def commitToDatabase(self):
processdir = self.params['rundir']
runname = self.params['runname']
# insertTomoRun
self.fullrundata = apTomo.insertFullTomoRun(self.sessiondata,
processdir, runname,
self.params['method'])
reconname = self.seriesname + "_full"
if os.path.exists(os.path.join(processdir, reconname + '.rec')):
#insertTomograma and z projection
if 'bin' not in self.params.keys():
self.params['bin'] = 1
bin = self.params['bin']
zerotiltimage = self.orig_imagelist[0]
zprojectfile = apImod.projectFullZ(processdir, runname,
self.seriesname, bin, True,
False)
q = leginon.leginondata.AcquisitionImageData()
zimagedata = apTomo.uploadZProjection(runname, zerotiltimage,
zprojectfile)
excludeimages = apTomo.getExcludedImageIds(self.ordered_imagelist,
self.excludelist)
reconparamdata = self.getReconParams()
self.fulltomodata = apTomo.insertFullTomogram(
self.sessiondata, self.tiltdatalist[0], self.alignerdata,
self.fullrundata, reconname, self.params['description'],
zimagedata, self.params['thickness'], reconparamdata, bin,
excludeimages)
def commitToDatabase(self):
processdir = self.params['rundir']
runname = self.params['runname']
# insertTomoRun
self.fullrundata = apTomo.insertFullTomoRun(self.sessiondata,processdir,runname,self.params['method'])
reconname = self.seriesname+"_full"
if os.path.exists(os.path.join(processdir,reconname+'.rec')):
#insertTomograma and z projection
if 'bin' not in self.params.keys():
self.params['bin']=1
bin = self.params['bin']
zerotiltimage = self.orig_imagelist[0]
zprojectfile = apImod.projectFullZ(processdir, runname, self.seriesname,bin,True,False)
q=leginon.leginondata.AcquisitionImageData()
zimagedata = apTomo.uploadZProjection(runname,zerotiltimage,zprojectfile)
excludeimages = apTomo.getExcludedImageIds(self.ordered_imagelist,self.excludelist)
reconparamdata = self.getReconParams()
self.fulltomodata = apTomo.insertFullTomogram(self.sessiondata,self.tiltdatalist[0],self.alignerdata,
self.fullrundata,reconname,self.params['description'],zimagedata,self.params['thickness'],reconparamdata,bin,excludeimages)
def start(self):
cleanlist = []
# imod needs the recon files named as .rec It may need some fix later
if self.params["name"] is None:
self.setNewFileName()
apDisplay.printColor("Naming tomogram as: " + self.params["name"], "cyan")
newtomopath = os.path.join(self.params["rundir"], self.params["name"] + ".rec")
origtomopath = self.params["file"]
origxfpath = self.params["oldxffile"]
apParam.createDirectory(self.params["aligndir"])
newxfpath = os.path.join(self.params["aligndir"], self.params["newxffile"])
order = self.params["order"]
voltransform = self.params["transform"]
bin = self.params["bin"]
self.getImageShapeFromTiltSeries()
self.getOriginalVolumeShape()
if os.path.isfile(newtomopath):
uploaded_before = self.checkExistingFile()
if uploaded_before:
return
else:
currenttomopath = origtomopath
if self.params["full"]:
### full tomogram upload, may need to pad to the image size
if self.params["order"] == "XZY" and not voltransform:
apDisplay.printMsg("Default full tomogram orientation with original handness")
else:
if voltransform:
apDisplay.printMsg("Transforming original tomogram....")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
cleanlist.append(currenttomopath)
### padding the XZY tomogram to the image size
currentheader = mrc.readHeaderFromFile(currenttomopath)
currentshape = currentheader["shape"]
