def fixed_align_frames(self,maxDisplacement=50):
'''perform fixed alignment on the framestack
maxDisplacement=50 - maximum allowed displacement, frames with > than this will be removed from the stack'''
if self.data is None:
logger.warning('No frames found')
return
if self.data.templateFrame is None:
logger.warning('template frame not set')
return
framesToProcess = [i for i in self.data.frameIds if i != self.data.templateFrameId]
midRow = int(self.data.frameWidth / 2)
midCol = int(self.data.frameHeight / 2)
targetFrame = self.data.templateFrame
targetFrame = targetFrame[midRow - self.largeFrameSize : midRow + self.largeFrameSize,
midCol - self.largeFrameSize : midRow + self.largeFrameSize]
results = []
#ensure the target frame is included in the output
results.append({'frameid':self.data.templateFrameId,
'correlation':1,
'shift':(0,0)})
for iFrame in framesToProcess:
templateFrame = self.data.get_frame_by_id(iFrame)
templateFrame = templateFrame[midRow - self.smallFrameSize : midRow + self.smallFrameSize,
midCol - self.smallFrameSize : midCol + self.smallFrameSize]
displacement = ImageTools.find_frame_shift(targetFrame,
templateFrame,
topLeft=[(midRow - self.largeFrameSize,midCol - self.largeFrameSize),
(midRow - self.smallFrameSize,midCol - self.smallFrameSize)],
applyBlur=True,
method='xcorr',
attemptSubPixelAlignment=False)
results.append({'frameid':iFrame,
'correlation':displacement['maxcorr'],
'shift':displacement['coords']})
#Check displacement is les than 50 pixels
good_results = [result for result in results
if abs(result['shift'][1])<=maxDisplacement
and abs(result['shift'][0]) <= maxDisplacement]
bad_results = [result['frameid'] for result in results
if abs(result['shift'][1]) > maxDisplacement
or abs(result['shift'][0]) > maxDisplacement]
logger.info('Removing frames {} for too large displacements'.format(bad_results))
if not good_results:
#no good frames found
logger.warning('frame displacements are too large')
raise RuntimeError('frame displacements are too large')
alignedData = StackTools.apply_displacements(self.data,good_results)
self.data = alignedData
self.currentStack = alignedData
def create_average_frame(self,type='mean'):
assert type in ['lucky','mean']
#check to see if an error has occured before this
if self.data is None:
logger.debug('')
if type == 'lucky':
#creating a lucky average
if self.data.frameCount > 20:
self.currentAverageFrame = StackTools.compute_lucky_image(self.data)
else:
self.currentAverageFrame = None
logger.warning('Too few frames to create lucky average')
else:
self.currentAverageFrame = self.data.mean(axis=0)
def create_average_frame(self, type='mean'):
assert type in ['lucky', 'mean']
#check to see if an error has occured before this
if self.data is None:
logger.debug('')
if type == 'lucky':
#creating a lucky average
if self.data.frameCount > 20:
self.currentAverageFrame = StackTools.compute_lucky_image(
self.data)
else:
self.currentAverageFrame = None
logger.warning('Too few frames to create lucky average')
else:
self.currentAverageFrame = self.data.mean(axis=0)
def compute_stdev_image(stack):
'''Compute the standard deviation image'''
nFrames, height, width = stack.shape
if nFrames < 10:
logger.error('stdev image requires at least 10 frames')
return None
global results
results = np.empty(stack.shape)
stack = StackTools.getMaskedStack(stack)
medianImage = np.median(stack,axis=0)
#pool = mp.Pool()
for idxFrame in range(stack.shape[0]):
srcImg = stack[idxFrame,:,:]
#pool.apply_async(compute_variance_image,
#args=(srcImg,
#medianImage,
#idxFrame),
#callback=_compute_stdev_image_callback)
results[idxFrame,:,:] = compute_variance_image(srcImg,medianImage,idxFrame)[1]
#pool.close
#pool.join
#newStack = np.ma.array(results)
imageStdev = results.std(axis=0)
imageAvg = results.mean(axis=0)
#some values in imageAvg can be 0, create this as a masked array
imageAvg = np.ma.MaskedArray(data = imageAvg,
mask = imageAvg == 0)
