def start(self):
self.setFileName()
scale = float(self.params['oldapix'])/self.params['newapix']
mrcname = os.path.join(self.params['rundir'], self.params['name']+".mrc")
origmodel = self.params['file']
if os.path.isfile(mrcname):
apDisplay.printError("File exists")
if (abs(self.params['oldapix'] - self.params['newapix']) > 1.0e-2 or
abs(self.params['oldbox'] - self.params['newbox']) > 1.0e-1):
### rescale old model to a new size
apDisplay.printWarning("rescaling original model to a new size")
scale = float(self.params['oldapix'])/self.params['newapix']
apDisplay.printMsg("rescaling model by scale factor of %.4f"%(scale))
apVolume.rescaleVolume(origmodel, mrcname,
self.params['oldapix'], self.params['newapix'], self.params['newbox'])
else:
### simple upload, just copy file to models folder
apDisplay.printMsg("copying original model to a new location: "+mrcname)
shutil.copyfile(origmodel, mrcname)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['newapix'])
### render chimera images of model
contour = self.params['contour']
if self.params['mass'] is not None:
apChimera.setVolumeMass(mrcname, self.params['newapix'], self.params['mass'])
contour = 1.0
apChimera.renderSnapshots(mrcname, contour=contour,
zoom=self.params['zoom'], sym=self.params['symdata']['eman_name'])
self.insertModel(mrcname)
def processVolume(self, spivolfile, iternum=0):
### set values
apix = apStack.getStackPixelSizeFromStackId(
self.params['tiltstackid']) * self.params['tiltbin']
boxsize = self.getBoxSize()
rawspifile = os.path.join(
self.params['rundir'],
"rawvolume%s-%03d.spi" % (self.timestamp, iternum))
mrcvolfile = os.path.join(
self.params['rundir'],
"volume%s-%03d.mrc" % (self.timestamp, iternum))
lowpass = self.params['lowpassvol']
### copy original to raw file
shutil.copy(spivolfile, rawspifile)
### convert to mrc
emancmd = ("proc3d " + spivolfile + " " + mrcvolfile +
" norm=0,1 apix=" + str(apix))
apEMAN.executeEmanCmd(emancmd, verbose=False)
### median filter
rawvol = mrc.read(mrcvolfile)
medvol = ndimage.median_filter(rawvol, size=self.params['median'])
mrc.write(medvol, mrcvolfile)
### low pass filter
emancmd = ("proc3d " + mrcvolfile + " " + mrcvolfile +
" center norm=0,1 apix=" + str(apix) + " lp=" +
str(lowpass))
apEMAN.executeEmanCmd(emancmd, verbose=False)
### set origin
emancmd = "proc3d " + mrcvolfile + " " + mrcvolfile + " origin=0,0,0 "
apEMAN.executeEmanCmd(emancmd, verbose=False)
### mask volume
emancmd = "proc3d " + mrcvolfile + " " + mrcvolfile + " mask=" + str(
self.params['radius'])
apEMAN.executeEmanCmd(emancmd, verbose=False)
### convert to spider
apFile.removeFile(spivolfile)
emancmd = "proc3d " + mrcvolfile + " " + spivolfile + " spidersingle"
apEMAN.executeEmanCmd(emancmd, verbose=False)
### image with chimera
if self.params['skipchimera'] is False:
if self.params['mass'] is not None:
apDisplay.printMsg("Using scale by mass method")
apChimera.setVolumeMass(mrcvolfile,
apix=apix,
mass=self.params['mass'])
apChimera.renderSnapshots(mrcvolfile, self.params['contour'],
self.params['zoom'], 'c1')
return mrcvolfile
def start(self):
mrcfile = self.params['file']
### bin the volume
if self.params['bin'] is not None and self.params['bin'] > 1:
apDisplay.printMsg("Binning volume")
newmrcfile = os.path.join(os.getcwd(), "binned.mrc")
voldata = mrc.read(mrcfile)
voldata = imagefun.bin3(voldata, self.params['bin'])
mrc.write(voldata, newmrcfile)
del voldata
self.params['apix'] *= self.params['bin']
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### scale by mass
if self.params['mass'] is not None:
apDisplay.printMsg("Using scale by mass method")
newmrcfile = os.path.join(os.getcwd(), "setmass.mrc")
shutil.copy(self.params['file'], newmrcfile)
apChimera.setVolumeMass(newmrcfile, apix=self.params['apix'], mass=self.params['mass'])
self.params['contour'] = 1.0
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### print stats
box = apVolume.getModelDimensions(mrcfile)
apDisplay.printColor("Box: %d Apix: %.2f File: %s"%
(box, self.params['apix'], os.path.basename(mrcfile)), "green")
