def makeFilesForETomoSampleRecon(processdir, stackdir,aligndir, templatedir, seriesname, thickness, pixelsize,yspacing,has_rotation=False):
'''
Make or link local files required by etomo to redo sampling, creating tomopitch model, and reconstruct the volume.
'''
# etomo status file
createETomoBoundaryModelEDF(processdir,templatedir,seriesname,thickness,pixelsize)
# required by remaking sample tomograms inside etomo
if has_rotation:
apDisplay.printWarning('eTomo wants to regenerate global alignment from non-rotated local alignment. This alignment with rotation will not work right')
else:
# prexf file is generated from database values if this function is called from tomomaker. It is better not to change it if exists.
prexf = seriesname+".prexf"
alignprexf = os.path.join(aligndir,prexf)
localprexf = os.path.join(processdir,prexf)
apFile.safeCopy(alignprexf,localprexf)
writeETomoNewstComTemplate(processdir, seriesname)
rawtltname = '%s.rawtlt' % (seriesname)
shutil.copy(os.path.join(stackdir,rawtltname),os.path.join(processdir,rawtltname))
# required by tomopitch model making
tomopitchname = 'tomopitch.com'
imodcomdir = os.path.join(os.environ['IMOD_DIR'],'com')
tomopitchpath = os.path.join(processdir,tomopitchname)
shutil.copy(os.path.join(imodcomdir,tomopitchname),tomopitchpath)
apFile.replaceUniqueLinePatternInTxtFile(tomopitchpath,'SpacingInY','SpacingInY\t%.1f\n' % yspacing)
# required by "Final Aligned Stack" step
stackname = '%s.st' % (seriesname)
apFile.safeSymLink(os.path.join(stackdir,stackname),os.path.join(processdir,stackname))
def start(self):
### Set FSC resolution criterion
self.fscResCriterion = 0.145
### database entry parameters
package_table = 'ApRelionIterData|relionParams'
### set projection-matching path
#self.projmatchpath = os.path.abspath(os.path.join(self.params['rundir'], "recon"))
self.projmatchpath = os.path.abspath(self.params['rundir'])
### determine which iterations to upload
lastiter = self.findLastCompletedIteration()
uploadIterations = self.verifyUploadIterations(lastiter)
for iteration in uploadIterations:
apDisplay.printColor("uploading iteration %d" % iteration, "cyan")
package_database_object = self.instantiateProjMatchParamsData(iteration)
### move FSC file to results directory
self.FSCExists = self.convertFSCFileForIteration(iteration)
### create a text file with particle information
self.createParticleDataFile(iteration, package_database_object)
# Use Dmitrys code to combine the 2 halves mrcs
### create mrc file of map for iteration and reference number
half1vol = os.path.join(self.projmatchpath, "recon_it%.3d_half1_class001.mrc" % iteration)
half2vol = os.path.join(self.projmatchpath, "recon_it%.3d_half2_class001.mrc" % iteration)
newvol = os.path.join(self.resultspath, "recon_%s_it%.3d_vol001.mrc" % (self.params['timestamp'], iteration))
self.combineMRCs( half1vol, half2vol, newvol )
if iteration == lastiter:
oldvol = os.path.join(self.projmatchpath, "recon_class001.mrc")
apFile.safeCopy(oldvol, newvol)
### make chimera snapshot of volume
self.createChimeraVolumeSnapshot(newvol, iteration)
### instantiate database objects
self.insertRefinementRunData(iteration)
self.insertRefinementIterationData(iteration, package_table, package_database_object)
### make symlink only after successful insertion
# if os.path.isfile(newvol):
# if os.path.isfile(oldvol):
# apFile.removeFile(oldvol,True)
# try:
# os.symlink(newvol, oldvol)
# except IOError, e:
# print e
### calculate Euler jumps
self.calculateEulerJumpsAndGoodBadParticles(uploadIterations)
def start(self):
### Set FSC resolution criterion
self.fscResCriterion = 0.145
