python4astronomers.github.com/vo/webmodules.html at master · python4astronomers/python4astronomers.github.com

History

550 lines (490 loc) · 29 KB

Raw

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

356

357

358

359

360

361

362

363

364

365

366

367

368

369

370

371

372

373

374

375

376

377

378

379

380

381

382

383

384

385

386

387

388

389

390

391

392

393

394

395

396

397

398

399

400

401

402

403

404

405

406

407

408

409

410

411

412

413

414

415

416

417

418

419

420

421

422

423

424

425

426

427

428

429

430

431

432

433

434

435

436

437

438

439

440

441

442

443

444

445

446

447

448

449

450

451

452

453

454

455

456

457

458

459

460

461

462

463

464

465

466

467

468

469

470

471

472

473

474

475

476

477

478

479

480

481

482

483

484

485

486

487

488

489

490

491

492

493

494

495

496

497

498

499

500

501

502

503

504

505

506

507

508

509

510

511

512

513

514

515

516

517

518

519

520

521

522

523

524

525

526

527

528

529

530

531

532

533

534

535

536

537

538

539

540

541

542

543

544

545

546

547

548

549

550

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"

"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<head>

<title>Standard Python Tools — Python4Astronomers 2.0 documentation</title>

var DOCUMENTATION_OPTIONS = {

URL_ROOT: '../',

VERSION: '2.0',

COLLAPSE_INDEX: false,

FILE_SUFFIX: '.html',

HAS_SOURCE: true

};

</script>

$(document).ready(function(){

$(".flip0").click(function(){

$(".panel0").slideToggle("normal");

});

$(".flip1").click(function(){

$(".panel1").slideToggle("normal");

});

$(".flip2").click(function(){

$(".panel2").slideToggle("normal");

});

$(".flip3").click(function(){

$(".panel3").slideToggle("normal");

});

$(".flip4").click(function(){

$(".panel4").slideToggle("normal");

});

$(".flip5").click(function(){

$(".panel5").slideToggle("normal");

});

$(".flip6").click(function(){

$(".panel6").slideToggle("normal");

});

$(".flip7").click(function(){

$(".panel7").slideToggle("normal");

});

$(".flip8").click(function(){

$(".panel8").slideToggle("normal");

});

$(".flip9").click(function(){

$(".panel9").slideToggle("normal");

});

</script>

div.panel0,p.flip0

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip0

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel0

{

display:none;

}

div.panel1,p.flip1

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip1

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel1

{

display:none;

}

div.panel2,p.flip2

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip2

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel2

{

display:none;

}

div.panel3,p.flip3

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip3

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel3

{

display:none;

}

div.panel4,p.flip4

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip4

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel4

{

display:none;

}

div.panel5,p.flip5

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip5

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel5

{

display:none;

}

div.panel6,p.flip6

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip6

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel6

{

display:none;

}

div.panel7,p.flip7

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip7

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel7

{

display:none;

}

div.panel8,p.flip8

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip8

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel8

{

display:none;

}

div.panel9,p.flip9

{

font-size: 0.9em;

margin: 0;

padding: 0.1em 0 0.1em 0.5em;

border-bottom: 1px solid #86989B;

}

p.flip9

{

color: white;

font-weight: bold;

background-color: #AFC1C4;

}

div.panel9

{

display:none;

}

</style>

var _gaq = _gaq || [];

_gaq.push(['_setAccount', 'UA-18709417-2']);

_gaq.push(['_trackPageview']);

(function() {

var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;

ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';

var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);

})();

</script>

</head>

<a class="brand" title="Documentation Home" href="../index.html">python4astronomers</a>

<ul>

</ul>

</div>

<h3>Navigation</h3>

<ul>

</a>

</li>

« previous

</a>

</li>

<li>

<a href="../index.html">Python4Astronomers 2.0 documentation</a>

</li>

<li><a href="vo.html" accesskey="U">Online Astronomy and the virtual observatory</a> »</li>

<li>Standard Python Tools</li>

</ul>

</div>

<h1>Standard Python Tools<a class="headerlink" href="#standard-python-tools" title="Permalink to this headline">¶</a></h1>

There are two standard “core” Python modules that provide much of the

functionality necessary to access internet resources from inside python:

<a class="reference external" href="http://docs.python.org/library/urllib2">urllib2</a> and <a class="reference external" href="http://docs.python.org/library/urllib">urllib</a>. You have seen <code class="docutils literal">urllib2</code> in each of the prior

workshops when downloading example files or datasets, like this:

<div class="highlight-python"><div class="highlight"><pre>import urllib2

url = 'http://python4astronomers.github.com/_downloads/image_sources.csv'

open('image_sources.csv', 'wb').write(urllib2.urlopen(url).read())

</pre></div>

</div>

<h2>Webpage Retrieval<a class="headerlink" href="#webpage-retrieval" title="Permalink to this headline">¶</a></h2>

It is useful to write the example above a bit differently since

readability counts and we want to highlight a few steps.