currentxyshape = currentshape[0], currentshape[2]
imageshape = self.imageshape
if currentxyshape[0] < imageshape[0] / bin or currentxyshape[1] < imageshape[1] / bin:
currenttomopath = apImod.pad(currenttomopath, currentxyshape, imageshape, bin, "XZY")
cleanlist.append(currenttomopath)
else:
### subtomogram simple upload, just copy file to Tomo folder
if self.params["order"] == "XYZ" and not voltransform:
apDisplay.printMsg("Default sub tomogram orientation")
else:
if voltransform:
apDisplay.printMsg("Transforming original tomogram....")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
cleanlist.append(currenttomopath)
### simple upload, just copy file to Tomo folder
apDisplay.printMsg("Copying original tomogram to a new location: " + newtomopath)
shutil.copyfile(currenttomopath, newtomopath)
if origxfpath and os.path.isfile(origxfpath):
apDisplay.printMsg("Copying original alignment to a new location: " + newxfpath)
shutil.copyfile(origxfpath, newxfpath)
if self.params["image"]:
shutil.copyfile(self.params["image"], self.params["rundir"] + "/snapshot.png")
### inserting tomogram
tomoheader = mrc.readHeaderFromFile(newtomopath)
self.params["shape"] = tomoheader["shape"]
if self.params["full"]:
seriesname = "%s_%03d" % (self.params["sessionname"], self.params["tiltseriesnumber"])
self.params["zprojfile"] = apImod.projectFullZ(
self.params["rundir"], self.params["runname"], seriesname, bin, True, False
)
else:
apTomo.makeMovie(newtomopath)
apTomo.makeProjection(newtomopath)
apTomo.uploadTomo(self.params)
### clean up
for tmpfilepath in cleanlist:
apFile.removeFile(tmpfilepath)
def start(self):
# set local parameters
commit = self.params['commit']
tiltdatalist = apTomo.getTiltdataList(self.params['tiltseries'],
self.params['othertiltseries'])
sessiondata = tiltdatalist[0]['session']
description = self.params['description']
runname = self.params['runname']
alignmethod = self.params['alignmethod']
reconbin = int(self.params['reconbin'])
thickness_pixel = int(self.params['reconthickness'])
markersize_nm = int(self.params['markersize'])
markernumber = int(self.params['markernumber'])
apDisplay.printMsg("getting imagelist")
imagelist = apTomo.getImageList(tiltdatalist)
tilts, ordered_imagelist, ordered_mrc_files, refimg = apTomo.orderImageList(
imagelist)
apDisplay.printMsg("getting pixelsize")
pixelsize = apTomo.getTomoPixelSize(ordered_imagelist[refimg])
imgshape = apTomo.getTomoImageShape(ordered_imagelist[refimg])
#thickness_binnedpixel = int(thickness_nm * 1e-9 / (pixelsize * reconbin))
markersize_pixel = int(markersize_nm * 1e-9 / pixelsize)
processdir = os.path.abspath(self.params['rundir'])
imodseriesname = apTomo.getFilename(tiltdatalist)
seriesname = imodseriesname
# Write tilt series stack images and tilt angles
stackdir = self.params['tiltseriesdir']
stackname = imodseriesname + ".st"
apTomo.writeTiltSeriesStack(stackdir, stackname, ordered_mrc_files,
1e10 * pixelsize)
apRaptor.linkStToMrcExtension(stackdir, imodseriesname)
apImod.writeRawtltFile(stackdir, imodseriesname, tilts)
# Get Leginon tomography settings
leginontomosettingslist = []
for tiltdata in tiltdatalist:
settingsdata = apTomo.getTomographySettings(sessiondata, tiltdata)
leginontomosettingslist.append(settingsdata)
aligndir = processdir
# run the script and get alignment results when raptor can output alignment results in the future. raptoraligndata is None for now.
