def combine_polished_stacks(self):
oldmovieid = None
nmic = 0
for part in self.stackparts:
self.dd.setImageData(part['particle']['image'])
movieid = part['particle']['image'].dbid
alignpairdata = self.dd.getAlignImagePairData(
None, query_source=not self.dd.getIsAligned())
if alignpairdata is False:
apDisplay.printWarning(
'Image not used for nor a result of alignment.')
if movieid != oldmovieid:
ddstack = orig_dd_file = alignpairdata['source'][
'filename'] + "_lmbfgs.mrc"
particlestack = os.path.join(self.params['rundir'],
"Particles", ddstack)
a = mrc.read(particlestack)
apDisplay.printMsg("appending stack %s" % ddstack)
if oldmovieid is None:
mrc.write(a, "polished.mrc")
else:
mrc.append(a, "polished.mrc")
oldmovieid = movieid
def makeStack(self, tiltseries, mrc_files): stackname = self.getFilename(tiltseries) + '_stack.mrc' stackname = os.path.join(self.settings['path'], stackname) shutil.copy(mrc_files[0], stackname) for mrcfile in mrc_files: im = mrc.read(mrcfile) mrc.append(im, stackname)
def mergeResults(self):
allout = 'all_out.mrc'
for proc in range(self.params['nproc']):
infilepath = 'proc%03d/out.mrc' % (proc)
a = mrc.read(infilepath)
if proc == 0:
mrc.write(a, allout)
else:
mrc.append(a, allout)
return allout
def mergeResults(self):
allout = 'all_out.mrc'
for proc in range(self.params['nproc']):
infilepath = 'proc%03d/out.mrc' % (proc)
a = mrc.read(infilepath)
if proc == 0:
mrc.write(a,allout)
else:
mrc.append(a,allout)
return allout
def mergeResults(self):
allout = "all_out.mrc"
for proc in range(self.params["nproc"]):
infilepath = "proc%03d/out.mrc" % (proc)
a = mrc.read(infilepath)
if proc == 0:
mrc.write(a, allout)
else:
mrc.append(a, allout)
return allout
def writeMrcStack(path, stackname, mrc_files, binning=1):
apDisplay.printMsg("Writing MRC stack file... ")
stackname = os.path.join(path, stackname)
im = mrc.read(mrc_files[0])
image = imagefun.bin(im, binning)
mrc.write(image,stackname)
del mrc_files[0]
for mrcfile in mrc_files:
im = mrc.read(mrcfile)
image = imagefun.bin(im, binning)
mrc.append(image, stackname)
def writeMrcStack(path, stackname, mrc_files, binning=1):
apDisplay.printMsg("Writing MRC stack file... ")
stackname = os.path.join(path, stackname)
im = mrc.read(mrc_files[0])
image = imagefun.bin(im, binning)
mrc.write(image, stackname)
del mrc_files[0]
for mrcfile in mrc_files:
im = mrc.read(mrcfile)
image = imagefun.bin(im, binning)
mrc.append(image, stackname)
def makeMovie(self,framepaths_wild,moviepath):
files = os.listdir(self.params['rundir'])
moviepath += '.mrc'
for filename in files:
bits = framepaths_wild.split('*')
if bits[0] in filename:
print filename
array = mrc.read(os.path.join(self.params['rundir'],filename))
if os.path.isfile(moviepath):
mrc.append(array,moviepath)
else:
mrc.write(array,moviepath)
def makeStack(self, tiltseries, mrc_files):
stackname = self.getFilename(tiltseries) + '.st'
stackname = os.path.join(self.settings['path'], stackname)
im = mrc.read(mrc_files[0])
image = imagefun.bin(im, int(self.settings['binning']))
mrc.write(image, stackname)
#shutil.copy(mrc_files[0], stackname)
del mrc_files[0]
for mrcfile in mrc_files:
im = mrc.read(mrcfile)
image = imagefun.bin(im, int(self.settings['binning']))
mrc.append(image, stackname)
def makeStack(self, tiltseries, mrc_files):
stackname = self.getFilename(tiltseries) + '.st'
stackname = os.path.join(self.settings['path'], stackname)
im = mrc.read(mrc_files[0])
image = imagefun.bin(im, int(self.settings['binning']))
mrc.write(image,stackname)
#shutil.copy(mrc_files[0], stackname)
