def boxerFrameStack(framestackpath, parttree, outstack, boxsize,framelist):
"""
boxes the particles and returns them as a list of numpy arrays
"""
start_frame = framelist[0]
nframe = len(framelist)
apDisplay.printMsg("boxing %d particles from sum of total %d frames starting from frame %d using mmap" % (len(parttree),nframe,start_frame))
boxedparticles = []
stack = mrc.mmap(framestackpath)
for partdict in parttree:
x1,x2,y1,y2 = getBoxBoundary(partdict, boxsize)
apDisplay.printDebug(' crop range of (x,y)=(%d,%d) to (%d,%d)' % (x1,y1,x2-1,y2-1))
#numpy arrays are rows,cols --> y,x not x,y
boxpart = numpy.sum(stack[tuple(framelist),y1:y2,x1:x2],axis=0)
boxedparticles.append(boxpart)
apImagicFile.writeImagic(boxedparticles, outstack)
return True
def _getAllImages(self):
startt = time.time()
allfiles = glob.glob("*.dwn.mrc")
self.imgtree = []
for i, filename in enumerate(allfiles):
imagedict = FileImageData()
imagedict.dbid = i + 1
imagedict['filename'] = filename[:-8]
imagedict['image'] = mrc.mmap(filename)
self.imgtree.append(imagedict)
precount = len(self.imgtree)
apDisplay.printMsg("Found " + str(precount) + " images in " +
apDisplay.timeString(time.time() - startt))
### REMOVE PROCESSED IMAGES
apDisplay.printMsg("Remove processed images")
self._removeProcessedImages()
### SET IMAGE ORDER
if self.params['shuffle'] is True:
self.imgtree = self._shuffleTree(self.imgtree)
apDisplay.printMsg("Process images shuffled")
elif self.params['reverse'] is True:
apDisplay.printMsg("Process images new to old")
else:
# by default images are new to old
apDisplay.printMsg("Process images old to new")
self.imgtree.reverse()
### LIMIT NUMBER
if self.params['limit'] is not None:
lim = self.params['limit']
if len(self.imgtree) > lim:
apDisplay.printMsg("Limiting number of images to " + str(lim))
self.imgtree = self.imgtree[:lim]
if len(self.imgtree) > 0:
# Fake apix
self.params['apix'] = self.getPixelSize(self.imgtree[0])
self.stats['imagecount'] = len(self.imgtree)
def _getAllImages(self):
startt = time.time()
allfiles = glob.glob("*.dwn.mrc")
self.imgtree = []
for i, filename in enumerate(allfiles):
imagedict = FileImageData()
imagedict.dbid = i+1
imagedict['filename'] = filename[:-8]
imagedict['image'] = mrc.mmap(filename)
self.imgtree.append(imagedict)
precount = len(self.imgtree)
apDisplay.printMsg("Found "+str(precount)+" images in "+apDisplay.timeString(time.time()-startt))
### REMOVE PROCESSED IMAGES
apDisplay.printMsg("Remove processed images")
self._removeProcessedImages()
### SET IMAGE ORDER
if self.params['shuffle'] is True:
self.imgtree = self._shuffleTree(self.imgtree)
apDisplay.printMsg("Process images shuffled")
elif self.params['reverse'] is True:
apDisplay.printMsg("Process images new to old")
else:
# by default images are new to old
apDisplay.printMsg("Process images old to new")
self.imgtree.reverse()
### LIMIT NUMBER
if self.params['limit'] is not None:
lim = self.params['limit']
if len(self.imgtree) > lim:
apDisplay.printMsg("Limiting number of images to "+str(lim))
self.imgtree = self.imgtree[:lim]
if len(self.imgtree) > 0:
# Fake apix
self.params['apix'] = self.getPixelSize(self.imgtree[0])
self.stats['imagecount'] = len(self.imgtree)
def readFileData(self, filename):
"""
takes any file type and returns a list of 2D arrays
use memory mapping (mmap) to prevent memory overloads
"""
#Determine extension
if filename.endswith('.mrc') or filename.endswith('.mrcs'):
data = mrc.mmap(filename)
if len(data.shape) == 2:
#convert to 3D
self.single = True
data.resize((1, data.shape[0], data.shape[1], ))
elif filename.endswith('.hed') or filename.endswith('.img'):
data = imagic.read(filename)
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")
return data
def memmapMRC(fileref): fullname = os.path.join(fileref.path, fileref.filename) im = mrc.mmap(fullname) return im
def memmapMRC(fileref):
fullname = os.path.join(fileref.path, fileref.filename)
im = mrc.mmap(fullname)
return im
