def start(self):
### some of this should go in preloop functions
###create param file
param_out = self.params['seriesname'] + '.param'
tiltfilename = self.params['seriesname'] + '.tlt'
iters = self.params['iters']
self.params['cos_alpha'] = math.cos(self.params['maxtilt'] * math.pi /
180)
self.params['raw_path'] = os.path.join(self.params['rundir'], 'raw')
param_in = apProTomo2Prep.getPrototypeParamPath()
paramdict = apProTomo2Prep.createParamDict(self.params)
apProTomo2Prep.modifyParamFile(param_in, param_out, paramdict)
seriesparam = protomo.param(param_out)
apDisplay.printMsg('Starting protomo alignment')
###using presence of i3t to determine if protomo has been run once already
#create series object
i3tfile = self.params['seriesname'] + '.i3t'
if os.path.exists(i3tfile):
series = protomo.series(seriesparam)
else:
seriesgeom = protomo.geom(tiltfilename)
series = protomo.series(seriesparam, seriesgeom)
#figure out starting number
start = 0
previters = glob.glob(self.params['seriesname'] + '*.corr')
if len(previters) > 0:
previters.sort()
lastiter = previters[-1]
start = int(
lastiter.split(self.params['seriesname'])[1].split('.')[0]) + 1
for n in range(iters):
series.align()
basename = '%s%02d' % (self.params['seriesname'], (n + start))
corrfile = basename + '.corr'
series.corr(corrfile)
series.fit()
series.update()
#archive results
tiltfile = basename + '.tlt'
geom = series.geom()
geom.write(tiltfile)
def start(self):
### some of this should go in preloop functions
###create param file
param_out=self.params['seriesname']+'.param'
tiltfilename=self.params['seriesname']+'.tlt'
iters = self.params['iters']
self.params['cos_alpha']=math.cos(self.params['maxtilt']*math.pi/180)
self.params['raw_path']=os.path.join(self.params['rundir'],'raw')
param_in=apProTomo2Prep.getPrototypeParamPath()
paramdict = apProTomo2Prep.createParamDict(self.params)
apProTomo2Prep.modifyParamFile(param_in, param_out, paramdict)
seriesparam=protomo.param(param_out)
apDisplay.printMsg('Starting protomo alignment')
###using presence of i3t to determine if protomo has been run once already
#create series object
i3tfile=self.params['seriesname']+'.i3t'
if os.path.exists(i3tfile):
series=protomo.series(seriesparam)
else:
seriesgeom=protomo.geom(tiltfilename)
series=protomo.series(seriesparam,seriesgeom)
#figure out starting number
start=0
previters=glob.glob(self.params['seriesname']+'*.corr')
if len(previters) > 0:
previters.sort()
lastiter=previters[-1]
start=int(lastiter.split(self.params['seriesname'])[1].split('.')[0])+1
for n in range(iters):
series.align()
basename='%s%02d' % (self.params['seriesname'],(n+start))
corrfile=basename+'.corr'
series.corr(corrfile)
series.fit()
series.update()
#archive results
tiltfile=basename+'.tlt'
geom=series.geom()
geom.write(tiltfile)
def run(self):
# use the tilt angles to set the reference image, which is the image with tilt values closest to zero.
self.setRefImg(self.tilts)
apDisplay.printMsg("Setting Reference image to: %d" % (self.refimg, ))
# Write a default parameter file if it does not already exist
self.params['protomo2paramfile'] = self.writeDefaultParamFile()
apDisplay.printMsg("Setting Parameter file to: %s" %
(self.params['protomo2paramfile'], ))
# Create the parameter object
try:
protomo2param = protomo.param(self.params['protomo2paramfile'])
except Exception:
msg = "The protomo2 config file (%s) has an error. Could not create the parameter object." % (
self.params['protomo2paramfile'], )
apDisplay.printWarning(msg)
raise
# Write a default tilt geometry file if it does not already exist
geomParamFilePath = self.writeTiltGeomFile()
apDisplay.printMsg("Setting tilt geometry file to: %s" %
(geomParamFilePath, ))
# Create the protomo2 geometry object
try:
protomo2geom = protomo.geom(geomParamFilePath)
except:
apDisplay.printWarning(
"Failed to create the protomo2 geometry object with the geometry parameter file, %s"
% (geomParamFilePath, ))
raise
# Modify the parameter object with the user input values
self.setUserModifiedParams(protomo2param)
# Create a tilt series object (contains input geometry, creates updated geometry, info to do the alignment)
try:
protomo2series = protomo.series(protomo2param, protomo2geom)
except:
apDisplay.printWarning(
"Failed to create the protomo2 tilt series object.")