del mrc_files[0]
for mrcfile in mrc_files:
im = mrc.read(mrcfile)
image = imagefun.bin(im, int(self.settings['binning']))
mrc.append(image, stackname)
def makeMovie(self,framepaths_wild,moviepath):
files = os.listdir(self.params['rundir'])
moviepath += '.mrc'
for filename in files:
bits = framepaths_wild.split('*')
if bits[0] in filename:
print filename
array = mrc.read(os.path.join(self.params['rundir'],filename))
if os.path.isfile(moviepath):
mrc.append(array,moviepath)
else:
mrc.write(array,moviepath)
def appendParticleListToStackFile(self, partlist, filename):
"""
takes any file type and adds a list of particles
use memory mapping (mmap) to prevent memory overloads
"""
if self.particlesWritten < 1 and os.path.exists(filename) and self.params['append'] is False:
if filename.endswith('.hed') or filename.endswith('.img'):
root = os.path.splitext(filename)[0]
headerfile = root+".hed"
datafile = root+".img"
os.remove(headerfile)
os.remove(datafile)
else:
os.remove(filename)
#Determine extension
if filename.endswith('.mrc'):
if os.path.exists(filename):
partarray = numpy.array(partlist)
mrc.append(partarray, filename)
else:
f = open(filename, "wb+")
partarray = numpy.array(partlist)
mrc.write(partarray, f)
f.close()
apix = self.params['apix']
pixeldict = {'x': apix, 'y': apix, 'z': apix, }
mrc.updateFilePixelSize(filename, pixeldict)
elif filename.endswith('.hed') or filename.endswith('.img'):
apImagicFile.appendParticleListToStackFile(partlist, filename,
msg=self.params['debug'])
elif filename.endswith('.spi'):
### to be implemented
apDisplay.printError("SPIDER is not implemented yet")
elif filename.endswith('.hdf'):
### to be implemented
apDisplay.printError("HDF is not implemented yet")
else:
apDisplay.printError("unknown stack type")
self.particlesWritten += len(partlist)
return True
def combine_polished_stacks(self):
oldmovieid = None
nmic = 0
for part in self.stackparts:
self.dd.setImageData(part['particle']['image'])
movieid = part['particle']['image'].dbid
alignpairdata = self.dd.getAlignImagePairData(None,query_source=not self.dd.getIsAligned())
if alignpairdata is False:
apDisplay.printWarning('Image not used for nor a result of alignment.')
if movieid != oldmovieid:
ddstack = orig_dd_file = alignpairdata['source']['filename']+"_lmbfgs.mrc"
particlestack = os.path.join(self.params['rundir'], "Particles", ddstack)
a = mrc.read(particlestack)
apDisplay.printMsg("appending stack %s" % ddstack)
if oldmovieid is None:
mrc.write(a, "polished.mrc")
else:
mrc.append(a, "polished.mrc")
oldmovieid = movieid
def _getImage(self):
self.custom_setup()
if not self.validateGeometry():
raise ValueError('invalid image geometry')
for axis in ['x', 'y']:
if self.dimension[axis] * self.binning[axis] > self.getCameraSize(
)[axis]:
raise ValueError('invalid dimension/binning combination')
columns = self.dimension['x']
rows = self.dimension['y']
shape = (rows, columns)
t0 = time.time()
## exposure time
time.sleep(self.exposure_time)
t1 = time.time()
self.exposure_timestamp = (t1 + t0) / 2.0
nframes = self.getNumberOfFrames()
exptime = self.frame_time
if self.useframes:
useframes = []
for f in self.useframes:
if 0 <= f < nframes:
useframes.append(f)
else:
# use all frames in final image
useframes = range(nframes)
self.useframes = useframes
print 'SAVERAWFRAMES', self.save_frames
if self.save_frames:
self.rawframesname = time.strftime('frames_%Y%m%d_%H%M%S')
self.rawframesname += '_%02d' % (idcounter.next(), )
else:
return self.getSyntheticImage(shape)
sum = numpy.zeros(shape, numpy.float32)
