Script for importing data file from WinEDR to MATLAB

I put this script together a few years ago for importing data from WinEDR into MATLAB:

	function [data, h] = import_edr(file)
	% function [data, h] = import_edr(file)
	%
	% Imports .edr file to matrix
	% for use with files output by WinEDR,
	% http://spider.science.strath.ac.uk/sipbs/page.php?show=software_ses
	% but created independently
	%
	% ---------------inputs------------------------------
	% file .edr file name ( e.g. 'File_001.EDR')
	%
	% ---------------outputs-----------------------------
	% data m x (n+1) matrix of data, where n is number of channels
	% and m is total number of samples
	% h structure array with header data
	%
	% created by Peter Weir, California Institute of Technology, June, 2007
	% no guarantees
	% Adapted from import_abf by Michele Giugliano (http://www.giugliano.info)
	if ~strncmpi(fliplr(file),'rde.',4);
	file = strcat(file,'.EDR');
	end
	fid = fopen(file);
	num_left = 2048;
	while ~feof(fid)
	s = fgetl(fid);
	num_left = num_left-length(s);
	if num_left<0, break, end
	k = strfind(s,'=');
	if ~(isempty(k))
	key = s(1:k-1);
	if strncmp(key,'YN',2) | strncmp(key,'YU',2) | strcmp(key,'TU') | strcmp(key,'ID') | strcmp(key,'BAK') | strcmp(key,'WCPFNAM')
	h.(key) = s(k+1:length(s));
	else
	h.(key) = str2num(s(k+1:length(s)));
	end
	end
	end
	fseek(fid, h.NBH, 'bof');
	data = fread(fid, h.NP, 'short');
	data = reshape(data,h.NC,h.NP/h.NC)';
	for Ch = 0:h.NC-1
	YCFCh = strcat('YCF',int2str(Ch));
	data(:,Ch+1) = (h.AD/((h.ADCMAX+1)*h.(YCFCh)))*data(:,Ch+1);
	end
	time = [0:h.DT:h.DT*(h.NP/h.NC-1)];
	data = [time' data];
	fclose(fid);

view raw import_edr.m hosted with ❤ by GitHub

Ubuntu 12.04 boot times on solid state vs. regular hard drive

Comparing (almost) completely clean new installations of Ubuntu 12.04 on my home (an old hp Pentium 4) on

1) 1.0 TB Western Digital SATA 64MB Cache 3Gbps?
I got to the login screen about 37.5 seconds after pressing the power button, and to the desktop about 10.3 seconds later.

and 2) 80 Gb Intel SSD? (I already screwed it to the inside of the box...)
I got to the login screen about 30.5 seconds after pressing the power button, and to the desktop about 7 seconds later.

So, the SSD saves about 10 seconds per startup.

Installing php and apache

In the spirit of logging changes I make to my new laptop: I'm setting up php and apache to test some little php scripts:


sudo apt-get install apache2
sudo apt-get install php5
sudo /etc/init.d/apache2 restart
And it seems to have worked.

Plot binned mean and mean plus/minus std using python

python scripts to plot mean and mean plus/minus std for data in time bin:

	def binMeanPlot(X,Y,ax=None,numBins=8,xmin=None,xmax=None):
	if xmin is None:
	xmin = X.min()
	if xmax is None:
	xmax = X.max()
	if ax is None:
	fig = pylab.figure()
	ax = fig.add_subplot(111)
	bins = np.linspace(xmin,xmax,numBins+1)
	XX = np.array([np.mean((bins[binInd], bins[binInd+1])) for binInd in range(numBins)])
	YY = np.array([np.mean(Y[(X > bins[binInd]) & (X <= bins[binInd+1])]) for binInd in range(numBins)])
	lineHandles = ax.plot(XX,YY)
	return lineHandles[0], XX, YY
	def binMeanStdPlot(X,Y,ax=None,numBins=8,xmin=None,xmax=None):
	if xmin is None:
	xmin = X.min()
	if xmax is None:
	xmax = X.max()
	if ax is None:
	fig = pylab.figure()
	ax = fig.add_subplot(111)
	bins = np.linspace(xmin,xmax,numBins+1)
	XX = np.array([np.mean((bins[binInd], bins[binInd+1])) for binInd in range(numBins)])
	YY = np.array([np.mean(Y[(X > bins[binInd]) & (X <= bins[binInd+1])]) for binInd in range(numBins)])
	#XX[np.isnan(YY)]=np.nan
	YYstd = np.array([np.std(Y[(X > bins[binInd]) & (X <= bins[binInd+1])]) for binInd in range(numBins)])
	lineHandles = ax.plot(XX,YY)
	patchHandle = ax.fill_between(XX[~np.isnan(YY)],YY[~np.isnan(YY)]-YYstd[~np.isnan(YY)],YY[~np.isnan(YY)]+YYstd[~np.isnan(YY)])
	patchHandle.set_facecolor([.8, .8, .8])
	patchHandle.set_edgecolor('none')
	return lineHandles[0], patchHandle, XX, YY, YYstd

view raw binPlots.py hosted with ❤ by GitHub

National Instruments Setup in WinWCP

Mounting an external hard drive in Ubuntu

Lately Ubuntu hasn't been recognizing my external hard drives when I plug them into the USB ports. Here is a manual way to mount one named "weir17":


sudo mkdir /media/weir17
sudo mount /dev/disk/by-label/weir17 /media/weir17  

I'm not sure why this is not happening automatically, maybe something to do with them being formatted in NTFS?