def upgradeLeginonDB(self): if not self.leginon_dbupgrade.columnExists('SessionData', 'frame path'): return sessions = leginondata.SessionData().query() for sessiondata in sessions: if sessiondata['frame path']: continue imagepath = sessiondata['image path'] if not imagepath: continue framepath = ddinfo.getRawFrameSessionPathFromImagePath(imagepath) self.leginon_dbupgrade.updateColumn('SessionData', 'frame path',"'"+framepath+"'",'`DEF_id`=%d' % sessiondata.dbid,True)
def upgradeLeginonDB(self): if not self.leginon_dbupgrade.columnExists('SessionData', 'frame path'): return sessions = leginondata.SessionData().query() for sessiondata in sessions: if sessiondata['frame path']: continue imagepath = sessiondata['image path'] if not imagepath: continue framepath = ddinfo.getRawFrameSessionPathFromImagePath(imagepath) self.leginon_dbupgrade.updateColumn( 'SessionData', 'frame path', "'" + framepath + "'", '`DEF_id`=%d' % sessiondata.dbid, True)
def getRawFrameDirFromImage(self,imagedata): if self.getRawFrameType() == 'singles': return super(GatanK2Processing,self).getRawFrameDirFromImage(imagedata) ''' K2 raw frames are now saved as image stack for feeding into gpu program. RawFrameDir here is now actually the filename with mrc extension. ''' # strip off DOS path in rawframe directory name rawframename = imagedata['camera']['frames name'].split('\\')[-1] if not rawframename: apDisplay.printWarning('No Raw Frame Saved for %s' % imagedata['filename']) # raw frames are saved in a subdirctory of image path imagepath = imagedata['session']['image path'] rawframe_basepath = ddinfo.getRawFrameSessionPathFromImagePath(imagepath) # frame stackfile is image filename plus '.frames.mrc' rawframedir = os.path.join(rawframe_basepath,'%s.frames.mrc' % imagedata['filename']) if not self.waitForPathExist(rawframedir,30): apDisplay.printError('Raw Frame Dir %s does not exist.' % rawframedir) return rawframedir
def getRawFrameDirFromImage(self, imagedata): if self.getRawFrameType() == 'singles': return super(GatanK2Processing, self).getRawFrameDirFromImage(imagedata) ''' K2 raw frames are now saved as image stack for feeding into gpu program. RawFrameDir here is now actually the filename with mrc extension. ''' # strip off DOS path in rawframe directory name rawframename = imagedata['camera']['frames name'].split('\\')[-1] if not rawframename: apDisplay.printWarning('No Raw Frame Saved for %s' % imagedata['filename']) # raw frames are saved in a subdirctory of image path imagepath = imagedata['session']['image path'] rawframe_basepath = ddinfo.getRawFrameSessionPathFromImagePath( imagepath) # frame stackfile is image filename plus '.frames.mrc' rawframedir = os.path.join(rawframe_basepath, '%s.frames.mrc' % imagedata['filename']) if not self.waitForPathExist(rawframedir, 30): apDisplay.printError('Raw Frame Dir %s does not exist.' % rawframedir) return rawframedir