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VectorPython.html
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VectorPython.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta http-equiv="Content-Style-Type" content="text/css" />
<meta name="generator" content="pandoc" />
<meta name="author" content="Jan Verbesselt, Jorge Mendes de Jesus, Aldo Bergsma, Dainius Masiliunas" />
<title></title>
<style type="text/css">code{white-space: pre;}</style>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- jQuery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.0.3/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.10.3/jquery-ui.min.js"></script>
<!-- bootstrap -->
<!--<link href="https://netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap.min.css" rel="stylesheet" id="style">-->
<script src="https://netdna.bootstrapcdn.com/bootstrap/3.0.0/js/bootstrap.min.js"></script>
<!-- highlight.js -->
<!--<link href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/7.3/styles/default.min.css" rel="stylesheet" id="code-style">-->
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/7.3/highlight.min.js"></script>
<script>
hljs.LANGUAGES.r=function(a){var b="([a-zA-Z]|\\.[a-zA-Z.])[a-zA-Z0-9._]*";return{c:[a.HCM,{b:b,l:b,k:{keyword:"function if in break next repeat else for return switch while try tryCatch|10 stop warning require library attach detach source setMethod setGeneric setGroupGeneric setClass ...|10",literal:"NULL NA TRUE FALSE T F Inf NaN NA_integer_|10 NA_real_|10 NA_character_|10 NA_complex_|10"},r:0},{cN:"number",b:"0[xX][0-9a-fA-F]+[Li]?\\b",r:0},{cN:"number",b:"\\d+(?:[eE][+\\-]?\\d*)?L\\b",r:0},{cN:"number",b:"\\d+\\.(?!\\d)(?:i\\b)?",r:0},{cN:"number",b:"\\d+(?:\\.\\d*)?(?:[eE][+\\-]?\\d*)?i?\\b",r:0},{cN:"number",b:"\\.\\d+(?:[eE][+\\-]?\\d*)?i?\\b",r:0},{b:"`",e:"`",r:0},{cN:"string",b:'"',e:'"',c:[a.BE],r:0},{cN:"string",b:"'",e:"'",c:[a.BE],r:0}]}}(hljs); </script>
<!--<script type="text/javascript", src="https://yandex.st/highlightjs/7.3/languages/r.min.js"></script>-->
<!-- Manific Popup -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/magnific-popup.js/0.8.9/jquery.magnific-popup.min.js"></script>
<script type="text/javascript"
src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
<script defer="defer">
// Function to generate the dynamic table of contents
jQuery.fn.generate_TOC = function () {
var base = $(this[0]);
var selectors = ['h1', 'h2', 'h3', 'h4'];
var last_ptr = [{}, {}, {}, {}];
var anchors = {};
generate_anchor = function (text) {
var test = text.replace(/\W/g, '_');
while(test in anchors){
//if no suffix, add one
if(test.match(/_\d+$/) === null){
test = test + "_2";
}
//else generate unique id for duplicates by adding one to the suffix
else {
test = test.replace(/_(\d+)$/, function(match, number){ var num=+number+1; return("_" + num) });
}
}
anchors[test]=1;
return(test);
}
$(selectors.join(',')).filter(function(index) { return $(this).parent().attr("id") != 'header'; }).each(function () {
var heading = $(this);
var idx = selectors.indexOf(heading.prop('tagName').toLowerCase());
var itr = 0;
while (itr <= idx) {
if (jQuery.isEmptyObject(last_ptr[itr])) {
last_ptr[itr] = $('<ul>').addClass('nav');
if (itr === 0) {
base.append(last_ptr[itr])
} else {
