Created
May 13, 2013 16:25
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A script to obtain acquisition parameters from [OME XML](http://www.openmicroscopy.org/site/support/ome-model/) files created by Prairie View.
Prairie View is a microscope acquisition software for multiphoton microscopes by [Prairie Technologies](http://www.prairie-technologies.com/products/photon/Ultima.html).
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#! /usr/bin/env python | |
#pyPrairieTiffXMLparams.py | |
#Created by James B. Ackman 4/1/2011 | |
''' | |
A tool to obtain relevant experimental parameters from a Prairie View (microscope acquisition program from Prairie Technologies) | |
formatted XML file contained with folders of Prairie View acquired TIFFs. Output is to stdout as well as a log file in the users python home directory. | |
''' | |
import os, sys, wx | |
from xml.dom import minidom | |
rootdir=os.getcwd() | |
class MyApp(wx.App): | |
def OnInit(self): | |
# Args below are: parent, question, dialog title, default answer | |
dd = wx.DirDialog(None, "Select directory to open", "~/", 0, (10, 10), wx.Size(400, 300)) | |
ret = dd.ShowModal() | |
if ret == wx.ID_OK: | |
#print('You selected: %s\n' % dd.GetPath()) | |
selectedDir.append(dd.GetPath()) | |
else: | |
print('You clicked cancel') | |
dd.Destroy() | |
return True | |
selectedDir = [] | |
app = MyApp(redirect = 0) | |
app.MainLoop() | |
print selectedDir[0] | |
#--Parse relevant experimental parameters from OME XML file------------------------------------- | |
#fnm = "/Users/ackman/Desktop/TSeries-03232011-1321-003.xml" | |
splitpath=os.path.split(str(selectedDir[0])) | |
fname = splitpath[1] + '.xml' | |
fnm = os.path.join(str(selectedDir[0]),fname) | |
f = open(fnm) | |
xmldoc = minidom.parse(f) | |
seqtype = xmldoc.getElementsByTagName('Sequence')[0].getAttribute('type') | |
datetime = xmldoc.getElementsByTagName('PVScan').item(0).getAttribute('date') | |
frlist = xmldoc.getElementsByTagName('Frame') | |
nframes = frlist.length | |
if nframes > 1: | |
keylist = frlist[0].getElementsByTagName('Key') | |
nodes = len(keylist) | |
nchannels = len(frlist[0].getElementsByTagName('File')) | |
headers = ['filename'] | |
data = [fname] | |
headers.append('sequencetype') | |
data.append(str(seqtype)) | |
headers.append('nchannels') | |
data.append(nchannels) | |
headers.append('datetime') | |
data.append(str(datetime)) | |
L = ['objectiveLens','pixelsPerLine','linesPerFrame','frameAveraging','framePeriod','scanlinePeriod','dwellTime','positionCurrent_XAxis','positionCurrent_YAxis','positionCurrent_ZAxis','opticalZoom','micronsPerPixel_XAxis','micronsPerPixel_YAxis'] | |
for i in range(nodes): | |
keyname = keylist.item(i).getAttribute('key') | |
if keyname in L: | |
val = keylist.item(i).getAttribute('value') | |
#headers = headers + '\t' + keyname | |
headers.append(str(keyname)) | |
#data = data + '\t' + val | |
data.append(str(val)) | |
#print keyname + '\t' + val | |
if str(keyname) == 'framePeriod': | |
#print keyname | |
framerate = 1/float(val) | |
#print framerate | |
#print str(framerate) | |
headers.append('framerate') | |
data.append(framerate) | |
#add no.of.frames to the header and data list | |
headers.append('nframes') | |
data.append(nframes) | |
#add the movie length to the header and data list | |
ind = headers.index('framePeriod') | |
mov_length = float(data[ind]) * nframes | |
headers.append('mov_length.s') | |
data.append(mov_length) | |
#--Format for printing to stdout and to log file---------------------------------------------- | |
pheaders = headers[0] | |
pdata = data[0] | |
for i in range(1,len(headers)): | |
pheaders = pheaders + '\t' + headers[i] | |
pdata = pdata + '\t' + str(data[i]) | |
print pheaders | |
print pdata | |
logfile = 'log_expParams.txt' | |
logfilepath=os.path.join(rootdir, logfile) | |
if os.path.isfile(logfilepath): | |
log = open(logfilepath,'a') | |
print >> log, pdata | |
else: | |
log = open(logfilepath,'w') | |
print >> log, pheaders | |
print >> log, pdata | |
log.close() |
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