raise
# Run the specified number of alignment iterations
for i in range(0, self.params['max_iterations']):
protomo2series.align()
# correction factors, automatically generates a file name using the iteration number(? TODO: Hanspeter to implement)
protomo2series.corr() #( self.correctionFactorFile )
protomo2series.fit()
protomo2series.update()
def run(self):
# use the tilt angles to set the reference image, which is the image with tilt values closest to zero.
self.setRefImg(self.tilts)
apDisplay.printMsg("Setting Reference image to: %d" % (self.refimg, ))
# Write a default parameter file if it does not already exist
self.params['protomo2paramfile'] = self.writeDefaultParamFile()
apDisplay.printMsg("Setting Parameter file to: %s" % (self.params['protomo2paramfile'], ))
# Create the parameter object
try:
protomo2param = protomo.param( self.params['protomo2paramfile'] )
except Exception:
msg = "The protomo2 config file (%s) has an error. Could not create the parameter object." % (self.params['protomo2paramfile'], )
apDisplay.printWarning(msg)
raise
# Write a default tilt geometry file if it does not already exist
geomParamFilePath = self.writeTiltGeomFile()
apDisplay.printMsg("Setting tilt geometry file to: %s" % (geomParamFilePath, ))
# Create the protomo2 geometry object
try:
protomo2geom = protomo.geom( geomParamFilePath )
except:
apDisplay.printWarning("Failed to create the protomo2 geometry object with the geometry parameter file, %s" % (geomParamFilePath, ))
raise
# Modify the parameter object with the user input values
self.setUserModifiedParams( protomo2param )
# Create a tilt series object (contains input geometry, creates updated geometry, info to do the alignment)
try:
protomo2series = protomo.series(protomo2param, protomo2geom)
except:
apDisplay.printWarning("Failed to create the protomo2 tilt series object.")
raise
# Run the specified number of alignment iterations
for i in range(0, self.params['max_iterations']):
protomo2series.align()
# correction factors, automatically generates a file name using the iteration number(? TODO: Hanspeter to implement)
protomo2series.corr() #( self.correctionFactorFile )
protomo2series.fit()
protomo2series.update()
import sys
import glob
import os
def parseOptions():
parser = optparse.OptionParser()
parser.add_option('--param', dest='param', help='Param file')
parser.add_option('--map',
dest='map',
help='Output map name, e.g. series1.img')
options, args = parser.parse_args()
if len(args) != 0 or len(sys.argv) == 1:
parser.print_help()
sys.exit()
return options
if __name__ == '__main__':
options = parseOptions()
param = protomo.param(options.param)
series = protomo.series(param)
series.mapfile(options.map)
print "Done!"
import protomo
import optparse
import sys
import glob
import os
def parseOptions():
parser=optparse.OptionParser()
parser.add_option('--param', dest='param', help= 'Param file')
parser.add_option('--map', dest='map', help= 'Output map name, e.g. series1.img')
options, args=parser.parse_args()
if len(args) != 0 or len(sys.argv) == 1:
parser.print_help()
sys.exit()
return options
if __name__=='__main__':
options=parseOptions()
param=protomo.param(options.param)
series=protomo.series(param)
series.mapfile(options.map)
print "Done!"
