Note: The default ITS GitLab runner is a shared resource and is subject to slowdowns during heavy usage.
You can run your own GitLab runner that is dedicated just to your group if you need to avoid processing delays.

DOCUMENTATION.markdown 12.2 KB
Newer Older
Qusai Al Shidi's avatar
Qusai Al Shidi committed
1
2
3
# Table of Contents

* [swmfpy](#.swmfpy)
4
  * [write\_imf\_from\_omni](#.swmfpy.write_imf_from_omni)
5
6
7
8
* [swmfpy.web](#.swmfpy.web)
  * [get\_omni\_data](#.swmfpy.web.get_omni_data)
  * [download\_magnetogram\_hmi](#.swmfpy.web.download_magnetogram_hmi)
  * [download\_magnetogram\_adapt](#.swmfpy.web.download_magnetogram_adapt)
9
10
11
12
13
* [swmfpy.io](#.swmfpy.io)
  * [write\_imf\_input](#.swmfpy.io.write_imf_input)
  * [read\_wdc\_ae](#.swmfpy.io.read_wdc_ae)
  * [read\_wdc\_asy\_sym](#.swmfpy.io.read_wdc_asy_sym)
  * [read\_gm\_log](#.swmfpy.io.read_gm_log)
Qusai Al Shidi's avatar
Qusai Al Shidi committed
14
15
16
* [swmfpy.paramin](#.swmfpy.paramin)
  * [replace\_command](#.swmfpy.paramin.replace_command)
  * [read\_command](#.swmfpy.paramin.read_command)
17
* [swmfpy.tools](#.swmfpy.tools)
Qusai Al Shidi's avatar
Qusai Al Shidi committed
18

Qusai Al Shidi's avatar
Qusai Al Shidi committed
19
20
<a name=".swmfpy"></a>
## swmfpy
21

Qusai Al Shidi's avatar
Autodoc    
Qusai Al Shidi committed
22
23
A collection of tools to read, write, visualize with the
Space Weather Modeling Framework (SWMF).
24

25
### Modules
26

Qusai Al Shidi's avatar
Autodoc    
Qusai Al Shidi committed
27
These are automatically imported.
28

29
30
31
- `swmfpy.io` Input/Output tools.
- `swmfpy.paramin` PARAM.in editing tools.
- `swmfpy.web` Internet data downloading/uploading tools.
32

33
### Extra Modules
34

Qusai Al Shidi's avatar
Autodoc    
Qusai Al Shidi committed
35
These are not automatically imported. Might have extra dependancies.
36

Qusai Al Shidi's avatar
Autodoc    
Qusai Al Shidi committed
37
*None yet.*
38

39
40
<a name=".swmfpy.write_imf_from_omni"></a>
#### write\_imf\_from\_omni
41
42

```python
43
write_imf_from_omni(time_from, time_to, filename='IMF.dat', **kwargs)
44
45
```

46
47
Writes an IMF.dat file for the geospace model runs for a specific time
period.
48
49
50

**Arguments**:

51
52
53
- `time_from` _datetime.datetime_ - Time to begin omni data retrieval
- `time_to` _datetime.datetime_ - Time to end omni data retrieval
- `filename` _str_ - The filename for the dat file, defaults to 'IMF.dat'.
54
  
55
56
  **kwargs:
  see `swmfpy.io.write_imf_input()` and `swmfpy.web.get_omni_data()`
57
58
59
60
  

**Examples**:

61
  Using this function is simple:
62
  ```python
63
64
65
66
67
68
69
  import swmfpy
  import datetime as dt
  times = (dt.datetime(2014, 2, 2), dt.datetime(2014, 2, 4))
  # Usually the kwargs are unecessary
  swmfpy.write_imf_input(*times)
  # Sometimes this
  swmfpy.write_imf_input(*times, filename='run/IMF.dat')
70
71
  ```

72
73
74
<a name=".swmfpy.web"></a>
## swmfpy.web

75
### Tools to download/upload data on the web
76
77

Here are a collection of tools to work with data on the internet. Thus,
78
79
80
this module mostly requires an internet connection. Which on some
supercomputers would be turned off during a job run. In scripts, make sure to
use these to preprocess before submitting jobs.
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100

<a name=".swmfpy.web.get_omni_data"></a>
#### get\_omni\_data

```python
get_omni_data(time_from, time_to, **kwargs)
```

Retrieve omni solar wind data over http.

This will download omni data from https://spdf.gsfc.nasa.gov/pub/data/omni
and put it into a dictionary. If your data is large, then make a csv and
use swmfpy.io.read_omni_data().

**Arguments**:

- `time_from` _datetime.datetime_ - The start time of the solar wind
  data that you want to receive.
- `time_to` _datetime.datetime_ - The end time of the solar wind data
  you want to receive.
101
102
103
104
105
106
107
108
  **kwargs:
- `original_colnames` _bool_ - Use the original column names from the
  spdf specification. The alternative is
  nicer and shorter names. Defaults to
  False.
- `resolution` _str_ - (default: 'high') Here you can choose 'high' or
  'low' resolution omni data. Some columns appear
  in one but not the other.
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
  

**Returns**:

- `dict` - This will be a list of *all* columns
  available in the omni data set.
  

