def hello(self, im):
" filename is the classavg image "
if self.docfile == "" or self.serfile == "":
self.callTemplates()
filename = im.info['filename']
#print "hello from " + filename
tmp = self.doctemplate.get()
fn = Spiderutils.template2filename(tmp, os.path.basename(filename))
if len(fn) < 1:
return
if not os.path.exists(fn):
print "Unable to find " + fn
return
D = Spiderutils.readdoc(fn, keys='all')
plist = []
files = D.keys()
for f in files:
num = int(D[f][0]) # each element is a list (of column data)
imgfilename = Spiderutils.template2filename(self.serfile, num)
plist.append(imgfilename)
title = "images for class: " + os.path.basename(filename)
newtop = Toplevel(self.top)
m = montage.montage(newtop, imagelist=plist, title=title,
useLabels=0)
m.makeMenus()
m.createMontage()
def getdata(self, filename=None, xcol=None, ycol=None):
if filename == None or filename == "":
filename = self.filename
if self.filename == None or self.filename == "":
return
try:
#D = spiderutils.readSpiderDocFile(filename, [xcol,ycol])
D = Spiderutils.readdoc(filename, keys='all')
except:
print "Unable to get data from %s" % filename
return
keys = D.keys()
if len(keys) < 1:
print "%s contains no data" % filename
return
f = D[keys[0]]
xmin = f[0]
xmax = f[0]
ymin = f[1]
ymax = f[1]
for k in keys:
x = D[k][0]
y = D[k][1]
if x < xmin: xmin = x
elif x > xmax: xmax = x
if y < ymin: ymin = y
elif y > ymax: ymax = y
vector_x = (xmin,xmax)
vector_y = (ymin,ymax)
return (D, vector_x, vector_y)
def readDefocus(filename):
" returns list of (mic#, defocus) pairs (mic=int defocus=string)"
# F = spiderutils.readSpiderDocFile(filename, col_list=(1,2))
F = Spiderutils.readdoc(filename, keys='all')
if F == None: return []
keys = F.keys()
keys.sort()
M = []
for key in keys:
mic = int(F[key][0])
defocus = str(int(F[key][1]))
M.append((mic, defocus))
return M
def readDefocus(filename):
" returns list of (mic#, defocus) pairs (mic=int defocus=string)"
# F = spiderutils.readSpiderDocFile(filename, col_list=(1,2))
F = Spiderutils.readdoc(filename, keys='all')
if F == None: return []
keys = F.keys()
keys.sort()
M = []
for key in keys:
mic = int(F[key][0])
defocus = str(int(F[key][1]))
M.append( (mic, defocus) )
return M
def readdoc(filename, factor=1.0, squared=1):
F = Spiderutils.readdoc(filename, keys='all')
if F == None: return []
roofile = 0
A = []
B = []
C = []
D = []
E = []
keys = F.keys()
keys.sort()
# get the 1st line of data, test if roo (cols 3 & 4 = 1)
k = keys[0]
vals = F[k]
vlen = len(vals)
if vlen < 4:
roofile = 1
else: #
if vals[2] == 1 and vals[3] == 1:
roofile = 1
# get the data
for key in keys:
if roofile:
a = factor * F[key][0]
D.append(a)
else:
freq = F[key][0]
bgd = factor * F[key][1]
sub = factor * F[key][2]
env = factor * F[key][3]
roo = bgd + sub # get original spectrum
if squared == 1:
k = env + bgd
roo = roo * roo # square the spectrum
bgd = bgd * bgd # square the background
sub = roo - bgd # new subtracted curve
env = k * k - bgd # new envelope
A.append(freq)
B.append(bgd)
C.append(sub)
D.append(env)
E.append(roo)
if roofile:
return [D]
else:
return [A, B, C, D, E]
def readdoc(filename, factor=1.0, squared=1):
F = Spiderutils.readdoc(filename, keys='all')
if F == None: return []
roofile = 0
A = []; B = []; C = []; D = []; E = []
keys = F.keys()
keys.sort()
# get the 1st line of data, test if roo (cols 3 & 4 = 1)
k = keys[0]
vals = F[k]
vlen = len(vals)
if vlen < 4:
roofile = 1
else: #
if vals[2] == 1 and vals[3] == 1:
roofile = 1
# get the data
for key in keys:
if roofile:
a = factor * F[key][0]
D.append(a)
else:
freq = F[key][0]
bgd = factor * F[key][1]
sub = factor * F[key][2]
env = factor * F[key][3]
roo = bgd + sub # get original spectrum
if squared == 1:
k = env + bgd
roo = roo * roo # square the spectrum
bgd = bgd * bgd # square the background
sub = roo - bgd # new subtracted curve
env = k*k - bgd # new envelope
A.append(freq)
B.append(bgd)
C.append(sub)
D.append(env)
E.append(roo)
if roofile:
return [D]
else:
return [A,B,C,D,E]
def saveDefocus(self, filename=None):
"save current defocus and file number to a doc file"
if filename != None:
self.savefile = filename
if self.savefile == "":
filename = asksaveasfilename()
if filename == "":
return
self.savefile = filename
self.setFileLabels()
if self.tfedfile == "":
print "defocus data will be saved to %s" % self.savefile
return
micnum = self.filenumber(os.path.basename(self.tfedfile))
defocus = int(float(self.defocus.get()))
outfile = self.savefile
headers = Spiderutils.getDocfileHeaders(outfile)
if os.path.exists(outfile):
# try to replace the line
d = Spiderutils.readdoc(outfile, keys='all')
keys = d.keys()
found = 0
for k in keys:
mic = d[k][0]
if mic == micnum:
d[k][1] = defocus
found = 1
break
if found:
Spiderutils.writedoc(outfile, columns=d)
else:
Spiderutils.writedoc(outfile,
columns=[[micnum], [defocus]],
mode='a')
else:
Spiderutils.writedoc(outfile,
columns=[[micnum], [defocus]],
headers=headers)
#if writedoc(self.savefile, column1=micnum, column2=defocus):
print "defocus %s saved to %s" % (defocus, outfile)
def saveDefocus(self, filename=None):
"save current defocus and file number to a doc file"
if filename != None:
self.savefile = filename
if self.savefile == "":
filename = asksaveasfilename()
if filename == "":
return
self.savefile = filename
self.setFileLabels()
if self.tfedfile == "":
print "defocus data will be saved to %s" % self.savefile
return
micnum = self.filenumber(os.path.basename(self.tfedfile))
defocus = int(float(self.defocus.get()))
outfile = self.savefile
headers = Spiderutils.getDocfileHeaders(outfile)
if os.path.exists(outfile):
# try to replace the line
d = Spiderutils.readdoc(outfile, keys='all')
keys = d.keys()
found = 0
for k in keys:
mic = d[k][0]
if mic == micnum:
d[k][1] = defocus
found = 1
break
if found:
Spiderutils.writedoc(outfile,columns=d)
else:
Spiderutils.writedoc(outfile,columns=[[micnum],[defocus]],mode='a')
else:
Spiderutils.writedoc(outfile,columns=[[micnum],[defocus]],headers=headers)
#if writedoc(self.savefile, column1=micnum, column2=defocus):
print "defocus %s saved to %s" % (defocus, outfile)