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 GetIconName(self):
if not self.IsExpandable():
name, ext = os.path.splitext(self.path)
if ext in ['.py']: #, '.pyc','.pyo']:
return "python"
if ext.lower() in self.imagetypes:
return "image"
typ = Spiderutils.istextfile(self.path)
if typ == 1:
if Spiderutils.isSpiderDocfile(self.path):
return "docfile"
elif Spiderutils.isSpiderBatchfile(self.path):
return "procfile"
elif Spiderutils.isSpiderProcedurefile(self.path):
return "procfile"
else:
return "text"
elif typ == -1:
return "unknown"
spi = Spiderutils.isSpiderBin(self.path)
if spi == "image" or spi == "Fourier" or spi == "stack":
return "spider"
elif spi == "volume":
return "volume"
return "binary" # i.e. a non-spider binary file
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 callTemplates(self):
gtwin = Toplevel(self.top)
self.getTemplates(gtwin)
self.top.wait_window(gtwin) # wait til template window gone
# if they typed in w/o asterisks..
doc = self.doctemplate.get()
if len(doc) > 0:
self.docfile = doc
if string.find(doc, "*") < 0:
tmp = Spiderutils.name2template(doc)
self.doctemplate.set(tmp)
ser = self.sertemplate.get()
if len(ser) > 0:
self.serfile = ser
if string.find(ser, "*") < 0:
tmp = Spiderutils.name2template(ser)
self.sertemplate.set(tmp)
def writedoc(filename, column1=1, column2=0):
column1 = integer(column1)
column2 = integer(column2)
# if file already exists
if os.path.exists(filename):
# if it's a doc file, try to get the last key
if Spiderutils.isSpiderDocfile(filename):
lastline = getoutput("tail -1 %s" % filename)
if len(lastline) > 0:
key = 1 + int(string.split(lastline)[0])
else:
key = 1
else:
# if it's not a doc file...
os.remove(filename)
key = 1
data = "%5d 2 %11d% 11d\n" % (key, column1, column2)
try:
fp = open(filename, 'a') # append
fp.write(data)
fp.close()
except:
print "unable to write to %s" % filename
return 0
# if it's a new file
else:
try:
fp = open(filename, 'w')
fname = os.path.basename(filename)
ext = os.path.splitext(filename)[1]
ext = ext[1:] # remove dot
date, time, id = Spiderutils.nowisthetime()
h = " ;ctf/%s %s AT %s %s\n" % (ext, date, time, fname)
fp.write(h)
fp.write(" ; / MICROGRAPH DEFOCUS\n")
key = 1
data = "%5d 2 %11d %11d\n" % (key, column1, column2)
fp.write(data)
fp.close()
except:
print "unable to create %s" % filename
return 0
return 1
def setTemplates(self, parent, which='doc'):
filename = askopenfilename(parent=parent, filetypes=self.filetypes)
if len(filename) < 1:
return
tmp = Spiderutils.name2template(filename)
if which == 'doc':
self.doctemplate.set(tmp)
else:
self.sertemplate.set(tmp)
def saveSelectedMarkers(self, filename=None):
if self.selectedPolygon == "":
self.statusMessage("no polygon selected")
return
if filename == None:
filename = asksaveasfilename(title="Save points into a doc file")
if len(filename) == 0:
return
print filename
if type(filename) == type((1, 2)):
print 'filename is a tuple!'
