#If running from editor
if (get_exec_pars().source == CommandSource.ui):
    ROI = {"Region1": [10,5,20, 10], "Region2": [60,60,40, 40]}
    SAVE_SPECTRUM = True
    SAVE_IMAGES = True
    WITH_I0 = False
    SWITCH_POL = False
    EXPOSURE = 1.0
    AVERAGE = 2
    NUMBER_SCANS =1       
    RANGES = [[500.0, 1000.0, 100.0]]

print "Starting AbsSpec: ",SAVE_SPECTRUM, SAVE_IMAGES, WITH_I0, SWITCH_POL, EXPOSURE, AVERAGE, NUMBER_SCANS, RANGES

run("eiger")
machine_cur=sin
Keithley_1_raw = cv
def get_dry_run():
    return True
def set_outliers_threshold(value):
    set_setting("OUTLIERS_THRESHOLD", int(value))
def get_outliers_threshold():
    try:
        return int(get_setting("OUTLIERS_THRESHOLD"))
    except:
        return 0
def get_outliers_mask_file():
    return get_setting("OUTLIERS_MASK_FILE")    

if SWITCH_POL:
    init_pol_switch("Normal")


log("ROIs: " + str(ROI))

if len(RANGES) == 0: 
    raise Exception("No scan range defined")    

start = time.time()

init_eiger(exposure=EXPOSURE)

set_exec_pars(name="AbsortionSpectrum",  format="csv", layout="table")
tag= "AbsortionSpectrum_{seq}%03d_{count}%02d"

rois = create_roi_devices(ROI)

if AVERAGE>1:
    for i in range(len(rois)):  
        rois[i].monitored = True  
        rois[i] = create_averager(rois[i], AVERAGE, -1)
        rois[i].monitored = True


frames=[]


class SyncEnergy(Writable):
    def write(self,pos):
        if not get_dry_run():
            put_energy(pos)
        else:
            print "Energy=" + str(pos)
sync_energy=SyncEnergy()
set_device_alias(sync_energy, "Energy") #Set display name

sensors = rois + [machine_cur]
if WITH_I0:
    sensors = sensors + [Keithley_1_raw]


####
def __save_as_tiff(index, data, filename,metadata={}):
    if type(data) == Data:
        ip = load_array(data.matrix)
    else:
        ip = data
    
    metadata["Timestamp"] = time.strftime("%y/%m/%d %H:%M:%S",time.localtime())
    if not os.path.exists(os.path.dirname(filename)):
        os.makedirs(os.path.dirname(filename))    
    save_image(ip, filename,"tiff", metadata)    
           
    d = get_ip_array(ip)
    import java.util.Arrays  as Arrays
    ip=open_image(filename)
    read = get_ip_array(ip)        
    if not Arrays.deepEquals(read, d):
        print  "Error reading array"  
    print index, filename  
    index=0
    for name,r in ROI.items():
          s=0.0
          for i in range(r[2]):
            for j in range(r[3]):
                #s = s + d[r[0]+i][r[1]+j]
                el=data.getElement(r[0]+i, r[1]+j, False)
                s = s + (0 if (math.isnan(el)) else el)
          roi = data.getRoi(Rectangle(r[0],r[1], r[2], r[3]))
          
          print name, s, rois[index].take(), roi.integrate(False)      
          index=index+1

    
####


av=None
def grab_image(position, scan):
   global av  
   av = average_eiger_frames(AVERAGE, roi=None, wait_next=True)
   
   if SAVE_IMAGES:
       filename = get_exec_pars().path + "/" + str(scan.currentPass) + "/s" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)       
       filename = get_context().setup.expandPath(filename)
       #print filename       
       #save_as_tiff(av, filename, metadata={}) 
       #fork((__save_as_tiff,(scan.recordIndex, av, filename)),)  
       __save_as_tiff(scan.recordIndex, av, filename)
class Average(ReadableMatrix):
    def read(self):
        return av.matrix
    def getWidth(self):
        return image.getData().getWidth()
    def getHeight(self):
        return image.getData().getHeight()       
averager=Average()
set_device_alias(averager, "Image") #Set display name
sensors.append(averager) 

#Initialize vartiables
if not get_dry_run() and str(get_setting("AUTO_SWITCH_VALVE")).lower() == "true":
    open_vg10()


def after_pass(pass_number, scan):
    if SWITCH_POL:
        if pass_number<scan.numberOfPasses:        
           switch_pol()
try:                
    rscan(sync_energy, sensors, RANGES, latency = 0.0 , passes = NUMBER_SCANS, tag=tag, before_read=grab_image, save=SAVE_SPECTRUM,  split=True, keep=False, after_pass=after_pass)
finally:
    if AVERAGE>1:
        for i in range(len(rois)):  
            rois[i].parent.monitored = False # Remove listeners on the image
    if not get_dry_run() and str(get_setting("AUTO_SWITCH_VALVE")).lower() == "true":
        close_vg10()   
    restore_eiger()
    print "Running time: " + str(time.time() - start)