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