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EnergyScanMockup.py
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import os
import time
import gevent
import logging
from matplotlib.figure import Figure
from matplotlib.backends.backend_agg import FigureCanvasAgg
from HardwareRepository.TaskUtils import *
from AbstractEnergyScan import AbstractEnergyScan
from HardwareRepository.BaseHardwareObjects import HardwareObject
try:
import PyChooch
except:
print ("PyChooch not found")
scan_test_data = [(10841.0, 20.0), (10842.0, 20.0), (10843.0, 20.0),
(10844.0, 20.0), (10845.0, 20.0), (10846.0, 20.0), (10847.0, 20.0),
(10848.0, 20.0), (10849.0, 20.0), (10850.0, 20.0), (10851.0, 20.0),
(10852.0, 20.0), (10853.0, 20.0), (10854.0, 20.0), (10855.0, 20.0),
(10856.0, 20.0), (10857.0, 20.0), (10858.0, 20.00), (10859.0, 20.0),
(10860.0, 20.0), (10861.0, 20.1), (10862.0, 21.4), (10863.0, 30.4),
(10864.9, 80.7), (10865.9, 299.0), (10866.7, 820.8), (10867.5, 2009.2),
(10868.2, 4305.5), (10869.0, 8070.2), (10869.8, 13246.7), (10870.6, 19124.1),
(10871.4, 24430.5), (10872.2, 27843.1), (10873.0, 28654.8), (10873.8, 27092.5),
(10874.6, 24138.5), (10875.4, 20957.3), (10876.0, 18373.6), (10877.0, 16373.8),
(10878.0, 15474.8), (10879.0, 15163.9), (10880.0, 15080.5), (10881.0, 15063.0),
(10882.0, 15060.3), (10883.0, 15059.8), (10884.0, 15059.7), (10885.0, 15059.0),
(10886.0, 15059.0), (10887.0, 15059.0), (10888.0, 15059.0), (10889.0, 15059.0),
(10890.0, 15059.0), (10891.0, 15059.0), (10892.0, 15059.0), (10893.0, 15059.0),
(10894.0, 15059.0), (10895.0, 15059.0), (10896.0, 15059.0), (10897.0, 15059.0),
(10898.0, 15059.0), (10899.0, 15059.0), (10900.0, 15059.0), (10901.0, 15059.0),
(10902.0, 15059.0), (10903.0, 15059.0), (10904.0, 15059.0), (10905.0, 15059.0),
(10906.0, 15059.0), (10907.0, 15059.0), (10908.0, 15059.0), (10909.0, 15059.0),
(10910.0, 15059.0)]
class EnergyScanMockup(AbstractEnergyScan, HardwareObject):
def __init__(self, name):
AbstractEnergyScan.__init__(self)
HardwareObject.__init__(self, name)
def init(self):
self.ready_event = gevent.event.Event()
self.scan_info = {}
self.result_value_emitter = None
self.scan_data = []
self.thEdgeThreshold = 5
self.energy2WavelengthConstant = 12.3980
self.defaultWavelength = 0.976
def emit_result_values(self):
for value_tuple in scan_test_data:
x = value_tuple[0]
y = value_tuple[1]
if not (x == 0 and y == 0):
# if x is in keV, transform into eV otherwise let it like it is
# if point larger than previous point (for chooch)
if len(self.scan_data) > 0:
if x > self.scan_data[-1][0]:
self.scan_data.append([(x < 1000 and x*1000.0 or x), y])
else:
self.scan_data.append([(x < 1000 and x*1000.0 or x), y])
self.emit('scanNewPoint', (x < 1000 and x*1000.0 or x), y)
time.sleep(0.05)
self.scanCommandFinished()
def startEnergyScan(self, element, edge, directory, prefix,
session_id=None, blsample_id=None, exptime=3):
self._element = element
self._edge = edge
self.scan_info = {"sessionId": session_id, "blSampleId": blsample_id,
"element": element,"edgeEnergy": edge}
self.scan_info['transmissionFactor'] = 0
self.scan_info['exposureTime'] = exptime
self.scan_info['startEnergy'] = 0
self.scan_info['endEnergy'] = 0
self.scan_info['beamSizeHorizontal'] = 0
self.scan_info['beamSizeVertical'] = 0
self.scan_data = []
self.scanCommandStarted()
self.result_value_emitter = gevent.spawn(self.emit_result_values)
#self.emit('energyScanFinished', (self.scan_info,))
#self.ready_event.set()
def doChooch(self, elt, edge, scan_directory, archive_directory, prefix):
"""
Descript. :
"""
symbol = "_".join((elt, edge))
pk = 7.519
ip = 7.516
rm = 7.54
fpPeak = -12.6
fppPeak = 20.7
fpInfl = -21.1
fppInfl = 11.9
comm = "Results from mockuResults from mockupp"
self.scan_info['edgeEnergy'] = 0.1