def start(self):
it="%03d" % (self.params['recon_iter'])
itt="%03d" % (self.params['recon_iter']-1)
global wd
wd=self.params['rundir']
raw_path=os.path.join(wd, 'raw')
os.chdir(self.params['rundir'])
seriesnumber = "%04d" % int(self.params['tiltseries'])
seriesname='series'+seriesnumber
param_out=seriesname+'.param'
param_out_full=self.params['rundir']+'/'+param_out
tilt_out_full=self.params['rundir']+'/'+seriesname+itt+'.tlt'
recon_dir=self.params['rundir']+'/recons/'
os.system('mkdir %s 2>/dev/null' % recon_dir)
recon_param_out_full=recon_dir+'/'+param_out
recon_tilt_out_full=recon_dir+'/'+seriesname+'.tlt'
recon_cache_dir=recon_dir+'/cache'
recon_out_dir=recon_dir+'out'
os.system('cp %s %s' % (tilt_out_full, recon_tilt_out_full))
os.system('cp %s %s' % (param_out_full,recon_param_out_full))
#CTF Correction
if (self.params['ctf_correct'] == 'True'):
apProTomo2Prep.ctfCorrect(seriesname, self.params['rundir'], self.params['projectid'], self.params['sessionname'], int(self.params['tiltseries']), recon_tilt_out_full, self.params['frame_aligned'], self.params['pixelsize'], self.params['DefocusTol'], self.params['iWidth'], self.params['amp_contrast'])
#Dose Compensation
if (self.params['dose_presets'] != 'False'):
apProTomo2Prep.doseCompensate(seriesname, self.params['rundir'], self.params['sessionname'], int(self.params['tiltseries']), self.params['frame_aligned'], raw_path, self.params['pixelsize'], self.params['dose_presets'], self.params['dose_a'], self.params['dose_b'], self.params['dose_c'])
# Remove high tilts from .tlt file if user requests
if (self.params['positive'] < 90) or (self.params['negative'] > -90):
removed_images, mintilt, maxtilt = apProTomo2Aligner.removeHighTiltsFromTiltFile(recon_tilt_out_full, self.params['negative'], self.params['positive'])
apDisplay.printMsg("Images %s have been removed before reconstruction by weighted back-projection" % removed_images)
else:
cmd1="awk '/ORIGIN /{print}' %s | wc -l" % (recon_tilt_out_full)
proc=subprocess.Popen(cmd1, stdout=subprocess.PIPE, shell=True)
(numimages, err) = proc.communicate()
numimages=int(numimages)
cmd2="awk '/IMAGE /{print $2}' %s | head -n +1" % (recon_tilt_out_full)
proc=subprocess.Popen(cmd2, stdout=subprocess.PIPE, shell=True)
(tiltstart, err) = proc.communicate()
tiltstart=int(tiltstart)
mintilt=0
maxtilt=0
for i in range(tiltstart-1,tiltstart+numimages):
try: #If the image isn't in the .tlt file, skip it
cmd="awk '/IMAGE %s /{print}' %s | awk '{for (j=1;j<=NF;j++) if($j ~/TILT/) print $(j+2)}'" % (i+1, recon_tilt_out_full)
proc=subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
(tilt_angle, err) = proc.communicate()
tilt_angle=float(tilt_angle)
mintilt=min(mintilt,tilt_angle)
maxtilt=max(maxtilt,tilt_angle)
except:
pass
# Backup then edit the Refinement param file, changing the map size, map sampling, cache dir, and out dir
refine_param_full=self.params['rundir']+'/'+'refine_'+param_out
command="cp %s %s" % (param_out_full, refine_param_full)
os.system(command)
command1="grep -n 'AP sampling' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(command1, stdout=subprocess.PIPE, shell=True)
(samplingline, err) = proc.communicate()
samplingline=int(samplingline)
command2="grep -n 'AP reconstruction map size' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(command2, stdout=subprocess.PIPE, shell=True)
(mapsizeline, err) = proc.communicate()
mapsizeline=int(mapsizeline)
command3="grep -n 'AP reconstruction map sampling' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(command3, stdout=subprocess.PIPE, shell=True)
(mapsamplingline, err) = proc.communicate()
mapsamplingline=int(mapsamplingline)
command11="sed -i \"%ss/.*/ S = %s (* AP sampling *)/\" %s" % (samplingline, self.params['recon_map_sampling'], recon_param_out_full)
os.system(command11)
command22="sed -i \"%ss/.*/ size: { %s, %s, %s } (* AP reconstruction map size *)/\" %s" % (mapsizeline, int(self.params['recon_map_size_x']/self.params['recon_map_sampling']), int(self.params['recon_map_size_y']/self.params['recon_map_sampling']), int(round(self.params['recon_thickness']/(self.params['pixelsize']*self.params['recon_map_sampling']))), recon_param_out_full)
os.system(command22)
command33="sed -i \"%ss/.*/ sampling: %s (* AP reconstruction map sampling *)/\" %s" % (mapsamplingline, self.params['recon_map_sampling'], recon_param_out_full)
os.system(command33)
command4="grep -n 'cachedir' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(command4, stdout=subprocess.PIPE, shell=True)
(cachedirline, err) = proc.communicate()
cachedirline=int(cachedirline)
command5="grep -n 'outdir' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(command5, stdout=subprocess.PIPE, shell=True)
(outdirline, err) = proc.communicate()
outdirline=int(outdirline)
command44="sed -i \'%ss|.*| cachedir: \"%s\" (* AP directory where cache files are stored *)|\' %s" % (cachedirline, recon_cache_dir, recon_param_out_full)
os.system(command44)
command55="sed -i \'%ss|.*| outdir: \"%s\" (* AP directory where other output files are stored *)|\' %s" % (outdirline, recon_out_dir, recon_param_out_full)
os.system(command55)
#Lowpass filter reconstruction?
