bdunnette’s gists

bdunnette / process-svs.sh

Last active November 20, 2020 06:30

Process Aperio SVS files into web tiles (with Leaflet-based viewer)

	#!/bin/bash

	# Copyright (c) 2014 Regents of the University of Minnesota

	# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

	# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

	# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR

bdunnette / gist:9075479

Created February 18, 2014 17:24

tar -cf - . | ssh [email protected] "tar -xf - -C /www/basic/ahc/labmed/slides.pathology.umn.edu/htdocs"

bdunnette / images-to-alfresco.py

Last active August 29, 2015 13:56

	import sys
	import cmislib

	cmisClient = cmislib.CmisClient('https://lmp-alfresco.ahc.umn.edu/alfresco/cmisatom', sys.argv[1], sys.argv[2])
	print cmisClient
	repo = cmisClient.getRepository('48ebc2be-3a2c-4856-8e68-877ec40d9a20')
	print repo.id
	imaging = repo.getObjectByPath("/Sites/lmp-imaging/documentLibrary/Grosslab")
	print imaging
	new_folder = imaging.createFolder(sys.argv[3])

bdunnette / fusion-tables-sandbox.html

Last active May 24, 2018 13:36

	<html>
	<head>
	<title>Google Fusion Tables API Example</title>
	</head>
	<body>
	<div id="content"></div>
	<script>
	function handler(response) {
	for (var i = 0; i < response.items.length; i++) {
	var item = response.items[i];

bdunnette / aperiotilesource.js

Created March 20, 2014 22:36 — forked from richstoner/aperiotilesource.js

	// hacked together aperio support

	(function( $ ){

	/**
	* A client implementation of the Aperio ImageServer Format
	*
	* @class
	* @extends OpenSeadragon.TileSource
	* @param {Number\|Object} width - the pixel width of the image or the idiomatic

bdunnette / aperio-delete-label.py

Created March 20, 2014 22:36 — forked from bgilbert/README.md

-#!/usr/bin/python
-#
-#  Delete the label image from an Aperio SVS file.
-#
-#  Copyright (c) 2012-2013 Carnegie Mellon University
-#  All rights reserved.
-#
-#  This program is free software: you can redistribute it and/or modify
-#  it under the terms of the GNU Lesser General Public License as
-#  published by the Free Software Foundation, version 2.1.

bdunnette / html5-geo.html

Created March 28, 2014 14:11

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset=utf-8>
	<meta name="viewport" content="width=620">
	<title>HTML5 Demo: geolocation</title>
	<link rel="stylesheet" href="css/html5demos.css">
	<script src="js/h5utils.js"></script></head>
	<body>
	<section id="wrapper">

bdunnette / odp2anki.py

Last active August 29, 2015 13:57

	import sys
	import os
	import os.path
	import zipfile
	from lxml import etree
	from lxml import objectify

	tempdir = 'temp'
	docfile = zipfile.ZipFile(sys.argv[1])
	docfile.extractall(tempdir)

bdunnette / backup-checksums.py

Last active August 29, 2015 13:58

	#!/usr/bin/env python
	import hashlib
	import os
	import sys
	import csv

	# Set the directory you want to start from
	rootDir = sys.argv[1]
	BLOCKSIZE = 65536
	csv_filename = "checksums.csv"

bdunnette / get-lastfm-free-tracks.py

Last active August 29, 2015 13:58

	import feedparser
	import urllib

	feed = feedparser.parse('http://ws.audioscrobbler.com/2.0/user/lazymofo/podcast.rss')

	for item in feed.entries:
	item_url = item.links[0].href
	print item_url
	file = urllib.urlretrieve(item_url)

Brian Dunnette bdunnette