def postProcessingRecon(self):
# Full tomogram created with imod is left-handed XZY
voltransform = 'flipx'
origtomopath = os.path.join(self.params['rundir'],
self.seriesname + "_full.rec")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
shutil.move(currenttomopath, origtomopath)
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 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 postProcessingRecon(self):
# Full tomogram created with imod is left-handed XZY
voltransform = "flipx"
origtomopath = os.path.join(self.params["rundir"], self.seriesname + "_full.rec")
currenttomopath = apImod.transformVolume(origtomopath, voltransform)
shutil.move(currenttomopath, origtomopath)