10,11 +10,13 @@ if get_exec_pars().source == CommandSource.ui:
     NUMBER_SCANS =1       
     RANGES = [[500.0, 1000.0, 100.0]]
 
-DRY_RUN=False
+DRY_RUN=True
 
 if len(RANGES) == 0: 
     raise Exception("No scan range defined")    
 
+start = time.time()
+
 eiger.stop()
 eiger.grabMode=eiger.GrabMode.Single
 eiger.setExposure(EXPOSURE)
@@ -110,4 +112,5 @@ finally:
     if not DRY_RUN:
         close_vg10()   
     eiger.grabMode=eiger.GrabMode.Continuous
-    eiger.start()
+    eiger.start()
+    print "Running time: " + str(time.time() - start)

script/test/BenchGrab.py

@@ -0,0 +1,21 @@
+eiger.stop()
+eiger.grabMode=eiger.GrabMode.Single
+eiger.setExposure(0.1)
+AVERAGE=1
+
+def grab_image(position, scan):
+    eiger.start()
+    #eiger.getDataArray().waitCacheChange(2000)
+    image.waitNext(2000)
+
+def grab_image(position, scan):    
+   #av = grab_frame(image, roi=None, wait_next=True, rmv_outliers=False)
+   frames = grab_frames(image, AVERAGE, roi=None, wait_next=True)   
+   av = average_frames(frames)
+   if True:
+       filename = get_exec_pars().path + "/" + ("%03d.tif" % scan.recordIndex)       
+       filename = get_context().setup.expandPath(filename)
+       print filename
+       save_as_tiff(av, filename, parallel=True)
+
+tscan(eiger.dataMatrix, 10, 0.01, before_read=grab_image, save=False, plot_disabled=True)