schluppeck

% use anonymous function to wrap Matlab plot3. Pass on options as per plot3
myPlot3 = @(P,varargin) plot3(P(:,1), P(:,2), P(:,3), varargin{:});

% e.g. make a noisy spiral
t = transpose( linspace(0, 2.*pi, 100) );
X =[sin(2.*t), cos(2.*t)+rand(size(t)), t]
% plot
figure
myPlot3(X, '.-', 'color', 'r', 'linewidth', 2)
axis vis3d

schluppeck

#!/bin/bash
#
# downloading pubmed data into json files
#
# used curl --help and stackoverflow for inspiration. also check out the posts here:
# http://superuser.com/questions/149329/what-is-the-curl-command-line-syntax-to-do-a-post-request

# define some variables - change as appropriate
author="schluppeck-d"
# pubmed search cgi is located here

schluppeck

# pmid2bibtex.rb
# convert a PubMed PMID to BibTeX citation format
# updated version of http://chrisamiller.com/science/2010/12/13/using-bioruby-to-fetch-citations-from-pubmed/
# works as of 2015-03-18

require 'bio'
Bio::NCBI.default_email = "me@me.com" # required for EUtils

id  = "18265351"
pm  = Bio::PubMed::efetch(id)         # array of MEDLINE-formatted string

schluppeck

function [ fHandle ] = jneurosci(fHandle, colWidth)
%jneurosci - provide some defaults for figures to get to JNeurosci style
%
%      usage: [ fHandle ] = jneurosci( fHandle )
%         by: lpzds1
%       date: May 28, 2015
%
%     inputs: fHandle, colWidth [1, 1.5, 2]
%    outputs: fHandle
%

schluppeck

#!/bin/bash
#
# example of how to use a simple BASH loop w/ FSL to traverse
# directories and create summary images of rendered_thresh_zstat?.hdr
# in a nice way

# input 1 is folder name	
if [[ ! -d $1 ]]; then
	echo "(uhoh) directory $1 does not exist"
	echo " usage:"

schluppeck

% spectrovis.m
%
%        $Id: spectrovis.m 1022 2012-08-07 10:29:58Z svnuser $
%      usage: spectrovis(varargin)
%         by: denis schluppeck based on mglRetinotopy by justin gardner
%       date: 2010-06-06
%
%    purpose: Displays a retinotopy stimulus, there are many
%             parameters you can set, you can set as many
%             or as few as you like.

schluppeck

% make random coordinates on [0..1]
xy = rand(50,2)

% plot them with scatter
figure, scatter(xy(:,1), xy(:,2))

% get convex hull of cloud + plot
k = convhull(xy(:,1), xy(:,2))
hold on
plot(xy(k,1), xy(k,2), 'r-')

schluppeck

function [  ] = rmText(f_)
%rmText - remove text objects from a figure 
%
%      usage: [  ] = rmText( f_ )
%         by: lpzds1, Denis Schluppeck
%       date: Aug 20, 2015
%     inputs: f_
%    outputs: 
%
%    purpose: matlab figure exporting is a bit of a pain, so sometime one

schluppeck

#! /bin/bash
#
# creating a table that contains a given term week (2,3,4...)
# and the corresponding dates. using bash / unix. e.g.

	# Week 2 - Wed 30 Sep 2015
	# Week 3 - Wed 7 Oct 2015
	# Week 4 - Wed 14 Oct 2015
	# Week 5 - Wed 21 Oct 2015

schluppeck

function	[dip,xl,xu, ifault, gcm, lcm, mn, mj] = HartigansDipTest(xpdf)

% function	[dip,xl,xu, ifault, gcm, lcm, mn, mj]=HartigansDipTest(xpdf)
%
% This is a direct translation by F. Mechler (August 27 2002)
% into MATLAB from the original FORTRAN code of Hartigan's Subroutine DIPTST algorithm 
% Ref: Algorithm AS 217 APPL. STATIST. (1985) Vol. 34. No.3 pg 322-325
%
% Appended by F. Mechler (September 2 2002) to deal with a perfectly unimodal input
% This check the original Hartigan algorithm omitted, which leads to an infinite cycle