imageNorm = imageAvg / imageAvg.max()
imageRatio = imageStdev / imageNorm
imageRatio[imageRatio > 0.3] = 0.3
imageRatio = cv2.medianBlur(imageRatio.astype(np.float32),3)
return imageRatio
def fixed_align_frames(self, maxDisplacement=50):
'''perform fixed alignment on the framestack
maxDisplacement=50 - maximum allowed displacement, frames with > than this will be removed from the stack'''
if self.data is None:
logger.warning('No frames found')
return
if self.data.templateFrame is None:
logger.warning('template frame not set')
return
framesToProcess = [
i for i in self.data.frameIds if i != self.data.templateFrameId
]
framesToProcess2 = [
i for i in self.data2.frameIds if i != self.data2.templateFrameId
]
midRow = int(self.data.frameWidth / 2)
midCol = int(self.data.frameHeight / 2)
midRow2 = int(self.data2.frameWidth / 2)
midCol2 = int(self.data2.frameHeight / 2)
targetFrame = self.data.templateFrame
targetFrame = targetFrame[midRow - self.largeFrameSize:midRow +
self.largeFrameSize,
midCol - self.largeFrameSize:midRow +
self.largeFrameSize]
targetFrame2 = self.data2.templateFrame
targetFrame2 = targetFrame2[midRow2 - self.largeFrameSize:midRow2 +
self.largeFrameSize,
midCol2 - self.largeFrameSize:midRow2 +
self.largeFrameSize]
results = []
results2 = []
#ensure the target frame is included in the output
results.append({
'frameid': self.data.templateFrameId,
'correlation': 1,
'shift': (0, 0)
})
results2.append({
'frameid': self.data2.templateFrameId,
'correlation': 1,
'shift': (0, 0)
})
for iFrame in framesToProcess:
templateFrame = self.data.get_frame_by_id(iFrame)
templateFrame = templateFrame[midRow - self.smallFrameSize:midRow +
self.smallFrameSize,
midCol - self.smallFrameSize:midCol +
self.smallFrameSize]
templateFrame2 = self.data2.get_frame_by_id(iFrame)
templateFrame2 = templateFrame2[midRow2 -
self.smallFrameSize:midRow2 +
self.smallFrameSize, midCol2 -
self.smallFrameSize:midCol2 +
self.smallFrameSize]
displacement = ImageTools.find_frame_shift(
targetFrame,
templateFrame,
topLeft=[(midRow - self.largeFrameSize,
midCol - self.largeFrameSize),
(midRow - self.smallFrameSize,
midCol - self.smallFrameSize)],
applyBlur=True,
method='xcorr',
attemptSubPixelAlignment=False)
displacement2 = ImageTools.find_frame_shift(
targetFrame2,
templateFrame2,
topLeft=[(midRow2 - self.largeFrameSize,
midCol2 - self.largeFrameSize),
(midRow2 - self.smallFrameSize,
midCol2 - self.smallFrameSize)],
applyBlur=True,
method='xcorr',
attemptSubPixelAlignment=False)
results.append({
'frameid': iFrame,
'correlation': displacement['maxcorr'],
'shift': displacement['coords']
})
results2.append({
'frameid': iFrame,
'correlation': displacement['maxcorr'],
'shift': displacement['coords']
})
#Check displacement is les than 50 pixels
good_results = [
result for result in results
if abs(result['shift'][1]) <= maxDisplacement
and abs(result['shift'][0]) <= maxDisplacement
]
good_results2 = [
result2 for result2 in results2
if abs(result2['shift'][1]) <= maxDisplacement
and abs(result2['shift'][0]) <= maxDisplacement
]
bad_results = [
result['frameid'] for result in results
if abs(result['shift'][1]) > maxDisplacement
or abs(result['shift'][0]) > maxDisplacement
]
bad_results2 = [
result2['frameid'] for result2 in results2
if abs(result2['shift'][1]) > maxDisplacement
or abs(result2['shift'][0]) > maxDisplacement
]
logger.info('Removing frames {} for too large displacements'.format(
bad_results))
if not good_results:
#no good frames found
logger.warning('frame displacements are too large')
raise RuntimeError('frame displacements are too large')
alignedData = StackTools.apply_displacements(self.data, good_results)
self.data = alignedData
alignedData2 = StackTools.apply_displacements(self.data2,
good_results2)
self.data2 = alignedData2
self.currentStack = alignedData
self.currentStack2 = alignedData2
def fixInterlace(self):
StackTools.interlaceStack(self.data)
def fixInterlace(self):
StackTools.interlaceStack(self.data)
