mhl’s gists

mhl / gist:2700917

Created May 15, 2012 11:14

beautify-javascript.bash

	#!/bin/bash

	D=$(dirname $(readlink -nf $BASH_SOURCE))
	SD=$(readlink -nf $D/../httpdocs)

	# The js-beautify directory. (It can be cloned from
	# https://github.com/einars/js-beautify .)
	JSB=~/js-beautify/

	if [ ! -e "$JSB/beautify-cl.js" ]

mhl / convert-stitching-results.py

Created February 23, 2012 14:13

Convert TileConfiguration.registered.txt to a format TrakEM2 can load

	#!/usr/bin/env python

	# This script takes the output of Stephan Preibisch's stitching plugins
	# for 3D stacks and outputs tab separated data suitable for loading
	# into TrakEM2. What TrakEM2 expects is described here:
	#
	# http://www.ini.uzh.ch/~acardona/trakem2_manual.html#importing_list

	import sys, re

mhl / generate-st-tng-html.py

Created January 3, 2012 13:37

	#!/usr/bin/python

	import re, csv, sys, urllib, urllib2, time, cgi
	from collections import defaultdict

	spreadsheet_url = 'https://docs.google.com/spreadsheet/ccc?key=0Am9Hd8ELMkEsdDg4QVd6d0JGeS1WQ0VpTnNBSm5xS2c&output=csv'

	season_output = defaultdict(list)

	decision_data = {

mhl / git-show-all-objects.sh

Created September 12, 2011 16:05

A script to show all the objects in a git repository

	#!/bin/sh

	set -e

	cd "$(git rev-parse --show-cdup)"

	# Find all the objects that are in packs:

	for p in .git/objects/pack/pack-*.idx
	do

mhl / wilson-interval.rb

Created July 1, 2011 17:10

Naive pairwise comparisons power

mhl / git-fetch-and-fast-forward-all-branches.sh

Created April 22, 2011 11:35

An example script to show how to fetch from all default remotes and do any fast-forwards of local branches from upstream possible

	#!/bin/sh

	set -e

	CURRENT_BRANCH="$(git symbolic-ref HEAD)"
	CURRENT_BRANCH_UPSTREAM="$(git rev-parse --symbolic-full-name @{u} 2> /dev/null)"

	# Update the remote-tracking branches for every remote for which
	# remote.<name>.skipDefaultUpdate is not true:
	git remote update default

mhl / Convert_Traces_to_SWC.py

Created March 26, 2011 05:39

Batch convert Simple Neurite Tracer's .traces files to SWC format

	import os
	import re
	from tracing import PathAndFillManager

	# An example script showing how to convert all the .traces
	# files in a directory to SWC files. (The .traces format
	# is the native file format of Simple Neurite Tracer.)

	def run():
	d = IJ.getDirectory("Choose your directory of .traces files...")

mhl / squash-all.bash

Created March 11, 2011 06:38

A script that squashes your entire branch down to a single commit

	#!/bin/bash

	# A script that squashes your entire current branch down to a single commit,
	# if this repository has a single root commit. This will change the object
	# name of the root commit. This is for an answer to the Stack Overflow
	# question: http://stackoverflow.com/questions/5266340/

	if [ -n "$(git status --porcelain)" ]
	then
	echo "git status wasn't clean - refusing to run..."

mhl / SWC_Display.py

Created February 22, 2011 14:00

In Fiji display SWC files in the 3D Viewer

	import re
	import os

	from java.awt import Color
	from ij3d import Image3DUniverse

	univ = Image3DUniverse(512, 512)
	univ.show()

	# d = '/home/mark/painting-demo/static/data'

mhl / gist:816543

Created February 8, 2011 15:02

	Checking prerequisites of (fiji.build.SubFake) jars/weka.jar <- fiji jars/Fiji.jar ...
	Building (fiji.build.SubFake) jars/weka.jar <- fiji jars/Fiji.jar ...
	Building in modules/weka/
	Checking prerequisites of (fiji.build.ExecuteProgram) weka.jar <- weka/dist/weka.jar
	Checking prerequisites of (fiji.build.ExecuteProgram) weka/dist/weka.jar <-
	Building (fiji.build.ExecuteProgram) weka/dist/weka.jar <-
	Executing: '../../fiji' '--ant' '-f' 'weka/build.xml' 'exejar'
	Found that JAVA_HOME was: '/usr/lib/jvm/java-6-openjdk/'
	Buildfile: weka/build.xml

Mark Longair mhl