def __correctFrameImage(self,framelist,use_full_raw_area=False): # load raw frames corrected_array = self.sumupFrames(self.rawframe_dir,framelist) if corrected_array is False: return False if save_jpg: numpil.write(corrected,'%s_gain_corrected.jpg' % ddtype,'jpeg') return corrected_array
def __correctFrameImage(self, framelist, use_full_raw_area=False):
# load raw frames
corrected_array = self.sumupFrames(self.rawframe_dir, framelist)
if corrected_array is False:
return False
if save_jpg:
numpil.write(corrected, '%s_gain_corrected.jpg' % ddtype, 'jpeg')
return corrected_array
def array2jpg(pictpath,im,imin=None,imax=None,size=512):
jpgpath = pictpath+'.jpg'
imshape = im.shape
scale = float(size)/imshape[1]
im = apImage.scaleImage(im,scale)
stats = arraystats.all(im)
if imin is not None and imax is not None:
range = (imin,imax)
else:
range = stats['mean']-3*stats['std'],stats['mean']+3*stats['std']
numpil.write(im,jpgpath, format = 'JPEG', limits=range)
def array2jpg(pictpath, im, imin=None, imax=None, size=512):
jpgpath = pictpath + '.jpg'
imshape = im.shape
scale = float(size) / imshape[1]
im = apImage.scaleImage(im, scale)
stats = arraystats.all(im)
if imin is not None and imax is not None:
range = (imin, imax)
else:
range = stats['mean'] - 3 * stats['std'], stats[
'mean'] + 3 * stats['std']
numpil.write(im, jpgpath, format='JPEG', limits=range)
def start(self):
self.params['output_fileformat'] = 'mrc'
newstackname='framealigned.hed'
stackdata=apStack.getStackParticlesFromId(self.params['stackid'])
stackrundata=apStack.getOnlyStackData(self.params['stackid'])
apix=stackrundata['pixelsize']*1e10
kev=stackdata[0]['particle']['image']['scope']['high tension']/1000
origstackpath=os.path.join(stackrundata['path']['path'],stackrundata['name'])
boxsize=stackdata[0]['stackRun']['stackParams']['boxSize']
binning=stackdata[0]['stackRun']['stackParams']['bin']
#determine camera type
cameratype=stackdata[0]['particle']['image']['camera']['ccdcamera']['name']
if self.params['override_camera'] is not None:
cameratype=self.params['override_camera']
#create sorted boxfiles
imagedict={}
masterlist=[]
for particle in stackdata:
parentimage=particle['particle']['image']['filename']
if parentimage in imagedict.keys():
imagedict[parentimage].append(particle['particle'])
else:
imagedict[parentimage]=[]
imagedict[parentimage].append(particle['particle'])
index=len(imagedict[parentimage])-1
masterlist.append({'particle':particle,'key':parentimage,'index':index})
#print masterlist
for key in imagedict:
particlelst=imagedict[key]
parentimage=key
framespath=particlelst[0]['image']['session']['frame path']
print cameratype
if 'Gatan' in cameratype:
#prepare frames
print framespath
#prepare frame directory
framespathname=os.path.join(self.params['rundir'],parentimage+'.frames')
if os.path.exists(framespathname):
pass
else:
os.mkdir(framespathname)
print framespathname
mrcframestackname=parentimage+'.frames.mrc'
print mrcframestackname
nframes=particlelst[0]['image']['camera']['nframes']
print "Extracting frames for", mrcframestackname
for n in range(nframes):
a=mrc.read(os.path.join(framespath,mrcframestackname),n)
numpil.write(a,imfile=os.path.join(framespathname,'RawImage_%d.tif' % (n)), format='tiff')
elif 'DE' in cameratype:
framespathname=os.path.join(framespath,parentimage+'.frames')
print os.getcwd()
print framespathname
#generate DE script call
if os.path.exists(framespathname):
print "found frames for", parentimage
nframes=particlelst[0]['image']['camera']['nframes']
boxname=parentimage + '.box'
boxpath=os.path.join(framespathname,boxname)
shiftdata={'scale':1,'shiftx':0,'shifty':0}
#flatfield references
brightrefpath=particlelst[0]['image']['bright']['session']['image path']
brightrefname=particlelst[0]['image']['bright']['filename']
brightnframes=particlelst[0]['image']['bright']['camera']['nframes']
darkrefpath=particlelst[0]['image']['dark']['session']['image path']
