def checkNumberOfParticles(self):
#determine number of particle in input stack
header = mrc.readHeaderFromFile(self.splitStacks['right'])
#print header['shape']
rightnumpart = header['shape'][0] - 1
rightboxsize = max(header['shape'][1], header['shape'][2])
apDisplay.printColor(
"Found %d particles in the right stack file with box size %d x %d"
% (rightnumpart, header['shape'][1], header['shape'][2]), "green")
#determine number of particle in input stack
header = mrc.readHeaderFromFile(self.splitStacks['left'])
#print header['shape']
leftnumpart = header['shape'][0] - 1
leftboxsize = max(header['shape'][1], header['shape'][2])
apDisplay.printColor(
"Found %d particles in the left stack file with box size %d x %d" %
(leftnumpart, header['shape'][1], header['shape'][2]), "green")
if leftboxsize != rightboxsize:
apDisplay.printError("particles have different box size")
self.boxsize = leftboxsize
if leftnumpart != rightnumpart:
apDisplay.printWarning("particles have different count")
self.numpart = min(leftnumpart, rightnumpart)
return
def checkNumberOfParticles(self):
#determine number of particle in input stack
header = mrc.readHeaderFromFile(self.splitStacks['right'])
#print header['shape']
rightnumpart = header['shape'][0]-1
rightboxsize = max(header['shape'][1], header['shape'][2])
apDisplay.printColor("Found %d particles in the right stack file with box size %d x %d"
%(rightnumpart, header['shape'][1], header['shape'][2]), "green")
#determine number of particle in input stack
header = mrc.readHeaderFromFile(self.splitStacks['left'])
#print header['shape']
leftnumpart = header['shape'][0]-1
leftboxsize = max(header['shape'][1], header['shape'][2])
apDisplay.printColor("Found %d particles in the left stack file with box size %d x %d"
%(leftnumpart, header['shape'][1], header['shape'][2]), "green")
if leftboxsize != rightboxsize:
apDisplay.printError("particles have different box size")
self.boxsize = leftboxsize
if leftnumpart != rightnumpart:
apDisplay.printWarning("particles have different count")
self.numpart = min(leftnumpart, rightnumpart)
return
def getSubTomoBoundary(processdir,seriesname,axis):
'''
Get the start and end coordinate at a particular axis.
The definition of origin may or may not apply to tomograms
generated outside imod.
'''
fulltomopath = os.path.join(processdir,seriesname+'_full.rec')
subtomopath = os.path.join(processdir,seriesname+'.rec')
fullheader = mrc.readHeaderFromFile(fulltomopath)
subheader = mrc.readHeaderFromFile(subtomopath)
lenkey = axis+'len'
originkey = axis+'origin'
mkey = 'm'+axis
# There is a rotation around x-axis in full tomogram
fullorigin = {'xorigin':fullheader['xorigin'],'yorigin':fullheader['zorigin'],'zorigin':fullheader['yorigin']}
fullm = {'mx':fullheader['mx'],'my':fullheader['mz'],'mz':fullheader['my']}
# full and sub tomo should have the same pixelsize
pixelsize = subheader[lenkey] / subheader[mkey]
if axis != 'z':
start = int((fullorigin[originkey] - subheader[originkey]) / pixelsize)
else:
# z origin is defined different from x and y
start = -int((fullorigin[originkey] + subheader[originkey]) / pixelsize) + int(fullm[mkey])
end = start + int(subheader[mkey])
return (start,end)
def shiftToCenter(infile,shiftfile,isEMAN=False):
'''
EMAN defines the rotation origin differently from other packages.
Therefore, it needs to be recenterred according to the package
after using EMAN proc3d rotation functions.
'''
# center of rotation for eman is not at length/2.
if isEMAN:
formatoffset = getEmanCenter()
prefix = ''
else:
formatoffset = (0,0,0)
prefix = 'non-'
apDisplay.printMsg('Shifting map center for %sEMAN usage' % (prefix,))
# Find center of mass of the density map
a = mrc.read(infile)
t = a.mean()+2*a.std()
numpy.putmask(a,a>=t,t)
numpy.putmask(a,a<t,0)
center = ndimage.center_of_mass(a)
offset = (center[0]+formatoffset[0]-a.shape[0]/2,center[1]+formatoffset[1]-a.shape[1]/2,center[2]+formatoffset[2]-a.shape[2]/2)
offset = (-offset[0],-offset[1],-offset[2])
apDisplay.printMsg('Shifting map center by (x,y,z)=(%.2f,%.2f,%.2f)' % (offset[2],offset[1],offset[0]))
# shift the map
a = mrc.read(infile)
a = ndimage.interpolation.shift(a,offset)
mrc.write(a,shiftfile)
h = mrc.readHeaderFromFile(infile)
mrc.update_file_header(shiftfile,h)
def checkExistingFile(self):
savedtomopath = os.path.join(self.params['rundir'], self.params['name']+".rec")
origtomopath = self.params['file']
apDisplay.printWarning("A Tomogram by the same filename already exists: '"+savedtomopath+"'")
### a tomogram by the same name already exists
savedheader = mrc.readHeaderFromFile(savedtomopath)
savedshape = savedheader['shape']
origheader = self.origheader
origshape = self.origshape
order = self.params['order']
if self.params['full']:
newshape = (self.imageshape[0], origshape[order.find('Z')], self.imageshape[1])
else:
newshape = (origshape[order.find('X')], origshape[order.find('Y')], origshape[order.find('Z')])
# not using md5 for file comparison because it takes too long. With padding, only min and max are stable
if newshape != savedshape or savedheader['amax'] != origheader['amax'] or savedheader['amin'] != origheader['amin']:
different = True
else:
different = False
mdnew = None
if different:
apDisplay.printWarning("The tomograms are different, cannot overwrite")
return True
elif apDatabase.isTomoInDB(mdnew,self.params['full'],savedtomopath):
### they are the same and its in the database already
apDisplay.printWarning("Identical Tomogram already exists in the database!")