<div class="highlight-python"><div class="highlight"><pre>with open('image_sources.csv','wb') as outfile:

handler = urllib2.urlopen(url)

data = handler.read()

outfile.write(data)

handler.close()

</pre></div>

</div>

First, <a class="reference external" href="http://docs.python.org/library/urllib2">urllib2</a> has returned a file like object <code class="docutils literal">handler</code> that

points to a specific web resource. Various attributes about the

webpage are available:

<div class="highlight-python"><div class="highlight"><pre>print(handler.code)

print(handler.headers['content-type'])

</pre></div>

</div>

In this particular example the data request is handled after the

initial response has been examined; the data is streamed into a local

variable <code class="docutils literal">data</code> and then saved to a local file. As demonstrated in

the <a class="reference internal" href="../files/asciifiles.html">ASCII files portion</a> of the <a class="reference internal" href="../files/files.html">Reading

and Writing Files</a> workshop, one alternatively could

parse the returned data stream into a table for further use.

</div>

<h2>Building Queries<a class="headerlink" href="#building-queries" title="Permalink to this headline">¶</a></h2>

Now we are getting closer to searching for data online via python.

Traditionally, each data archive has implemented its own set of

query parameters; more often then not you experience it as a web

form with lots of check and input boxes. Most of the time these web

forms are simply input wrappers that build a query string and

process the result.

Here is a very simple query example: search for HST

images near M 51. It is worth noting that you have

to find and read the <a class="reference external" href="http://archive.stsci.edu/vo/mast_services.html">MAST HST documentation</a> to

learn which <a class="reference external" href="http://archive.stsci.edu/vo/general_params.html">parameters</a> are needed to build the query.

<div class="highlight-python"><div class="highlight"><pre>import urllib2, urllib

# this is the query url for this service.

url = 'http://archive.stsci.edu/hst/search.php'

# make a dictionary of search parameters

p = {}

p['target']="M 51"

p['radius']=1.0

p['max_records']=10

p['outputformat']='CSV'

p['action']='Search'

# encode the http string

query = urllib.urlencode(p)

# create the full URL for a GET query

get_url = url + "?" + query

# create the GET handler

# check it

print(handler.code)

# save it

with open('hst_m51.csv','wb') as f:

f.write(handler.read())

</pre></div>

</div>

The magic is that <a class="reference external" href="http://docs.python.org/library/urllib">urllib</a> module takes care of encoding the

parameters using standard HTTP rules. You can compare the input

dictionary key,value pairs with the HTTP url encoding.

<div class="highlight-python"><div class="highlight"><pre># some simple formatting where the format %-M.Ns means

# "-" :: 'left justified'

# "M" :: 'minimum string length, padded'

# "N" :: 'maximum string length, sequence sliced'

# "s" :: 'format as string'

sform = "%-20.20s %-10.10s %-30.30s"

# make a header

print(sform % ('parameter','value','encoded'))

print(sform % (3*(100*'-',)))

# for each paramter show the input items from the dictionary

# "p" and the output query string.

for a,b in zip(p.items(),query.split('&')):

print(sform % (a+(b,)))

</pre></div>

</div>

Exercise: import WISE catalog data for a young cluster

In this exerice you will use a different service (IRSA) and

with a different overall goal for these data.

<div class="highlight-python"><div class="highlight"><pre>import atpy, urllib, urllib2

url = "http://irsa.ipac.caltech.edu/cgi-bin/Gator/nph-query"

p = {}

p['spatial'] = "Cone"

p['objstr'] = "IC 348"

p['outfmt'] = 1 # IPAC table format

p['catalog'] = 'wise_prelim_p3as_psd'

p['radius'] = 300

get_url = url + "?" + query

raw = handler.read()

print(raw[0:255])

with open('ic348_wise.tbl', 'wb') as f:

f.write(raw)

</pre></div>

</div>

The challenge is to immediately analyze the results of this query. The

exercise is to make a simple color-color plot of these objects.

