def makeDenoisedParticleJPGFrames(self,partdatas,shiftdata,shortname):
'''
Denoise the boxed particles and then read in the resulting frame stack of the particle for saving as movie frames.
'''
if not partdatas:
return
if not self.is_dd_stack:
apDisplay.printError('Denoising works only with ddstack for now')
imgdata = partdatas[0]['image']
ddstackdir,stackfile = self.getDDStackDirFile(imgdata)
framestacks = []
for p,partdata in enumerate(partdatas):
# denoise within the particle box
col_start,row_start = apBoxer.getBoxStartPosition(imgdata,self.half_box,partdata, shiftdata)
row_end = row_start + self.boxsize
col_end = col_start + self.boxsize
roi = ((row_start,row_end),(col_start,col_end))
paramstr = self.denoise.setupKSVDdenoise(self.frameavg,self.firstframe,self.nframe,roi)
apDisplay.printMsg('denoise param string: %s' % paramstr)
self.denoise.makeDenoisedStack(ddstackdir, stackfile)
outputstackfile = '%s_%s.mrc' % (stackfile[:-4], paramstr)
framestacks.append(outputstackfile)
for i,start_frame in enumerate(range(self.firstframe,self.nframe-self.frameavg-self.firstframe+1,self.framestep)):
for p,partdata in enumerate(partdatas):
array = mrc.read(os.path.join(self.params['rundir'],'results/mrc',framestacks[p]),i)
# bin is not used for now
movieframe_number = start_frame
self.saveFrameFromArray(array,shortname,p,movieframe_number)
def makeParticleJPGFrames(self, partdatas, shiftdata, shortname):
'''
Make corrected frame images and then box off the particles.
'''
imgdata = partdatas[0]['image']
for start_frame in range(
self.firstframe,
self.nframe - self.frameavg - self.firstframe + 1,
self.framestep):
if self.is_dd_frame:
corrected = self.dd.correctFrameImage(start_frame,
self.frameavg)
else:
ddstackdir, stackfile = self.getDDStackDirFile(imgdata)
corrected = self.dd.getDDStackFrameSumImage(
start_frame, self.frameavg)
for p, partdata in enumerate(partdatas):
col_start, row_start = apBoxer.getBoxStartPosition(
imgdata, self.half_box, partdata, shiftdata)
row_end = row_start + self.boxsize
col_end = col_start + self.boxsize
array = corrected[row_start:row_end, col_start:col_end]
# bin is not used for now
movieframe_number = start_frame
self.saveFrameFromArray(array, shortname, p, movieframe_number)
def removeBoxOutOfImage(self,imgdata,partdatas,shiftdata): imgdims = imgdata['camera']['dimension'] newpartdatas = [] for partdata in partdatas: start_x,start_y = apBoxer.getBoxStartPosition(imgdata,self.half_box,partdata, shiftdata) if apBoxer.checkBoxInImage(imgdims,start_x,start_y,self.boxsize): newpartdatas.append(partdata) return newpartdatas
def removeBoxOutOfImage(self, imgdata, partdatas, shiftdata):
imgdims = imgdata['camera']['dimension']
newpartdatas = []
for partdata in partdatas:
start_x, start_y = apBoxer.getBoxStartPosition(
imgdata, self.half_box, partdata, shiftdata)
if apBoxer.checkBoxInImage(imgdims, start_x, start_y,
self.boxsize):
newpartdatas.append(partdata)
return newpartdatas
def makeParticleJPGFrames(self,partdatas,shiftdata,shortname):
'''
Make corrected frame images and then box off the particles.
'''
imgdata = partdatas[0]['image']
for start_frame in range(self.firstframe,self.nframe-self.frameavg-self.firstframe+1,self.framestep):
if self.is_dd_frame:
corrected = self.dd.correctFrameImage(start_frame,self.frameavg)
else:
ddstackdir,stackfile = self.getDDStackDirFile(imgdata)
corrected = self.dd.getDDStackFrameSumImage(start_frame,self.frameavg)
for p,partdata in enumerate(partdatas):
col_start,row_start = apBoxer.getBoxStartPosition(imgdata,self.half_box,partdata, shiftdata)
row_end = row_start + self.boxsize
col_end = col_start + self.boxsize
array = corrected[row_start:row_end,col_start:col_end]
# bin is not used for now
movieframe_number = start_frame
self.saveFrameFromArray(array,shortname,p,movieframe_number)
def makeDenoisedParticleJPGFrames(self, partdatas, shiftdata, shortname):
'''
Denoise the boxed particles and then read in the resulting frame stack of the particle for saving as movie frames.
'''
if not partdatas:
return
if not self.is_dd_stack:
apDisplay.printError('Denoising works only with ddstack for now')
imgdata = partdatas[0]['image']
ddstackdir, stackfile = self.getDDStackDirFile(imgdata)
framestacks = []
for p, partdata in enumerate(partdatas):
# denoise within the particle box
col_start, row_start = apBoxer.getBoxStartPosition(
imgdata, self.half_box, partdata, shiftdata)
row_end = row_start + self.boxsize
col_end = col_start + self.boxsize
roi = ((row_start, row_end), (col_start, col_end))
paramstr = self.denoise.setupKSVDdenoise(self.frameavg,
self.firstframe,
self.nframe, roi)
apDisplay.printMsg('denoise param string: %s' % paramstr)
self.denoise.makeDenoisedStack(ddstackdir, stackfile)
outputstackfile = '%s_%s.mrc' % (stackfile[:-4], paramstr)
framestacks.append(outputstackfile)
for i, start_frame in enumerate(
range(self.firstframe,
self.nframe - self.frameavg - self.firstframe + 1,
self.framestep)):
for p, partdata in enumerate(partdatas):
array = mrc.read(
os.path.join(self.params['rundir'], 'results/mrc',
framestacks[p]), i)
# bin is not used for now
movieframe_number = start_frame
self.saveFrameFromArray(array, shortname, p, movieframe_number)