apDisplay.printWarning("Upload Not Allowed")
self.params['commit'] = False
return True
else:
### they are the same, but it is not in the database
apDisplay.printWarning("The same tomogram with name '"+savedtomopath+"' already exists, but is not uploaded!")
if self.params['commit'] is True:
apDisplay.printMsg("Inserting tomogram into database...")
def shiftToCenter(infile, shiftfile, isEMAN=False):
'''
EMAN defines the rotation origin differently from other packages.
Therefore, it needs to be recenterred according to the package
after using EMAN proc3d rotation functions.
'''
# center of rotation for eman is not at length/2.
if isEMAN:
formatoffset = getEmanCenter()
prefix = ''
else:
formatoffset = (0, 0, 0)
prefix = 'non-'
apDisplay.printMsg('Shifting map center for %sEMAN usage' % (prefix, ))
# Find center of mass of the density map
a = mrc.read(infile)
t = a.mean() + 2 * a.std()
numpy.putmask(a, a >= t, t)
numpy.putmask(a, a < t, 0)
center = ndimage.center_of_mass(a)
offset = (center[0] + formatoffset[0] - a.shape[0] / 2,
center[1] + formatoffset[1] - a.shape[1] / 2,
center[2] + formatoffset[2] - a.shape[2] / 2)
offset = (-offset[0], -offset[1], -offset[2])
apDisplay.printMsg('Shifting map center by (x,y,z)=(%.2f,%.2f,%.2f)' %
(offset[2], offset[1], offset[0]))
# shift the map
a = mrc.read(infile)
a = ndimage.interpolation.shift(a, offset)
mrc.write(a, shiftfile)
h = mrc.readHeaderFromFile(infile)
mrc.update_file_header(shiftfile, h)
def checkExistingFile(self):
savedtomopath = os.path.join(self.params['rundir'], self.params['name']+".rec")
origtomopath = self.params['file']
apDisplay.printWarning("A Tomogram by the same filename already exists: '"+savedtomopath+"'")
### a tomogram by the same name already exists
savedheader = mrc.readHeaderFromFile(savedtomopath)
savedshape = savedheader['shape']
origheader = self.origheader
origshape = self.origshape
order = self.params['order']
if self.params['full']:
newshape = (self.imageshape[0], origshape[order.find('Z')], self.imageshape[1])
else:
newshape = (origshape[order.find('X')], origshape[order.find('Y')], origshape[order.find('Z')])
# not using md5 for file comparison because it takes too long. With padding, only min and max are stable
if newshape != savedshape or savedheader['amax'] != origheader['amax'] or savedheader['amin'] != origheader['amin']:
different = True
else:
different = False
mdnew = None
if different:
apDisplay.printWarning("The tomograms are different, cannot overwrite")
return True
elif apDatabase.isTomoInDB(mdnew,self.params['full'],savedtomopath):
### they are the same and its in the database already
apDisplay.printWarning("Identical Tomogram already exists in the database!")
apDisplay.printWarning("Upload Not Allowed")
self.params['commit'] = False
return True
else:
### they are the same, but it is not in the database
apDisplay.printWarning("The same tomogram with name '"+savedtomopath+"' already exists, but is not uploaded!")
if self.params['commit'] is True:
apDisplay.printMsg("Inserting tomogram into database...")
