def alreadyAcquired(self, targetdata, presetname):
'''
determines if image already acquired using targetdata and presetname
'''
## if image exists with targetdata and presetdata, no acquire
## we expect target to be exact, however, presetdata may have
## changed so we only query on preset name
# seems to have trouple with using original targetdata as
# a query, so use a copy with only some of the fields
presetquery = leginondata.PresetData(name=presetname)
targetquery = leginondata.AcquisitionImageTargetData(initializer=targetdata)
## don't care if drift correction was done on target after image was
## acquired, so ignore version, delta row/col, parentimage, and fromtarget
targetquery['version'] = None
targetquery['delta row'] = None
targetquery['delta column'] = None
targetquery['image'] = None
targetquery['fromtarget'] = None
imagequery = leginondata.AcquisitionImageData(target=targetquery, preset=presetquery)
## other things to fill in
imagequery['scope'] = leginondata.ScopeEMData()
imagequery['camera'] = leginondata.CameraEMData()
imagequery['session'] = leginondata.SessionData()
datalist = self.research(datainstance=imagequery)
if datalist:
## no need to acquire again, but need to republish
self.reportStatus('output', 'Image was acquired previously, republishing')
imagedata = datalist[0]
self.publishDisplayWait(imagedata)
return True
else:
return False
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()
file = open('contourpickerTubeCircleData-' + sessionname + '.txt', 'w')
file.write('experiment_name ' + sessionname + '\n')
file.write('experiment_description ' + sessiond[0]['comment'] + '\n')
numimages = 0
for imgdata in imgtree:
partq['image'] = imgdata
partd = partq.query()
if len(partd) > 0:
numimages += 1
file.write('nimages ' + str(numimages) + '\n')
numparticles = 0.0
numcircles = 0.0
numtubes = 0.0
for imgdata in imgtree:
partq['image'] = imgdata
partd = partq.query()
maxversion = 0
for part in partd:
if int(part['version']
) > maxversion and part['runname'] == runname:
maxversion = int(part['version'])
for part in partd:
if int(part['version']
) == maxversion and part['runname'] == runname:
numparticles += 1
if part['particleType'] == 'Circle':
numcircles += 1
if part['particleType'] == 'Tube':
numtubes += 1
file.write('nparticles ' + str(numparticles) + '\n')
if numparticles == 0:
precenttubes = 0
file.write('%tubes ' + str(0.0))
else:
percenttubes = numtubes / numparticles
percent = percenttubes * 100
percent *= 100
percent = int(percent)
percent = percent / 100.0
file.write('%tubes ' + str(percent))
def getDoseFromSessionPresetNames(sessionname, presetname):
''' returns dose, in electrons per Angstrom '''
sessiondata = leginondata.SessionData(name=sessionname).query()[0]
presetdata = leginondata.PresetData(
name=presetname, session=sessiondata).query(results=1)[0]
dose = presetdata['dose']
if not dose:
raise RunTimeError("dose not available for %s session and preset %s" %
(sessionname, presetname))
return dose / 1e20
def makeAlignedImageData(old_imagedata,
new_camdata,
new_array,
alignlabel='a'):
'''
Prepare ImageData to be uploaded after alignment
'''
label_string = '-%s' % (alignlabel)
camdata = leginondata.CameraEMData(
initializer=new_camdata) # new CameraEMData for the aligned image
align_presetdata = leginondata.PresetData(
initializer=old_imagedata['preset'])
if old_imagedata['preset'] is None:
old_name = 'ma'
align_presetdata = leginondata.PresetData(
name='ma-%s' % (label_string),
magnification=old_imagedata['scope']['magnification'],
defocus=old_imagedata['scope']['defocus'],
tem=old_imagedata['scope']['tem'],
ccdcamera=camdata['ccdcamera'],
session=old_imagedata['session'],
)
else:
old_name = align_presetdata['name']
align_presetdata['name'] = old_name + label_string
align_presetdata['dimension'] = camdata['dimension']
align_presetdata['binning'] = camdata['binning']
align_presetdata['offset'] = camdata['offset']
align_presetdata['exposure time'] = camdata['exposure time']
# make new imagedata with the align_preset amd aligned CameraEMData
imagedata = leginondata.AcquisitionImageData(initializer=old_imagedata)
imagedata['preset'] = align_presetdata
imagefilename = imagedata['filename']
bits = imagefilename.split(old_name)
before_string = old_name.join(bits[:-1])
newfilename = align_presetdata['name'].join((before_string, bits[-1]))
imagedata['camera'] = camdata
imagedata['camera']['align frames'] = True
imagedata['image'] = new_array
imagedata['filename'] = makeUniqueImageFilename(imagedata, old_name,
align_presetdata['name'])
return imagedata
def importLastPresets(self):
# some presets such as fa and fc is never used in image acquisition
print 'importing all last version of presets....'
