def _getAllSeries(self):
startt = time.time()
self.seriestree = []
if self.params['mrcnames'] is not None:
mrcfileroot = self.params['mrcnames'].split(",")
if self.params['sessionname'] is not None:
images = apDatabase.getSpecificImagesFromSession(mrcfileroot, self.params['sessionname'])
else:
images = apDatabase.getSpecificImagesFromDB(mrcfileroot)
elif self.params['sessionname'] is not None:
if self.params['preset'] is not None:
images = apDatabase.getImagesFromDB(self.params['sessionname'], self.params['preset'])
else:
self.seriestree = apDatabase.getAllTiltSeriesFromSessionName(self.params['sessionname'])
else:
if self.params['mrcnames'] is not None:
apDisplay.printMsg("MRC List: "+str(len(self.params['mrcnames']))+" : "+str(self.params['mrcnames']))
apDisplay.printMsg("Session: "+str(self.params['sessionname'])+" : "+str(self.params['preset']))
apDisplay.printError("no files specified")
# Only use finished tilt series
if len(self.seriestree) > 0:
indices_to_pop = []
for tiltseriesdata in self.seriestree:
if not apDatabase.getTiltSeriesDoneStatus(tiltseriesdata):
indices_to_pop.append(self.seriestree.index(tiltseriesdata))
indices_to_pop.sort()
indices_to_pop.reverse()
for index in indices_to_pop:
self.seriestree.pop(index)
else:
for image in images:
tiltseriesdata = image['tilt series']
if tiltseriesdata and tiltseriesdata not in self.seriestree and apDatabase.getTiltSeriesDoneStatus(tiltseriesdata):
self.seriestree.append(tiltseriesdata)
precount = len(self.seriestree)
apDisplay.printMsg("Found "+str(precount)+" tilt series in "+apDisplay.timeString(time.time()-startt))
### REMOVE PROCESSED IMAGES
apDisplay.printMsg("Remove processed series")
self._removeProcessedSeries()
### SET SERIES ORDER
if self.params['reverse'] is True:
apDisplay.printMsg("Process series new to old")
else:
# by default series are new to old
apDisplay.printMsg("Process series old to new")
self.seriestree.sort(self._reverseSortSeriesTree)
### LIMIT NUMBER
if self.params['limit'] is not None:
lim = self.params['limit']
if len(self.seriestree) > lim:
apDisplay.printMsg("Limiting number of series to "+str(lim))
self.seriestree = self.seriestree[:lim]
self.stats['seriescount'] = len(self.seriestree)
def _getAllImages(self):
startt = time.time()
if self.params['mrcnames'] is not None:
mrcfileroot = self.params['mrcnames'].split(",")
if self.params['sessionname'] is not None:
self.imgtree = apDatabase.getSpecificImagesFromSession(
mrcfileroot, self.params['sessionname'])
else:
self.imgtree = apDatabase.getSpecificImagesFromDB(mrcfileroot)
elif self.params['sessionname'] is not None:
if self.params['preset'] is not None:
self.imgtree = apDatabase.getImagesFromDB(
self.params['sessionname'], self.params['preset'])
else:
self.imgtree = apDatabase.getAllImagesFromDB(
self.params['sessionname'])
else:
if self.params['mrcnames'] is not None:
apDisplay.printMsg("MRC List: " +
str(len(self.params['mrcnames'])) + " : " +
str(self.params['mrcnames']))
apDisplay.printMsg("Session: " + str(self.params['sessionname']) +
" : " + str(self.params['preset']))
apDisplay.printError("no files specified")
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.sort(self._reverseSortImgTree)
### 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:
self.params['apix'] = apDatabase.getPixelSize(self.imgtree[0])
self.stats['imagecount'] = len(self.imgtree)
def _getAllImages(self):
startt = time.time()
if self.params['mrcnames'] is not None:
mrcfileroot = self.params['mrcnames'].split(",")
if self.params['sessionname'] is not None:
self.imgtree = apDatabase.getSpecificImagesFromSession(mrcfileroot, self.params['sessionname'])
else:
self.imgtree = apDatabase.getSpecificImagesFromDB(mrcfileroot)
elif self.params['sessionname'] is not None:
if self.params['preset'] is not None:
self.imgtree = apDatabase.getImagesFromDB(self.params['sessionname'], self.params['preset'])
else:
self.imgtree = apDatabase.getAllImagesFromDB(self.params['sessionname'])
else:
if self.params['mrcnames'] is not None:
apDisplay.printMsg("MRC List: "+str(len(self.params['mrcnames']))+" : "+str(self.params['mrcnames']))
apDisplay.printMsg("Session: "+str(self.params['sessionname'])+" : "+str(self.params['preset']))
apDisplay.printError("no files specified")
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.sort(self._reverseSortImgTree)
### 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:
self.params['apix'] = apDatabase.getPixelSize(self.imgtree[0])
self.stats['imagecount'] = len(self.imgtree)