def checkReconVolume(self):
from pyami import mrc
h = mrc.readHeaderFromFile(self.tasklogfile)
if h['amax'] == h['amin']:
apDisplay.printError(
'Reconstruction gives no real density. Is the mask too tight? If not, consider using larger "hard" value to exclude fewer images in recostruction.',
False)
def readFileHeader(self, filename):
"""
reads header information for any type of image or stack file
"""
try:
return self.headercache[filename]
except KeyError:
pass
if not os.path.exists(filename):
return None
#Determine extension
if filename.endswith('.mrc') or filename.endswith('.mrcs'):
header = mrc.readHeaderFromFile(filename)
elif filename.endswith('.hed') or filename.endswith('.img'):
header = imagic.readImagicHeader(filename)
elif filename.endswith('.spi'):
### to be implemented
apDisplay.printError("SPIDER is not implemented yet")
elif filename.endswith('.hdf'):
### to be implemented
apDisplay.printError("HDF is not implemented yet")
else:
apDisplay.printError("unknown stack type")
self.headercache[filename] = header
return header
def shiftMRCStartToZero(filename):
h = mrc.readHeaderFromFile(filename)
if h['nxstart'] != 0 or h['nystart'] != 0:
apDisplay.printMsg("Shifting image header start to zero on %s" %
(os.path.basename(filename)))
a = mrc.read(filename)
mrc.write(a, filename)
def writeTiltSeriesStack(stackdir, stackname, ordered_mrc_files, apix=1):
stackpath = os.path.join(stackdir, stackname)
print stackpath
apixdict = {'x': apix, 'y': apix}
if os.path.exists(stackpath):
stheader = mrc.readHeaderFromFile(stackpath)
stshape = stheader['shape']
imageheader = mrc.readHeaderFromFile(ordered_mrc_files[0])
imageshape = imageheader['shape']
if stshape[1:] == imageshape and stshape[0] == len(ordered_mrc_files):
apDisplay.printMsg("No need to get new stack of the tilt series")
else:
apImage.writeMrcStack(stackdir, stackname, order3dmrc_files, 1)
mrc.updateFilePixelSize(stackpath, apixdict)
else:
apImage.writeMrcStack(stackdir, stackname, ordered_mrc_files, 1)
mrc.updateFilePixelSize(stackpath, apixdict)
def getModelDimensions(mrcfile):
print "calculating dimensions..."
h = mrc.readHeaderFromFile(mrcfile)
(x, y, z) = h['mx'], h['my'], h['mz']
if x != y != z:
apDisplay.printWarning("starting model is not a cube")
return max(x, y, z)
return x
def getImageDimensions(self, mrcfile):
'''
Returns dictionary of x,y dimension for an mrc image/image stack
'''
mrcheader = mrc.readHeaderFromFile(mrcfile)
x = int(mrcheader['nx'].astype(numpy.uint16))
y = int(mrcheader['ny'].astype(numpy.uint16))
return {'x': x, 'y': y}
def writeTiltSeriesStack(stackdir,stackname,ordered_mrc_files,apix=1):
stackpath = os.path.join(stackdir, stackname)
print stackpath
apixdict = {'x':apix,'y':apix}
if os.path.exists(stackpath):
stheader = mrc.readHeaderFromFile(stackpath)
stshape = stheader['shape']
imageheader = mrc.readHeaderFromFile(ordered_mrc_files[0])
imageshape = imageheader['shape']
if stshape[1:] == imageshape and stshape[0] == len(ordered_mrc_files):
apDisplay.printMsg("No need to get new stack of the tilt series")
else:
apImage.writeMrcStack(stackdir,stackname,order3dmrc_files, 1)
mrc.updateFilePixelSize(stackpath,apixdict)
else:
apImage.writeMrcStack(stackdir,stackname,ordered_mrc_files, 1)
mrc.updateFilePixelSize(stackpath,apixdict)
def getModelDimensions(mrcfile):
print "calculating dimensions..."
h=mrc.readHeaderFromFile(mrcfile)
(x,y,z)=h['mx'],h['my'],h['mz']
if x!=y!=z:
apDisplay.printWarning("starting model is not a cube")
return max(x,y,z)
return x
def getFullTomoShape(self): ''' This function returns tuple of array shape as int, not numpy.int without reading the whole map ''' fulltomopath = os.path.join(self.fulltomodata['reconrun']['path']['path'], self.seriesname+"_full.rec") fulltomoheader = mrc.readHeaderFromFile(fulltomopath) # conversion to int is important for sinedon insert return tuple(map((lambda x:int(x)),fulltomoheader['shape']))
def getImageDimensions(self, mrcfile):
'''
Returns dictionary of x,y dimension for an mrc image/image stack
'''
mrcheader = mrc.readHeaderFromFile(mrcfile)
x = int(mrcheader['nx'].astype(numpy.uint16))
y = int(mrcheader['ny'].astype(numpy.uint16))
return {'x': x, 'y': y}
def start(self):
commit = self.params['commit']
description = self.params['description']
processdir = self.params['fulltomodir']
runname = self.params['runname']
offsetz = self.params['offsetz']
subbin = self.params['bin']
invert = self.params['invert']
fulltomodata = apTomo.getFullTomoData(self.params['fulltomoId'])
#subvolume making
if (self.params['selexonId'] is not None or self.params['stackId']) and fulltomodata is not None:
sessiondata = fulltomodata['session']
seriesname = fulltomodata['name'].rstrip('_full')
fullbin = fulltomodata['bin']
if not fullbin:
apDisplay.printWarning("no binning in full tomogram, something is wrong, use alignment bin for now")