poly = self.Polygons[self.selectedPolygon]
e = poly.elements
e.sort()
E = []
# make header for doc file and column headings
E.append(Spiderutils.makeDocfileHeader(filename))
xaxis = self.xaxisVar.get()
if xaxis == "": xaxis = 'x axis'
if len(xaxis) > 11:
xaxis = xaxis[:11] # just use first 11 chars
else:
xaxis = string.center(xaxis, 11)
yaxis = self.yaxisVar.get()
if yaxis == "": yaxis = 'y axis'
if len(yaxis) > 11:
yaxis = yaxis[:11] # just use first 11 chars
else:
yaxis = string.center(yaxis, 11)
keyhdr = string.center('keys', 11)
E.append(" ; / %s %s %s\n" % (keyhdr, xaxis, yaxis))
n = len(e)
for i in range(n):
key = i + 1
val = e[i]
x, y = self.D[val][0], self.D[val][1]
line = "%5d %2d %11.1f %11f %11f\n" % (key, 3, float(e[i]), x, y)
E.append(line)
try:
fp = open(filename, 'w')
fp.writelines(E)
fp.close()
self.statusMessage('Data written to %s' % filename)
except:
self.statusMessage('ERROR: unable to write to %s' % filename,
timeout=0)
def getSpiderInfo(self, filename):
info = Spiderutils.spiderInfo(filename)
if info == 0:
return ""
type = info[0]
dims = info[1]
infotxt = os.path.basename(filename) + "\n"
infotxt += "Spider %s file %s\n" % (type, str(dims))
if len(info) > 2:
stats = info[2]
infotxt += "max %5.4f, min %5.4f, avg %5.4f, stdev %5.4f\n" % (
stats[0], stats[1], stats[2], stats[3])
return infotxt
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 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 processargs(args):
" returns (serverflag, filelist, directory) "
serverflag = 0
readall = 0
filenames = []
cwd = os.getcwd()
for item in args:
if item == '-s':
serverflag = 1
elif item == '-h' or item == '-help':
helpmessage()
elif os.path.isdir(item):
# qview dir : reads all files in directory, but
# qview * : should not read subdirectories
if len(filenames) > 0:
continue
cwd = os.path.abspath(item)
os.chdir(cwd)
filenames = os.listdir(os.getcwd())
break
else:
filenames.append(item)
if filenames == []:
helpmessage()
if readall:
files = os.listdir(os.getcwd())
filenames = []
for file in files:
if not os.path.exists(file): # why is this needed?
continue
# only include binary files
if not os.path.isdir(file) \
and not Spiderutils.istextfile(file) \
and file[0] != '.':
filenames.append(file)
if len(filenames) == 0:
print "no images found in %s" % os.getcwd()
sys.exit()
return (serverflag, filenames, cwd)
def OnDoubleClick(self):
"""Called on a double-click on the icon."""
self.status.set(self.path)
# Directories: list them in window
if os.path.isdir(self.path):
dirmax = int(self.textbox.limits[3].get())
dirsize = os.path.getsize(self.path)
if dirsize > dirmax:
basename = os.path.basename(self.path)
txt = "%s may contain a very large number of files.\nDisplay anyway?" % (
basename)
if not askyesno("Warning", txt):
return
cmd = "ls -lF %s " % self.path
out = getoutput(cmd)
filelisting = self.path + "\n" + out
self.textbox.clear()
self.textbox.settext(filelisting)
# view text files in window (sometimes pdfs slip thru)
elif self.ext != ".pdf" and Spiderutils.istextfile(self.path):
# check if html files are sent to browser
if self.ext == ".html" or self.ext == ".htm":
browser = self.textbox.limits[4].get()
if browser:
webbrowser.open(self.path)
return
textmax = self.textbox.limits[2]
tmax = int(textmax.get())
textsize = os.path.getsize(self.path)
if textsize > tmax:
basename = os.path.basename(self.path)
txt = "%s is %d bytes.\nDisplay anyway?" % (basename, textsize)
if not askyesno("Warning", txt):
return
try:
fp = open(self.path, 'r')
B = fp.readlines()
except:
pass
fp.close()
self.textbox.clear()
for line in B:
self.textbox.component('text').insert(END, str(line))
# binaries
else:
spidertype = Spiderutils.isSpiderBin(self.path)
if spidertype != 0: #== "image":
infotxt = self.getSpiderInfo(self.path)
self.textbox.clear()
self.textbox.component('text').insert(END, infotxt)
if spidertype == "image":
self.putImage(self.path, clear=0)
elif self.ext.lower() in self.imagetypes:
self.putImage(self.path)