-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
355 lines (298 loc) · 13.9 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8"/>
<title>Tools for analysis of geospatial time series data.</title>
<meta name="author" content="(Christoph Paulik, Sebastian Hahn, Andreea Plocon, Christoph Reimer, Alexander Gruber)"/>
<link rel="stylesheet" href="http://cdn.jsdelivr.net/reveal.js/3.0.0/css/reveal.css"/>
<link rel="stylesheet" href="http://cdn.jsdelivr.net/reveal.js/3.0.0/css/theme/black.css" id="theme"/>
<link rel="stylesheet" href="./code_formatting.css"/>
<!-- If the query includes 'print-pdf', include the PDF print sheet -->
<script>
if( window.location.search.match( /print-pdf/gi ) ) {
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = 'http://cdn.jsdelivr.net/reveal.js/3.0.0/css/print/pdf.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
}
</script>
</head>
<body>
<div class="reveal">
<div class="slides">
<section id="sec-title-slide" data-background="" data-background-size="200px" data-background-repeat="" data-background-transition="">
<h1>Tools for analysis of geospatial time series data.</h1> <h2>Christoph Paulik, Sebastian Hahn, Andreea Plocon, Christoph Reimer, Alexander Gruber</h2> <h2><a href="mailto:[email protected]">[email protected]</a></h2> <h2></h2> <img width="200px" src="./GEO Logo Blau-Weiß.svg">
</section>
<section>
<section id="slide-orgheadline16">
<h2 id="orgheadline16">Background</h2>
<ul>
<li>Remote sensing of soil moisture</li>
<li>Time series based retrieval algorithm</li>
<li>Temporal dynamics are often more important for analysis than spatial distribution</li>
<li>Grew out of soil moisture validation</li>
</ul>
<div class="figure">
<p><img src="http://www.esa-soilmoisture-cci.org/sites/default/files/images/soilmoisture_logo_small.png" alt="soilmoisture_logo_small.png" />
</p>
</div>
</section>
<section id="slide-orgheadline1">
<h3 id="orgheadline1">Data preparation for time series analysis</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/data-prep.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline2">
<h3 id="orgheadline2">Typical workflow for time series analysis</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/workflow.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline3">
<h3 id="orgheadline3">Spatial referencing</h3>
<ul>
<li>Grid systems
<ul>
<li>UTM system</li>
<li>Equi7 system [<a class='org-ref-reference' href="#bauer2014optimisation">bauer2014optimisation</a>]</li>
</ul></li>
<li>Discrete Global grids
<ul>
<li>SMOS grid - Icosahedron Snyder Equal Area (ISEA)</li>
<li>Gaussian Grids - used by ECMWF</li>
</ul></li>
</ul>
<div class="figure">
<p><img src="./img/dgg-globe.png" alt="dgg-globe.png" />
</p>
</div>
</section>
<section id="slide-orgheadline4">
<h3 id="orgheadline4">pygeogrids</h3>
<ul>
<li><a href="https://github.com/TUW-GEO/pygeogrids">pygeogrids <img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a> is a package for managing discrete (global) grids</li>
<li>has a notion of subdivision that can correspond to I/O units (e.g. netCDF files)</li>
</ul>
<div class="figure">
<p><img src="./img/cells-dgg.png" alt="cells-dgg.png" />
</p>
</div>
</section>
<section id="slide-orgheadline5">
<h3 id="orgheadline5">How to store time series</h3>
<ul>
<li>Resample to data cube</li>
<li>Store as compressed sparse arrays</li>
<li>Climate and Forecast (CF) Metadata conventions <a href="http://cfconventions.org/">http://cfconventions.org/</a></li>
</ul>
</section>
<section id="slide-orgheadline6">
<h3 id="orgheadline6">CF - Orthogonal multidimensional</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/CF-DSG-orthogonal-multidim.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline7">
<h3 id="orgheadline7">CF - Incomplete multidimensional</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/CF-DSG-incomplete-multidim.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline8">
<h3 id="orgheadline8">CF - Contiguous ragged</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/CF-DSG-contigous-ragged.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline9">
<h3 id="orgheadline9">CF - Indexed ragged</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/CF-DSG-indexed-ragged.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline10">
<h3 id="orgheadline10">Interface for data I/O</h3>
<p>
