def testSurface():
array = readMrc()
if array.shape[0] < 2:
array = randomSurface()
print "Shape of array: ", array.shape
tifs = time.time()
surfareabyifs = surfaceAreaByIfs(array, test=True)
print "Surface area by ifs = %.3f pixels"%(surfareabyifs)
fifs = time.time()
tints = time.time()
surfareabyints = surfaceAreaByInts(array, test=True)
print "Surface area by ints = %.3f pixels"%(surfareabyints)
fints = time.time()
import apDisplay
size = float(array.shape[0]*array.shape[1]*array.shape[2])
print ""
print "*** Surface area by ifs = %.3f pixels"%(surfareabyifs)
print apDisplay.timeString((fifs-tifs)), "total time"
print apDisplay.timeString((fifs-tifs)/size), "per voxel"
print ""
print "*** Surface area by ints = %.3f pixels"%(surfareabyints)
print apDisplay.timeString((fints-tints)), "total time"
print apDisplay.timeString((fints-tints)/size), "per voxel"
print ""
def run(self):
t0 = time.time()
imgarray = self.openFile()
self.imgshape = imgarray.shape
self.printImageInfo(imgarray)
coordlist = self.setupCoordList()
ctfdict = {}
self.count = 0
### process image pieces
print "processing %d image pieces" % (len(coordlist))
keys = coordlist.keys()
keys.sort()
for key in keys:
(xstr, ystr) = key.split('x')
x = int(xstr)
y = int(ystr)
self.count += 1
subarray = self.getSubImage(imgarray, x, y)
#self.printImageInfo(subarray)
imgfile = "splitimage-" + key + ".dwn.mrc"
mrc.write(subarray, imgfile)
ctfvalues = None
reproc = 0
edgeblur = 8
while ctfvalues is None and reproc < 3:
ctfvalues = self.processImage(imgfile, edgeblur)
reproc += 1
edgeblur += 2
if ctfvalues is not None:
sys.stderr.write("#")
else:
sys.stderr.write("!")
ctfdict[key] = ctfvalues
apFile.removeFilePattern(imgfile + "*", False)
sys.stderr.write("\n")
### calculate ctf parameters
self.fitPlaneToCtf(ctfdict)
apDisplay.printMsg("Time: %s" %
(apDisplay.timeString(time.time() - t0)))
def run(self):
t0 = time.time()
imgarray = self.openFile()
self.imgshape = imgarray.shape
self.printImageInfo(imgarray)
coordlist = self.setupCoordList()
ctfdict = {}
self.count = 0
### process image pieces
print "processing %d image pieces"%(len(coordlist))
keys = coordlist.keys()
keys.sort()
for key in keys:
(xstr,ystr) = key.split('x')
x = int(xstr)
y = int(ystr)
self.count += 1
subarray = self.getSubImage(imgarray, x, y)
#self.printImageInfo(subarray)
imgfile = "splitimage-"+key+".dwn.mrc"
mrc.write(subarray, imgfile)
ctfvalues = None
reproc = 0
edgeblur = 8
while ctfvalues is None and reproc < 3:
ctfvalues = self.processImage(imgfile, edgeblur)
reproc += 1
edgeblur += 2
if ctfvalues is not None:
sys.stderr.write("#")
else:
sys.stderr.write("!")
ctfdict[key] = ctfvalues
apFile.removeFilePattern(imgfile+"*", False)
sys.stderr.write("\n")
### calculate ctf parameters
self.fitPlaneToCtf(ctfdict)
apDisplay.printMsg("Time: %s"%(apDisplay.timeString(time.time()-t0)))