fullbin = fulltomodata['aligner']['alignrun']['bin']
fulltomopath = os.path.join(fulltomodata['reconrun']['path']['path'], seriesname+"_full.rec")
fulltomoheader = mrc.readHeaderFromFile(fulltomopath)
fulltomoshape = fulltomoheader['shape']
if self.params['sizez'] > fulltomoshape[1]*fullbin :
self.params['sizez'] = fulltomoshape[1]*fullbin
subrunname = self.params['subrunname']
volumeindex = apTomo.getLastVolumeIndex(fulltomodata) + 1
dimension = {'x':int(self.params['sizex']),'y':int(self.params['sizey']),'z':int(self.params['sizez'])}
zprojimagedata = fulltomodata['zprojection']
apDisplay.printMsg("getting pixelsize")
pixelsize = apTomo.getTomoPixelSize(zprojimagedata) * fullbin * subbin
gtransform = [1,0,0,1,0,0]
if self.params['selexonId']:
particles = apParticle.getParticles(zprojimagedata, self.params['selexonId'])
if self.params['stackId']:
particles,stackparticles = apStack.getImageParticles(zprojimagedata, self.params['stackId'])
stackdata = apStack.getOnlyStackData(self.params['stackId'])
for p, particle in enumerate(particles):
print particle['xcoord'],particle['ycoord'],fullbin
center = apTomo.transformParticleCenter(particle,fullbin,gtransform)
size = (dimension['x']/fullbin,dimension['y']/fullbin,dimension['z']/fullbin)
volumename = 'volume%d'% (volumeindex,)
volumedir = os.path.join(processdir,subrunname+'/',volumename+'/')
apParam.createDirectory(volumedir)
apImod.trimVolume(processdir, subrunname,seriesname,volumename,center,offsetz,size,True)
long_volumename = seriesname+'_'+volumename
subvolumepath = os.path.join(processdir, runname+"/",volumename+"/",long_volumename+".rec")
if subbin > 1 or invert:
apTomo.modifyVolume(subvolumepath,subbin,invert)
if commit:
subtomorundata = apTomo.insertSubTomoRun(sessiondata,
self.params['selexonId'],self.params['stackId'],subrunname,invert,subbin)
subtomodata = apTomo.insertSubTomogram(fulltomodata,subtomorundata,
particle,offsetz,dimension,
volumedir,long_volumename,volumeindex,pixelsize,
description)
apTomo.makeMovie(subvolumepath)
apTomo.makeProjection(subvolumepath)
volumeindex += 1
def start(self):
commit = self.params['commit']
description = self.params['description']
processdir = self.params['fulltomodir']
runname = self.params['runname']
offsetz = self.params['offsetz']
subbin = self.params['bin']
invert = self.params['invert']
fulltomodata = apTomo.getFullTomoData(self.params['fulltomoId'])
#subvolume making
if (self.params['selexonId'] is not None or self.params['stackId']) and fulltomodata is not None:
sessiondata = fulltomodata['session']
seriesname = fulltomodata['name'].rstrip('_full')
fullbin = fulltomodata['bin']
if not fullbin:
apDisplay.printWarning("no binning in full tomogram, something is wrong, use alignment bin for now")
fullbin = fulltomodata['aligner']['alignrun']['bin']
fulltomopath = os.path.join(fulltomodata['reconrun']['path']['path'], seriesname+"_full.rec")
fulltomoheader = mrc.readHeaderFromFile(fulltomopath)
fulltomoshape = fulltomoheader['shape']
if self.params['sizez'] > fulltomoshape[1]*fullbin :
self.params['sizez'] = fulltomoshape[1]*fullbin
subrunname = self.params['subrunname']
volumeindex = apTomo.getLastVolumeIndex(fulltomodata) + 1
dimension = {'x':int(self.params['sizex']),'y':int(self.params['sizey']),'z':int(self.params['sizez'])}
zprojimagedata = fulltomodata['zprojection']
apDisplay.printMsg("getting pixelsize")
pixelsize = apTomo.getTomoPixelSize(zprojimagedata) * fullbin * subbin
gtransform = [1,0,0,1,0,0]
if self.params['selexonId']:
particles = apParticle.getParticles(zprojimagedata, self.params['selexonId'])
if self.params['stackId']:
particles,stackparticles = apStack.getImageParticles(zprojimagedata, self.params['stackId'])
stackdata = apStack.getOnlyStackData(self.params['stackId'])
for p, particle in enumerate(particles):
print particle['xcoord'],particle['ycoord'],fullbin
center = apTomo.transformParticleCenter(particle,fullbin,gtransform)
size = (dimension['x']/fullbin,dimension['y']/fullbin,dimension['z']/fullbin)
volumename = 'volume%d'% (volumeindex,)
volumedir = os.path.join(processdir,subrunname+'/',volumename+'/')
apParam.createDirectory(volumedir)
apImod.trimVolume(processdir, subrunname,seriesname,volumename,center,offsetz,size,True)
long_volumename = seriesname+'_'+volumename
subvolumepath = os.path.join(processdir, runname+"/",volumename+"/",long_volumename+".rec")
if subbin > 1 or invert:
apTomo.modifyVolume(subvolumepath,subbin,invert)
if commit:
subtomorundata = apTomo.insertSubTomoRun(sessiondata,
self.params['selexonId'],self.params['stackId'],subrunname,invert,subbin)
subtomodata = apTomo.insertSubTomogram(fulltomodata,subtomorundata,
particle,offsetz,dimension,
volumedir,long_volumename,volumeindex,pixelsize,
description)
apTomo.makeMovie(subvolumepath)
apTomo.makeProjection(subvolumepath)
volumeindex += 1
def getFullTomoShape(self):
'''