cmd="grep -n 'AP lowpass map' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
(lowpassmapline, err) = proc.communicate()
lowpassmapline=int(lowpassmapline)
if self.params['recon_lowpass'] == "False":
lp=''
#Remove lowpass filter from param
cmd2="sed -i \"%ss/.*//\" %s;" % (lowpassmapline, recon_param_out_full)
cmd2+="sed -i \"%ss/.*//\" %s;" % (lowpassmapline+1, recon_param_out_full)
cmd2+="sed -i \"%ss/.*//\" %s;" % (lowpassmapline+2, recon_param_out_full)
cmd2+="sed -i \"%ss/.*//\" %s" % (lowpassmapline+3, recon_param_out_full)
#Set preprocessing to false
cmd3="grep -n 'AP enable or disable preprocessing of raw images' %s | awk '{print $1}' | sed 's/://'" % (recon_param_out_full)
proc=subprocess.Popen(cmd3, stdout=subprocess.PIPE, shell=True)
(preprocessingline, err) = proc.communicate()
preprocessingline=int(preprocessingline)
cmd33="sed -i \'%ss|.*| preprocessing: false (* AP enable or disable preprocessing of raw images *)|\' %s" % (preprocessingline, recon_param_out_full)
os.system(cmd33)
else:
lpavg = int((self.params['recon_lp_diam_x']+self.params['recon_lp_diam_y'])/2)
lp='.lp%s' % lpavg
self.params['recon_lp_diam_x'] = 2*self.params['pixelsize']*self.params['recon_map_sampling']/self.params['recon_lp_diam_x']
self.params['recon_lp_diam_y'] = 2*self.params['pixelsize']*self.params['recon_map_sampling']/self.params['recon_lp_diam_y']
cmd2="sed -i \"%ss/.*/ diameter: { %s, %s } * S/\" %s" % (lowpassmapline+1, self.params['recon_lp_diam_x'], self.params['recon_lp_diam_y'], recon_param_out_full)
os.system(cmd2)
dim='%sx%s' % (self.params['recon_map_size_x'],self.params['recon_map_size_y'])
ang='%sto%s' % (round(mintilt,1),round(maxtilt,1))
img=seriesname+'00_bck.img'
mrcf=seriesname+'_ite'+it+'_dim'+dim+'_ang'+ang+'_bck.bin'+str(self.params['recon_map_sampling'])+lp+'.mrc'
mrcfn=seriesname+'_ite'+it+'_dim'+dim+'_ang'+ang+'_bck.bin'+str(self.params['recon_map_sampling'])+lp+'.norm.mrc'
img_full=recon_out_dir+'/'+img
mrc_full=recon_out_dir+'/'+mrcf
mrcn_full=recon_out_dir+'/'+mrcfn
# AP Get param files ready for batch processing
batchdir=self.params['rundir']+'/'+'ready_for_batch'
coarse_param_full=self.params['rundir']+'/coarse_out/'+'coarse_'+param_out
recon_param='recon_'+param_out
command="mkdir %s 2>/dev/null; cp %s %s; cp %s %s; cp %s %s/%s; rm -r %s %s %s*i3t %s/cache %s/out 2>/dev/null" % (batchdir, coarse_param_full, batchdir, refine_param_full, batchdir, param_out_full, batchdir, recon_param, img_full, mrc_full, recon_dir, recon_dir, recon_dir)
os.system(command)
# Create reconstruction
os.chdir(recon_dir)
os.system("rm %s/cache/%s* %s/*i3t 2>/dev/null" % (recon_dir, seriesname, recon_dir))
seriesparam=protomo.param(recon_param_out_full)
seriesgeom=protomo.geom(recon_tilt_out_full)
series=protomo.series(seriesparam,seriesgeom)
series.setparam("map.logging","true")
series.mapfile()
os.chdir(self.params['rundir'])
# Restore refine param file
command="cp %s %s" % (refine_param_full, param_out_full)
os.system(command)
# Convert to mrc
os.system("i3cut -fmt mrc %s %s" % (img_full, mrc_full))
os.system("rm %s" % img_full)
# Normalize
try:
command="e2proc3d.py %s %s --process=normalize" % (mrc_full, mrcn_full)
proc=subprocess.Popen(command, stdout=subprocess.PIPE, shell=True)
(code, err) = proc.communicate()
except:
pass
if proc.returncode != 0:
apDisplay.printMsg("\ne2proc3d not found or failed to process reconstruction. Trying proc3d...")