### animation
if self.params['type'] != "snapshot":
apDisplay.printMsg("Creating animation")
apChimera.renderAnimation(mrcfile, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.params['sym'],
color=self.params['color'], xvfb=self.params['xvfb'],
name=self.params['file'], silhouette=self.params['silhouette'])
### snapshot
if self.params['type'] != "animate":
apDisplay.printMsg("Creating snapshots")
apChimera.renderSnapshots(mrcfile, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.params['sym'],
color=self.params['color'], xvfb=self.params['xvfb'],
pdb=self.params['pdb'], name=self.params['file'],
silhouette=self.params['silhouette'])
### clean up
if self.params['mass'] is not None or self.params['bin'] is not None:
images = glob.glob(mrcfile+"*")
for img in images:
newimg = re.sub(mrcfile, self.params['file'], img)
shutil.move(img, newimg)
apFile.removeFile(mrcfile)
def processVolume(self, spivolfile, iternum=0):
### set values
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin']
boxsize = self.getBoxSize()
rawspifile = os.path.join(self.params['rundir'], "rawvolume%s-%03d.spi"%(self.timestamp, iternum))
mrcvolfile = os.path.join(self.params['rundir'], "volume%s-%03d.mrc"%(self.timestamp, iternum))
lowpass = self.params['lowpassvol']
### copy original to raw file
shutil.copy(spivolfile, rawspifile)
### convert to mrc
emancmd = ("proc3d "+spivolfile+" "+mrcvolfile+" norm=0,1 apix="+str(apix))
apEMAN.executeEmanCmd(emancmd, verbose=False)
### median filter
rawvol = mrc.read(mrcvolfile)
medvol = ndimage.median_filter(rawvol, size=self.params['median'])
mrc.write(medvol, mrcvolfile)
### low pass filter
emancmd = ("proc3d "+mrcvolfile+" "+mrcvolfile+" center norm=0,1 apix="
+str(apix)+" lp="+str(lowpass))
apEMAN.executeEmanCmd(emancmd, verbose=False)
### set origin
emancmd = "proc3d "+mrcvolfile+" "+mrcvolfile+" origin=0,0,0 "
apEMAN.executeEmanCmd(emancmd, verbose=False)
### mask volume
emancmd = "proc3d "+mrcvolfile+" "+mrcvolfile+" mask="+str(self.params['radius'])
apEMAN.executeEmanCmd(emancmd, verbose=False)
### convert to spider
apFile.removeFile(spivolfile)
emancmd = "proc3d "+mrcvolfile+" "+spivolfile+" spidersingle"
apEMAN.executeEmanCmd(emancmd, verbose=False)
### image with chimera
if self.params['skipchimera'] is False:
if self.params['mass'] is not None:
apDisplay.printMsg("Using scale by mass method")
apChimera.setVolumeMass(mrcvolfile, apix=apix, mass=self.params['mass'])
apChimera.renderSnapshots(mrcvolfile, self.params['contour'], self.params['zoom'], 'c1')
return mrcvolfile
def start(self):
self.setFileName()
scale = float(self.params['oldapix']) / self.params['newapix']
mrcname = os.path.join(self.params['rundir'],
self.params['name'] + ".mrc")
origmodel = self.params['file']
if os.path.isfile(mrcname):
apDisplay.printError("File exists")
if (abs(self.params['oldapix'] - self.params['newapix']) > 1.0e-2 or
abs(self.params['oldbox'] - self.params['newbox']) > 1.0e-1):
### rescale old model to a new size
apDisplay.printWarning("rescaling original model to a new size")
scale = float(self.params['oldapix']) / self.params['newapix']
apDisplay.printMsg("rescaling model by scale factor of %.4f" %
(scale))
apVolume.rescaleVolume(origmodel, mrcname, self.params['oldapix'],
self.params['newapix'],
self.params['newbox'])
else:
### simple upload, just copy file to models folder
apDisplay.printMsg("copying original model to a new location: " +
mrcname)
shutil.copyfile(origmodel, mrcname)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['newapix'])
### render chimera images of model
contour = self.params['contour']
if self.params['mass'] is not None:
apChimera.setVolumeMass(mrcname, self.params['newapix'],
self.params['mass'])
contour = 1.0
apChimera.renderSnapshots(mrcname,
contour=contour,
zoom=self.params['zoom'],
sym=self.params['symdata']['eman_name'])
self.insertModel(mrcname)
def start(self):
self.apix = None
self.mass = None
self.setFileName()
mrcname = self.params['name'] + ".mrc"
ccp4name = self.params['name'] + ".ccp4"
### get emdb from web
emdbfile = self.fetchEMDB(self.params['emdbid'], ccp4name)