returncode, raptoraligndata, raptorfailed = apRaptor.alignAndRecon(
stackdir, stackname, processdir, markersize_pixel, reconbin,
thickness_pixel, markernumber, commit)
# Create Aligned Stack for record, not done in apRaptor yet, currently raptoraligndata is None
if not raptorfailed:
alifilename = imodseriesname + '.ali'
alifilepath = os.path.join(aligndir, 'align', alifilename)
print alifilepath
# commit to database
if commit:
# parameters
raptorparamsdata = apRaptor.insertRaptorParams(
markersize_nm, markernumber)
alignrun = apTomo.insertTomoAlignmentRun(
sessiondata, None, None, None, raptorparamsdata, 1,
self.params['runname'], self.params['rundir'],
self.params['description'], raptorfailed)
# to accomodate iterative alignment, one alignmentrun may have
# used the aligner several times, for this case a single
# aligner params data is inserted as in the case of Imod xcorr
alignerdata = apTomo.insertAlignerParams(alignrun, self.params)
#results
if raptoraligndata:
# if raptor has alignment result, it is converted to protomo
# format which is more parameterized and saved
prexgfile = os.path.join(aligndir, imodseriesname + '.prexg')
shifts = apImod.readShiftPrexgFile(aligndir, imodseriesname)
resulttltparams = apProTomo.convertShiftsToParams(
tilts, shifts, center)
if resulttltparams:
modeldata = apProTomo.insertModel(alignerdata,
resulttltparams)
for i, imagedata in enumerate(ordered_imagelist):
apProTomo.insertTiltAlignment(alignerdata, imagedata,
i, resulttltparams[0][i],
center)
# multiple tilt series in one alignrun
for i in range(0, len(tiltdatalist)):
if i == 0:
primary = True
else:
primary = False
# Record tilts in align run allows more than one tilt series to be
# used in one align run.
apTomo.insertTiltsInAlignRun(alignrun, tiltdatalist[i],
leginontomosettingslist[i],
primary)
if not raptorfailed:
apTomo.makeAlignStackMovie(alifilepath)
os.chdir(processdir)
# Full tomogram created with raptor is ???? handness?????
if not raptorfailed:
'''
voltransform = '????'
origtomopath = os.path.join(processdir, seriesname+"_full.rec")
currenttomopath = apImod.transformVolume(origtomopath,voltransform)
shutil.move(currenttomopath, origtomopath)
'''
zprojectfile = apImod.projectFullZ(processdir, runname,
seriesname, reconbin, False,
False)
try:
zimagedata = apTomo.uploadZProjection(
runname, imagelist[0], zprojectfile)
except:
zimagedata = None
fullrundata = apTomo.insertFullTomoRun(sessiondata, processdir,
runname, 'imod-wbp')
fulltomodata = apTomo.insertFullTomogram(
sessiondata, tiltdatalist[0], alignerdata, fullrundata,
runname, description, zimagedata, thickness_pixel,
reconbin)
# if raptor succeeded, upload data and parameters to database
session_time = sessiondata.timestamp
description = self.params['description']
raptordatabase = apRaptor.commitToJensenDatabase(
session_time, fulltomodata, stackdir, processdir,
stackname, description)
if raptordatabase == 0:
apDisplay.printMsg(
"RAPTOR and uploading to Jensen database done.")
else:
apDisplay.printWarning(
"Uploading to Jensen database failed.")
