def getParticleParamsData(self):
tiltparamsq = appiondata.ApTiltAlignParamsData()
tiltparamsq['output_type'] = self.params['outtype']
if self.params['pickrunids'] is not None:
self.params['pickrunidlist'] = self.params['pickrunids'].split(",")
tiltparamsq['oldselectionrun'] = apParticle.getSelectionRunDataFromID(self.params['pickrunidlist'][0])
return tiltparamsq
def start(self):
sessionname = self.params['sessionname']
runname = self.params['runname']
preset = self.params['preset']
sessionq = leginondata.SessionData(name=sessionname)
presetq=leginondata.PresetData(name=preset)
imgquery = leginondata.AcquisitionImageData()
imgquery['preset'] = presetq
imgquery['session'] = sessionq
imgtree = imgquery.query(readimages=False)
partq = appiondata.ApContourData()
sessiond = sessionq.query()
selectionid = apParticle.getSelectionIdFromName(runname, sessionname)
if not selectionid:
apDisplay.printWarning('No Object Tracing Run found in database, Skipping.......')
return
selectionrundata = apParticle.getSelectionRunDataFromID(selectionid)
file = open('contourpickerData-' + sessionname + '.txt','w')
file.write('session_id ' + runname + '\n')
file.write('usr_id ' + os.getlogin() + '\n')
file.write('experiment_name ' + sessionname + '\n')
file.write('experiment_description ' + sessiond[0]['comment'].strip() + '\n')
file.write('nimages ' + str(len(imgtree)) + '\n')
for imgdata in imgtree:
file.write('START_IMAGE' + '\n')
partq['image'] = imgdata
partq['selectionrun'] = selectionrundata
partd = partq.query()
if len(partd)>0:
file.write('image_refID ' + str(partd[0]['image'].dbid) + '\n')
file.write('image_name ' + imgdata['filename'] + '\n')
if len(partd)>0:
file.write('time_roi ' + str(partd[0].timestamp) + '\n')
#file.write('time_roi ' + partd[0]['DEF_timestamp'] + '\n')
file.write('dfac = 1\n')
maxversion = 0
numparticles = 0
for part in partd:
if int(part['version'])>maxversion:
maxversion = int(part['version'])
for part in partd:
if int(part['version'])==maxversion:
numparticles+=1
file.write('version_id ' + str(maxversion) + '\n')
file.write('ncontours ' + str(numparticles) + '\n')
pointq = appiondata.ApContourPointData()
for part in partd:
if int(part['version'])==maxversion:
# file.write('contour_number ' + )
file.write('method_used ' + part['method'] + ' ')
pointq['contour'] = part
pointd = pointq.query()
for point in pointd:
file.write(str(point['x']) + ',' + str(point['y']) + ';')
file.write('\n')
file.write('END_IMAGE' + '\n')
def getParticleParamsData(self): manparamsq=appiondata.ApManualParamsData() manparamsq['trace'] = self.trace if self.params['helicalstep'] is not None: manparamsq['helicalstep'] = self.params['helicalstep'] manparamsq['diam'] = self.params['diam'] if self.params['pickrunid'] is not None: manparamsq['oldselectionrun'] = apParticle.getSelectionRunDataFromID(self.params['pickrunid']) return manparamsq
def getParticlePicks(self, imgdata): if not self.params['pickrunid']: if not self.params['pickrunname']: return [] self.params['pickrunid'] = apParticle.getSelectionRun(imgdata, self.params['pickrunname']) if not self.params['pickrunname']: rundata = apParticle.getSelectionRunDataFromID(self.params['pickrunid']) self.params['pickrunname'] = rundata['name'] particles = apParticle.getParticles(imgdata, self.params['pickrunid']) targets = self.particlesToTargets(particles) return targets
def preLoopFunctions(self):
self.is_dd_frame = False
self.is_dd_stack = False
self.is_dd = False
self.checkIsDD()
self.batchboxertimes = []
self.ctftimes = []
self.mergestacktimes = []
self.meanreadtimes = []
self.insertdbtimes = []
self.noimages = False
self.totalpart = 0
self.selectiondata = None
# Different class needed depending on if ddstack is specified or available
if self.is_dd:
from appionlib import apDDprocess
if self.is_dd_frame:
apDisplay.printMsg('DD Frame Processing')
self.dd = apDDprocess.initializeDDFrameprocess(
self.params['sessionname'])
self.dd.setUseGS(self.params['useGS'])
if self.is_dd_stack:
apDisplay.printMsg('DD Stack Processing')
self.dd = apDDprocess.DDStackProcessing()
if len(self.imgtree) == 0:
apDisplay.printWarning("No images were found to process")
self.noimages = True
# Still need to set attributes if waiting for more images
if not self.params['wait']:
return
if self.params['selectionid'] is not None:
self.selectiondata = apParticle.getSelectionRunDataFromID(
self.params['selectionid'])
if self.params['particlelabel'] == 'fromtrace':
if (not self.selectiondata['manparams']
or not self.selectiondata['manparams']['trace']):
apDisplay.printError(
"Can not use traced object center to extract boxed area without tracing"
)
else:
self.params['particlelabel'] = '_trace'
self.checkPixelSize()
self.existingParticleNumber = 0
self.setStartingParticleNumber()
apDisplay.printMsg("Starting at particle number: " +
str(self.particleNumber))
if self.params[
'partlimit'] is not None and self.particleNumber > self.params[
'partlimit']:
apDisplay.printError(
"Number of particles in existing stack already exceeds limit!")