### database entry parameters
package_table = 'ApRelionIterData|relionParams'
### set projection-matching path
#self.projmatchpath = os.path.abspath(os.path.join(self.params['rundir'], "recon"))
self.projmatchpath = os.path.abspath(self.params['rundir'])
### determine which iterations to upload
lastiter = self.findLastCompletedIteration()
uploadIterations = self.verifyUploadIterations(lastiter)
for iteration in uploadIterations:
apDisplay.printColor("uploading iteration %d" % iteration, "cyan")
package_database_object = self.instantiateProjMatchParamsData(iteration)
### move FSC file to results directory
self.FSCExists = self.convertFSCFileForIteration(iteration)
### create a text file with particle information
self.createParticleDataFile(iteration, package_database_object)
# Use Dmitrys code to combine the 2 halves mrcs
### create mrc file of map for iteration and reference number
half1vol = os.path.join(self.projmatchpath, "recon_it%.3d_half1_class001.mrc" % iteration)
half2vol = os.path.join(self.projmatchpath, "recon_it%.3d_half2_class001.mrc" % iteration)
newvol = os.path.join(self.resultspath, "recon_%s_it%.3d_vol001.mrc" % (self.params['timestamp'], iteration))
self.combineMRCs( half1vol, half2vol, newvol )
if iteration == lastiter:
oldvol = os.path.join(self.projmatchpath, "recon_class001.mrc")
apFile.safeCopy(oldvol, newvol)
### make chimera snapshot of volume
self.createChimeraVolumeSnapshot(newvol, iteration)
### instantiate database objects
self.insertRefinementRunData(iteration)
self.insertRefinementIterationData(iteration, package_table, package_database_object)
### make symlink only after successful insertion
# if os.path.isfile(newvol):
# if os.path.isfile(oldvol):
# apFile.removeFile(oldvol,True)
# try:
# os.symlink(newvol, oldvol)
# except IOError, e:
# print e
### calculate Euler jumps
self.calculateEulerJumpsAndGoodBadParticles(uploadIterations)
def sampleRecon(stackdir,
processdir,
aligndir,
seriesname,
samplesize=10,
sampleoffset=0.66,
thickness=100,
excludelist=[]):
inputparams = {
'alignedstack': seriesname + ".ali",
'xf': seriesname + ".xf",
'rawtilts': os.path.join(stackdir, seriesname + ".rawtlt"),
'tilts': os.path.join(seriesname + ".tlt"),
'tiltstack': os.path.join(stackdir, seriesname + ".st"),
'recon': seriesname + "_full.rec",
'scale': 250.0,
'thickness': thickness,
}
alignxf = os.path.join(aligndir, seriesname + ".xf")
linkxf = inputparams['xf']
files_to_copy = [(alignxf, linkxf),
(inputparams['rawtilts'], inputparams['tilts'])]
for filepair in files_to_copy:
apFile.safeCopy(filepair[0], filepair[1])
st_shape = apFile.getMrcFileShape(inputparams['tiltstack'])
# shape is in (z, y, x) size for imod is in (x,y)
inputparams['size'] = (st_shape[2], st_shape[1])
total_tilts = st_shape[0]
if samplesize == 'all' or samplesize > total_tilts:
samplesize = total_tilts
# calculate sampletilt range that reduces the process time
sampletilt_start = max(int((total_tilts - samplesize) / 2.0), 1)
sampletilt_end = min(sampletilt_start + samplesize - 1, total_tilts)
# calculate the 3 offsets
sampleoffset = int(st_shape[1] * sampleoffset / 2.0)
st_y_center = int(st_shape[1] / 2.0)
sampleoffsets = {'mid': 0, 'top': sampleoffset, 'bot': (-1) * sampleoffset}
# write basic tilt.com without processdir
comfilename = writeTiltCom(processdir, inputparams['alignedstack'],
inputparams['recon'], inputparams['tilts'],
inputparams['size'], inputparams['thickness'],
0.0, 0.0, (0, inputparams['scale']),
excludelist)
# make commandlines
commands = []
for key in sampleoffsets.keys():
commands.extend([
'$newstack -size ,%d -offset 0,%d -xf %s %s %s' %
(total_tilts, sampleoffsets[key], inputparams['xf'],