def start(self):
# set local parameters
commit = self.params['commit']
tiltdatalist = apTomo.getTiltdataList(self.params['tiltseries'],self.params['othertiltseries'])
sessiondata = tiltdatalist[0]['session']
description = self.params['description']
runname = self.params['runname']
alignmethod = self.params['alignmethod']
reconbin = int(self.params['reconbin'])
thickness_pixel = int(self.params['reconthickness'])
markersize_nm = int(self.params['markersize'])
markernumber = int(self.params['markernumber'])
apDisplay.printMsg("getting imagelist")
imagelist = apTomo.getImageList(tiltdatalist)
tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(imagelist)
apDisplay.printMsg("getting pixelsize")
pixelsize = apTomo.getTomoPixelSize(ordered_imagelist[refimg])
imgshape = apTomo.getTomoImageShape(ordered_imagelist[refimg])
#thickness_binnedpixel = int(thickness_nm * 1e-9 / (pixelsize * reconbin))
markersize_pixel = int(markersize_nm * 1e-9 / pixelsize)
processdir = os.path.abspath(self.params['rundir'])
imodseriesname = apTomo.getFilename(tiltdatalist)
seriesname = imodseriesname
# Write tilt series stack images and tilt angles
stackdir = self.params['tiltseriesdir']
stackname = imodseriesname+".st"
apTomo.writeTiltSeriesStack(stackdir,stackname,ordered_mrc_files,1e10*pixelsize)
apRaptor.linkStToMrcExtension(stackdir,imodseriesname)
apImod.writeRawtltFile(stackdir,imodseriesname,tilts)
# Get Leginon tomography settings
leginontomosettingslist = []
for tiltdata in tiltdatalist:
settingsdata = apTomo.getTomographySettings(sessiondata,tiltdata)
leginontomosettingslist.append(settingsdata)
aligndir = processdir
# run the script and get alignment results when raptor can output alignment results in the future. raptoraligndata is None for now.
returncode, raptoraligndata, raptorfailed = apRaptor.alignAndRecon(stackdir, stackname, processdir, markersize_pixel, reconbin, thickness_pixel, markernumber, commit)
# Create Aligned Stack for record, not done in apRaptor yet, currently raptoraligndata is None
if not raptorfailed:
alifilename = imodseriesname+'.ali'
alifilepath = os.path.join(aligndir,'align',alifilename)
print alifilepath
# commit to database
if commit:
# parameters
raptorparamsdata = apRaptor.insertRaptorParams(markersize_nm,markernumber)
alignrun = apTomo.insertTomoAlignmentRun(sessiondata,None,None,None,raptorparamsdata,1,self.params['runname'],self.params['rundir'],self.params['description'],raptorfailed)
# to accomodate iterative alignment, one alignmentrun may have
# used the aligner several times, for this case a single
# aligner params data is inserted as in the case of Imod xcorr
alignerdata = apTomo.insertAlignerParams(alignrun,self.params)
#results
if raptoraligndata:
# if raptor has alignment result, it is converted to protomo
# format which is more parameterized and saved
prexgfile = os.path.join(aligndir,imodseriesname+'.prexg')
shifts = apImod.readShiftPrexgFile(aligndir, imodseriesname)
resulttltparams = apProTomo.convertShiftsToParams(tilts,shifts,center)
if resulttltparams:
modeldata = apProTomo.insertModel(alignerdata, resulttltparams)
for i,imagedata in enumerate(ordered_imagelist):
apProTomo.insertTiltAlignment(alignerdata,imagedata,i,resulttltparams[0][i],center)
# multiple tilt series in one alignrun
for i in range(0,len(tiltdatalist)):
if i == 0:
primary = True
else:
primary = False
# Record tilts in align run allows more than one tilt series to be
# used in one align run.
apTomo.insertTiltsInAlignRun(alignrun, tiltdatalist[i],leginontomosettingslist[i],primary)
if not raptorfailed:
apTomo.makeAlignStackMovie(alifilepath)
os.chdir(processdir)
# Full tomogram created with raptor is ???? handness?????
if not raptorfailed:
'''
voltransform = '????'
origtomopath = os.path.join(processdir, seriesname+"_full.rec")
currenttomopath = apImod.transformVolume(origtomopath,voltransform)
shutil.move(currenttomopath, origtomopath)
'''
zprojectfile = apImod.projectFullZ(processdir, runname, seriesname,reconbin,False,False)
try:
zimagedata = apTomo.uploadZProjection(runname,imagelist[0],zprojectfile)
except:
zimagedata = None
fullrundata = apTomo.insertFullTomoRun(sessiondata,processdir,runname,'imod-wbp')
fulltomodata = apTomo.insertFullTomogram(sessiondata,tiltdatalist[0],alignerdata,
fullrundata,runname,description,zimagedata,thickness_pixel,reconbin)
# if raptor succeeded, upload data and parameters to database
session_time = sessiondata.timestamp
description = self.params['description']
raptordatabase = apRaptor.commitToJensenDatabase(session_time, fulltomodata, stackdir, processdir, stackname, description)
if raptordatabase == 0:
apDisplay.printMsg("RAPTOR and uploading to Jensen database done.")
