def getSubTomogramData(subtomorundata, stackpdata):
pdata = stackpdata['particle']
tomoq = appiondata.ApTomogramData(subtomorun=subtomorundata, center=pdata)
results = tomoq.query()
if results:
tomo = results[0]
return tomo
def getLastVolumeIndex(fulltomodata):
tomoq = appiondata.ApTomogramData(fulltomogram=fulltomodata)
results = tomoq.query()
if results:
return results[0]['number']
else:
return 0
def setRunDir(self):
"""
this function only runs if no rundir is defined at the command line
"""
subtomorunq = appiondata.ApSubTomogramRunData()
subtomorundata = subtomorunq.direct_query(self.params['subtomoId'])
subtomoq = appiondata.ApTomogramData(subtomorun=subtomorundata)
results = subtomoq.query(results=1)
if results:
subtomodir = results[0]['path']['path']
tiltdirs = subtomodir.split('/tiltseries')
self.params['rundir'] = os.path.join(tiltdirs[0],"average",self.params['runname'])
def isTomoInDB(md5sum, full=False, recfile=''):
abspath = os.path.abspath(recfile)
rundir = os.path.dirname(abspath)
basename = os.path.basename(abspath)
rootname = os.path.splitext(basename)
if not full:
tomoq = appiondata.ApTomogramData(name=rootname[0])
tomoq['md5sum'] = md5sum
else:
tomoq = appiondata.ApFullTomogramData(name=rootname[0])
tomod = tomoq.query(results=1)
if tomod:
tomodata = tomod[0]
# old style
if tomodata['path'] is not None and tomodata['path']['path'] == rundir:
return True
# new style
if tomodata['reconrun']['path']['path'] == rundir:
return True
return False
def insertSubTomogram(fulltomodata, rundata, center, offsetz, dimension, path,
name, index, pixelsize, description):
tomoq = appiondata.ApTomogramData(fulltomogram=fulltomodata)
tomoq['session'] = fulltomodata['session']
tomoq['tiltseries'] = fulltomodata['tiltseries']
tomoq['subtomorun'] = rundata
tomoq['path'] = appiondata.ApPathData(path=os.path.abspath(path))
tomoq['name'] = name
tomoq['number'] = index
tomoq['center'] = center
# offsetz is in pixel of the full tomogram
tomoq['offsetz'] = offsetz
# dimension is that of the original tilt images, i.e., before binning of the full tomogram
tomoq['dimension'] = dimension
# pixelsize is of the full_bin * sub_bin tomogram
tomoq['pixelsize'] = pixelsize
tomoq['description'] = description
filepath = os.path.join(path, name + ".rec")
tomoq['md5sum'] = apFile.md5sumfile(filepath)
return publish(tomoq)
def getSubvolumeInfo(subtomorundata):
tomoq = appiondata.ApTomogramData(subtomorun=subtomorundata)
results = tomoq.query(results=1)
if results:
tomo = results[0]
subbin = subtomorundata['subbin']
fullq = appiondata.ApFullTomogramData()
fulltomogram = tomo['fulltomogram']
if fulltomogram['alignrun'] is None:
# new data has no alignrun
fullbin = tomo['fulltomogram']['aligner']['alignrun']['bin']
else:
# old data has no aligner
fullbin = tomo['fulltomogram']['alignrun']['bin']
totalbin = subbin * fullbin
shape = (tomo['dimension']['z'] / totalbin,
tomo['dimension']['y'] / totalbin,
tomo['dimension']['x'] / totalbin)
pixelsize = tomo['pixelsize']
return shape, totalbin, pixelsize
else:
return None, 1, None
def uploadTomo(params):
if not params['commit']:
apDisplay.printWarning("not commiting tomogram to database")
return
apDisplay.printMsg("Commiting tomogram to database")
sessiondata = apDatabase.getSessionDataFromSessionName(
params['sessionname'])
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
params['tiltseriesnumber'], sessiondata)
runname = params['runname']
name = params['name']
if params['full']:
fullbin = params['bin']
else:
fullbin = 1
subbin = params['bin']
alignrun = insertTomoAlignmentRun(sessiondata, None, None, None, None,
fullbin, runname, params['aligndir'],
'manual alignment from upload')
# only tilt series in one alignrun for now
insertTiltsInAlignRun(alignrun, tiltdata, None, True)
alignerdata = insertAlignerParams(alignrun, params)
firstimagedata = getFirstImage(tiltdata)
path = os.path.abspath(params['rundir'])
description = params['description']
if params['full']:
thickness = params['shape'][0] * fullbin
uploadfile = params['zprojfile']
projectimagedata = uploadZProjection(runname, firstimagedata,
uploadfile)
fullrundata = insertFullTomoRun(sessiondata, path, runname, 'upload')
return insertFullTomogram(sessiondata, tiltdata, alignerdata,
fullrundata, name, description,
projectimagedata, thickness, None, fullbin,
[])
else:
projectimagedata = None
fulltomopath = params['rundir'].replace('/' + params['volume'], '')
dummyname = 'dummy'
dummydescription = 'fake full tomogram for subtomogram upload'
thickness = params['shape'][0] * subbin
fullrundata = insertFullTomoRun(sessiondata, fulltomopath, runname,
'upload')
fulltomogram = insertFullTomogram(sessiondata, tiltdata, alignerdata,
fullrundata, dummyname,
dummydescription, projectimagedata,
thickness, None, fullbin, [])
apix = apDatabase.getPixelSize(firstimagedata)
tomoq = appiondata.ApTomogramData()
tomoq['session'] = sessiondata
tomoq['tiltseries'] = tiltdata
results = tomoq.query()
index = len(results) + 1
pixelsize = 1e-10 * apix * subbin
runname = params['volume']
shape = map((lambda x: x * subbin), params['shape'])
dimension = {'x': shape[2], 'y': shape[1], 'z': shape[0]}
subtomorundata = insertSubTomoRun(sessiondata, None, None, runname,
params['invert'], subbin)
return insertSubTomogram(fulltomogram, subtomorundata, None, 0,
dimension, path, name, index, pixelsize,
description)