inputparams['tiltstack'], inputparams['alignedstack']),
'$sampletilt %d %d %d %s %s.rec tilt.com' %
(sampletilt_start, sampletilt_end,
sampleoffsets[key] + st_y_center, seriesname, key)
])
writeCommandAndRun(processdir, 'sample', commands,
[inputparams['alignedstack'], 'sample.log'])
def start(self):
### database entry parameters
package_table = 'ApFrealignIterData|frealignParams'
### set projection-matching path
self.projmatchpath = os.path.abspath(
os.path.join(self.params['rundir'], "recon"))
### determine which iterations to upload
lastiter = self.findLastCompletedIteration()
uploadIterations = self.verifyUploadIterations(lastiter)
for iteration in uploadIterations:
apDisplay.printColor("uploading iteration %d" % iteration, "cyan")
package_database_object = self.instantiateProjMatchParamsData(
iteration)
if not self.params['euleronly']:
### move FSC file to results directory
self.FSCExists = self.convertFSCFileForIteration(iteration)
### create a text file with particle information
self.createParticleDataFile(iteration, package_database_object)
if not self.params['euleronly']:
### create mrc file of map for iteration and reference number
oldvol = os.path.join(self.projmatchpath,
"threed.%03da.mrc" % iteration)
newvol = os.path.join(
self.resultspath, "recon_%s_it%.3d_vol001.mrc" %
(self.params['timestamp'], iteration))
apFile.safeCopy(oldvol, newvol)
### make chimera snapshot of volume
self.createChimeraVolumeSnapshot(newvol, iteration)
### instantiate database objects
self.insertRefinementRunData(iteration)
self.insertRefinementIterationData(iteration, package_table,
package_database_object)
### make symlink only after successful insertion
if not self.params['euleronly'] and os.path.isfile(newvol):
if os.path.isfile(oldvol):
apFile.removeFile(oldvol, True)
try:
os.symlink(newvol, oldvol)
except IOError, e:
print e
def start(self):
### database entry parameters
package_table = 'ApFrealignIterData|frealignParams'
### set projection-matching path
self.projmatchpath = os.path.abspath(os.path.join(self.params['rundir'], "recon"))
### determine which iterations to upload
lastiter = self.findLastCompletedIteration()
uploadIterations = self.verifyUploadIterations(lastiter)
for iteration in uploadIterations:
apDisplay.printColor("uploading iteration %d" % iteration, "cyan")
package_database_object = self.instantiateProjMatchParamsData(iteration)
if not self.params['euleronly']:
### move FSC file to results directory
self.FSCExists = self.convertFSCFileForIteration(iteration)
### create a text file with particle information
self.createParticleDataFile(iteration, package_database_object)
if not self.params['euleronly']:
### create mrc file of map for iteration and reference number
oldvol = os.path.join(self.projmatchpath, "threed.%03da.mrc" % iteration)
newvol = os.path.join(self.resultspath, "recon_%s_it%.3d_vol001.mrc" % (self.params['timestamp'], iteration))
apFile.safeCopy(oldvol, newvol)
### make chimera snapshot of volume
self.createChimeraVolumeSnapshot(newvol, iteration)
### instantiate database objects
self.insertRefinementRunData(iteration)
self.insertRefinementIterationData(iteration, package_table, package_database_object)
### make symlink only after successful insertion
if not self.params['euleronly'] and os.path.isfile(newvol):
if os.path.isfile(oldvol):
apFile.removeFile(oldvol,True)
try:
os.symlink(newvol, oldvol)
except IOError, e:
print e
def makeFilesForETomoSampleRecon(processdir,
stackdir,
aligndir,
templatedir,
seriesname,
thickness,
pixelsize,
yspacing,
has_rotation=False):
'''
Make or link local files required by etomo to redo sampling, creating tomopitch model, and reconstruct the volume.