try:
command="proc3d %s %s norm" % (mrc_full, mrcn_full)
proc=subprocess.Popen(command, stdout=subprocess.PIPE, shell=True)
(code, err) = proc.communicate()
except:
pass
if proc.returncode != 0:
apDisplay.printMsg("\nproc3d not found or failed to process reconstruction. Skipping normalization.")
else:
os.system('rm %s' % mrc_full)
# Link reconstruction to directory
try:
cmd1="mkdir -p %s 2>/dev/null; rm %s/%s %s/%s 2>/dev/null; ln -f %s %s 2>/dev/null" % (self.params['link_recon'], self.params['link_recon'], mrcf, self.params['link_recon'], mrcfn, mrc_full, self.params['link_recon'])
cmd2="mkdir -p %s 2>/dev/null; rm %s/%s %s/%s 2>/dev/null; ln -f %s %s" % (self.params['link_recon'], self.params['link_recon'], mrcf, self.params['link_recon'], mrcfn, mrcn_full, self.params['link_recon'])
try:
proc=subprocess.Popen(cmd1, stdout=subprocess.PIPE, shell=True)
(code, err) = proc.communicate()
except:
pass
if proc.returncode != 0:
try:
proc=subprocess.Popen(cmd2, stdout=subprocess.PIPE, shell=True)
(code, err) = proc.communicate()
except:
pass
apDisplay.printMsg("Reconstruction can be found in this directory:")
if (self.params['link_recon'] == None) or (self.params['link_recon'] == "") or (len(self.params['link_recon']) < 1):
print "\n%s\n" % (recon_out_dir)
else:
print "\n%s\n" % (self.params['link_recon'])
except:
apDisplay.printMsg("Reconstruction can be found in this directory:")
print "\n%s\n" % (recon_out_dir)
if proc.returncode != 0:
apDisplay.printMsg("The reconstruction in the above directory is not normalized because EMAN1 and EMAN2 were either not found or failed to process the reconstruction.")
os.system("rm %s/cache/%s* %s/*i3t" % (recon_dir, seriesname, recon_dir))
options, args=parser.parse_args()
if len(args) != 0 or len(sys.argv) == 1:
parser.print_help()
sys.exit()
return options
if __name__ == "__main__":
options=parseOptions()
seriesparam=protomo.param(options.param)
if options.i3tfile:
series=protomo.series( seriesparam )
else:
seriesgeom=protomo.geom( options.tlt )
options.i3tfile=options.tlt
series=protomo.series( seriesparam, seriesgeom )
seriesname=options.i3tfile.split('.')[0]
iters=options.iters
#figure out starting number
start=0
previters=glob.glob(seriesname+'*.corr')
if len(previters) > 0:
previters.sort()
lastiter=previters[-1]
start=int(lastiter.split(seriesname)[1].split('.')[0])+1
def start(self):
it = "%03d" % (self.params['recon_iter'])
itt = "%03d" % (self.params['recon_iter'] - 1)
global wd
wd = self.params['rundir']
raw_path = os.path.join(wd, 'raw')
os.chdir(self.params['rundir'])
seriesnumber = "%04d" % int(self.params['tiltseries'])
seriesname = 'series' + seriesnumber
param_out = seriesname + '.param'
param_out_full = self.params['rundir'] + '/' + param_out
tilt_out_full = self.params['rundir'] + '/' + seriesname + itt + '.tlt'
recon_dir = self.params['rundir'] + '/recons/'
os.system('mkdir %s 2>/dev/null' % recon_dir)
recon_param_out_full = recon_dir + '/' + param_out
recon_tilt_out_full = recon_dir + '/' + seriesname + '.tlt'
recon_cache_dir = recon_dir + '/cache'
recon_out_dir = recon_dir + 'out'
os.system('cp %s %s' % (tilt_out_full, recon_tilt_out_full))
os.system('cp %s %s' % (param_out_full, recon_param_out_full))
#CTF Correction
if (self.params['ctf_correct'] == 'True'):
apProTomo2Prep.ctfCorrect(
seriesname, self.params['rundir'],
self.params['projectid'], self.params['sessionname'],
int(self.params['tiltseries']), recon_tilt_out_full,
self.params['frame_aligned'], self.params['pixelsize'],
self.params['DefocusTol'], self.params['iWidth'],
self.params['amp_contrast'])
#Dose Compensation
if (self.params['dose_presets'] != 'False'):
apProTomo2Prep.doseCompensate(
seriesname, self.params['rundir'], self.params['sessionname'],
int(self.params['tiltseries']), self.params['frame_aligned'],
raw_path, self.params['pixelsize'],