This function returns tuple of array shape as int, not numpy.int without reading the whole map
'''
fulltomopath = os.path.join(
self.fulltomodata['reconrun']['path']['path'],
self.seriesname + "_full.rec")
fulltomoheader = mrc.readHeaderFromFile(fulltomopath)
# conversion to int is important for sinedon insert
return tuple(map((lambda x: int(x)), fulltomoheader['shape']))
def collectResults(self, imgdata, targetdict):
"""
Overwrite collectResults to do final processing of the
queue job result and commit
"""
#cleanup and reformat image
try:
innamepath = glob.glob(os.path.join(targetdict['outpath'],
'*.mrc'))[0]
print innamepath
except IndexError:
apDisplay.printWarning('queued job for %s failed' %
(imgdata['filename']))
return
outname = imgdata['filename'] + '-' + self.params['alignlabel'] + '.mrc'
outnamepath = os.path.join(targetdict['outpath'], outname)
if self.params['border'] != 0:
command = ['proc2d', innamepath, outnamepath]
header = mrc.readHeaderFromFile(innamepath)
origx = header['nx']
origy = header['ny']
newx = origx - self.params['border']
newy = origy - self.params['border']
command.append('clip=%d,%d' % (newx, newy))
print command
subprocess.call(command)
command = ['proc2d', outnamepath, outnamepath]
command.append('clip=%d,%d' % (origx, origy))
command.append('edgenorm')
print command
subprocess.call(command)
newimg_array = mrc.read(outnamepath)
self.commitAlignedImageToDatabase(imgdata, newimg_array,
self.params['alignlabel'])
# return None since everything is committed within this function.
if self.params['hackcopy'] is True:
origpath = imgdata['session']['image path']
archivecopy = os.path.join(origpath,
imgdata['filename'] + '.orig.mrc')
if os.path.exists(archivecopy) is True:
apDisplay.printMsg(
'archive copy for %s already exists, so skipping archive' %
(archivecopy))
else:
shutil.move(
os.path.join(origpath, imgdata['filename'] + '.mrc'),
archivecopy)
shutil.copyfile(
outnamepath,
os.path.join(origpath, imgdata['filename'] + '.mrc'))
return None
def __init__(self,filepath): if not os.path.isfile(filepath): print "ERROR: file does not exist" self.file_bytes = os.path.getsize(filepath) self.header = mrc.readHeaderFromFile(filepath) self.valid_exttypes = ['CCP4','MRCO','SERI','AGAR','FEI1'] self.is2D = True self.isCrystal = False self.errors = [] self.updates = [] self.infos = []
def __init__(self, filepath):
if not os.path.isfile(filepath):
print "ERROR: file does not exist"
self.file_bytes = os.path.getsize(filepath)
self.header = mrc.readHeaderFromFile(filepath)
self.valid_exttypes = ['CCP4', 'MRCO', 'SERI', 'AGAR', 'FEI1']
self.is2D = True
self.isCrystal = False
self.errors = []
self.updates = []
self.infos = []
def getSubTomoBoundary(processdir, seriesname, axis):
'''
Get the start and end coordinate at a particular axis.
The definition of origin may or may not apply to tomograms
generated outside imod.
'''
fulltomopath = os.path.join(processdir, seriesname + '_full.rec')
subtomopath = os.path.join(processdir, seriesname + '.rec')
fullheader = mrc.readHeaderFromFile(fulltomopath)
subheader = mrc.readHeaderFromFile(subtomopath)
lenkey = axis + 'len'
originkey = axis + 'origin'
mkey = 'm' + axis
# There is a rotation around x-axis in full tomogram
fullorigin = {
'xorigin': fullheader['xorigin'],
'yorigin': fullheader['zorigin'],
'zorigin': fullheader['yorigin']
}
fullm = {
'mx': fullheader['mx'],
'my': fullheader['mz'],
'mz': fullheader['my']
}
# full and sub tomo should have the same pixelsize
pixelsize = subheader[lenkey] / subheader[mkey]
if axis != 'z':
start = int((fullorigin[originkey] - subheader[originkey]) / pixelsize)
else:
# z origin is defined different from x and y
start = -int(
(fullorigin[originkey] + subheader[originkey]) / pixelsize) + int(
fullm[mkey])
end = start + int(subheader[mkey])
return (start, end)
def collectResults(self, imgdata,targetdict):
"""
Overwrite collectResults to do final processing of the
queue job result and commit
"""
#cleanup and reformat image
try:
innamepath=glob.glob(os.path.join(targetdict['outpath'],'*.mrc'))[0]
print innamepath
except IndexError:
apDisplay.printWarning('queued job for %s failed' % (imgdata['filename']))
return
outname=imgdata['filename']+'-'+self.params['alignlabel']+'.mrc'
outnamepath=os.path.join(targetdict['outpath'],outname)
if self.params['border'] != 0:
command=['proc2d',innamepath, outnamepath]
header=mrc.readHeaderFromFile(innamepath)
origx=header['nx']
origy=header['ny']
newx=origx-self.params['border']
newy=origy-self.params['border']
command.append('clip=%d,%d' % (newx,newy))
print command
subprocess.call(command)
command=['proc2d',outnamepath,outnamepath]
command.append('clip=%d,%d' % (origx,origy))
command.append('edgenorm')
print command
subprocess.call(command)
newimg_array = mrc.read(outnamepath)
self.commitAlignedImageToDatabase(imgdata,newimg_array,self.params['alignlabel'])
