def getDefocPairParticles(imgdata, selectionid, particlelabel=None):
### get defocal pair
if imgdata['preset'] is not None:
defimgdata = apDefocalPairs.getDefocusPair(imgdata)
else:
# For pairs from Leginon Manual Application
defimgdata = apDefocalPairs.getManualDefocusPair(imgdata)
if defimgdata is None:
apDisplay.printWarning(
"Could not find defocal pair for image %s (id %d)" %
(apDisplay.short(imgdata['filename']), imgdata.dbid))
return ([], {'shiftx': 0, 'shifty': 0, 'scale': 1})
apDisplay.printMsg(
"Found defocus pair %s (id %d) for image %s (id %d)" %
(apDisplay.short(defimgdata['filename']), defimgdata.dbid,
apDisplay.short(imgdata['filename']), imgdata.dbid))
### get particles
partq = appiondata.ApParticleData()
partq['image'] = defimgdata
partq['selectionrun'] = appiondata.ApSelectionRunData.direct_query(
selectionid)
if particlelabel is not None:
partq['label'] = particlelabel
partdatas = partq.query()
apDisplay.printMsg("Found %d particles for defocal pair %s (id %d)" % (
len(partdatas),
apDisplay.short(defimgdata['filename']),
defimgdata.dbid,
))
if len(partdatas) == 0:
return ([], {'shiftx': 0, 'shifty': 0, 'scale': 1})
### get shift information
has_tried = False
while True:
shiftq = appiondata.ApImageTransformationData()
shiftq['image1'] = defimgdata
shiftdatas = shiftq.query()
if shiftdatas:
shiftdata = shiftdatas[0]
apDisplay.printMsg(
"Shifting particles by %.1f,%.1f (%d X)" %
(shiftdata['shiftx'], shiftdata['shifty'], shiftdata['scale']))
break
else:
if has_tried == True:
apDisplay.printError(
"No shift inserted to database after one try")
apDisplay.printMsg("Calculating shift....")
shiftpeak = apDefocalPairs.getShift(defimgdata, imgdata)
apDefocalPairs.insertShift(defimgdata, imgdata, shiftpeak)
has_tried = True
return (partdatas, shiftdata)
def getTransformedDefocPair(imgdata, direction):
simgq = appiondata.ApImageTransformationData()
base = 'image'
direction = str(direction)
if direction == '2':
sfrom = base + '2'
sto = base + '1'
if direction == '1':
sfrom = base + '1'
sto = base + '2'
simgq[sfrom] = imgdata
simgresults = simgq.query(readimages=False)
if simgresults:
sbimgref = simgresults[0].special_getitem(sto, dereference=False)
sbimgdata = leginon.leginondata.AcquisitionImageData.direct_query(
sbimgref.dbid, readimages=False)
else:
return None
return sbimgdata
def insertShift(imgdata, siblingdata, peak):
if not siblingdata or not peak:
apDisplay.printWarning("No sibling or peak found. No database insert")
return False
shiftq = appiondata.ApImageTransformationData()
shiftq['image1'] = imgdata
shiftdata = shiftq.query()
if shiftdata:
apDisplay.printWarning("Shift values already in database")
return False
shiftq['image2'] = siblingdata
shiftq['shiftx'] = peak['shift'][1]
shiftq['shifty'] = peak['shift'][0]
shiftq['scale'] = peak['scalefactor']
if not peak['subfailed']:
shiftq['correlation'] = peak['subpixel peak value']
else:
shiftq['correlation'] = 0.0
apDisplay.printMsg("Inserting shift beteween "+apDisplay.short(imgdata['filename'])+\
" and "+apDisplay.short(siblingdata['filename'])+" into database")
shiftq.insert()
return True