def __init__(self, path = None, histo_bins_t = -1):
self._helper = BinLoadHelper()
# initialize mouse click
self._mouseListener = MouseListener()
self._mouseListener.on_click = self.onMouseClick
# load file
if not path is None:
self.loadFile(path, histo_bins_t)
class QuokkaBinLoader:
Histogram = None
HistogramPlot = None
TimeHistogram = None
TimeHistogramPlot = None
Masks = None
Timestamps = None
# reference file
NeXusPath = None
def __init__(self, path = None, histo_bins_t = -1):
self._helper = BinLoadHelper()
# initialize mouse click
self._mouseListener = MouseListener()
self._mouseListener.on_click = self.onMouseClick
# load file
if not path is None:
self.loadFile(path, histo_bins_t)
def close(self):
if not self.Histogram is None:
self.Histogram.close()
self.Histogram = None
if not self.TimeHistogram is None:
self.TimeHistogram.close()
self.TimeHistogram = None
self.Masks = []
self.Timestamps = []
def getTimeBinLength(self):
return self._helper.getTimeBinLength()
def getBinPath(self):
return self._helper.getBinPath()
def getNxPath(self):
return self.NeXusPath
def getCenterX(self):
return self._helper.getCenterX()
def getCenterY(self):
return self._helper.getCenterY()
def setCenter(self, centerX = -1, centerY = -1, minPixelCount = -1):
if minPixelCount == -1:
self._helper.setCenter(centerX, centerY)
else:
self._helper.setCenter(centerX, centerY, minPixelCount)
def setNeXusFile(self, path):
self.NeXusPath = path;
# event handling
def onMouseClick(self, e):
print 'clicked on (' + str(int(e.getX())) + ', ' + str(int(e.getY())) + ')'
# functions
def loadFile(self, path, histo_bins_t = -1):
print 'loading bin file'
self._helper.loadFile(path, histo_bins_t)
print 'bin file loaded'
def loadHistogram(self, startTime = 0, endTime = -1):
print 'loading histogram'
self._helper.loadHistogram(startTime, endTime)
self.Histogram = Dataset(Array(self._helper.getHistogram()))
self.Histogram.title = 'Histogram'
axis0 = self.Histogram.axes[0]
axis0.title = 'y'
axis0.units = 'pixels'
axis1 = self.Histogram.axes[1]
axis1.title = 'x'
axis1.units = 'pixels'
print 'histogram loaded'
def loadTimeHistogram(self, centerX = -1, centerY = -1):
print 'loading time histogram'
if (centerX == -1) and (centerY == -1):
self._helper.loadTimeHistogram()
else:
self._helper.loadTimeHistogram(centerX, centerY)
self.TimeHistogram = Dataset(Array(self._helper.getTimeHistogram()))
self.TimeHistogram.title = 'Time-Histogram'
axis0 = self.TimeHistogram.axes[0]
axis0.title = 'radius'
axis0.units = 'pixels'
axis1 = self.TimeHistogram.axes[1]
axis1.title = 'time'
axis1.units = 'seconds'
# adjust axes
axis1.copy_from(axis1 * self._helper.getTimeBinLength())
print 'time histogram loaded'
def showHistogram(self):
if self.Histogram is None:
self.loadHistogram()
if (self.HistogramPlot is None) or self.HistogramPlot.pv.isDisposed():
self.HistogramPlot = image(self.Histogram)
self.HistogramPlot.add_mouse_listener(self._mouseListener)
else:
self.HistogramPlot.set_dataset(self.Histogram)
def showTimeHistogram(self):
if self.TimeHistogram is None:
self.loadTimeHistogram()
if (self.TimeHistogramPlot is None) or self.TimeHistogramPlot.pv.isDisposed():
self.TimeHistogramPlot = image(self.TimeHistogram)
else:
self.TimeHistogramPlot.set_dataset(self.TimeHistogram)
def exportTimeHistogram(self, folder, file_q, file_t, file_i, upsideDown=False):
# fetch information
ds = self.TimeHistogram
axis_r = ds.axes[0]