self.params['dose_presets'], self.params['dose_a'],
self.params['dose_b'], self.params['dose_c'])
# Remove high tilts from .tlt file if user requests
if (self.params['positive'] < 90) or (self.params['negative'] > -90):
removed_images, mintilt, maxtilt = apProTomo2Aligner.removeHighTiltsFromTiltFile(
recon_tilt_out_full, self.params['negative'],
self.params['positive'])
apDisplay.printMsg(
"Images %s have been removed before reconstruction by weighted back-projection"
% removed_images)
else:
cmd1 = "awk '/ORIGIN /{print}' %s | wc -l" % (recon_tilt_out_full)
proc = subprocess.Popen(cmd1, stdout=subprocess.PIPE, shell=True)
(numimages, err) = proc.communicate()
numimages = int(numimages)
cmd2 = "awk '/IMAGE /{print $2}' %s | head -n +1" % (
recon_tilt_out_full)
proc = subprocess.Popen(cmd2, stdout=subprocess.PIPE, shell=True)
(tiltstart, err) = proc.communicate()
tiltstart = int(tiltstart)
mintilt = 0
maxtilt = 0
for i in range(tiltstart - 1, tiltstart + numimages):
try: #If the image isn't in the .tlt file, skip it
cmd = "awk '/IMAGE %s /{print}' %s | awk '{for (j=1;j<=NF;j++) if($j ~/TILT/) print $(j+2)}'" % (
i + 1, recon_tilt_out_full)
proc = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
shell=True)
(tilt_angle, err) = proc.communicate()
tilt_angle = float(tilt_angle)
mintilt = min(mintilt, tilt_angle)
maxtilt = max(maxtilt, tilt_angle)
except:
pass
# Backup then edit the Refinement param file, changing the map size, map sampling, cache dir, and out dir
refine_param_full = self.params['rundir'] + '/' + 'refine_' + param_out
command = "cp %s %s" % (param_out_full, refine_param_full)
os.system(command)
command1 = "grep -n 'AP sampling' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(command1, stdout=subprocess.PIPE, shell=True)
(samplingline, err) = proc.communicate()
samplingline = int(samplingline)
command2 = "grep -n 'AP reconstruction map size' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(command2, stdout=subprocess.PIPE, shell=True)
(mapsizeline, err) = proc.communicate()
mapsizeline = int(mapsizeline)
command3 = "grep -n 'AP reconstruction map sampling' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(command3, stdout=subprocess.PIPE, shell=True)
(mapsamplingline, err) = proc.communicate()
mapsamplingline = int(mapsamplingline)
command11 = "sed -i \"%ss/.*/ S = %s (* AP sampling *)/\" %s" % (
samplingline, self.params['recon_map_sampling'],
recon_param_out_full)
os.system(command11)
command22 = "sed -i \"%ss/.*/ size: { %s, %s, %s } (* AP reconstruction map size *)/\" %s" % (
mapsizeline,
int(self.params['recon_map_size_x'] /
self.params['recon_map_sampling']),
int(self.params['recon_map_size_y'] /
self.params['recon_map_sampling']),
int(
round(self.params['recon_thickness'] /
(self.params['pixelsize'] *
self.params['recon_map_sampling']))),
recon_param_out_full)
os.system(command22)
command33 = "sed -i \"%ss/.*/ sampling: %s (* AP reconstruction map sampling *)/\" %s" % (
mapsamplingline, self.params['recon_map_sampling'],
recon_param_out_full)
os.system(command33)
command4 = "grep -n 'cachedir' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(command4, stdout=subprocess.PIPE, shell=True)
(cachedirline, err) = proc.communicate()
cachedirline = int(cachedirline)
command5 = "grep -n 'outdir' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(command5, stdout=subprocess.PIPE, shell=True)
(outdirline, err) = proc.communicate()
outdirline = int(outdirline)
command44 = "sed -i \'%ss|.*| cachedir: \"%s\" (* AP directory where cache files are stored *)|\' %s" % (
cachedirline, recon_cache_dir, recon_param_out_full)
os.system(command44)
command55 = "sed -i \'%ss|.*| outdir: \"%s\" (* AP directory where other output files are stored *)|\' %s" % (
outdirline, recon_out_dir, recon_param_out_full)
os.system(command55)
#Lowpass filter reconstruction?