self.thEdge = self.scan_info['edgeEnergy']
logging.getLogger("HWR").info("th. Edge %s ; chooch results are pk=%f, ip=%f, rm=%f" % (self.thEdge, pk,ip,rm))
self.scan_info["peakEnergy"] = pk
self.scan_info["inflectionEnergy"] = ip
self.scan_info["remoteEnergy"] = rm
self.scan_info["peakFPrime"] = fpPeak
self.scan_info["peakFDoublePrime"] = fppPeak
self.scan_info["inflectionFPrime"] = fpInfl
self.scan_info["inflectionFDoublePrime"] = fppInfl
self.scan_info["comments"] = comm
chooch_graph_x, chooch_graph_y1, chooch_graph_y2 = zip(*chooch_graph_data)
chooch_graph_x = list(chooch_graph_x)
for i in range(len(chooch_graph_x)):
chooch_graph_x[i] = chooch_graph_x[i] / 1000.0
#logging.getLogger("HWR").info("EMBLEnergyScan: Saving png" )
# prepare to save png files
title = "%s %s %s\n%.4f %.2f %.2f\n%.4f %.2f %.2f" % \
("energy", "f'", "f''", pk, fpPeak, fppPeak, ip, fpInfl, fppInfl)
fig = Figure(figsize = (15, 11))
ax = fig.add_subplot(211)
ax.set_title("%s\n%s" % (scan_file_efs_filename, title))
ax.grid(True)
ax.plot(*(zip(*scan_data)), **{"color": 'black'})
ax.set_xlabel("Energy")
ax.set_ylabel("MCA counts")
ax2 = fig.add_subplot(212)
ax2.grid(True)
ax2.set_xlabel("Energy")
ax2.set_ylabel("")
handles = []
handles.append(ax2.plot(chooch_graph_x, chooch_graph_y1, color = 'blue'))
handles.append(ax2.plot(chooch_graph_x, chooch_graph_y2, color = 'red'))
canvas = FigureCanvasAgg(fig)
self.scan_info["jpegChoochFileFullPath"] = str(archive_file_png_filename)
try:
logging.getLogger("HWR").info("Rendering energy scan and Chooch " + \
"graphs to PNG file : %s", scan_file_png_filename)
canvas.print_figure(scan_file_png_filename, dpi = 80)
except:
logging.getLogger("HWR").exception("could not print figure")
try:
logging.getLogger("HWR").info("Saving energy scan to archive " +\
"directory for ISPyB : %s", archive_file_png_filename)
canvas.print_figure(archive_file_png_filename, dpi = 80)
except:
logging.getLogger("HWR").exception("could not save figure")
self.store_energy_scan()
logging.getLogger("HWR").info("<chooch> returning" )
self.emit('choochFinished', (pk, fppPeak, fpPeak, ip, fppInfl, fpInfl,
rm, chooch_graph_x, chooch_graph_y1, chooch_graph_y2, title))
return pk, fppPeak, fpPeak, ip, fppInfl, fpInfl, rm, chooch_graph_x, \
chooch_graph_y1, chooch_graph_y2, title
def getCurrentEnergy(self):
return 12
def getCurrentWavelength(self):
return 12
def getElements(self):
elements=[]
try:
for el in self["elements"]:
elements.append({"symbol":el.symbol, "energy":el.energy})
except IndexError:
pass
return elements
def getDefaultMadEnergies(self):
energies=[]
try:
for el in self["mad"]:
energies.append([float(el.energy), el.directory])
except IndexError:
pass
return energies
def canMoveEnergy(self):
return False
def isConnected(self):
return True
def scanCommandStarted(self, *args):
"""
Descript. :
"""
title = "%s %s: %s %s" % (self.scan_info["sessionId"],
self.scan_info["blSampleId"], self.scan_info["element"], self.scan_info["edgeEnergy"])
dic = {'xlabel': 'energy',
'ylabel': 'counts',
'scaletype': 'normal',
'title': title}
self.emit('scanStart', dic)
self.emit('energyScanStarted', dic)
self.scan_info['startTime'] = time.strftime("%Y-%m-%d %H:%M:%S")
self.scanning = True
def scanCommandFinished(self, *args):
"""
Descript. :
"""
with cleanup(self.ready_event.set):
self.scan_info['endTime'] = time.strftime("%Y-%m-%d %H:%M:%S")
logging.getLogger("HWR").debug("EMBLEnergyScan: energy scan finished")
self.scanning = False
self.scan_info["startEnergy"] = self.scan_data[-1][0]
self.scan_info["endEnergy"] = self.scan_data[-1][1]
self.emit('energyScanFinished', self.scan_info)
def get_scan_data(self):
"""
Descript. :
"""
return self.scan_data
def store_energy_scan(self):
"""
Descript. :
"""
return