# return None since everything is committed within this function.
if self.params['hackcopy'] is True:
origpath=imgdata['session']['image path']
archivecopy=os.path.join(origpath,imgdata['filename']+'.orig.mrc')
if os.path.exists(archivecopy) is True:
apDisplay.printMsg('archive copy for %s already exists, so skipping archive' % (archivecopy))
else:
shutil.move(os.path.join(origpath,imgdata['filename']+'.mrc'), archivecopy)
shutil.copyfile(outnamepath, os.path.join(origpath,imgdata['filename']+'.mrc'))
return None
def getMrcFileShape(mrcpath): header = mrc.readHeaderFromFile(mrcpath) return header['shape']
def checkReconVolume(self):
from pyami import mrc
h = mrc.readHeaderFromFile(self.tasklogfile)
if h['amax'] == h['amin']:
apDisplay.printError('Reconstruction gives no real density. Is the mask too tight? If not, consider using larger "hard" value to exclude fewer images in recostruction.',False)
def getSubTomogramSize(self,subtomopath): tomoheader = mrc.readHeaderFromFile(subtomopath) # conversion to int is important for sinedon insert return (int(tomoheader['mx']),int(tomoheader['my']),int(tomoheader['mz']))
def getNumberOfFrames(self, mrcfile): ''' Returns number of frames of an mrc image/image stack ''' mrcheader = mrc.readHeaderFromFile(mrcfile) return max(1,int(mrcheader['nz'].astype(numpy.uint16)))
def getNumberOfFrames(self, mrcfile): mrcheader = mrc.readHeaderFromFile(mrcfile) return max(1,int(mrcheader['nz'].astype(numpy.uint16)))
def shiftMRCStartToZero(filename):
h = mrc.readHeaderFromFile(filename)
if h['nxstart'] != 0 or h['nystart'] !=0:
apDisplay.printMsg("Shifting image header start to zero on %s" %(os.path.basename(filename)))
a = mrc.read(filename)
mrc.write(a, filename)
def getMrcFileShape(mrcpath):
header = mrc.readHeaderFromFile(mrcpath)
return header['shape']
def getNumberOfFrames(self, mrcfile):
'''
Returns number of frames of an mrc image/image stack
'''
mrcheader = mrc.readHeaderFromFile(mrcfile)
return max(1, int(mrcheader['nz'].astype(numpy.uint16)))
from optparse import OptionParser
if __name__ == '__main__':
parser = OptionParser()
parser.add_option("-f", "--file", dest="mrcfile",
help="MRC file", metavar="FILE")
parser.add_option("-c", "--contour", "--threshold", dest="threshold", default=1.0,
help="Contour threshold for density", metavar="#", type="float")
(options, args) = parser.parse_args()
mrcfile = options.mrcfile
if not mrcfile or not os.path.isfile(mrcfile):
parser.print_help()
floatdata = mrc.read(mrcfile)
header = mrc.readHeaderFromFile(mrcfile)
#del floatdata
s = numpy.ones((3,3,3))
print s
print "Median filter"
floatdata = ndimage.median_filter(floatdata, size=3)
print "Closing operation"
booldata = numpy.array(floatdata > options.threshold, dtype=int)
closebooldata = ndimage.morphology.binary_closing(booldata, iterations=3)
floatdata = numpy.where(closebooldata > booldata, floatdata+options.threshold/1.5, floatdata)
mrc.write(numpy.array(closebooldata, dtype=int), "bool.mrc", header)
def getOriginalVolumeShape(self):
origtomopath = self.params['file']
self.origheader = mrc.readHeaderFromFile(origtomopath)
self.origshape = self.origheader['shape']
def start(self):
cleanlist = []
# imod needs the recon files named as .rec It may need some fix later
if self.params['name'] is None:
self.setNewFileName()
apDisplay.printColor("Naming tomogram as: " + self.params['name'],
"cyan")
newtomopath = os.path.join(self.params['rundir'],
self.params['name'] + ".rec")
origtomopath = self.params['file']
origxfpath = self.params['oldxffile']
apParam.createDirectory(self.params['aligndir'])
newxfpath = os.path.join(self.params['aligndir'],
self.params['newxffile'])
order = self.params['order']
voltransform = self.params['transform']
bin = self.params['bin']
self.getImageShapeFromTiltSeries()
self.getOriginalVolumeShape()
if os.path.isfile(newtomopath):
uploaded_before = self.checkExistingFile()
if uploaded_before:
return
else:
currenttomopath = origtomopath
if self.params['full']:
### full tomogram upload, may need to pad to the image size
if self.params['order'] == 'XZY' and not voltransform:
apDisplay.printMsg(
"Default full tomogram orientation with original handness"
)
else:
if voltransform:
apDisplay.printMsg(
"Transforming original tomogram....")