if(last_ptr[itr-1].children('li').length === 0){
last_ptr[itr-1].append(last_ptr[itr]);
}
else {
last_ptr[itr - 1].children('li').last().append(last_ptr[itr]);
}
}
}
itr++;
}
var anchor = generate_anchor(heading.text());
heading.attr('id', anchor);
var a = $('<a>')
.text(heading.text())
.attr('href', '#' + anchor);
var li = $('<li>')
.append(a);
last_ptr[idx].append(li);
for (i = idx + 1; i < last_ptr.length; i++) {
last_ptr[i] = {};
}
});
}
/* run scripts when document is ready */
$(function() {
"use strict";
var $window = $(window);
var $body = $(document.body);
/* size of thumbnails */
var hidden_types = ['source']
var output_types = ['output', 'message', 'warning', 'error']
/* style tables */
$('table').addClass('table table-striped table-bordered table-hover table-condensed');
$('pre code').each(function(i, e) {
hljs.highlightBlock(e);
});
/* Magnific Popup */
$(".thumbnail").each(function(){
$(this).magnificPopup({
disableOn: 768,
closeOnContentClick: true,
type: 'image',
items: {
src: $(this).find('img').attr('src'),
}
});
});
function toggle_block(obj, show) {
var span = obj.find('span');
if(show === true){
span.removeClass('glyphicon-chevron-up').addClass('glyphicon-chevron-down');
obj.next('pre').slideDown();
}
else {
span.removeClass('glyphicon-chevron-down').addClass('glyphicon-chevron-up');
obj.next('pre').slideUp();
}
}
function toggle_thumbnails(imgs, show){
if(show === true){
imgs.parents().show()
imgs.slideDown();
}
else {
imgs.slideUp(400, function(){ $(this).parent().hide(); });
}
}
function global_toggle(obj){
var type = obj.attr('type');
var show = !obj.parent('li').hasClass('active');
if(show === true){
obj.parent('li').addClass('active');
}
else{
obj.parent('li').removeClass('active');
}
if(type == 'figure'){
toggle_thumbnails($('.thumbnail img'), show);
}
else {
$('.toggle.' + type).each(function() { toggle_block($(this), show); });
}
}
/* onclick toggle next code block */
$('.toggle').click(function() {
var span = $(this).find('span');
toggle_block($(this), !span.hasClass('glyphicon-chevron-down'));
return false
})
// global toggles
$('.toggle-global').click(function(){
var type = $(this).attr('type');
if(type === 'all-source'){
$('li a.source').each(function() {
global_toggle($(this));
});
}
else if(type === 'all-output'){
$.each(output_types, function(i, val){
console.log(val);
global_toggle($('li a.' + val));
});
}
else {
console.log($(this));
global_toggle($(this));
}
return false;
});
/* table of contents */
if($(['h1', 'h2', 'h3', 'h4'].join(',')).length > 0){
$('body > #wrap > .container > .row').append('<div class="col-md-2"><div id="toc" class="well sidebar sidenav affix hidden-print"/></div>');
$('#toc').generate_TOC();
}
$.each(hidden_types, function(i, type) {
$('li[type=' + type + ']').each(function(){ global_toggle($(this)); });
});
/* remove paragraphs with no content */
$('p:empty').remove();
$body.scrollspy({
target: '.sidebar',
});
/* theme switch */
$('.theme-switch').click(function(){
var css = $('link[title=' + $(this).attr('title') + ']');
$('#theme[rel=stylesheet]').attr('href', css.attr('href'));
$('.theme-switch').closest('li').removeClass('active');
$(this).closest('li').addClass('active');
return false;
});
/* code style switch */ //TODO use same function for both of these?