<a href="https://github.com/TUW-GEO/pygeobase">pygeobase <img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a> defines abstract base classes for a common interface
</p>
<div class="org-src-container">
<pre class="src src-python">read_ts<span style="color: #e91e63;">(</span>gpi<span style="color: #e91e63;">)</span>
read_ts<span style="color: #e91e63;">(</span>lon, lat<span style="color: #e91e63;">)</span>
iter_ts<span style="color: #e91e63;">()</span>
read_img<span style="color: #e91e63;">(</span>datetime<span style="color: #e91e63;">)</span>
iter_img<span style="color: #e91e63;">(</span>startdate, enddate<span style="color: #e91e63;">)</span>
</pre>
</div>
</section>
<section id="slide-orgheadline11">
<h3 id="orgheadline11">Implemenation for netCDF CF</h3>
<ul>
<li><a href="https://github.com/TUW-GEO/pynetCF">pynetCF <img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a> implements the interface for netCDF
files according to the CF conventions</li>
<li>Works but writing of data can be optimized</li>
<li>integration with general purpose packages (<a href="http://xray.readthedocs.org/en/stable/">xray</a>)</li>
</ul>
</section>
<section id="slide-orgheadline12">
<h3 id="orgheadline12">Dataset that knows itself</h3>
<ul>
<li>Can traverse itself and return a time series per grid point</li>
<li>Optimized I/O because dataset object knows how data is stored</li>
</ul>
<div class="figure">
<p><object type="image/svg+xml" data="./img/Dataset.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
<section id="slide-orgheadline13">
<h3 id="orgheadline13">Algorithms and processing</h3>
<ul>
<li><a href="https://github.com/TUW-GEO/pytesmo">pytesmo
<img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a> implements temporal matching,
filtering, and algorithms specifically needed for soil moisture validation
e.g.
<a href="http://rs.geo.tuwien.ac.at/validation_tool/pytesmo/docs/examples.html#triple-collocation-and-triple-collocation-based-scaling">triple
collocation</a>.</li>
<li>Framework for time series based computations parallelized via
<a href="http://ipyparallel.readthedocs.org/en/latest/">ipyparallel</a> (formerly
IPython parallel)</li>
<li>I/O for soil moisture RS and in-situ datasets</li>
</ul>
</section>
<section id="slide-orgheadline14">
<h3 id="orgheadline14">Example - global validation</h3>
<div class="org-src-container">
<pre class="src src-python"><span style="color: #EF6C00;">ecmwf_reader</span> = ECMWF.ERA_Interim<span style="color: #e91e63;">()</span>
<span style="color: #EF6C00;">ascat_reader</span> = AscatH25_SSM<span style="color: #e91e63;">()</span>
<span style="color: #EF6C00;">datasets</span> = <span style="color: #e91e63;">{</span><span style="color: #689f38;">'ASCAT'</span>: <span style="color: #1565C0;">{</span><span style="color: #689f38;">'class'</span>: ascat_reader,
<span style="color: #689f38;">'columns'</span>: <span style="color: #EF6C00;">[</span><span style="color: #689f38;">'sm'</span><span style="color: #EF6C00;">]</span>,
<span style="color: #689f38;">'type'</span>: <span style="color: #689f38;">'reference'</span><span style="color: #1565C0;">}</span>,
<span style="color: #689f38;">'ERAINT'</span>: <span style="color: #1565C0;">{</span><span style="color: #689f38;">'class'</span>: ecmwf_reader,
<span style="color: #689f38;">'columns'</span>: <span style="color: #EF6C00;">[</span><span style="color: #689f38;">'soilm-l1'</span><span style="color: #EF6C00;">]</span>,
<span style="color: #689f38;">'type'</span>: <span style="color: #689f38;">'other'</span>,
<span style="color: #689f38;">'kwargs'</span>: <span style="color: #EF6C00;">{</span><span style="color: #689f38;">'period'</span>: period<span style="color: #EF6C00;">}</span>,
<span style="color: #689f38;">'grids_compatible'</span>: <span style="color: #558b2f;">False</span>,
<span style="color: #689f38;">'use_lut'</span>: <span style="color: #558b2f;">True</span>, <span style="color: #689f38;">'lut_max_dist'</span>: <span style="color: #689f38;">100000</span><span style="color: #1565C0;">}</span><span style="color: #e91e63;">}</span>
<span style="color: #EF6C00;">process</span> = Validation<span style="color: #e91e63;">(</span>datasets=datasets,
temporal_matcher=BasicTemporalMatching<span style="color: #1565C0;">()</span>,
scaling=<span style="color: #689f38;">'lin_cdf_match'</span>,
metrics_calculator=BasicMetrics<span style="color: #1565C0;">()</span>,