currenttomopath = apImod.transformVolume(
origtomopath, voltransform)
cleanlist.append(currenttomopath)
### padding the XZY tomogram to the image size
currentheader = mrc.readHeaderFromFile(currenttomopath)
currentshape = currentheader['shape']
currentxyshape = currentshape[0], currentshape[2]
imageshape = self.imageshape
if currentxyshape[0] < imageshape[0] / bin or currentxyshape[
1] < imageshape[1] / bin:
currenttomopath = apImod.pad(currenttomopath,
currentxyshape, imageshape,
bin, 'XZY')
cleanlist.append(currenttomopath)
else:
### subtomogram simple upload, just copy file to Tomo folder
if self.params['order'] == 'XYZ' and not voltransform:
apDisplay.printMsg("Default sub tomogram orientation")
else:
if voltransform:
apDisplay.printMsg(
"Transforming original tomogram....")
currenttomopath = apImod.transformVolume(
origtomopath, voltransform)
cleanlist.append(currenttomopath)
### simple upload, just copy file to Tomo folder
apDisplay.printMsg(
"Copying original tomogram to a new location: " + newtomopath)
shutil.copyfile(currenttomopath, newtomopath)
if origxfpath and os.path.isfile(origxfpath):
apDisplay.printMsg(
"Copying original alignment to a new location: " +
newxfpath)
shutil.copyfile(origxfpath, newxfpath)
if self.params['image']:
shutil.copyfile(self.params['image'],
self.params['rundir'] + '/snapshot.png')
### inserting tomogram
tomoheader = mrc.readHeaderFromFile(newtomopath)
self.params['shape'] = tomoheader['shape']
if self.params['full']:
seriesname = "%s_%03d" % (self.params['sessionname'],
self.params['tiltseriesnumber'])
self.params['zprojfile'] = apImod.projectFullZ(
self.params['rundir'], self.params['runname'], seriesname, bin,
True, False)
else:
apTomo.makeMovie(newtomopath)
apTomo.makeProjection(newtomopath)
apTomo.uploadTomo(self.params)
### clean up
for tmpfilepath in cleanlist:
apFile.removeFile(tmpfilepath)
def getOriginalVolumeShape(self):
origtomopath = self.params["file"]
self.origheader = mrc.readHeaderFromFile(origtomopath)
self.origshape = self.origheader["shape"]
print "Bisecting along Y-axis"
y_index = y_linedensity.argmax()
cut_1a = orig1.copy()
cut_1b = orig1.copy()
cut_2a = orig2.copy()
cut_2b = orig2.copy()
cut_1a[:, :y_index, :] = 0
cut_1b[:, y_index:, :] = 0
cut_2a[:, :y_index, :] = 0
cut_2b[:, y_index:, :] = 0
elif z_maxcrossarea == maxcrossarea:
print "Bisecting along Z-axis"
z_index = z_linedensity.argmax()
cut_1a = orig1.copy()
cut_1b = orig1.copy()
cut_2a = orig2.copy()
cut_2b = orig2.copy()
cut_1a[:, :, :z_index] = 0
cut_1b[:, :, z_index:] = 0
cut_2a[:, :, :z_index] = 0
cut_2b[:, :, z_index:] = 0
header = mrc.readHeaderFromFile(file1)
print "Writing %s to file" % (root1 + "-top.mrc")
mrc.write(cut_1a, root1 + "-top.mrc", header)
print "Writing %s to file" % (root1 + "-bot.mrc")
mrc.write(cut_1b, root1 + "-bot.mrc", header)
print "Writing %s to file" % (root2 + "-top.mrc")
mrc.write(cut_2a, root2 + "-top.mrc", header)
print "Writing %s to file" % (root2 + "-bot.mrc")
mrc.write(cut_2b, root2 + "-bot.mrc", header)
def start(self):
cleanlist = []
# imod needs the recon files named as .rec It may need some fix later
if self.params["name"] is None:
self.setNewFileName()
apDisplay.printColor("Naming tomogram as: " + self.params["name"], "cyan")
newtomopath = os.path.join(self.params["rundir"], self.params["name"] + ".rec")
origtomopath = self.params["file"]
origxfpath = self.params["oldxffile"]
apParam.createDirectory(self.params["aligndir"])
newxfpath = os.path.join(self.params["aligndir"], self.params["newxffile"])
order = self.params["order"]
voltransform = self.params["transform"]
bin = self.params["bin"]
self.getImageShapeFromTiltSeries()
self.getOriginalVolumeShape()
if os.path.isfile(newtomopath):
uploaded_before = self.checkExistingFile()
if uploaded_before:
return
else:
currenttomopath = origtomopath
if self.params["full"]:
### full tomogram upload, may need to pad to the image size
if self.params["order"] == "XZY" and not voltransform:
apDisplay.printMsg("Default full tomogram orientation with original handness")
else:
if voltransform:
apDisplay.printMsg("Transforming original tomogram....")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