### create density from emdb
self.getXMLInfoFromEMDB(self.params['emdbid'])
emancmd = ("proc3d " + ccp4name + " " + mrcname)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
apFile.removeFile(ccp4name)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.apix)
### lowpass filter, do both atan2 and Gaussian filter to sum up to requested lowpass
### total lowpass = sqrt( lp1^2 + lp2^2 )
if self.params['lowpass'] is not None:
lp = self.params['lowpass'] / math.sqrt(2.0)
emancmd = "proc3d %s %s apix=%.3f origin=0,0,0 norm=0,1 " % (
mrcname, mrcname, self.apix)
if self.params['lowpass'] is not None:
emancmd += "tlp=%.2f lp=%.2f" % (lp, lp)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
if self.mass is not None:
apChimera.setVolumeMass(mrcname, apix=self.apix, mass=self.mass)
### chimera imaging
apChimera.renderSnapshots(mrcname,
contour=1.0,
zoom=1.0,
sym=self.params['symdata']['eman_name'])
### upload it
self.uploadDensity(mrcname)
def start(self):
self.apix = None
self.mass = None
self.setFileName()
mrcname = self.params['name']+".mrc"
ccp4name = self.params['name']+".ccp4"
### get emdb from web
emdbfile = self.fetchEMDB(self.params['emdbid'], ccp4name)
### create density from emdb
self.getXMLInfoFromEMDB(self.params['emdbid'])
emancmd = ("proc3d "+ccp4name+" "+mrcname)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
apFile.removeFile(ccp4name)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.apix)
### lowpass filter, do both atan2 and Gaussian filter to sum up to requested lowpass
### total lowpass = sqrt( lp1^2 + lp2^2 )
if self.params['lowpass'] is not None:
lp = self.params['lowpass']/math.sqrt(2.0)
emancmd = "proc3d %s %s apix=%.3f origin=0,0,0 norm=0,1 " %(mrcname, mrcname, self.apix)
if self.params['lowpass'] is not None:
emancmd += "tlp=%.2f lp=%.2f" % (lp, lp)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
if self.mass is not None:
apChimera.setVolumeMass(mrcname, apix=self.apix, mass=self.mass)
### chimera imaging
apChimera.renderSnapshots(mrcname, contour=1.0, zoom=1.0, sym=self.params['symdata']['eman_name'])
### upload it
self.uploadDensity(mrcname)
def start(self):
mrcfile = self.params['file']
### bin the volume
if self.params['bin'] is not None and self.params['bin'] > 1:
apDisplay.printMsg("Binning volume")
newmrcfile = os.path.join(os.getcwd(), "binned.mrc")
voldata = mrc.read(mrcfile)
voldata = imagefun.bin3(voldata, self.params['bin'])
mrc.write(voldata, newmrcfile)
del voldata
self.params['apix'] *= self.params['bin']
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### scale by mass
if self.params['mass'] is not None:
apDisplay.printMsg("Using scale by mass method")
newmrcfile = os.path.join(os.getcwd(), "setmass.mrc")
shutil.copy(self.params['file'], newmrcfile)
apChimera.setVolumeMass(newmrcfile,
apix=self.params['apix'],
mass=self.params['mass'])
self.params['contour'] = 1.0
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### print stats
box = apVolume.getModelDimensions(mrcfile)
apDisplay.printColor(
"Box: %d Apix: %.2f File: %s" %
(box, self.params['apix'], os.path.basename(mrcfile)), "green")
### animation
if self.params['type'] != "snapshot":
apDisplay.printMsg("Creating animation")
apChimera.renderAnimation(mrcfile,
contour=self.params['contour'],
zoom=self.params['zoom'],
sym=self.params['sym'],
color=self.params['color'],
xvfb=self.params['xvfb'],
name=self.params['file'],
silhouette=self.params['silhouette'])
### snapshot
if self.params['type'] != "animate":
apDisplay.printMsg("Creating snapshots")
apChimera.renderSnapshots(mrcfile,
contour=self.params['contour'],
zoom=self.params['zoom'],
sym=self.params['sym'],
color=self.params['color'],
xvfb=self.params['xvfb'],
pdb=self.params['pdb'],
name=self.params['file'],
silhouette=self.params['silhouette'])
### clean up
if self.params['mass'] is not None or self.params['bin'] is not None:
images = glob.glob(mrcfile + "*")
for img in images:
newimg = re.sub(mrcfile, self.params['file'], img)
shutil.move(img, newimg)
apFile.removeFile(mrcfile)
