#If running from editor
if (get_exec_pars().source == CommandSource.ui) and (get_exec_pars().script == "EigerAbsSpec") :
    ROI = {"Region1": [10,5,20, 10], "Region2": [20,15,20, 10]}
    SAVE_SPECTRUM = True
    SAVE_IMAGES = True
    WITH_I0 = True
    SWITCH_POL = False
    EXPOSURE = 1.0
    AVERAGE = 2
    NUMBER_SCANS =1       
    RANGES = [[500.0, 1000.0, 100.0]]
    DRIFT_CORRECTION = True

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

SAVE_DIAGS = True
calculated_shifts={}

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(path="{data}/{year}_{month}/{date}/{seq}%03d_AbsortionSpectrum",  format="csv", layout="table")
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]



av=None
def grab_image(position, scan):
   global av  
   av = average_eiger_frames(AVERAGE, roi=None, wait_next=True)
   
   if SAVE_IMAGES:
       #Scan_Nr = (scan.recordIndex-1)/NUMBER_SCANS           
       #filename = get_exec_pars().path + "/" + ("%02d" % Scan_Nr) + "/s" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)       
       filename = get_exec_pars().path + "/" + str(scan.currentPass) + "/s" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)       
       filename = get_context().setup.expandPath(filename)
       print filename       
       metadata = get_diags() if SAVE_DIAGS else {}
       save_as_tiff(av, filename, metadata=metadata)
       if DRIFT_CORRECTION and (calc_roi is not None):
            global ref_image
            filename = get_exec_pars().path + "/" + str(scan.currentPass) + "_corr/cs" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)       
            filename = get_context().setup.expandPath(filename)
            if ref_image is None:
                ref_image = av
                save_as_tiff(av, filename, metadata=metadata)
            else:
                shift_and_save_as_tiff(av, filename, ref_image, calc_roi, metadata=metadata)
                   
           
class Average(ReadableMatrix):
    def read(self):
        return av.matrix
    def getWidth(self):
        return eiger.dataMatrix.getWidth()
    def getHeight(self):
        return eiger.dataMatrix.getHeight()       
averager=Average()
set_device_alias(averager, "Image") #Set display name
sensors.append(averager) #sensors.append(eiger.getDataMatrix())

#Initialize vartiables
if not get_dry_run() and str(get_setting("AUTO_SWITCH_VALVE")).lower() == "true":
    open_vg10()
if not get_dry_run() and str(get_setting("AUTO_SWITCH_SHUTTER")).lower() == "true":
    caput(FAST_SHTR, 'Open')

#put_id_offset(1, OFFSET_ID_1) #offset on ID1
#put_id_offset(2, OFFSET_ID_2) #offset on ID2


"""
if ID == "ID1":
    current_pol=POL_IDS[POL_ID_1] #get_id_pol(1)
    put_id_pol(1,current_pol)
    caput('X11MA-ID2-GAP:SET',100) #open Gap ID2
elif ID == "ID2":    
    current_pol=POL_IDS[POL_ID_2]#get_id_pol(2)
    put_id_pol(2,current_pol)

    caput('X11MA-Ivg10D1-GAP:SET',100) #open Gap ID1
elif ID == "ID1_ID2":
    polID1=POL_IDS[POL_ID_1]
    polID2=POL_IDS[POL_ID_2]
    put_id_pol(1,polID1)
    put_id_pol(2,polID2)
wait_channel("X11PHS:alldone", 1)
"""


if DRIFT_CORRECTION:
    roi = IMAGING_ROI
    if roi is None:
        roi = DEFAULT_ROI
    calc_roi = Roi(roi.x,roi.y,roi.width, roi.height)
    ref_image = None # grab_frame(image, None, True)

def after_pass(pass_number, scan):
    if SWITCH_POL:
        if pass_number<scan.numberOfPasses:        
           switch_pol()
try:                
    #tscan(rois, 10, 0.1, format="csv", before_read=grab_image, passes = NUMBER_SCANS, tag=tag)
    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()
    if not get_dry_run() and str(get_setting("AUTO_SWITCH_SHUTTER")).lower() == "true":
        caput(FAST_SHTR, 'Close')
    restore_eiger()
    print "Running time: " + str(time.time() - start)