def writeTiltSeriesStack(stackdir,stackname,ordered_mrc_files,apix=1):
stackpath = os.path.join(stackdir, stackname)
print stackpath
apixdict = {'x':apix,'y':apix}
if os.path.exists(stackpath):
stheader = mrc.readHeaderFromFile(stackpath)
stshape = stheader['shape']
imageheader = mrc.readHeaderFromFile(ordered_mrc_files[0])
imageshape = imageheader['shape']
if stshape[1:] == imageshape and stshape[0] == len(ordered_mrc_files):
apDisplay.printMsg("No need to get new stack of the tilt series")
else:
apImage.writeMrcStack(stackdir,stackname,order3dmrc_files, 1)
mrc.updateFilePixelSize(stackpath,apixdict)
else:
apImage.writeMrcStack(stackdir,stackname,ordered_mrc_files, 1)
mrc.updateFilePixelSize(stackpath,apixdict)
def writeTiltSeriesStack(stackdir, stackname, ordered_mrc_files, apix=1):
stackpath = os.path.join(stackdir, stackname)
print stackpath
apixdict = {'x': apix, 'y': apix}
if os.path.exists(stackpath):
stheader = mrc.readHeaderFromFile(stackpath)
stshape = stheader['shape']
imageheader = mrc.readHeaderFromFile(ordered_mrc_files[0])
imageshape = imageheader['shape']
if stshape[1:] == imageshape and stshape[0] == len(ordered_mrc_files):
apDisplay.printMsg("No need to get new stack of the tilt series")
else:
apImage.writeMrcStack(stackdir, stackname, order3dmrc_files, 1)
mrc.updateFilePixelSize(stackpath, apixdict)
else:
apImage.writeMrcStack(stackdir, stackname, ordered_mrc_files, 1)
mrc.updateFilePixelSize(stackpath, apixdict)
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