cmd = "grep -n 'AP lowpass map' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
(lowpassmapline, err) = proc.communicate()
lowpassmapline = int(lowpassmapline)
if self.params['recon_lowpass'] == "False":
lp = ''
#Remove lowpass filter from param
cmd2 = "sed -i \"%ss/.*//\" %s;" % (lowpassmapline,
recon_param_out_full)
cmd2 += "sed -i \"%ss/.*//\" %s;" % (lowpassmapline + 1,
recon_param_out_full)
cmd2 += "sed -i \"%ss/.*//\" %s;" % (lowpassmapline + 2,
recon_param_out_full)
cmd2 += "sed -i \"%ss/.*//\" %s" % (lowpassmapline + 3,
recon_param_out_full)
#Set preprocessing to false
cmd3 = "grep -n 'AP enable or disable preprocessing of raw images' %s | awk '{print $1}' | sed 's/://'" % (
recon_param_out_full)
proc = subprocess.Popen(cmd3, stdout=subprocess.PIPE, shell=True)
(preprocessingline, err) = proc.communicate()
preprocessingline = int(preprocessingline)
cmd33 = "sed -i \'%ss|.*| preprocessing: false (* AP enable or disable preprocessing of raw images *)|\' %s" % (
preprocessingline, recon_param_out_full)
os.system(cmd33)
else:
lpavg = int((self.params['recon_lp_diam_x'] +
self.params['recon_lp_diam_y']) / 2)
lp = '.lp%s' % lpavg
self.params['recon_lp_diam_x'] = 2 * self.params[
'pixelsize'] * self.params['recon_map_sampling'] / self.params[
'recon_lp_diam_x']
self.params['recon_lp_diam_y'] = 2 * self.params[
'pixelsize'] * self.params['recon_map_sampling'] / self.params[
'recon_lp_diam_y']
cmd2 = "sed -i \"%ss/.*/ diameter: { %s, %s } * S/\" %s" % (
lowpassmapline + 1, self.params['recon_lp_diam_x'],
self.params['recon_lp_diam_y'], recon_param_out_full)
os.system(cmd2)
dim = '%sx%s' % (self.params['recon_map_size_x'],
self.params['recon_map_size_y'])
ang = '%sto%s' % (round(mintilt, 1), round(maxtilt, 1))
img = seriesname + '00_bck.img'
mrcf = seriesname + '_ite' + it + '_dim' + dim + '_ang' + ang + '_bck.bin' + str(
self.params['recon_map_sampling']) + lp + '.mrc'
mrcfn = seriesname + '_ite' + it + '_dim' + dim + '_ang' + ang + '_bck.bin' + str(
self.params['recon_map_sampling']) + lp + '.norm.mrc'
img_full = recon_out_dir + '/' + img
mrc_full = recon_out_dir + '/' + mrcf
mrcn_full = recon_out_dir + '/' + mrcfn
# AP Get param files ready for batch processing
batchdir = self.params['rundir'] + '/' + 'ready_for_batch'
coarse_param_full = self.params[
'rundir'] + '/coarse_out/' + 'coarse_' + param_out
recon_param = 'recon_' + param_out
command = "mkdir %s 2>/dev/null; cp %s %s; cp %s %s; cp %s %s/%s; rm -r %s %s %s*i3t %s/cache %s/out 2>/dev/null" % (
batchdir, coarse_param_full, batchdir, refine_param_full, batchdir,
param_out_full, batchdir, recon_param, img_full, mrc_full,
recon_dir, recon_dir, recon_dir)
os.system(command)
# Create reconstruction
os.chdir(recon_dir)
os.system("rm %s/cache/%s* %s/*i3t 2>/dev/null" %
(recon_dir, seriesname, recon_dir))
seriesparam = protomo.param(recon_param_out_full)
seriesgeom = protomo.geom(recon_tilt_out_full)
series = protomo.series(seriesparam, seriesgeom)
series.setparam("map.logging", "true")