darkrefname=particlelst[0]['image']['dark']['filename']
darknframes=particlelst[0]['image']['dark']['camera']['nframes']
brightref=os.path.join(brightrefpath,brightrefname+'.mrc')
darkref=os.path.join(darkrefpath,darkrefname+'.mrc')
print brightref
print darkref
apBoxer.processParticleData(particle['particle']['image'],boxsize,particlelst,shiftdata,boxpath)
print framespathname
#set appion specific options
self.params['gainreference_filename']=brightref
self.params['gainreference_framecount']=brightnframes
self.params['darkreference_filename']=darkref
self.params['darkreference_framecount']=darknframes
self.params['input_framecount']=nframes
self.params['boxes_fromfiles']=1
#self.params['run_verbosity']=3
self.params['output_invert']=0
#self.params['radiationdamage_apix=']=apix
self.params['radiationdamage_voltage']=kev
#self.params['boxes_boxsize']=boxsize
outpath=os.path.join(self.params['rundir'],key)
if os.path.exists(outpath):
shutil.rmtree(outpath)
os.mkdir(outpath)
command=['deProcessFrames.py']
keys=self.params.keys()
keys.sort()
for key in keys:
param=self.params[key]
#print key, param, type(param)
if param == None or param=='':
pass
else:
option='--%s=%s' % (key,param)
command.append(option)
command.append(outpath)
command.append(framespathname)
print command
if self.params['dryrun'] is False:
subprocess.call(command)
#recreate particle stack
for n,particledict in enumerate(masterlist):
parentimage=particledict['key']
correctedpath=os.path.join(self.params['rundir'],parentimage)
print correctedpath
if os.path.exists(correctedpath):
correctedparticle=glob.glob(os.path.join(correctedpath,('%s.*.region_%03d.*' % (parentimage,particledict['index']))))
print os.path.join(correctedpath,('%s.*.region_%03d.*' % (parentimage,particledict['index'])))
print correctedparticle
#sys.exit()
command=['proc2d',correctedparticle[0], newstackname]
if self.params['output_rotation'] !=0:
command.append('rot=%d' % self.params['output_rotation'])
if self.params['show_DE_command'] is True:
print command
subprocess.call(command)
else:
print "did not find frames for ", parentimage
command=['proc2d', origstackpath, newstackname,('first=%d' % n), ('last=%d' % n)]
print command
if self.params['dryrun'] is False:
subprocess.call(command)
#upload stack
#make keep file
self.params['keepfile']='keepfile.txt'
f=open(self.params['keepfile'],'w')
for n in range(len(masterlist)):
f.write('%d\n' % (n))
f.close()
apStack.commitSubStack(self.params, newname=newstackname)
apStack.averageStack(stack=newstackname)
print "Done!!!!"
def start(self):
self.params['output_fileformat'] = 'mrc'
newstackname = 'framealigned.hed'
stackdata = apStack.getStackParticlesFromId(self.params['stackid'])
stackrundata = apStack.getOnlyStackData(self.params['stackid'])
apix = stackrundata['pixelsize'] * 1e10
kev = stackdata[0]['particle']['image']['scope']['high tension'] / 1000
origstackpath = os.path.join(stackrundata['path']['path'],
stackrundata['name'])
boxsize = stackdata[0]['stackRun']['stackParams']['boxSize']
binning = stackdata[0]['stackRun']['stackParams']['bin']
#determine camera type
cameratype = stackdata[0]['particle']['image']['camera']['ccdcamera'][
'name']
if self.params['override_camera'] is not None:
cameratype = self.params['override_camera']
#create sorted boxfiles
imagedict = {}
masterlist = []
for particle in stackdata:
parentimage = particle['particle']['image']['filename']
if parentimage in imagedict.keys():
imagedict[parentimage].append(particle['particle'])
else:
imagedict[parentimage] = []
imagedict[parentimage].append(particle['particle'])
index = len(imagedict[parentimage]) - 1
masterlist.append({
'particle': particle,
'key': parentimage,
'index': index
})
#print masterlist
for key in imagedict:
particlelst = imagedict[key]
parentimage = key
framespath = particlelst[0]['image']['session']['frame path']
print cameratype
if 'Gatan' in cameratype:
#prepare frames
print framespath
#prepare frame directory
framespathname = os.path.join(self.params['rundir'],
parentimage + '.frames')
if os.path.exists(framespathname):
pass
else:
os.mkdir(framespathname)
print framespathname
mrcframestackname = parentimage + '.frames.mrc'
print mrcframestackname
nframes = particlelst[0]['image']['camera']['nframes']
print "Extracting frames for", mrcframestackname
for n in range(nframes):
a = mrc.read(os.path.join(framespath, mrcframestackname),
n)
numpil.write(a,
imfile=os.path.join(framespathname,
'RawImage_%d.tif' % (n)),
format='tiff')
elif 'DE' in cameratype:
framespathname = os.path.join(framespath,
parentimage + '.frames')
print os.getcwd()
print framespathname
#generate DE script call
if os.path.exists(framespathname):
print "found frames for", parentimage
nframes = particlelst[0]['image']['camera']['nframes']
boxname = parentimage + '.box'
boxpath = os.path.join(framespathname, boxname)
shiftdata = {'scale': 1, 'shiftx': 0, 'shifty': 0}
#flatfield references
brightrefpath = particlelst[0]['image']['bright']['session'][
'image path']
brightrefname = particlelst[0]['image']['bright']['filename']
brightnframes = particlelst[0]['image']['bright']['camera'][
'nframes']
darkrefpath = particlelst[0]['image']['dark']['session'][
'image path']
darkrefname = particlelst[0]['image']['dark']['filename']
darknframes = particlelst[0]['image']['dark']['camera'][
'nframes']
brightref = os.path.join(brightrefpath, brightrefname + '.mrc')
darkref = os.path.join(darkrefpath, darkrefname + '.mrc')
print brightref
print darkref
apBoxer.processParticleData(particle['particle']['image'],
boxsize, particlelst, shiftdata,
boxpath)
print framespathname
#set appion specific options
self.params['gainreference_filename'] = brightref
self.params['gainreference_framecount'] = brightnframes
self.params['darkreference_filename'] = darkref
self.params['darkreference_framecount'] = darknframes
self.params['input_framecount'] = nframes
self.params['boxes_fromfiles'] = 1
#self.params['run_verbosity']=3
self.params['output_invert'] = 0
#self.params['radiationdamage_apix=']=apix
self.params['radiationdamage_voltage'] = kev
#self.params['boxes_boxsize']=boxsize
outpath = os.path.join(self.params['rundir'], key)
if os.path.exists(outpath):
shutil.rmtree(outpath)
os.mkdir(outpath)
command = ['deProcessFrames.py']
keys = self.params.keys()
keys.sort()
for key in keys:
param = self.params[key]
#print key, param, type(param)
if param == None or param == '':
pass
else:
option = '--%s=%s' % (key, param)
command.append(option)
command.append(outpath)
command.append(framespathname)
print command
if self.params['dryrun'] is False:
subprocess.call(command)
#recreate particle stack
for n, particledict in enumerate(masterlist):
parentimage = particledict['key']
correctedpath = os.path.join(self.params['rundir'], parentimage)
print correctedpath
if os.path.exists(correctedpath):
correctedparticle = glob.glob(
os.path.join(correctedpath,
('%s.*.region_%03d.*' %
(parentimage, particledict['index']))))
print os.path.join(correctedpath,
('%s.*.region_%03d.*' %
(parentimage, particledict['index'])))
print correctedparticle
#sys.exit()
command = ['proc2d', correctedparticle[0], newstackname]
if self.params['output_rotation'] != 0:
command.append('rot=%d' % self.params['output_rotation'])
if self.params['show_DE_command'] is True:
print command
subprocess.call(command)
else:
print "did not find frames for ", parentimage
command = [
'proc2d', origstackpath, newstackname, ('first=%d' % n),
('last=%d' % n)
]
print command
if self.params['dryrun'] is False:
subprocess.call(command)
#upload stack
#make keep file
self.params['keepfile'] = 'keepfile.txt'
f = open(self.params['keepfile'], 'w')
for n in range(len(masterlist)):
f.write('%d\n' % (n))
f.close()
apStack.commitSubStack(self.params, newname=newstackname)
apStack.averageStack(stack=newstackname)
print "Done!!!!"
