def loadStack(dataDir, start, stop, useImg = False, nCols=80, nRows=125):
frameTimes = np.arange(start, stop+1)
frames = []
for iTs,ts in enumerate(frameTimes):
try:
if useImg==False:
imagePath = os.path.join(dataDir,str(ts)+'.bin')
print imagePath
with open(imagePath,'rb') as dumpFile:
data = dumpFile.read()
nBytes = len(data)
nWords = nBytes/8 #64 bit words
#break into 64 bit words
words = np.array(struct.unpack('>{:d}Q'.format(nWords), data),dtype=object)
parseDict = parsePacketData(words,verbose=False)
image = parseDict['image']
else:
imagePath = os.path.join(dataDir,str(ts)+'.img')
print imagePath
image = np.fromfile(open(imagePath, mode='rb'),dtype=np.uint16)
image = np.transpose(np.reshape(image, (nCols, nRows)))
except (IOError, ValueError):
print "Failed to load ", imagePath
image = np.zeros((nRows, nCols),dtype=np.uint16)
frames.append(image)
stack = np.array(frames)
return stack
def bin2img(ts,
binPath='/mnt/data0/ScienceData/',
imgPath='/mnt/data0/ScienceDataIMGs/'):
imagePath = os.path.join(binPath, str(ts) + '.bin')
with open(imagePath, 'rb') as dumpFile:
data = dumpFile.read()
nBytes = len(data)
nWords = nBytes / 8 #64 bit words
#break into 64 bit words
words = np.array(struct.unpack('>{:d}Q'.format(nWords), data),
dtype=object)
parseDict = parsePacketData(words, verbose=False)
image = parseDict['image']
image = np.transpose(image)
#formattedImage = np.array(image, dtype=np.uint16)
image.flatten()
imagePath = os.path.join(imgPath, str(ts) + '.img')
image.tofile(imagePath)
print "Wrote IMG to ", imagePath
return
def bin2img(ts, binPath = '/mnt/data0/ScienceData/', imgPath = '/mnt/data0/ScienceDataIMGs/'):
imagePath = os.path.join(binPath,str(ts)+'.bin')
with open(imagePath,'rb') as dumpFile:
data = dumpFile.read()
nBytes = len(data)
nWords = nBytes/8 #64 bit words
#break into 64 bit words
words = np.array(struct.unpack('>{:d}Q'.format(nWords), data),dtype=object)
parseDict = parsePacketData(words,verbose=False)
image = parseDict['image']
image = np.transpose(image)
#formattedImage = np.array(image, dtype=np.uint16)
image.flatten()
imagePath = os.path.join(imgPath,str(ts)+'.img')
image.tofile(imagePath)
print "Wrote IMG to ", imagePath
return
def generateDarkFrame(self):
self.darkStart = int(self.lineEdit_darkStart.text())
self.darkEnd = int(self.lineEdit_darkEnd.text())
self.darkTimes = np.arange(self.darkStart, self.darkEnd + 1)
darkFrames = []
for iTs, ts in enumerate(self.darkTimes):
try:
imagePath = os.path.join(self.dataPath, str(ts) + '.bin')
print imagePath
with open(imagePath, 'rb') as dumpFile:
data = dumpFile.read()
nBytes = len(data)
nWords = nBytes / 8 #64 bit words
#break into 64 bit words
words = np.array(struct.unpack('>{:d}Q'.format(nWords), data),
dtype=object)
parseDict = parsePacketData(words, verbose=False)
image = parseDict['image']
if self.beammap is not None:
newImage = np.zeros(image.shape)
for y in range(len(newImage)):
for x in range(len(newImage[0])):
newX = int(self.beammap[y, x][0])
newY = int(self.beammap[y, x][1])
if newX > 0 and newY > 0:
newImage[newY, newX] = image[y, x]
image = newImage
except (IOError, ValueError):
image = np.zeros((imageShape['nRows'], imageShape['nCols']),
dtype=np.uint16)
print "Failed to load dark frame..."
darkFrames.append(image)
self.darkStack = np.array(darkFrames)
self.darkFrame = np.median(self.darkStack, axis=0)
print "Generated median dark frame from timestamps %i to %i" % (
self.darkStart, self.darkEnd)
self.darkLoaded = True
def loadImageStack(self):
self.timestampList = np.arange(self.startTstamp, self.endTstamp + 1)
images = []
self.photonTstamps = np.array([])
self.photonPhases = np.array([])
self.photonBases = np.array([])
self.photonXs = np.array([])
self.photonYs = np.array([])
self.photonPixelIDs = np.array([])
for iTs, ts in enumerate(self.timestampList):
try:
imagePath = os.path.join(self.dataPath, str(ts) + '.bin')
print imagePath
with open(imagePath, 'rb') as dumpFile:
data = dumpFile.read()
nBytes = len(data)
nWords = nBytes / 8 #64 bit words
#break into 64 bit words
words = np.array(struct.unpack('>{:d}Q'.format(nWords), data),
dtype=object)
parseDict = parsePacketData(words, verbose=False)
photonTimes = np.array(parseDict['photonTimestamps'])
phasesDeg = np.array(parseDict['phasesDeg'])
basesDeg = np.array(parseDict['basesDeg'])
xCoords = np.array(parseDict['xCoords'])
yCoords = np.array(parseDict['yCoords'])
pixelIds = np.array(parseDict['pixelIds'])
image = parseDict['image']
if self.beammap is not None:
newImage = np.zeros(image.shape)
for y in range(len(newImage)):
for x in range(len(newImage[0])):
newX = int(self.beammap[y, x][0])
newY = int(self.beammap[y, x][1])
if newX > 0 and newY > 0:
newImage[newY, newX] = image[y, x]
#print '('+str(x)+', '+str(y)+') --> ('+str(newX)+', '+str(newY)+')'
#else:
# print '('+str(x)+', '+str(y)+') --> 0'
# newImage[y,x]=0
image = newImage
except (IOError, ValueError):
image = np.zeros((imageShape['nRows'], imageShape['nCols']),
dtype=np.uint16)
self.photonTstamps = np.append(self.photonTstamps, photonTimes)
self.photonPhases = np.append(self.photonPhases, phasesDeg)
self.photonBases = np.append(self.photonBases, basesDeg)
self.photonXs = np.append(self.photonXs, xCoords)
self.photonYs = np.append(self.photonYs, yCoords)
self.photonPixelIDs = np.append(self.photonPixelIDs, pixelIds)
images.append(image)
self.imageStack = np.array(images)
if len(sys.argv) > 1:
path = sys.argv[1]
else:
path = 'photonDump.bin'
pathTstamp = os.path.splitext(os.path.basename(path))[0]
with open(path,'rb') as dumpFile:
data = dumpFile.read()
nBytes = len(data)
nWords = nBytes/8 #64 bit words
#break into 64 bit words
words = np.array(struct.unpack('>{:d}Q'.format(nWords), data),dtype=object)
parseDict = parsePacketData(words,verbose=True)
timestamps = parseDict['photonTimestamps']
phasesDeg = parseDict['phasesDeg']
basesDeg = parseDict['basesDeg']
pixelIds = parseDict['pixelIds']
image = parseDict['image']
xCoords = parseDict['xCoords']
yCoords = parseDict['yCoords']
selPixelId = pixelIds[np.where((xCoords==selPixelCol) & (yCoords==selPixelRow))][0]
print selPixelId
print 'selected pixel',selPixelId
print len(np.where(pixelIds==selPixelId)[0]),'photons for selected pixel'