$('.highlight-switch').click(function(){
var css = $('link[title="' + $(this).attr('title') + '"]');
$('#highlight[rel=stylesheet]').attr('href', css.attr('href'));
$('.highlight-switch').closest('li').removeClass('active');
$(this).closest('li').addClass('active');
return false;
});
//TODO refresh on show/hide
$window.on('load', function () {
$body.scrollspy('refresh');
})
});
</script>
<style>
/* Knitr_bootstrap styles */
#header {
display: none !important;
visibility: hidden !important;
}
#wrap .container-fluid {
padding: 0;
overflow: hidden;
}
.toggle{
text-transform: capitalize;
}
.toggle-global{
text-transform: capitalize;
}
/* Sticky footer styles */
* {
margin:0;
}
html,
body {
height: 100%;
padding:0 !important;
/* The html and body elements cannot have any padding or margin. */
/*overflow-x: hidden;*/
}
/* Wrapper for page content to push down footer */
#wrap {
min-height: 100%;
height: auto !important;
height: 100%;
/* Negative indent footer by it's height */
margin: 0 auto -120px;
}
/* Set the fixed height of the footer here */
#push,
#footer {
height: 120px;
}
#footer {
text-align: center;
}
/* Top level subheader elements. These are the first nested items underneath a header element. */
.header li {
font-size: 20px;
}
/* Makes the font smaller for all subheader elements. */
.sub-header li {
font-size: 12px;
}
button.thumbnails {
margin-left:0px;
}
/*
* Side navigation
*
* Scrollspy and affixed enhanced navigation to highlight sections and secondary
* sections of docs content.
*/
/* By default it's not affixed in mobile views, so undo that */
.sidebar.affix {
position: static;
}
/* First level of nav */
.sidenav {
margin-top: 30px;
margin-bottom: 30px;
padding-top: 10px;
padding-bottom: 10px;
border-radius: 5px;
}
/* All levels of nav */
.sidebar .nav > li > a {
display: block;
padding: 5px 20px;
}
.sidebar .nav > li > a:hover,
.sidebar .nav > li > a:focus {
text-decoration: none;
border-right: 1px solid;
}
.sidebar .nav > .active > a,
.sidebar .nav > .active:hover > a,
.sidebar .nav > .active:focus > a {
font-weight: bold;
background-color: transparent;
border-right: 1px solid;
}
/* Nav: second level (shown on .active) */
.sidebar .nav .nav {
display: none; /* Hide by default, but at >768px, show it */
margin-bottom: 8px;
}
.sidebar .nav .nav > li > a {
padding-top: 3px;
padding-bottom: 3px;
padding-left: 30px;
font-size: 90%;
}
.sidebar .nav .nav .nav > li > a {
padding-left: 40px;
}
.sidebar .nav .nav .nav .nav > li > a {
padding-left: 50px;
}
/* Show and affix the side nav when space allows it */
@media screen and (min-width: 992px) {
.sidebar .nav > .active > ul {
display: block;
}
/* Widen the fixed sidebar */
.sidebar.affix,
.sidebar.affix-bottom {
width: 213px;
}
.sidebar.affix-top,
.sidebar.affix {
position: fixed; /* Undo the static from mobile first approach */
top: 30px;
}
.sidebar.affix-bottom {
position: absolute; /* Undo the static from mobile first approach */
}
.sidebar.affix-bottom .sidenav,
.sidebar.affix .sidenav {
margin-top: 0;
margin-bottom: 0;
}
}
@media screen and (min-width: 1200px) {
/* Widen the fixed sidebar again */
.sidebar.affix-bottom,
.sidebar.affix {
width: 263px;
}
}
#toc {
padding: 10px 0px;
margin:0;
border:0;
}
.panel pre {
margin: 0;
padding: 0;
border: 0;
}
button + pre {
margin: 0;
padding: 0;
}
pre code {
border-radius: 0;
}
/* Magnific Popup CSS */
.mfp-bg {
top: 0;
left: 0;
width: 100%;
height: 100%;
z-index: 1042;
overflow: hidden;
position: fixed;
background: #0b0b0b;
opacity: 0.8;
filter: alpha(opacity=80); }
.mfp-wrap {
top: 0;
left: 0;
width: 100%;
height: 100%;
z-index: 1043;
position: fixed;
outline: none !important;
