def readApshDocFile(self, docfile, picklefile):
### eventually add this as apSpider.alignment.readAPSHDocFile()
apDisplay.printMsg("processing alignment doc file " + docfile)
if not os.path.isfile(docfile):
apDisplay.printError("Doc file, " + docfile + " does not exist")
docf = open(docfile, "r")
partlist = []
for line in docf:
data = line.strip().split()
if data[0] == ";":
continue
if len(data) < 15:
continue
"""
2 psi,
3 theta,
4 phi,
5 refNum,
6 particleNum,
7 sumRotation,
8 sumXshift,
9 sumYshift,
10 #refs,
11 anglechange,
12 cross-correlation,
13 currentRotation,
14 currentXshift,
15 currentYshift,
16 currentMirror
"""
partdict = {
'psi': float(data[2]),
'theta': float(data[3]),
'phi': float(data[4]),
'template': int(abs(float(data[5]))),
'num': int(float(data[6])),
'rot': alignment.wrap360(float(data[7])),
'xshift': float(data[8]),
'yshift': float(data[9]),
'mirror': alignment.checkMirror(float(data[16])),
'score': float(data[12]),
}
partlist.append(partdict)
docf.close()
picklef = open(picklefile, "w")
cPickle.dump(partlist, picklef)
picklef.close()
return partlist
def readApshDocFile(self, docfile, picklefile):
### eventually add this as apSpider.alignment.readAPSHDocFile()
apDisplay.printMsg("processing alignment doc file "+docfile)
if not os.path.isfile(docfile):
apDisplay.printError("Doc file, "+docfile+" does not exist")
docf = open(docfile, "r")
partlist = []
for line in docf:
data = line.strip().split()
if data[0] == ";":
continue
if len(data) < 15:
continue
"""
2 psi,
3 theta,
4 phi,
5 refNum,
6 particleNum,
7 sumRotation,
8 sumXshift,
9 sumYshift,
10 #refs,
11 anglechange,
12 cross-correlation,
13 currentRotation,
14 currentXshift,
15 currentYshift,
16 currentMirror
"""
partdict = {
'psi': float(data[2]),
'theta': float(data[3]),
'phi': float(data[4]),
'template': int(abs( float(data[5]) )),
'num': int(float(data[6])),
'rot': alignment.wrap360(float(data[7])),
'xshift': float(data[8]),
'yshift': float(data[9]),
'mirror': alignment.checkMirror( float(data[16]) ),
'score': float(data[12]),
}
partlist.append(partdict)
docf.close()
picklef = open(picklefile, "w")
cPickle.dump(partlist, picklef)
picklef.close()
return partlist
def readRefBasedDocFile(self, docfile, picklefile):
apDisplay.printMsg("processing alignment doc file " + docfile)
if not os.path.isfile(docfile):
apDisplay.printError("Doc file, " + docfile + " does not exist")
docf = open(docfile, "r")
partlist = []
angs = []
shifts = []
for line in docf:
data = line.strip().split()
if data[0][0] == ";":
continue
if len(data) < 6:
continue
templatenum = float(data[1])
angle = alignment.wrap360(float(data[2]))
partdict = {
'num': int(data[0]),
'template': int(abs(templatenum)),
'mirror': bool(data[5]),
'score': float(data[6]),
'rot': angle,
'xshift': float(data[3]),
'yshift': float(data[4]),
}
angs.append(angle)
shift = math.hypot(float(data[3]), float(data[4]))
shifts.append(shift)
partlist.append(partdict)
docf.close()
shifts = numpy.array(shifts, dtype=numpy.float32)
angs = numpy.array(angs, dtype=numpy.float32)
apDisplay.printMsg("Angles = %.3f +/- %.3f" %
(angs.mean(), angs.std()))
apDisplay.printMsg("Shifts = %.3f +/- %.3f" %
(shifts.mean(), shifts.std()))
picklef = open(picklefile, "w")
cPickle.dump(partlist, picklef)
picklef.close()
return partlist
def readRefBasedDocFile(self, docfile, picklefile):
apDisplay.printMsg("processing alignment doc file "+docfile)
if not os.path.isfile(docfile):
apDisplay.printError("Doc file, "+docfile+" does not exist")
docf = open(docfile, "r")
partlist = []
angs = []
shifts = []
for line in docf:
data = line.strip().split()
if data[0][0] == ";":
continue
if len(data) < 6:
continue
templatenum = float(data[1])
angle = alignment.wrap360(float(data[2]))
partdict = {
'num': int(data[0]),
'template': int(abs(templatenum)),
'mirror': bool(data[5]),
'score': float(data[6]),
'rot': angle,
'xshift': float(data[3]),
'yshift': float(data[4]),
}
angs.append(angle)
shift = math.hypot(float(data[3]), float(data[4]))
shifts.append(shift)
partlist.append(partdict)
docf.close()
shifts = numpy.array(shifts, dtype=numpy.float32)
angs = numpy.array(angs, dtype=numpy.float32)
apDisplay.printMsg("Angles = %.3f +/- %.3f"%(angs.mean(), angs.std()))
apDisplay.printMsg("Shifts = %.3f +/- %.3f"%(shifts.mean(), shifts.std()))
picklef = open(picklefile, "w")
cPickle.dump(partlist, picklef)
picklef.close()
return partlist