period=period<span style="color: #e91e63;">)</span>
<span style="color: #EF6C00;">jobs</span> = process.get_processing_jobs<span style="color: #e91e63;">()</span>
<span style="color: #00796b;">return</span> process, jobs
</pre>
</div>
</section>
<section id="slide-orgheadline15">
<h3 id="orgheadline15">Where do the packages fit in</h3>
<div class="figure">
<p><object type="image/svg+xml" data="./img/workflow-packages.svg" >
Sorry, your browser does not support SVG.</object>
</p>
</div>
</section>
</section>
<section>
<section id="slide-orgheadline17">
<h2 id="orgheadline17">Summary</h2>
<ul>
<li>Suite of Python packages for time series optimized processing</li>
<li><a href="https://github.com/TUW-GEO/pytesmo">pytesmo
<img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a>
<a href="http://badge.fury.io/py/pytesmo"><object type="image/svg+xml" data="https://badge.fury.io/py/pytesmo.svg" >
Sorry, your browser does not support SVG.</object></a>
<a href="http://dx.doi.org/10.5281/zenodo.29593"><object type="image/svg+xml" data="https://zenodo.org/badge/doi/10.5281/zenodo.29593.svg" >
Sorry, your browser does not support SVG.</object></a></li>
<li><a href="https://github.com/TUW-GEO/pygeogrids">pygeogrids
<img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a>
<a href="http://badge.fury.io/py/pygeogrids"><object type="image/svg+xml" data="https://badge.fury.io/py/pygeogrids.svg" >
Sorry, your browser does not support SVG.</object></a>
<a href="http://dx.doi.org/10.5281/zenodo.31613"><object type="image/svg+xml" data="https://zenodo.org/badge/doi/10.5281/zenodo.17406.svg" >
Sorry, your browser does not support SVG.</object></a></li>
<li><a href="https://github.com/TUW-GEO/pygeobase">pygeobase
<img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a>
<a href="http://badge.fury.io/py/pygeobase"><object type="image/svg+xml" data="https://badge.fury.io/py/pygeobase.svg" >
Sorry, your browser does not support SVG.</object></a></li>
<li><a href="https://github.com/TUW-GEO/pynetCF">pynetCF
<img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a></li>
<li>BSD licensed</li>
</ul>
</section>
</section>
<section>
<section id="slide-orgheadline18">
<h2 id="orgheadline18">Thank you, Questions?</h2>
<ul>
<li>Get in touch
<ul>
<li>You can find this presentation at <a href="http://cpaulik.github.io/2015-eoscience2.0">http://cpaulik.github.io/2015-eoscience2.0</a></li>
<li><a href="https://github.com/cpaulik">cpaulik <img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a></li>
<li><a href="https://github.com/TUW-GEO">TUW-GEO <img src="./img/GitHub-Mark-Light-64px.png" alt="GitHub-Mark-Light-64px.png" /></a></li>
<li>[email protected]</li>
</ul></li>
<li>Thanks to the Python open source community.</li>
</ul>
<div class="figure">
<p><a href="http://creativecommons.org/licenses/by/4.0/deed"><object type="image/svg+xml" data="http://mirrors.creativecommons.org/presskit/buttons/88x31/svg/by-sa.svg" >
Sorry, your browser does not support SVG.</object></a>
</p>
</div>
</section>
</section>
<section>
<section id="slide-orgheadline19">
<h2 id="orgheadline19">References</h2>
<p>
<h1 class='org-ref-bib-h1'>Bibliography</h1>
<ul class='org-ref-bib'><li><a id="bauer2014optimisation">[bauer2014optimisation] Bauer-Marschallinger, Sabel & Wagner, Optimisation of global grids for high-resolution remote sensing data, <i>Computers & Geosciences</i>, <b>72</b>, 84-93 (2014).</a></li>
</ul>
</p>
</section>
</section>
</div>
</div>
<script src="http://cdn.jsdelivr.net/reveal.js/3.0.0/lib/js/head.min.js"></script>
<script src="http://cdn.jsdelivr.net/reveal.js/3.0.0/js/reveal.js"></script>
<script>
// Full list of configuration options available here:
// https://github.com/hakimel/reveal.js#configuration
Reveal.initialize({
controls: true,
progress: true,
history: false,
center: true,
slideNumber: true,
rollingLinks: false,
keyboard: true,
overview: true,
theme: Reveal.getQueryHash().theme, // available themes are in /css/theme
transition: Reveal.getQueryHash().transition || 'default', // default/cube/page/concave/zoom/linear/fade/none
transitionSpeed: 'default',
multiplex: {
secret: '', // null if client
id: '', // id, obtained from socket.io server
url: '' // Location of socket.io server
},
// Optional libraries used to extend on reveal.js
dependencies: [
]
});
</script>
</body>
</html>