-webkit-backface-visibility: hidden; }
.mfp-container {
text-align: center;
position: absolute;
width: 100%;
height: 100%;
left: 0;
top: 0;
padding: 0 8px;
-webkit-box-sizing: border-box;
-moz-box-sizing: border-box;
box-sizing: border-box; }
.mfp-container:before {
content: '';
display: inline-block;
height: 100%;
vertical-align: middle; }
.mfp-align-top .mfp-container:before {
display: none; }
.mfp-content {
position: relative;
display: inline-block;
vertical-align: middle;
margin: 0 auto;
text-align: left;
z-index: 1045; }
.mfp-inline-holder .mfp-content,
.mfp-ajax-holder .mfp-content {
width: 100%;
cursor: auto; }
.mfp-ajax-cur {
cursor: progress; }
.mfp-zoom-out-cur,
.mfp-zoom-out-cur .mfp-image-holder .mfp-close {
cursor: -moz-zoom-out;
cursor: -webkit-zoom-out;
cursor: zoom-out; }
.mfp-zoom {
cursor: pointer;
cursor: -webkit-zoom-in;
cursor: -moz-zoom-in;
cursor: zoom-in; }
.mfp-auto-cursor .mfp-content {
cursor: auto; }
.mfp-close,
.mfp-arrow,
.mfp-preloader,
.mfp-counter {
-webkit-user-select: none;
-moz-user-select: none;
user-select: none; }
.mfp-loading.mfp-figure {
display: none; }
.mfp-hide {
display: none !important; }
.mfp-preloader {
color: #cccccc;
position: absolute;
top: 50%;
width: auto;
text-align: center;
margin-top: -0.8em;
left: 8px;
right: 8px;
z-index: 1044; }
.mfp-preloader a {
color: #cccccc; }
.mfp-preloader a:hover {
color: white; }
.mfp-s-ready .mfp-preloader {
display: none; }
.mfp-s-error .mfp-content {
display: none; }
button.mfp-close,
button.mfp-arrow {
overflow: visible;
cursor: pointer;
background: transparent;
border: 0;
-webkit-appearance: none;
display: block;
padding: 0;
z-index: 1046;
-webkit-box-shadow: none;
box-shadow: none; }
button::-moz-focus-inner {
padding: 0;
border: 0; }
.mfp-close {
width: 44px;
height: 44px;
line-height: 44px;
position: absolute;
right: 0;
top: 0;
text-decoration: none;
text-align: center;
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</style>
</head>
<body>
<title>
Week 3: Python for geo-scripting
</title>
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<div class="contents col-xs-12 col-md-10">
<h1 id="wur-geoscripting-wur-logo"><a href="https://geoscripting-wur.github.io/">WUR Geoscripting</a> <img src="http://www.wageningenur.nl/upload/f9a0b5f2-15c5-4b84-9e14-20ef02f5e265_wur-logo.png" alt="WUR logo" /></h1>
<h1 id="vector-data-handling-with-python">Vector data handling with Python</h1>
<p><em>Jan Verbesselt, Jorge Mendes de Jesus, Aldo Bergsma, Dainius Masiliunas</em> - 22 January, 2018</p>
<h2 id="gdalogr-using-python">GDAL/OGR using Python</h2>
<p>By now you should know what the following abbreviations stand for, and what can you do with the software:</p>
<ul>
<li>GDAL</li>
<li>OGR</li>
</ul>
<p>Whereas the following may be new to you:</p>
<ul>
<li>OSR: spatial reference (projections!)</li>
</ul>
<h2 id="ogr-and-the-data-drivers">OGR and the data drivers</h2>
<p>OGR supports many different vector formats:</p>
<ul>
<li>ESRI formats such as shapefiles, personal geodatabases and ArcSDE</li>
<li>Other software such as MapInfo, GRASS, Microstation</li>
<li>Open formats such TIGER/Line, SDTS, GML, KML</li>
<li>Databases such as MySQL, PostgreSQL, Oracle Spatial, etc.</li>
<li>Webservices such as Web Feature Service 1.0,1.1,2.0 (WFS output as GML)</li>
</ul>
<p><strong>OGR Data drivers:</strong> A driver is an object that knows how to interact with a certain data type (e.g. a shapefile). You need to know the right driver to read or write data. Some drivers might only be able to read content, but the majority can read and write.</p>
Start a terminal and see if you can load osgeo in Python.