for i in range(nframes):
if self.exposure_type == 'bias':
frame = self._simBias(shape)
elif self.exposure_type == 'dark':
frame = self._simDark(shape, exptime)
elif self.exposure_type == 'normal':
frame = self._simNormal(shape, exptime)
else:
raise RuntimeError('unknown exposure type: %s' %
(self.exposure_type, ))
#Keep it small
frame = self.convertToInt8(frame)
mrcname = '.mrc'
fname = os.path.join(FRAME_DIR, self.rawframesname + mrcname)
if self.save_frames:
print 'SAVE', i
if i == 0:
mrc.write(frame, fname)
else:
mrc.append(frame, fname)
if i in self.useframes:
print 'SUM', i
sum += frame
return sum
def _getImage(self):
self.custom_setup()
if not self.validateGeometry():
raise ValueError('invalid image geometry')
for axis in ['x', 'y']:
if self.dimension[axis] * self.binning[axis] > self.getCameraSize()[axis]:
raise ValueError('invalid dimension/binning combination')
columns = self.dimension['x']
rows = self.dimension['y']
shape = (rows, columns)
t0 = time.time()
## exposure time
time.sleep(self.exposure_time)
t1 = time.time()
self.exposure_timestamp = (t1 + t0) / 2.0
nframes = self.getNumberOfFrames()
exptime = self.frame_time
if self.useframes:
useframes = []
for f in self.useframes:
if 0 <= f < nframes:
useframes.append(f)
else:
# use all frames in final image
useframes = range(nframes)
self.useframes = useframes
print 'SAVERAWFRAMES', self.save_frames
if self.save_frames:
self.rawframesname = time.strftime('frames_%Y%m%d_%H%M%S')
self.rawframesname += '_%02d' % (idcounter.next(),)
else:
return self.getSyntheticImage(shape)
sum = numpy.zeros(shape, numpy.float32)
for i in range(nframes):
if self.exposure_type == 'bias':
frame = self._simBias(shape)
elif self.exposure_type == 'dark':
frame = self._simDark(shape, exptime)
elif self.exposure_type == 'normal':
frame = self._simNormal(shape, exptime)
else:
raise RuntimeError('unknown exposure type: %s' % (self.exposure_type,))
#Keep it small
frame = self.convertToInt8(frame)
mrcname = '.mrc'
fname = os.path.join(FRAME_DIR,self.rawframesname + mrcname)
if self.save_frames:
print 'SAVE', i
if i == 0:
mrc.write(frame, fname)
else:
mrc.append(frame, fname)
if i in self.useframes:
print 'SUM', i
sum += frame
return sum
""" # parameters to change size = (2048,2048) drift = 3.0 number_of_frames = 20 feature_size = 2 import numpy from pyami import mrc zeros = numpy.zeros(size) center_frame = number_of_frames / 2 start_center = (size[0]/2 - center_frame, size[1]/2 - center_frame) for i in range(number_of_frames): print 'writing frame %d' % (i,) a = zeros * 1.0 for p in range(feature_size): for q in range(feature_size): position = (int(round(start_center[0]+p+i*drift)),int(round(start_center[1]+q+i*drift))) a[position] = 5.0 print position if i == 0: mrc.write(a,'frames.mrc') else: mrc.append(a,'frames.mrc')
"""
Makes a small and simple stack for testing frame alignment program
It writes to local directory
"""
# parameters to change
size = (2048, 2048)
drift = 3.0
number_of_frames = 20
feature_size = 2
import numpy
from pyami import mrc
zeros = numpy.zeros(size)
center_frame = number_of_frames / 2
start_center = (size[0] / 2 - center_frame, size[1] / 2 - center_frame)
for i in range(number_of_frames):
print 'writing frame %d' % (i, )
a = zeros * 1.0
for p in range(feature_size):
for q in range(feature_size):
position = (int(round(start_center[0] + p + i * drift)),
int(round(start_center[1] + q + i * drift)))
a[position] = 5.0
print position
if i == 0:
mrc.write(a, 'frames.mrc')
else:
mrc.append(a, 'frames.mrc')