cleanlist.append(currenttomopath)
### padding the XZY tomogram to the image size
currentheader = mrc.readHeaderFromFile(currenttomopath)
currentshape = currentheader["shape"]
currentxyshape = currentshape[0], currentshape[2]
imageshape = self.imageshape
if currentxyshape[0] < imageshape[0] / bin or currentxyshape[1] < imageshape[1] / bin:
currenttomopath = apImod.pad(currenttomopath, currentxyshape, imageshape, bin, "XZY")
cleanlist.append(currenttomopath)
else:
### subtomogram simple upload, just copy file to Tomo folder
if self.params["order"] == "XYZ" and not voltransform:
apDisplay.printMsg("Default sub tomogram orientation")
else:
if voltransform:
apDisplay.printMsg("Transforming original tomogram....")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
cleanlist.append(currenttomopath)
### simple upload, just copy file to Tomo folder
apDisplay.printMsg("Copying original tomogram to a new location: " + newtomopath)
shutil.copyfile(currenttomopath, newtomopath)
if origxfpath and os.path.isfile(origxfpath):
apDisplay.printMsg("Copying original alignment to a new location: " + newxfpath)
shutil.copyfile(origxfpath, newxfpath)
if self.params["image"]:
shutil.copyfile(self.params["image"], self.params["rundir"] + "/snapshot.png")
### inserting tomogram
tomoheader = mrc.readHeaderFromFile(newtomopath)
self.params["shape"] = tomoheader["shape"]
if self.params["full"]:
seriesname = "%s_%03d" % (self.params["sessionname"], self.params["tiltseriesnumber"])
self.params["zprojfile"] = apImod.projectFullZ(
self.params["rundir"], self.params["runname"], seriesname, bin, True, False
)
else:
apTomo.makeMovie(newtomopath)
apTomo.makeProjection(newtomopath)
apTomo.uploadTomo(self.params)
### clean up
for tmpfilepath in cleanlist:
apFile.removeFile(tmpfilepath)
def getSubTomogramSize(self, subtomopath):
tomoheader = mrc.readHeaderFromFile(subtomopath)
# conversion to int is important for sinedon insert
return (int(tomoheader['mx']), int(tomoheader['my']),
int(tomoheader['mz']))
def getImageDimensions(self, mrcfile):
mrcheader = mrc.readHeaderFromFile(mrcfile)
x = int(mrcheader['nx'].astype(numpy.uint16))
y = int(mrcheader['ny'].astype(numpy.uint16))
return {'x': x, 'y': y}
# integration half box size
self.panel.box = box
self.sizer.Add(self.panel, 1, wx.EXPAND|wx.ALL)
frame.SetSizerAndFit(self.sizer)
self.SetTopWindow(frame)
frame.Show(True)
return True
array = None
if filename is None:
filename = raw_input('Enter file path: ')
if not filename:
array = None
elif filename[-4:] == '.mrc':
h = mrc.readHeaderFromFile(filename)
if h['mz'] == 0:
print 'invalid mz, assumes 1'
h['mz'] = 1
nframes = h['nz']/h['mz']
frame = 0
# 2D image stack
if h['mz'] == 1:
if nframes > 1:
# mrc2014 image stack
frame_str = raw_input('This is an image stack of %d frames.\n Enter 0 to %d to select a frame to load: ' % (nframes,nframes-1))
frame = int(frame_str)
else:
if nframes > 1:
slice_str = raw_input('This is a stack of %d volume.\n Enter 0 to %d to select a slice to load: ' % (nframes,h['nz']-1))
else:
z_maxcrossarea = 0
maxcrossarea = max(x_maxcrossarea, y_maxcrossarea, z_maxcrossarea)
if x_maxcrossarea == maxcrossarea:
print "Bisecting along X-axis"
x_index = x_linedensity.argmax()
cut_1 = orig.copy()
cut_2 = orig.copy()
cut_1[:x_index, :, :] = 0
cut_2[x_index:, :, :] = 0
elif y_maxcrossarea == maxcrossarea:
print "Bisecting along Y-axis"
y_index = y_linedensity.argmax()
cut_1 = orig.copy()
cut_2 = orig.copy()
cut_1[:, :y_index, :] = 0
cut_2[:, y_index:, :] = 0
elif z_maxcrossarea == maxcrossarea:
print "Bisecting along Z-axis"
z_index = z_linedensity.argmax()
cut_1 = orig.copy()
cut_2 = orig.copy()
cut_1[:, :, :z_index] = 0
cut_2[:, :, z_index:] = 0
header = mrc.readHeaderFromFile(filename)
print "Writing %s to file" % (rootname + "-top.mrc")
mrc.write(cut_1, rootname + "-top.mrc", header)
print "Writing %s to file" % (rootname + "-bot.mrc")
mrc.write(cut_2, rootname + "-bot.mrc", header)
def getImageDimensions(self, mrcfile):
mrcheader = mrc.readHeaderFromFile(mrcfile)
x = int(mrcheader["nx"].astype(numpy.uint16))
y = int(mrcheader["ny"].astype(numpy.uint16))
return {"x": x, "y": y}