</div>

Click to Show/Hide Solution <div class="panel9">There are MANY ways we have looked at in the workshops for converting

this result to a numpy array. Some of these examples parse the raw

web data directly, circumventing a need to write it to file. Some use

different means to try to deal with the data types and null values

in the result.

<div class="highlight-python"><div class="highlight"><pre>t1 = atpy.Table('ic348_wise.tbl',type="ipac")

t2 = asciitable.read(raw, Reader=asciitable.IpacReader)

t3 = atpy.Table(raw,type='ascii')

fill_values = [('null',numpy.nan)]

t4 = asciitable.read(raw, Reader=asciitable.IpacReader, \

fill_values=fill_values)

t5 = atpy.Table(raw,type='ascii', fill_values=fill_values)

</pre></div>

</div>

Its important to realize that YMMV as to how these differ in their output.

For example, lets look at the output table types and the data types for

a couple of columns:

<div class="highlight-python"><div class="highlight"><pre>t = [t1, t2, t3, t4, t5]

for i in t:

c = (type(i), i['j_m_2mass'].dtype, i['tmass_key'].dtype)

print("%40s%10s%10s" % c)

</pre></div>

</div>

The output table types (and hence their built-in utilities), column data types

and treatment of null values vary and this matters when trying to make a plot

or perform other types of analysis. We will use <code class="docutils literal">t1</code> as the data types are

correct. It also preserves more of the metadata of the query.

Just a quick plot that reuses some of this metadata in the plot title.

<div class="highlight-python"><div class="highlight"><pre>clf()

plot(t1['w2mag']-t1['w3mag'], t1['j_m_2mass']-t1['h_m_2mass'], 'ro')

xlabel('W2 - W3')

ylabel('J - H')

title(t1.keywords['SKYAREA'], fontsize='small')

</pre></div>

</div>

</div><div class="admonition-read-the-instructions admonition">

Read the instructions!

Because these web interfaces vary from archive to archive it is

worth emphasizing that building the query string for a particular

data archive begins with reading the documentation page

for that archive’s GET interface.

Here are some links to these documentation pages for some archives

</ul>

and the service url for these are:

<li>(IRSA) <a class="reference external" href="http://irsa.ipac.caltech.edu/cgi-bin/Gator/nph-query">http://irsa.ipac.caltech.edu/cgi-bin/Gator/nph-query</a></li>

<li>(MAST, HST) <a class="reference external" href="http://archive.stsci.edu/hst/search.php">http://archive.stsci.edu/hst/search.php</a></li>

</ul>

</div>

Warning

Nothing I’ve shown actually checks that the data expected is the

data retrieved. See also warnings in the documentation for

<a class="reference external" href="http://docs.python.org/library/urllib2">urllib2</a> and <a class="reference external" href="http://docs.python.org/library/urllib">urllib</a> about <code class="docutils literal">https</code> transactions. As with

everything web based, you should implement assertions or tests to

check your results before continuing.

</div>

<div class="sphinxsidebarwrapper"><h3>Page Contents</h3>

<ul>

<li><a class="reference internal" href="#">Standard Python Tools</a><ul>

<li><a class="reference internal" href="#webpage-retrieval">Webpage Retrieval</a></li>

<li><a class="reference internal" href="#building-queries">Building Queries</a></li>

</ul>

</li>

</ul>

<h4>Previous topic</h4>

<a href="install.html"

title="previous chapter">Modules</a>

<h4>Next topic</h4>

<a href="votools.html"

title="next chapter">Virtual Observatory</a>

</div>

</div>

<a href="../_sources/vo/webmodules.txt"

rel="nofollow">Page Source</a>

terms of <a rel="license"

href="http://creativecommons.org/licenses/by/3.0/">CC

Attribution 3.0</a>.

Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.3.1.

</footer>

</body>

</html>

pFad - Phone/Frame/Anonymizer/Declutterfier! Saves Data!

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Pfad - The Proxy pFad © 2024 Your Company Name. All rights reserved.

pFad - Phone/Frame/Anonymizer/Declutterfier! Saves Data!

FilesExpand file tree

webmodules.html

Latest commit

History

webmodules.html

File metadata and controls

Pfad - The Proxy pFad © 2024 Your Company Name. All rights reserved.