axis_t = ds.axes[1]
axis_q = Array(axis_r)
axis_rLen = len(axis_r)
# conversion radius to q
factor = 2 * pi / 5.0;
for index_r in xrange(axis_rLen):
alpha = atan(axis_r[index_r] * 0.00508 / 4.07163)
axis_q[index_r] = factor * alpha
#print "%15.6g" % axis_q[index_r]
# write q (1d)
f = None
try:
f = open(folder + file_q, 'w')
itr_q = axis_q
if upsideDown:
itr_q = reversed(itr_q)
for q in itr_q:
f.write(str(q) + '\n')
finally:
if f is not None:
f.close()
print file_q, 'saved'
# write time (1d)
f = None
try:
f = open(folder + file_t, 'w')
for t in axis_t:
f.write(str(t) + '\n')
finally:
if f is not None:
f.close()
print file_t, 'saved'
# write intensity map (2d)
f = None
try:
f = open(folder + file_i, 'w')
itr_r = xrange(axis_rLen)
if upsideDown:
itr_r = reversed(itr_r)
for index_r in itr_r:
for index_t in xrange(len(axis_t)):
f.write(str(ds[index_r, index_t]) + ',')
f.write('\n')
finally:
if f is not None:
f.close()
print file_i, 'saved'
# successful completion
print 'done'
def removeMasks(self):
if (not self.Masks is None) and (not self.TimeHistogramPlot is None) and not self.TimeHistogramPlot.pv.isDisposed():
for mask in self.Masks:
self.TimeHistogramPlot.remove_mask(mask)
self.Timestamps = []
self.Masks = []
def setManualTimeBins(self, timestamps):
self.showTimeHistogram()
self.removeMasks()
rCount = loader.TimeHistogram.storage.shape[0] # self._maxRIndex
tCount = loader.TimeHistogram.storage.shape[1]
is_inclusive = True
offsetY = 0.5
y_min = -offsetY
y_max = -offsetY + rCount
index = 0
t0 = 0
tN = tCount * self._helper.getTimeBinLength()
for timestamp in timestamps:
if timestamp < t0:
raise AttributeError('timestamps')
if timestamp == t0:
continue
t1 = timestamp
if t1 >= tN:
break
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, t1, y_min, y_max, str(index), is_inclusive))
index += 1
# shift time span
t0 = t1
# swap color
is_inclusive = not is_inclusive
# final mask
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, tN, y_min, y_max, str(index), is_inclusive))
def setEqualTimeBins(self, timespan):
if timespan <= 0:
raise AttributeError('timespan')
self.showTimeHistogram()
self.removeMasks()
rCount = loader.TimeHistogram.storage.shape[0]
tCount = loader.TimeHistogram.storage.shape[1]
is_inclusive = True
offsetY = 0.5
y_min = -offsetY
y_max = -offsetY + rCount
index = 0
t0 = 0
t1 = timespan
tN = tCount * self._helper.getTimeBinLength()
while t1 < tN:
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, t1, y_min, y_max, str(index), is_inclusive))
index += 1
# shift time span
t0 = t1
t1 += timespan
# swap color
is_inclusive = not is_inclusive
# final mask
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, tN, y_min, y_max, str(index), is_inclusive))
def setGeometricTimeBins(self, firstTimespan, startTime = 0, mirrored = False):
if firstTimespan <= 0:
raise AttributeError('firstTimespan')
if startTime < 0:
raise AttributeError('startTime')
self.showTimeHistogram()
self.removeMasks()
rCount = self.TimeHistogram.storage.shape[0]
tCount = self.TimeHistogram.storage.shape[1]
is_inclusive = True
offsetY = 0.5
y_min = -offsetY
y_max = -offsetY + rCount
index = 0
if startTime != 0:
if not mirrored:
self.Timestamps.append(0)
self.Masks.append(self.TimeHistogramPlot.add_mask(0, startTime, y_min, y_max, str(index), is_inclusive))
index += 1
# swap color
is_inclusive = not is_inclusive
else:
ts = firstTimespan
t0 = startTime - ts
t1 = startTime
while t0 > 0:
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, t1, y_min, y_max, None, is_inclusive))
# double time span
ts *= 2
# shift time span
t1 = t0
t0 -= ts
# swap color
is_inclusive = not is_inclusive
# final mask
self.Timestamps.append(0)
self.Masks.append(self.TimeHistogramPlot.add_mask(0, t1, y_min, y_max, None, is_inclusive))
# set correct names
self.Timestamps.reverse()
self.Masks.reverse()
for mask in self.Masks:
mask.setName(str(index))
index += 1
is_inclusive = False
ts = firstTimespan
t0 = startTime
t1 = startTime + ts
tN = tCount * self._helper.getTimeBinLength()
while t1 < tN:
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, t1, y_min, y_max, str(index), is_inclusive))
index += 1
# double time span
ts *= 2
# shift time span
t0 = t1
t1 += ts
# swap color
is_inclusive = not is_inclusive
# final mask
self.Timestamps.append(t0)
self.Masks.append(self.TimeHistogramPlot.add_mask(t0, tN, y_min, y_max, str(index), is_inclusive))
def exportDatasets(self, nexusReference = None):
print '0'
if not nexusReference is None:
self.NeXusPath = nexusReference
if self.NeXusPath is None:
raise NameError('no reference nexus file was specified')
if (self.Timestamps is None) or (self.Timestamps.count == 0):
raise NameError('no time bins were specified')
# check file name convention
directory = path.dirname(self.NeXusPath)
filename = path.basename(self.NeXusPath).upper()
number = filename[3:filename.find('.NX.HDF')]
print 'a'
if not filename.startswith('QKK') or not filename.endswith('.NX.HDF') or not number.isdigit():
raise NameError('the specified nx-hdf filename does not match the pattern QKK#######.nx.hdf')
number = int(number)
if number > 99999:
raise NameError('this version of the bin-loader only supports QKK files in the range of 0 to 99999')
print 'b'
# set up double array for argument
timestamps = jdoubles(len(self.Timestamps))
for i in xrange(len(self.Timestamps)):
timestamps[i] = self.Timestamps[i]
print 'c'
# load selected time bins
print 'loading time bins'
timeBins = self._helper.loadTimeBins(timestamps)
beamTime = self._helper.getBeamTime()
print 'time bins loaded'
print 'd'
ref = Dataset(self.NeXusPath)
ref.__iDictionary__.addEntry('total_counts', '$entry/data/total_counts' )
# monitor
ref.__iDictionary__.addEntry('bm1_counts' , '$entry/monitor/bm1_counts')
ref.__iDictionary__.addEntry('bm1_time' , '$entry/monitor/bm1_time' )
# beam time
ref.__iDictionary__.addEntry('start_time' , '$entry/instrument/detector/start_time')
ref.__iDictionary__.addEntry('stop_time' , '$entry/instrument/detector/stop_time')
print 'e'
bm1_rate = ref.bm1_counts / ref.bm1_time
time0 = ref.start_time[0]
n = len(self.Timestamps)
bt = -1 # beam time index
tm = -1 # time bin index
print 'f'
t1 = 0
while t1 < beamTime:
t0 = t1
bt += 1
if bt < n:
t1 = self.Timestamps[bt]
else:
t1 = beamTime
if t1 <= 0:
continue
tm += 1
if t1 <= t0:
continue
timeBin = Array(timeBins[tm])
ref.storage.copy_from(timeBin) # <---- ref.storage[0].copy_from(timeBin)
ref.total_counts = timeBin.sum()
ref.bm1_time = (t1 - t0)
ref.bm1_counts = (t1 - t0) * bm1_rate # assuming that the rate is correct and constant for the current beam time
ref.start_time = int(time0 + t0)
ref.stop_time = int(time0 + t1)
shortname = 'QKK%07i' % (number * 100 + tm)
ref.__iNXroot__.getDefaultEntry().setShortName(shortname)
ref.save_copy(path.join(directory, shortname + '.nx.hdf'))
print shortname, 'created'
print 'export completed'