series.mapfile()
os.chdir(self.params['rundir'])
# Restore refine param file
command = "cp %s %s" % (refine_param_full, param_out_full)
os.system(command)
# Convert to mrc
os.system("i3cut -fmt mrc %s %s" % (img_full, mrc_full))
os.system("rm %s" % img_full)
# Normalize
try:
command = "e2proc3d.py %s %s --process=normalize" % (mrc_full,
mrcn_full)
proc = subprocess.Popen(command,
stdout=subprocess.PIPE,
shell=True)
(code, err) = proc.communicate()
except:
pass
if proc.returncode != 0:
apDisplay.printMsg(
"\ne2proc3d not found or failed to process reconstruction. Trying proc3d..."
)
try:
command = "proc3d %s %s norm" % (mrc_full, mrcn_full)
proc = subprocess.Popen(command,
stdout=subprocess.PIPE,
shell=True)
(code, err) = proc.communicate()
except:
pass
if proc.returncode != 0:
apDisplay.printMsg(
"\nproc3d not found or failed to process reconstruction. Skipping normalization."
)
else:
os.system('rm %s' % mrc_full)
# Link reconstruction to directory
try:
cmd1 = "mkdir -p %s 2>/dev/null; rm %s/%s %s/%s 2>/dev/null; ln -f %s %s 2>/dev/null" % (
self.params['link_recon'], self.params['link_recon'], mrcf,
self.params['link_recon'], mrcfn, mrc_full,
self.params['link_recon'])
cmd2 = "mkdir -p %s 2>/dev/null; rm %s/%s %s/%s 2>/dev/null; ln -f %s %s" % (
self.params['link_recon'], self.params['link_recon'], mrcf,
self.params['link_recon'], mrcfn, mrcn_full,
self.params['link_recon'])
try:
proc = subprocess.Popen(cmd1,
stdout=subprocess.PIPE,
shell=True)
(code, err) = proc.communicate()
except:
pass
if proc.returncode != 0:
try:
proc = subprocess.Popen(cmd2,
stdout=subprocess.PIPE,
shell=True)
(code, err) = proc.communicate()
except:
pass
apDisplay.printMsg(
"Reconstruction can be found in this directory:")
if (self.params['link_recon']
== None) or (self.params['link_recon'] == "") or (len(
self.params['link_recon']) < 1):
print "\n%s\n" % (recon_out_dir)
else:
print "\n%s\n" % (self.params['link_recon'])
except:
apDisplay.printMsg(
"Reconstruction can be found in this directory:")
print "\n%s\n" % (recon_out_dir)
if proc.returncode != 0:
apDisplay.printMsg(
"The reconstruction in the above directory is not normalized because EMAN1 and EMAN2 were either not found or failed to process the reconstruction."
)
os.system("rm %s/cache/%s* %s/*i3t" %
(recon_dir, seriesname, recon_dir))
options, args = parser.parse_args()
if len(args) != 0 or len(sys.argv) == 1:
parser.print_help()
sys.exit()
return options
if __name__ == "__main__":
options = parseOptions()
seriesparam = protomo.param(options.param)
if options.i3tfile:
series = protomo.series(seriesparam)
else:
seriesgeom = protomo.geom(options.tlt)
options.i3tfile = options.tlt
series = protomo.series(seriesparam, seriesgeom)
seriesname = options.i3tfile.split('.')[0]
iters = options.iters
#figure out starting number
start = 0
previters = glob.glob(seriesname + '*.corr')
if len(previters) > 0:
previters.sort()
lastiter = previters[-1]
start = int(lastiter.split(seriesname)[1].split('.')[0]) + 1