source_session = self.getSourceSession()
q = leginondata.PresetData(session=source_session)
allpresets = self.research(q)
lastpresets = {}
for p in allpresets:
if p['name'] not in lastpresets:
lastpresets[p['name']] = p
lastpreset_list = map((lambda x: lastpresets[x]), lastpresets.keys())
self.publish(lastpreset_list)
def processImageData(self, imagedata):
'''
Gets and publishes target information of specified image leginondata.
'''
if self.settings['ignore images']:
return
for target_name in self.targetnames:
self.setTargets([], target_name, block=True)
self.setTargetImageVector(imagedata)
# check if there is already a target list for this image
# or any other versions of this image (all from same target/preset)
# exclude sublists (like rejected target lists)
qtarget = imagedata['target']
try:
pname = imagedata['preset']['name']
qpreset = leginondata.PresetData(name=pname)
except:
qpreset = None
qimage = leginondata.AcquisitionImageData(target=qtarget,
preset=qpreset)
previouslists = self.researchTargetLists(image=qimage, sublist=False)
if previouslists:
# I hope you can only have one target list on an image, right?
targetlist = previouslists[0]
db = False
self.logger.info('Existing target list on this image...')
self.displayPreviousTargets(targetlist)
else:
# no previous list, so create one and fill it with targets
targetlist = self.newTargetList(image=imagedata,
queue=self.settings['queue'])
db = True
if self.settings['allow append'] or len(previouslists) == 0:
self.findTargets(imagedata, targetlist)
self.logger.debug('Publishing targetlist...')
## if queue is turned on, do not notify other nodes of each target list publish
if self.settings['queue']:
pubevent = False
else:
pubevent = True
self.publish(targetlist, database=db, pubevent=pubevent)
self.logger.debug('Published targetlist %s' % (targetlist.dbid, ))
if self.settings['wait for done'] and not self.settings['queue']:
self.makeTargetListEvent(targetlist)
self.setStatus('waiting')
self.waitForTargetListDone()
self.setStatus('processing')
def recentImageVersion(self, imagedata):
# find most recent version of this image
p = leginondata.PresetData(name=imagedata['preset']['name'])
q = leginondata.AcquisitionImageData()
q['session'] = imagedata['session']
q['target'] = imagedata['target']
q['list'] = imagedata['list']
q['preset'] = p
allimages = q.query()
version = 0
for im in allimages:
if im['version'] > version:
version = im['version']
return version
def getTiltSeries(self, targetdata, presetdata): ''' targetdata argument is target about to be acquired. Find the tilt series that this new image will belong to if it exists, otherwise create a new tilt series. ''' commontarget = targetdata['image']['target'] targetnumber = targetdata['number'] qimage1 = leginondata.AcquisitionImageData(target=commontarget) qtarget = leginondata.AcquisitionImageTargetData(image=qimage1, number=targetnumber) qpreset = leginondata.PresetData(name=presetdata['name'], session=presetdata['session']) qimage2 = leginondata.AcquisitionImageData(target=qtarget, preset=qpreset, session=presetdata['session']) images = self.research(qimage2, readimages=False) if images: tiltseries = images[0]['tilt series'] defocus = images[0]['scope']['defocus'] else: tiltseries = None defocus = None return tiltseries, defocus
def getImageList(self):
self.childpreset = self.settings['child preset']
childpresetq = leginondata.PresetData(session=self.session,
name=self.childpreset)
q = leginondata.AcquisitionImageData(session=self.session,
preset=childpresetq)
images = self.research(datainstance=q, readimages=False)
self.imageids = []
nongrid = 0
for image in images:
if image['grid'] is None:
nongrid += 1
else:
anc = self.getAncestor(image)
if anc is not None:
self.imageids.append((image.dbid, anc.dbid))
if nongrid > 0:
self.logger.warning(
'%d images are not from grids loaded by a robot' % nongrid)
if not self.imageids:
self.logger.error('No %s images in session' % (self.childpreset, ))
self.currentindex = None
def getImageList(self):
preset = self.settings['preset']
self.parentdir = self.session['image path']
maskname = self.settings['run']
if self.settings['path'] is None or self.settings['path'] == '':
rundir = self.handleDefaultPath(maskname)
else:
rundir = os.path.join(self.settings['path'], maskname)
self.logger.info('mask run dir %s' % rundir)
self.bin = self.settings['bin']
presetq = leginondata.PresetData(session=self.session, name=preset)
q = leginondata.AcquisitionImageData(session=self.session,
preset=presetq)
allimages = self.research(datainstance=q, readimages=False)
self.maskrundata, self.maskparamsdata = apMask.getMaskParamsByRunName(
maskname, self.session)
if not self.maskrundata:
apMask.insertManualMaskRun(self.session, rundir, maskname,
self.bin)
self.maskrundata, self.maskparamsdata = apMask.getMaskParamsByRunName(
maskname, self.session)
images = allimages
try:
maskdir = os.path.join(rundir, "masks")
self.makeRecursivePath(maskdir)
except:
self.logger.warning('can not create mask directory')
else:
if self.settings['continueon']:
mode = 'continue'
else:
mode = 'overwrite empty masks'
self.logger.warning('Mask Run exists, will %s' % (mode, ))
savedbin = self.maskparamsdata['bin']
if self.bin != savedbin:
self.logger.warning('Change binning to that of the saved %s',
(savedbin, ))
self.bin = savedbin
savedrundir = self.maskrundata['path']['path']
if rundir != savedrundir:
self.logger.warning(
'Change mask run path to that of the saved %s',
(savedrundir, ))
rundir = savedrundir
images = []
for imgdata in allimages:
regions = apMask.getMaskRegions(self.maskrundata, imgdata)
maskfile = os.path.join(rundir, "masks",
imgdata['filename'] + '_mask.png')
if mode == 'continue':
if not os.path.exists(maskfile):
images.append(imgdata)
else:
if mode == 'overwrite empty masks':
if len(regions) == 0:
images.append(imgdata)
self.maskdir = os.path.join(self.maskrundata['path']['path'], "masks")
if images:
goodfiles = map((lambda x: x['filename']), images)
goodfiles.sort()
self.images = []
self.files = []
for i, filename in enumerate(goodfiles):
q = leginondata.AcquisitionImageData(session=self.session,
filename=filename)
imgdatalist = self.research(datainstance=q, readimages=False)
if imgdatalist:
imgdata = imgdatalist[0]
self.images.append(imgdata)
self.files.append(filename)
if self.noreject and apDatabase.getImgAssessmentStatus(
imgdata) == False:
self.files.pop()
self.images.pop()
else:
self.logger.error('No %s files in session' % (preset, ))
return
if len(self.files) > 0:
self.currentindex = 0
self.displayCurrent()
else:
self.logger.error('No %s files in session' % (preset, ))
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')
if test:
return True
# check stage position
if movetype == 'modeled stage position':
scopeparam = 'stage position'
else:
scopeparam = movetype
emtargetdata[scopeparam] = dict(scopedata[scopeparam])
emtargetdata['target'] = targetdata
#emtargetdata['preset'] = presetdata
query = leginondata.AcquisitionImageTargetData()
query['session'] = self.session
query['preset'] = leginondata.PresetData()
query['preset']['name'] = presetname
query['grid'] = griddata
try:
targetdata['number'] = max(
[r['number'] for r in self.research(query)]) + 1
except ValueError:
targetdata['number'] = 0
self.logger.debug('new number: %s' % (targetdata['number'], ))
targetdata['preset'] = presetdata
targetdata['grid'] = griddata
targetdata['version'] = 0
targetdata['status'] = 'done'
targetdata['list'] = None
targetdata['image'] = None
