149 lines
4.3 KiB
Python
149 lines
4.3 KiB
Python
#If running from editor
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if (get_exec_pars().source == CommandSource.ui):
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ROI = {"Region1": [10,5,20, 10], "Region2": [60,60,40, 40]}
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SAVE_SPECTRUM = True
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SAVE_IMAGES = True
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WITH_I0 = False
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SWITCH_POL = False
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EXPOSURE = 1.0
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AVERAGE = 2
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NUMBER_SCANS =1
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RANGES = [[500.0, 1000.0, 100.0]]
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print "Starting AbsSpec: ",SAVE_SPECTRUM, SAVE_IMAGES, WITH_I0, SWITCH_POL, EXPOSURE, AVERAGE, NUMBER_SCANS, RANGES
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run("eiger")
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machine_cur=sin
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Keithley_1_raw = cv
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def get_dry_run():
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return True
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def set_outliers_threshold(value):
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set_setting("OUTLIERS_THRESHOLD", int(value))
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def get_outliers_threshold():
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try:
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return int(get_setting("OUTLIERS_THRESHOLD"))
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except:
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return 0
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def get_outliers_mask_file():
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return get_setting("OUTLIERS_MASK_FILE")
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if SWITCH_POL:
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init_pol_switch("Normal")
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log("ROIs: " + str(ROI))
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if len(RANGES) == 0:
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raise Exception("No scan range defined")
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start = time.time()
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init_eiger(exposure=EXPOSURE)
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set_exec_pars(name="AbsortionSpectrum", format="csv", layout="table")
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tag= "AbsortionSpectrum_{seq}%03d_{count}%02d"
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rois = create_roi_devices(ROI)
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if AVERAGE>1:
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for i in range(len(rois)):
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rois[i].monitored = True
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rois[i] = create_averager(rois[i], AVERAGE, -1)
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rois[i].monitored = True
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frames=[]
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class SyncEnergy(Writable):
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def write(self,pos):
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if not get_dry_run():
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put_energy(pos)
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else:
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print "Energy=" + str(pos)
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sync_energy=SyncEnergy()
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set_device_alias(sync_energy, "Energy") #Set display name
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sensors = rois + [machine_cur]
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if WITH_I0:
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sensors = sensors + [Keithley_1_raw]
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####
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def __save_as_tiff(index, data, filename,metadata={}):
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if type(data) == Data:
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ip = load_array(data.matrix)
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else:
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ip = data
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metadata["Timestamp"] = time.strftime("%y/%m/%d %H:%M:%S",time.localtime())
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if not os.path.exists(os.path.dirname(filename)):
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os.makedirs(os.path.dirname(filename))
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save_image(ip, filename,"tiff", metadata)
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d = get_ip_array(ip)
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import java.util.Arrays as Arrays
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ip=open_image(filename)
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read = get_ip_array(ip)
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if not Arrays.deepEquals(read, d):
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print "Error reading array"
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print index, filename
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index=0
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for name,r in ROI.items():
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s=0.0
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for i in range(r[2]):
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for j in range(r[3]):
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#s = s + d[r[0]+i][r[1]+j]
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el=data.getElement(r[0]+i, r[1]+j, False)
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s = s + (0 if (math.isnan(el)) else el)
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roi = data.getRoi(Rectangle(r[0],r[1], r[2], r[3]))
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print name, s, rois[index].take(), roi.integrate(False)
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index=index+1
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####
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av=None
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def grab_image(position, scan):
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global av
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av = average_eiger_frames(AVERAGE, roi=None, wait_next=True)
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if SAVE_IMAGES:
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filename = get_exec_pars().path + "/" + str(scan.currentPass) + "/s" + "{seq}%03d" + "_" + ("%03d.tif" % scan.recordIndex)
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filename = get_context().setup.expandPath(filename)
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#print filename
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#save_as_tiff(av, filename, metadata={})
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#fork((__save_as_tiff,(scan.recordIndex, av, filename)),)
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__save_as_tiff(scan.recordIndex, av, filename)
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class Average(ReadableMatrix):
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def read(self):
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return av.matrix
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def getWidth(self):
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return image.getData().getWidth()
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def getHeight(self):
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return image.getData().getHeight()
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averager=Average()
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set_device_alias(averager, "Image") #Set display name
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sensors.append(averager)
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#Initialize vartiables
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if not get_dry_run() and str(get_setting("AUTO_SWITCH_VALVE")).lower() == "true":
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open_vg10()
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def after_pass(pass_number, scan):
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if SWITCH_POL:
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if pass_number<scan.numberOfPasses:
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switch_pol()
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try:
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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)
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finally:
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if AVERAGE>1:
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for i in range(len(rois)):
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rois[i].parent.monitored = False # Remove listeners on the image
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if not get_dry_run() and str(get_setting("AUTO_SWITCH_VALVE")).lower() == "true":
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close_vg10()
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restore_eiger()
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print "Running time: " + str(time.time() - start) |