def prepareRecon(self):
processdir = self.params['rundir']
stackdir = self.params['tiltseriesdir']
thickness = int(self.params['thickness'])
# Make Sample Tomogram for etomo manual positioning and exit
aligndir = self.alignerdata['alignrun']['path']['path']
templatedir = os.path.join(os.path.dirname(apImod.__file__), 'data')
yspacing_fraction = 0.66
apImod.sampleRecon(stackdir, processdir, aligndir, self.seriesname, 10,
0.66, thickness, self.excludelist)
stackpath = os.path.join(stackdir, self.seriesname + ".st")
yspacing_pixel = apFile.getMrcFileShape(
stackpath)[1] * yspacing_fraction * 0.5
has_rotation = False
if self.alignerdata['protomo']:
if self.alignerdata['refine_cycle']['cycle'] > 0:
has_rotation = True
apImod.makeFilesForETomoSampleRecon(processdir, stackdir, aligndir,
templatedir, self.seriesname,
thickness, self.pixelsize,
yspacing_pixel, has_rotation)
paramfile = os.path.join(processdir,
'%s_sample.params' % (self.params['runname']))
apParam.dumpParameters(self.params, paramfile)
return
def projectFullZ(processdir,
runname,
seriesname,
bin=1,
rotx=True,
flipyz=False):
"""
# Command for projecting full tomogram to z-axis
#
# Tomography reconstruction y and z are usually flipped
# full tomogram mrc file axes [x,z,y]
# clip average command need [x,y,z]
clip flipyz 09feb18c_002_full.rec temp.mrc
clip avg -2d -iz 0-199 temp.mrc projection.mrc
"""
inputparams = {
'recon': os.path.join(processdir, seriesname + "_full.rec"),
'temp': os.path.join(processdir, "temp.rec"),
'project': os.path.join(processdir, seriesname + "_zproject.mrc"),
}
fullshape = apFile.getMrcFileShape(inputparams['recon'])
commands = []
if rotx or flipyz:
op = ''
if rotx:
op += ' rotx'
if flipyz:
op += ' flipyz'
lookup = {'y': 0, 'z': 1}
inputparams['3d'] = inputparams['temp']
commands.append("$clip" + op + " %s %s" % (
inputparams['recon'],
inputparams['temp'],
))
else:
lookup = {'y': 1, 'z': 0}
inputparams['3d'] = inputparams['recon']
# limit slices for projection to 200 to save time.
zcenter = int(fullshape[lookup['z']] / 2)
zstart = max(0, zcenter - 100)
zend = min(fullshape[lookup['z']] - 1, zcenter + 99)
commands.append(
"$clip avg -2d -iz %d-%d %s %s" % (
zstart,
zend,
inputparams['3d'],
inputparams['project'],
), )
writeCommandAndRun(
processdir, 'projectZ', commands,
[inputparams['temp'], inputparams['project'], 'projectZ.log'])
if bin > 1:
# unbin the projection
a = mrc.read(inputparams['project'])
b = apImage.scaleImage(a, bin)
mrc.write(b, inputparams['project'])
return inputparams['project']
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 projectFullZ(processdir, runname, seriesname,bin=1,rotx=True,flipyz=False):
"""
# Command for projecting full tomogram to z-axis
#
# Tomography reconstruction y and z are usually flipped
# full tomogram mrc file axes [x,z,y]
# clip average command need [x,y,z]
clip flipyz 09feb18c_002_full.rec temp.mrc
clip avg -2d -iz 0-199 temp.mrc projection.mrc
"""
inputparams = {
'recon': os.path.join(processdir, seriesname+"_full.rec"),
'temp': os.path.join(processdir, "temp.rec"),
'project': os.path.join(processdir, seriesname+"_zproject.mrc"),
}
fullshape = apFile.getMrcFileShape(inputparams['recon'])
commands = []
if rotx or flipyz:
op = ''
if rotx:
op += ' rotx'
if flipyz:
op += ' flipyz'
lookup = {'y':0,'z':1}
inputparams['3d'] = inputparams['temp']
commands.append(
"$clip"+op+" %s %s"
% (inputparams['recon'],inputparams['temp'],
)
)
else:
lookup = {'y':1,'z':0}
inputparams['3d'] = inputparams['recon']