'''
# etomo status file
createETomoBoundaryModelEDF(processdir, templatedir, seriesname, thickness,
pixelsize)
# required by remaking sample tomograms inside etomo
if has_rotation:
apDisplay.printWarning(
'eTomo wants to regenerate global alignment from non-rotated local alignment. This alignment with rotation will not work right'
)
else:
# prexf file is generated from database values if this function is called from tomomaker. It is better not to change it if exists.
prexf = seriesname + ".prexf"
alignprexf = os.path.join(aligndir, prexf)
localprexf = os.path.join(processdir, prexf)
apFile.safeCopy(alignprexf, localprexf)
writeETomoNewstComTemplate(processdir, seriesname)
rawtltname = '%s.rawtlt' % (seriesname)
shutil.copy(os.path.join(stackdir, rawtltname),
os.path.join(processdir, rawtltname))
# required by tomopitch model making
tomopitchname = 'tomopitch.com'
imodcomdir = os.path.join(os.environ['IMOD_DIR'], 'com')
tomopitchpath = os.path.join(processdir, tomopitchname)
shutil.copy(os.path.join(imodcomdir, tomopitchname), tomopitchpath)
apFile.replaceUniqueLinePatternInTxtFile(tomopitchpath, 'SpacingInY',
'SpacingInY\t%.1f\n' % yspacing)
# required by "Final Aligned Stack" step
stackname = '%s.st' % (seriesname)
apFile.safeSymLink(os.path.join(stackdir, stackname),
os.path.join(processdir, stackname))
def sampleRecon(stackdir, processdir, aligndir, seriesname, samplesize=10, sampleoffset=0.66, thickness=100, excludelist=[]):
inputparams = {
'alignedstack': seriesname+".ali",
'xf': seriesname+".xf",
'rawtilts': os.path.join(stackdir, seriesname+".rawtlt"),
'tilts': os.path.join(seriesname+".tlt"),
'tiltstack': os.path.join(stackdir, seriesname+".st"),
'recon': seriesname+"_full.rec",
'scale': 250.0,
'thickness': thickness,
}
alignxf = os.path.join(aligndir, seriesname+".xf")
linkxf = inputparams['xf']
files_to_copy = [(alignxf,linkxf),(inputparams['rawtilts'],inputparams['tilts'])]
for filepair in files_to_copy:
apFile.safeCopy(filepair[0],filepair[1])
st_shape = apFile.getMrcFileShape(inputparams['tiltstack'])
# shape is in (z, y, x) size for imod is in (x,y)
inputparams['size']=(st_shape[2],st_shape[1])
total_tilts = st_shape[0]
if samplesize == 'all' or samplesize > total_tilts:
samplesize = total_tilts
# calculate sampletilt range that reduces the process time
sampletilt_start = max(int((total_tilts - samplesize)/2.0),1)
sampletilt_end = min(sampletilt_start + samplesize - 1,total_tilts)
# calculate the 3 offsets
sampleoffset = int (st_shape[1] * sampleoffset / 2.0)
st_y_center = int (st_shape[1] / 2.0)
sampleoffsets = {'mid':0,'top':sampleoffset,'bot':(-1)*sampleoffset}
# write basic tilt.com without processdir
comfilename = writeTiltCom(processdir,inputparams['alignedstack'],inputparams['recon'],inputparams['tilts'],inputparams['size'],inputparams['thickness'],0.0,0.0,(0,inputparams['scale']),excludelist)
# make commandlines
commands = []
for key in sampleoffsets.keys():
commands.extend([
'$newstack -size ,%d -offset 0,%d -xf %s %s %s' % (total_tilts,sampleoffsets[key],inputparams['xf'],inputparams['tiltstack'],inputparams['alignedstack']),
'$sampletilt %d %d %d %s %s.rec tilt.com' % (sampletilt_start,sampletilt_end,sampleoffsets[key]+st_y_center,seriesname,key)
])
writeCommandAndRun(processdir,'sample',commands,[inputparams['alignedstack'],'sample.log'])
def copyFrames(self,source,destination): apFile.safeCopy(source, destination)
def fakeOutput(imgname, ccmapfile, params):
a = apImage.mrcToArray(imgname)
a = numpy.zeros(a.shape)
apImage.arrayToMrc(a, ccmapfile)
apFile.safeCopy('/home/acheng/Projects/Gfindem/example.box',
getBoxFileName(ccmapfile))
def fakeOutput(imgname,ccmapfile,params):
a = apImage.mrcToArray(imgname)
a = numpy.zeros(a.shape)
apImage.arrayToMrc(a,ccmapfile)
apFile.safeCopy('/home/acheng/Projects/Gfindem/example.box', getBoxFileName(ccmapfile))