else:
apDisplay.printWarning("Uploading to Jensen database failed.")
def start(self):
cleanlist = []
# imod needs the recon files named as .rec It may need some fix later
if self.params['name'] is None:
self.setNewFileName()
apDisplay.printColor("Naming tomogram as: " + self.params['name'],
"cyan")
newtomopath = os.path.join(self.params['rundir'],
self.params['name'] + ".rec")
origtomopath = self.params['file']
origxfpath = self.params['oldxffile']
apParam.createDirectory(self.params['aligndir'])
newxfpath = os.path.join(self.params['aligndir'],
self.params['newxffile'])
order = self.params['order']
voltransform = self.params['transform']
bin = self.params['bin']
self.getImageShapeFromTiltSeries()
self.getOriginalVolumeShape()
if os.path.isfile(newtomopath):
uploaded_before = self.checkExistingFile()
if uploaded_before:
return
else:
currenttomopath = origtomopath
if self.params['full']:
### full tomogram upload, may need to pad to the image size
if self.params['order'] == 'XZY' and not voltransform:
apDisplay.printMsg(
"Default full tomogram orientation with original handness"
)
else:
if voltransform:
apDisplay.printMsg(
"Transforming original tomogram....")
currenttomopath = apImod.transformVolume(
origtomopath, voltransform)
cleanlist.append(currenttomopath)
### padding the XZY tomogram to the image size
currentheader = mrc.readHeaderFromFile(currenttomopath)
currentshape = currentheader['shape']
currentxyshape = currentshape[0], currentshape[2]
imageshape = self.imageshape
if currentxyshape[0] < imageshape[0] / bin or currentxyshape[
1] < imageshape[1] / bin:
currenttomopath = apImod.pad(currenttomopath,
currentxyshape, imageshape,
bin, 'XZY')
cleanlist.append(currenttomopath)
else:
### subtomogram simple upload, just copy file to Tomo folder
if self.params['order'] == 'XYZ' and not voltransform:
apDisplay.printMsg("Default sub tomogram orientation")
else:
if voltransform:
apDisplay.printMsg(
"Transforming original tomogram....")
currenttomopath = apImod.transformVolume(
origtomopath, voltransform)
cleanlist.append(currenttomopath)
### simple upload, just copy file to Tomo folder
apDisplay.printMsg(
"Copying original tomogram to a new location: " + newtomopath)
shutil.copyfile(currenttomopath, newtomopath)
if origxfpath and os.path.isfile(origxfpath):
apDisplay.printMsg(
"Copying original alignment to a new location: " +
newxfpath)
shutil.copyfile(origxfpath, newxfpath)
if self.params['image']:
shutil.copyfile(self.params['image'],
self.params['rundir'] + '/snapshot.png')
### inserting tomogram
tomoheader = mrc.readHeaderFromFile(newtomopath)
self.params['shape'] = tomoheader['shape']
if self.params['full']:
seriesname = "%s_%03d" % (self.params['sessionname'],
self.params['tiltseriesnumber'])
self.params['zprojfile'] = apImod.projectFullZ(
self.params['rundir'], self.params['runname'], seriesname, bin,
True, False)
else:
apTomo.makeMovie(newtomopath)
apTomo.makeProjection(newtomopath)
apTomo.uploadTomo(self.params)
### clean up
for tmpfilepath in cleanlist:
apFile.removeFile(tmpfilepath)