# limit slices for projection to 200 to save time.
zcenter = int(fullshape[lookup['z']] / 2)
zstart = max(0,zcenter - 100)
zend = min(fullshape[lookup['z']]-1,zcenter + 99)
commands.append(
"$clip avg -2d -iz %d-%d %s %s"
% (zstart,zend,
inputparams['3d'],inputparams['project'],
),
)
writeCommandAndRun(processdir,'projectZ',commands,[inputparams['temp'],inputparams['project'],'projectZ.log'])
if bin > 1:
# unbin the projection
a = mrc.read(inputparams['project'])
b = apImage.scaleImage(a,bin)
mrc.write(b,inputparams['project'])
return inputparams['project']
def trimVolume(processdir, runname, seriesname, volumename, center, offsetz, size,rotx=True):
"""
# Command for triming reconstructed volume
#
# Full Tomography reconstruction is X,Z,Y need to rotate around x
# full tomogram array axes [z,y,x]
# imod full_rec axes [y,z,x]
# center and size axes [x,y,z]
trimvol -x 390,460 -z 477,537 -rx 08aug14f_008_full.rec test.rec
"""
inputparams = {
'recon': os.path.join(processdir, seriesname+"_full.rec"),
'subvolume': os.path.join(processdir, runname+"/",volumename+"/",seriesname+"_"+volumename+".rec"),
'xrange0': max(1,center[0] - size[0]/2),
'yrange0': max(1,center[1] - size[1]/2),
}
if rotx:
lookup = {'y':0,'z':1}
else:
lookup = {'y':1,'z':0}
fullshape = apFile.getMrcFileShape(inputparams['recon'])
center = list(center)
center.append(fullshape[lookup['z']]/2+offsetz)
inputparams['zrange0'] = max(1,center[2] - size[2]/2)
inputparams['xrange1'] = min(fullshape[2],inputparams['xrange0'] + size[0]-1)
inputparams['yrange1'] = min(fullshape[lookup['y']],inputparams['yrange0'] + size[1]-1)
inputparams['zrange1'] = min(fullshape[lookup['z']],inputparams['zrange0'] + size[2]-1)
if rotx:
commands = [
"$trimvol -x %d,%d -y %d,%d -z %d,%d -rx %s %s"
% (inputparams['xrange0'],inputparams['xrange1'],
inputparams['zrange0'],inputparams['zrange1'],
inputparams['yrange0'],inputparams['yrange1'],
inputparams['recon'],
inputparams['subvolume'],
),
]
else:
commands = [
"$trimvol -x %d,%d -y %d,%d -z %d,%d %s %s"
% (inputparams['xrange0'],inputparams['xrange1'],
inputparams['yrange0'],inputparams['yrange1'],
inputparams['zrange0'],inputparams['zrange1'],
inputparams['recon'],
inputparams['subvolume'],
),
]
writeCommandAndRun(processdir,'trimvol',commands,[inputparams['subvolume'],'trimvol.log'])
def prepareRecon(self):
processdir = self.params['rundir']
stackdir = self.params['tiltseriesdir']
thickness = int(self.params['thickness'])
# Make Sample Tomogram for etomo manual positioning and exit
aligndir = self.alignerdata['alignrun']['path']['path']
templatedir = os.path.join(os.path.dirname(apImod.__file__),'data')
yspacing_fraction = 0.66
apImod.sampleRecon(stackdir, processdir, aligndir, self.seriesname, 10, 0.66, thickness, self.excludelist)
stackpath = os.path.join(stackdir, self.seriesname+".st")
yspacing_pixel = apFile.getMrcFileShape(stackpath)[1] * yspacing_fraction * 0.5
has_rotation = False
if self.alignerdata['protomo']:
if self.alignerdata['refine_cycle']['cycle'] > 0:
has_rotation = True
apImod.makeFilesForETomoSampleRecon(processdir, stackdir,aligndir, templatedir, self.seriesname, thickness, self.pixelsize,yspacing_pixel,has_rotation)
paramfile = os.path.join(processdir,'%s_sample.params' % (self.params['runname']))
apParam.dumpParameters(self.params, paramfile)
return
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 trimVolume(processdir,
runname,
seriesname,
volumename,
center,
offsetz,
size,
rotx=True):
"""
# Command for triming reconstructed volume
#
# Full Tomography reconstruction is X,Z,Y need to rotate around x
# full tomogram array axes [z,y,x]
# imod full_rec axes [y,z,x]
# center and size axes [x,y,z]
trimvol -x 390,460 -z 477,537 -rx 08aug14f_008_full.rec test.rec
"""
inputparams = {
'recon':
os.path.join(processdir, seriesname + "_full.rec"),
'subvolume':
os.path.join(processdir, runname + "/", volumename + "/",
seriesname + "_" + volumename + ".rec"),
'xrange0':
max(1, center[0] - size[0] / 2),
'yrange0':
max(1, center[1] - size[1] / 2),
}
if rotx:
lookup = {'y': 0, 'z': 1}
else:
lookup = {'y': 1, 'z': 0}
fullshape = apFile.getMrcFileShape(inputparams['recon'])
center = list(center)
center.append(fullshape[lookup['z']] / 2 + offsetz)
inputparams['zrange0'] = max(1, center[2] - size[2] / 2)
inputparams['xrange1'] = min(fullshape[2],
inputparams['xrange0'] + size[0] - 1)
inputparams['yrange1'] = min(fullshape[lookup['y']],
inputparams['yrange0'] + size[1] - 1)
inputparams['zrange1'] = min(fullshape[lookup['z']],
inputparams['zrange0'] + size[2] - 1)
if rotx:
commands = [
"$trimvol -x %d,%d -y %d,%d -z %d,%d -rx %s %s" % (
inputparams['xrange0'],
inputparams['xrange1'],
inputparams['zrange0'],
inputparams['zrange1'],
inputparams['yrange0'],
inputparams['yrange1'],
inputparams['recon'],
inputparams['subvolume'],
),
]
else:
commands = [
"$trimvol -x %d,%d -y %d,%d -z %d,%d %s %s" % (
inputparams['xrange0'],
inputparams['xrange1'],
inputparams['yrange0'],
inputparams['yrange1'],
inputparams['zrange0'],
inputparams['zrange1'],
inputparams['recon'],
inputparams['subvolume'],
),
]
writeCommandAndRun(processdir, 'trimvol', commands,
[inputparams['subvolume'], 'trimvol.log'])