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<pre style=""><code class="source bash">python</code></pre>
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<pre style=""><code class="source python">try:
from osgeo import ogr
except:
import ogr</code></pre>
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From the terminal you can also type the following to obtain an overview of supported formats:
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<pre style=""><code class="source bash">echo "Terminal command to obtain an overview of supported formats"
ogrinfo --formats</code></pre>
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<p><a href="http://www.gdal.org/ogr_formats.html">More info about the different OGR formats</a>.</p>
<h2 id="setting-up-environment">Setting up environment</h2>
<p>Before we continue with scripting, you need to setup your Python environment. In the previous Python lesson you learned about Conda and Jupyter Notebooks. We will use both again today. Check if you have made any conda environment named geoscripting.</p>
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<pre style=""><code class="source bash">## Display all your conda environments
conda info --envs</code></pre>
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<p>If you don't have a conda environment called 'geoscripting', create it first.</p>
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<pre style=""><code class="source bash">## Create conda environment called geoscripting
conda create --name geoscripting python=3 numpy jupyter</code></pre>
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<p>Then install todays modules in your conda environment and start your Jupyter Notebook.</p>
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<pre style=""><code class="source bash">## Install gdal and folium
conda install --name geoscripting --channel conda-forge gdal folium
source activate geoscripting
jupyter notebook</code></pre>
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<p>Open a new Ipython Notebook in an appropriate location. Output of the Python scripts from Jupyter Notebook will be saved in the repository where the .ipynb is stored.</p>
<h2 id="points">Points</h2>
<p>Now we continue with the tutorial. Try the script below and find out what "WKT" means.</p>
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<pre style=""><code class="source python">from osgeo import ogr
# Create a point geometry
wkt = "POINT (173914.00 441864.00)"
pt = ogr.CreateGeometryFromWkt(wkt)
print(pt)
# print(help(osgeo.ogr))</code></pre>
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<pre style=""><code class="output python">## POINT (173914 441864)
</code></pre>
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<p>WKT (Well Known Text) is a sort of markup language that describes spatial information in a clean text format, there is an equivalent in binary format (easier for computers to process and more efficient for data transfer).</p>
<p>Explanation of WKT: <a href="https://en.wikipedia.org/wiki/Well-known_text">Wikipedia</a></p>
<h2 id="defining-a-spatial-reference">Defining a spatial reference</h2>
<p>A spatial reference defines: an ellipsoid, a datum using that ellipsoid, and either a geocentric, geographic or projected coordinate system.</p>
<p>Therefore spatial references come in multiple forms according to our data needs. There is even a search engine for it: <a href="http://spatialreference.org/ref/epsg/wgs-84/">http://spatialreference.org</a>.</p>
<p>The following example is based on WGS84, see: <a href="http://spatialreference.org/ref/epsg/wgs-84/" class="uri">http://spatialreference.org/ref/epsg/wgs-84/</a></p>
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<pre style=""><code class="source python">from osgeo import osr
## Spatial reference
spatialRef = osr.SpatialReference()
spatialRef.ImportFromEPSG(4326) # from EPSG - Lat/long</code></pre>
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<h2 id="reproject-a-point">Reproject a point</h2>
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<pre style=""><code class="source python">## lat/long definition
source = osr.SpatialReference()
source.ImportFromEPSG(4326)
# http://spatialreference.org/ref/sr-org/6781/
# http://spatialreference.org/ref/epsg/28992/
target = osr.SpatialReference()
target.ImportFromEPSG(28992)
# transform from lat/long to Dutch coord. system
transform = osr.CoordinateTransformation(source, target)
point = ogr.CreateGeometryFromWkt("POINT (5.6660 51.9872)") #ogr uses lon, lat
point.Transform(transform)
print(point.ExportToWkt())</code></pre>
</div>
<p>Are you still keeping track of your data and coordinate system?</p>
<blockquote>