def createTransformFile(self):
# Get alignment from database
specimen_euler, tiltaz, origins, rotations = apTomo.getAlignmentFromDB(self.alignerdata,self.imgcenter)
centertuple = (self.imgcenter['x'],self.imgcenter['y'])
imodaffines = apProTomo.convertProtomoToImod(specimen_euler, tiltaz, origins, rotations,centertuple)
processdir = self.params['rundir']
apImod.writeTransformFile(processdir, self.seriesname,imodaffines,ext='xf')
imodlocalaffines = apTomo.convertGlobalToLocalAffines(imodaffines)
apImod.writeTransformFile(processdir, self.seriesname,imodlocalaffines,ext='prexf')
def start(self):
###do queries
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
self.params['tiltseries'], sessiondata)
tiltseriessettings = apTomo.getTomographySettings(
sessiondata, tiltseriesdata)
tiltdata = apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
print "ordering list"
tilts, ordered_imagelist, ordered_mrc_files, refimg = apTomo.orderImageList(
tiltdata)
#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int
###set up files
seriesname = 'series' + str(self.params['tiltseries'])
tiltfilename = seriesname + '.tlt'
param_out = seriesname + '.param'
maxtilt = max([abs(tilts[0]), abs(tilts[-1])])
apDisplay.printMsg("highest tilt angle is %f" % maxtilt)
self.params['cos_alpha'] = math.cos(maxtilt * math.pi / 180)
self.params['raw_path'] = os.path.join(self.params['rundir'], 'raw')
rawexists = apParam.createDirectory(self.params['raw_path'])
apDisplay.printMsg("copying raw images")
newfilenames = apProTomo.getImageFiles(ordered_imagelist,
self.params['raw_path'],
link=False)
#get alignment data
alignerdata = apTomo.getAlignerdata(self.params['alignerid'])
imgshape = apTomo.getTomoImageShape(ordered_imagelist[0])
imgcenter = {'x': self.imgshape[1] / 2, 'y': self.imgshape[0] / 2}
specimen_euler, azimuth, origins, rotations = apTomo.getAlignmentFromDB(
alignerdata, imgcenter)
#write protomo2 tilt file
outtltfile = 'series.tlt'
seriesname = 'series'
apProTomo.writeTiltFile2(outfilename, seriesname, specimen_eulers,
azimuth, referenceimage)
def createTransformFile(self):
# Get alignment from database
specimen_euler, tiltaz, origins, rotations = apTomo.getAlignmentFromDB(
self.alignerdata, self.imgcenter)
centertuple = (self.imgcenter['x'], self.imgcenter['y'])
imodaffines = apProTomo.convertProtomoToImod(specimen_euler, tiltaz,
origins, rotations,
centertuple)
processdir = self.params['rundir']
apImod.writeTransformFile(processdir,
self.seriesname,
imodaffines,
ext='xf')
imodlocalaffines = apTomo.convertGlobalToLocalAffines(imodaffines)
apImod.writeTransformFile(processdir,
self.seriesname,
imodlocalaffines,
ext='prexf')
def start(self):
###do queries
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseries'],sessiondata)
tiltseriessettings= apTomo.getTomographySettings(sessiondata,tiltseriesdata)
tiltdata=apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
print "ordering list"
tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(tiltdata)
#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int
###set up files
seriesname='series'+str(self.params['tiltseries'])
tiltfilename=seriesname+'.tlt'
param_out=seriesname+'.param'
maxtilt=max([abs(tilts[0]),abs(tilts[-1])])
apDisplay.printMsg("highest tilt angle is %f" % maxtilt)
self.params['cos_alpha']=math.cos(maxtilt*math.pi/180)
self.params['raw_path']=os.path.join(self.params['rundir'],'raw')
rawexists=apParam.createDirectory(self.params['raw_path'])
apDisplay.printMsg("copying raw images")
newfilenames=apProTomo.getImageFiles(ordered_imagelist,self.params['raw_path'], link=False)
#get alignment data
alignerdata = apTomo.getAlignerdata(self.params['alignerid'])
imgshape = apTomo.getTomoImageShape(ordered_imagelist[0])
imgcenter = {'x':self.imgshape[1]/2,'y':self.imgshape[0]/2}
specimen_euler, azimuth, origins, rotations = apTomo.getAlignmentFromDB(alignerdata,imgcenter)
#write protomo2 tilt file
outtltfile='series.tlt'
seriesname='series'
apProTomo.writeTiltFile2(outfilename, seriesname, specimen_eulers, azimuth, referenceimage )