def runTestShift(img1name, img2name, imgpath, tiltdiff, coord): img1path = os.path.join(imgpath, img1name) img2path = os.path.join(imgpath, img2name) print img1path print img2path img1 = apImage.binImg(apImage.mrcToArray(img1path),4) img2 = apImage.binImg(apImage.mrcToArray(img2path),4) apImage.arrayToMrc(img1,"img1a-raw.mrc") apImage.arrayToMrc(img2,"img2a-raw.mrc") origin, newpart, snr = apTiltShift.getTiltedCoordinates(img1, img2, tiltdiff, coord) apImage.arrayToJpegPlusPeak(img1, "img1a-guess.jpg", (origin[1], origin[0])) apImage.arrayToJpegPlusPeak(img2, "img2a-guess.jpg", (newpart[1], newpart[0]))
def processTiltPair(self, imgfile1, imgfile2, picks1, picks2, tiltangle, outfile, pixdiam=20.0, tiltaxis=-7.0, msg=True):
"""
Inputs:
imgfile1
imgfile2
picks1, 2xN numpy array
picks2, 2xN numpy array
tiltangle
outfile
Modifies:
outfile
Output:
None, failed
True, success
"""
### pre-load particle picks
if len(picks1) < 10 or len(picks2) < 10:
if msg is True:
apDisplay.printWarning("Not enough particles ot run program on image pair")
return None
### setup tilt data
self.data['theta'] = tiltangle
self.data['shiftx'] = 0.0
self.data['shifty'] = 0.0
self.data['gamma'] = tiltaxis
self.data['phi'] = tiltaxis
self.data['scale'] = 1.0
self.data['pixdiam'] = pixdiam
### open image file 1
img1 = self.openImageFile(imgfile1)
if img1 is None:
apDisplay.printWarning("Could not read image: "+imgfile1)
return None
### open tilt file 2
img2 = self.openImageFile(imgfile2)
if img1 is None:
apDisplay.printWarning("Could not read image: "+imgfile1)
return None
### guess the shift
t0 = time.time()
if msg is True:
apDisplay.printMsg("Refining tilt axis angles")
origin, newpart, snr, bestang = apTiltShift.getTiltedCoordinates(img1, img2, tiltangle, picks1, True, tiltaxis, msg=msg)
self.data['gamma'] = float(bestang)
self.data['phi'] = float(bestang)
if snr < 2.0:
if msg is True:
apDisplay.printWarning("Low confidence in initial shift")
return None
self.currentpicks1 = [origin]
self.currentpicks2 = [newpart]
### search for the correct particles
self.importPicks(picks1, picks2, tight=False, msg=msg)
if len(self.currentpicks1) < 4:
apDisplay.printWarning("Failed to find any particle matches")
return None
self.deleteFirstPick()
self.printData(msg)
for i in range(4):
self.clearBadPicks(msg)
if len(self.currentpicks1) < 5 or len(self.currentpicks2) < 5:
if msg is True:
apDisplay.printWarning("Not enough particles to optimize angles")
return None
self.optimizeAngles(msg)
self.printData(msg)
self.clearBadPicks(msg)
self.clearBadPicks(msg)
if len(self.currentpicks1) < 5 or len(self.currentpicks2) < 5:
if msg is True:
apDisplay.printWarning("Not enough particles to optimize angles")
return None
self.optimizeAngles(msg)
self.printData(msg)
self.clearBadPicks(msg)
self.importPicks(picks1, picks2, tight=False, msg=msg)
self.clearBadPicks(msg)
self.printData(msg)
if len(self.currentpicks1) < 5 or len(self.currentpicks2) < 5:
if msg is True:
apDisplay.printWarning("Not enough particles to optimize angles")
return None
self.optimizeAngles(msg)
self.printData(msg)
self.getOverlap(img1,img2,msg)
if msg is True:
apDisplay.printMsg("Completed alignment of "+str(len(self.currentpicks1))
+" particle pairs in "+apDisplay.timeString(time.time()-t0))
self.saveData(imgfile1, imgfile2, outfile)
self.printData(msg)
return True
def processTiltPair(self,
imgfile1,
imgfile2,
picks1,
picks2,
tiltangle,
outfile,
pixdiam=20.0,
tiltaxis=-7.0,
msg=True):
"""
Inputs:
imgfile1
imgfile2
picks1, 2xN numpy array
picks2, 2xN numpy array
tiltangle
outfile
Modifies:
outfile
Output:
None, failed
True, success
"""
### pre-load particle picks
if len(picks1) < 10 or len(picks2) < 10:
if msg is True:
apDisplay.printWarning(
"Not enough particles ot run program on image pair")
return None
### setup tilt data
self.data['theta'] = tiltangle
self.data['shiftx'] = 0.0
self.data['shifty'] = 0.0
self.data['gamma'] = tiltaxis
self.data['phi'] = tiltaxis
self.data['scale'] = 1.0
self.data['pixdiam'] = pixdiam
### open image file 1
img1 = self.openImageFile(imgfile1)
if img1 is None:
apDisplay.printWarning("Could not read image: " + imgfile1)
return None
### open tilt file 2
img2 = self.openImageFile(imgfile2)
if img1 is None:
apDisplay.printWarning("Could not read image: " + imgfile1)
return None
### guess the shift
t0 = time.time()
if msg is True:
apDisplay.printMsg("Refining tilt axis angles")
origin, newpart, snr, bestang = apTiltShift.getTiltedCoordinates(
img1, img2, tiltangle, picks1, True, tiltaxis, msg=msg)
self.data['gamma'] = float(bestang)
self.data['phi'] = float(bestang)
if snr < 2.0:
if msg is True:
apDisplay.printWarning("Low confidence in initial shift")
return None
self.currentpicks1 = [origin]
self.currentpicks2 = [newpart]
### search for the correct particles
self.importPicks(picks1, picks2, tight=False, msg=msg)
if len(self.currentpicks1) < 4:
apDisplay.printWarning("Failed to find any particle matches")
return None
self.deleteFirstPick()
self.printData(msg)
for i in range(4):
self.clearBadPicks(msg)
if len(self.currentpicks1) < 5 or len(self.currentpicks2) < 5:
if msg is True:
apDisplay.printWarning(
"Not enough particles to optimize angles")
return None
self.optimizeAngles(msg)
self.printData(msg)
self.clearBadPicks(msg)
self.clearBadPicks(msg)
if len(self.currentpicks1) < 5 or len(self.currentpicks2) < 5:
if msg is True:
apDisplay.printWarning(
"Not enough particles to optimize angles")
return None
self.optimizeAngles(msg)
self.printData(msg)
self.clearBadPicks(msg)
self.importPicks(picks1, picks2, tight=False, msg=msg)
self.clearBadPicks(msg)
self.printData(msg)
if len(self.currentpicks1) < 5 or len(self.currentpicks2) < 5:
if msg is True:
apDisplay.printWarning(
"Not enough particles to optimize angles")
return None
self.optimizeAngles(msg)
self.printData(msg)
self.getOverlap(img1, img2, msg)
if msg is True:
apDisplay.printMsg("Completed alignment of " +
str(len(self.currentpicks1)) +
" particle pairs in " +
apDisplay.timeString(time.time() - t0))
self.saveData(imgfile1, imgfile2, outfile)
self.printData(msg)
return True