self.logpeaks = 2
def preLoopFunctions(self):
self.is_dd_frame = False
self.is_dd_stack = False
self.is_dd = False
self.checkIsDD()
self.batchboxertimes = []
self.ctftimes = []
self.mergestacktimes = []
self.meanreadtimes = []
self.insertdbtimes = []
self.noimages = False
self.totalpart = 0
self.selectiondata = None
# Different class needed depending on if ddstack is specified or available
if self.is_dd:
from appionlib import apDDprocess
if self.is_dd_frame:
apDisplay.printMsg('DD Frame Processing')
self.dd = apDDprocess.initializeDDFrameprocess(self.params['sessionname'])
self.dd.setUseGS(self.params['useGS'])
if self.is_dd_stack:
apDisplay.printMsg('DD Stack Processing')
self.dd = apDDprocess.DDStackProcessing()
if len(self.imgtree) == 0:
apDisplay.printWarning("No images were found to process")
self.noimages = True
# Still need to set attributes if waiting for more images
if not self.params['wait']:
return
if self.params['selectionid'] is not None:
self.selectiondata = apParticle.getSelectionRunDataFromID(self.params['selectionid'])
if self.params['particlelabel'] == 'fromtrace':
if (not self.selectiondata['manparams'] or not self.selectiondata['manparams']['trace']):
apDisplay.printError("Can not use traced object center to extract boxed area without tracing")
else:
self.params['particlelabel'] = '_trace'
self.checkPixelSize()
self.existingParticleNumber=0
self.setStartingParticleNumber()
apDisplay.printMsg("Starting at particle number: "+str(self.particleNumber))
if self.params['partlimit'] is not None and self.particleNumber > self.params['partlimit']:
apDisplay.printError("Number of particles in existing stack already exceeds limit!")
self.logpeaks = 2
def start(self):
sessionname = self.params['sessionname']
runname = self.params['runname']
preset = self.params['preset']
sessionq = leginondata.SessionData(name=sessionname)
presetq = leginondata.PresetData(name=preset)
imgquery = leginondata.AcquisitionImageData()
imgquery['preset'] = presetq
imgquery['session'] = sessionq
imgtree = imgquery.query(readimages=False)
partq = appiondata.ApContourData()
sessiond = sessionq.query()
selectionid = apParticle.getSelectionIdFromName(runname, sessionname)
if not selectionid:
apDisplay.printWarning(
'No Object Tracing Run found in database, Skipping.......')
return
selectionrundata = apParticle.getSelectionRunDataFromID(selectionid)
file = open('contourpickerData-' + sessionname + '.txt', 'w')
file.write('session_id ' + runname + '\n')
file.write('usr_id ' + os.getlogin() + '\n')
file.write('experiment_name ' + sessionname + '\n')
file.write('experiment_description ' + sessiond[0]['comment'].strip() +
'\n')
file.write('nimages ' + str(len(imgtree)) + '\n')
for imgdata in imgtree:
file.write('START_IMAGE' + '\n')
partq['image'] = imgdata
partq['selectionrun'] = selectionrundata
partd = partq.query()
if len(partd) > 0:
file.write('image_refID ' + str(partd[0]['image'].dbid) + '\n')
file.write('image_name ' + imgdata['filename'] + '\n')
if len(partd) > 0:
file.write('time_roi ' + str(partd[0].timestamp) + '\n')
#file.write('time_roi ' + partd[0]['DEF_timestamp'] + '\n')
file.write('dfac = 1\n')
maxversion = 0
numparticles = 0
for part in partd:
if int(part['version']) > maxversion:
maxversion = int(part['version'])
for part in partd:
if int(part['version']) == maxversion:
numparticles += 1
file.write('version_id ' + str(maxversion) + '\n')
file.write('ncontours ' + str(numparticles) + '\n')
pointq = appiondata.ApContourPointData()
for part in partd:
if int(part['version']) == maxversion:
# file.write('contour_number ' + )
file.write('method_used ' + part['method'] + ' ')
pointq['contour'] = part
pointd = pointq.query()
for point in pointd:
file.write(
str(point['x']) + ',' + str(point['y']) + ';')
file.write('\n')
file.write('END_IMAGE' + '\n')