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 start(self):
### some of this should go in preloop functions
###do queries
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseries'],sessiondata)
tiltdata=apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
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)
###create tilt file
#get image size from the first image
imagesizex=tiltdata[0]['image'].shape[0]
imagesizey=tiltdata[0]['image'].shape[1]
#shift half tilt series relative to eachother
#SS I'm arbitrarily making the bin parameter here 1 because it's not necessary to sample at this point
shifts = apTomo.getGlobalShift(ordered_imagelist, 1, refimg)
#OPTION: refinement might be more robust by doing one round of IMOD aligment to prealign images before doing protomo refine
origins=apProTomo2Prep.convertShiftsToOrigin(shifts, imagesizex, imagesizey)
#determine azimuth
azimuth=apTomo.getAverageAzimuthFromSeries(ordered_imagelist)
apProTomo2Prep.writeTileFile2(tiltfilename, seriesname, newfilenames, origins, tilts, azimuth, refimg)
def prepareTiltFile(sessionname, seriesname, tiltfilename, tiltseriesnumber, raw_path, frame_aligned_images, link=False, coarse=True):
'''
Creates tlt file from basic image information and copies raw images
'''
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(tiltseriesnumber,sessiondata)
tiltdata = apTomo.getImageList([tiltseriesdata])
apDisplay.printMsg("getting imagelist")
frame_tiltdata, non_frame_tiltdata = frameOrNonFrameTiltdata(tiltdata)
tilts,ordered_imagelist,accumulated_dose_list,ordered_mrc_files,refimg = apTomo.orderImageList(frame_tiltdata, non_frame_tiltdata, frame_aligned=frame_aligned_images)
if frame_aligned_images == "True": #Azimuth is only present in the non-frame aligned images
a,ordered_imagelist_for_azimuth,c,d,e = apTomo.orderImageList(frame_tiltdata, non_frame_tiltdata, frame_aligned="False")
#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int
maxtilt = max([abs(tilts[0]),abs(tilts[-1])])
apDisplay.printMsg("highest tilt angle is %f" % maxtilt)
if coarse == "True":
if frame_aligned_images == "True": #Azimuth is only present in the non-frame aligned images
azimuth = apTomo.getAverageAzimuthFromSeries(ordered_imagelist_for_azimuth)
else:
azimuth = apTomo.getAverageAzimuthFromSeries(ordered_imagelist)
rawexists = apParam.createDirectory(raw_path)
apDisplay.printMsg("Copying raw images, y-flipping, normalizing, and converting images to float32 for Protomo...") #Linking removed because raw images need to be y-flipped for Protomo:(.
newfilenames, new_ordered_imagelist = apProTomo.getImageFiles(ordered_imagelist, raw_path, link=False, copy="True")
###create tilt file
#get image size from the first image
imagesizex = tiltdata[0]['image'].shape[1]
imagesizey = tiltdata[0]['image'].shape[0]
#shift half tilt series relative to eachother
#SS I'm arbitrarily making the bin parameter here 1 because it's not necessary to sample at this point
shifts = apTomo.getGlobalShift(ordered_imagelist, 1, refimg)
#OPTION: refinement might be more robust by doing one round of IMOD aligment to prealign images before doing protomo refine
origins = convertShiftsToOrigin(shifts, imagesizex, imagesizey)
writeTiltFile2(tiltfilename, seriesname, newfilenames, origins, tilts, azimuth, refimg)
return tilts, accumulated_dose_list, new_ordered_imagelist, maxtilt
def doseCompensate(seriesname, rundir, sessionname, tiltseriesnumber, frame_aligned_images, raw_path, pixelsize, dose_presets, dose_a, dose_b, dose_c):
"""
Images will be lowpass filtered using equation (3) from Grant & Grigorieff, 2015.
No changes to the database are made. No backups are made.
"""
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(tiltseriesnumber,sessiondata)
tiltdata = apTomo.getImageList([tiltseriesdata])
frame_tiltdata, non_frame_tiltdata = frameOrNonFrameTiltdata(tiltdata)
tilts, ordered_imagelist, accumulated_dose_list, ordered_mrc_files, refimg = apTomo.orderImageList(frame_tiltdata, non_frame_tiltdata, frame_aligned="False")
if frame_aligned_images == "True": #For different image filenames
a, ordered_imagelist, c, d, e = apTomo.orderImageList(frame_tiltdata, non_frame_tiltdata, frame_aligned=frame_aligned_images)
newfilenames, new_ordered_imagelist = apProTomo.getImageFiles(ordered_imagelist, raw_path, link=False, copy=False)
if (dose_presets == "Light"):
dose_a = 0.245
dose_b = -1.6
dose_c = 12
elif (dose_presets == "Moderate"):
dose_a = 0.245
dose_b = -1.665
dose_c = 2.81
elif (dose_presets == "Heavy"):
dose_a = 0.245
dose_b = -1.4
dose_c = 2
apDisplay.printMsg('Dose compensating all tilt images with a=%s, b=%s, and c=%s...' % (dose_a, dose_b, dose_c))
for image, j in zip(new_ordered_imagelist, range(len(new_ordered_imagelist))):
lowpass = float(np.real(complex(dose_a/(accumulated_dose_list[j] - dose_c))**(1/dose_b))) #equation (3) from Grant & Grigorieff, 2015
if lowpass < 0.0:
lowpass = 0.0
im = mrc.read(image)
im = imagefilter.lowPassFilter(im, apix=pixelsize, radius=lowpass, msg=False)
im=imagenorm.normStdev(im)
mrc.write(im, image)
#Make plots
apProTomo2Aligner.makeDosePlots(rundir, seriesname, tilts, accumulated_dose_list, dose_a, dose_b, dose_c)
apDisplay.printMsg("Dose compensation finished for tilt-series #%s!" % tiltseriesnumber)
return
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 )
param_out = seriesname+'.param'
maxtilt = max([abs(tilts[0]),abs(tilts[-1])])
>>>>>>> .r18846
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'])
<<<<<<< .mine
=======
rawexists = apParam.createDirectory(self.params['raw_path'])
>>>>>>> .r18846
apDisplay.printMsg("copying raw images")
newfilenames = apProTomo.getImageFiles(ordered_imagelist,self.params['raw_path'], link=False)
###create tilt file
#get image size from the first image
<<<<<<< .mine
imagesizex = tiltdata[0]['image'].shape[1]
imagesizey = tiltdata[0]['image'].shape[0]
=======
imagesizex = tiltdata[0]['image'].shape[0]
imagesizey = tiltdata[0]['image'].shape[1]
>>>>>>> .r18846
#shift half tilt series relative to eachother
#SS I'm arbitrarily making the bin parameter here 1 because it's not necessary to sample at this point