**Examples**:

  ```python
  import datetime
  import swmfpy.web
  
  storm_start = datetime.datetime(year=2000, month=1, day=1)
  storm_end = datetime.datetime(year=2000, month=2, day=15)
  data = swmfpy.web.get_omni_data(time_from=storm_start,
  time_to=storm_end)
127
128
129
130
  # or for low res
  data = swmfpy.web.get_omni_data(time_from=storm_start,
  time_to=storm_end,
  resolution='low')
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
  ```

<a name=".swmfpy.web.download_magnetogram_hmi"></a>
#### download\_magnetogram\_hmi

```python
download_magnetogram_hmi(mag_time, hmi_map='hmi.B_720s', **kwargs)
```

Downloads HMI vector magnetogram fits files.

This will download vector magnetogram FITS files from
Joint Science Operations Center (JSOC) near a certain hour.

This unfortunately depends on sunpy and drms, if you don't have it try,


```bash
pip install -U --user sunpy drms
```

**Arguments**:

- `mag_time` _datetime.datetime_ - Time after which to find
  vector magnetograms.
- `hmi_map` _str_ - JSOC prefix for hmi maps. Currently can only do
  'hmi.B_720s' and 'hmi.b_synoptic.small'.
  
  **kwargs:
- `download_dir` _str_ - Relative directory to download to.
- `verbose` _bool_ - (default False) print out the files it's downloading.
  

**Returns**:

- `str` - list of filenames downloaded.
  

**Raises**:

- `ImportError` - If module `drms` is not found.
- `FileNotFoundError` - If the JSOC doesn't have the magnetograms for that
  time.
  

**Examples**:

  ```python
  from swmfpy.web import download_magnetogram_hmi
  import datetime as dt
  
  # I am interested in the hmi vector magnetogram from 2014, 2, 18
  time_mag = dt.datetime(2014, 2, 18, 10)  # Around hour 10
  
  # Calling it will download
  filenames = download_magnetogram_hmi(mag_time=time_mag,
  hmi_map='B_720s',
  download_dir='mydir/')
  
  # To see my list
  print('The magnetograms I downloaded are:', filenames)
  
  # You may call and ignore the file list
  download_magnetogram_hmi(mag_time=time_mag,
  hmi_map='b_synoptic_small',
  download_dir='mydir')
  ```

<a name=".swmfpy.web.download_magnetogram_adapt"></a>
#### download\_magnetogram\_adapt

```python
download_magnetogram_adapt(time, map_type='fixed', **kwargs)
```

This routine downloads GONG ADAPT magnetograms.

Downloads ADAPT magnetograms from ftp://gong2.nso.edu/adapt/maps/gong/
to a local directory. It will download all maps with the regex file
pattern: adapt4[0,1]3*yyyymmddhh

**Arguments**:

- `time` _datetime.datetime_ - Time in which you want the magnetogram.
- `map_type` _str_ - (default: 'fixed')
  Choose either 'fixed' or 'central' for
  the map type you want.
  
  **kwargs:
- `download_dir` _str_ - (default is current dir) Relative directory
  where you want the maps to be downloaded.
  

**Returns**:

- `str` - First unzipped filename found.
  

**Raises**:

- `NotADirectoryError` - If the adapt maps directory
  is not found on the server.
- `ValueError` - If map_type is not recognized.
  (i.e. not 'fixed' or 'central')
- `FileNotFoundError` - If maps were not found.
  

**Examples**:

  ```python
  import datetime as dt
  
  # Use datetime objects for the time
  time_flare = dt.datetime(2018, 2, 12, hour=10)
  swmfpy.web.download_magnetogram_adapt(time=time_flare,
  map_type='central',
  download_dir='./mymaps/')
  ```

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
<a name=".swmfpy.io"></a>
## swmfpy.io

### Input/Output tools

Here are tools to read and write files relating to SWMF.

<a name=".swmfpy.io.write_imf_input"></a>
#### write\_imf\_input

```python
write_imf_input(imf_data, filename='IMF.dat', **kwargs)
```

Creates the IMF.dat input file for the SWMF BATS-R-US geospace model.

`imf_data` must be a dictionary of array_like objects with same length
in data. In swmfpy Pythonic versions are always preferred so the 'times'
must be `datetime.datetime` array.
imf_data = dict(times, bx, by, bz, vx, vy, vz, density, temperature)

**Arguments**:

- `imf_data` _dict_ - This dictionary contains the solar wind data.
- `filename` _str_ - (default: 'IMF.dat') Filename to write to.
  **kwargs:
- `commands` _[str]_ - (default: None) List of commands to write to imf
  input file (indexed by line then by tabs on same
  line). *Note*: Must be a list if have one command
  str.
  

**Raises**:

- `TypeError` - If commands is not a list or tuple. It must be at least a
  one element list of strings.
- `AssertionError` - If inputs aren't prepared properly (key names)
  

**Examples**:

  ```python
  from swmfpy.io import write_imf_input
  
  # Prepare imf dictionary: imf_data
  write_imf_input(imf_data, filename='run/IMF.dat')
  ```

<a name=".swmfpy.io.read_wdc_ae"></a>
#### read\_wdc\_ae

```python
read_wdc_ae(wdc_filename)
```

Read an auroral electrojet (AE) indeces from Kyoto's World Data Center
text file into a dictionary of lists.

**Arguments**:

  
- `wdc_filename` _str_ - Filename of wdc data from
  http://wdc.kugi.kyoto-u.ac.jp/

**Returns**:

- `dict` - Auroral indeces 'AL', 'AE', 'AO', 'AU'
- `datetime.datetime` - 'times'
- `int` - 'values'

<a name=".swmfpy.io.read_wdc_asy_sym"></a>
#### read\_wdc\_asy\_sym

```python
read_wdc_asy_sym(wdc_filename)
```

Reads a WDC file for ASY/SYM data.

Reads an ASY/SYM file downloaded from
http://wdc.kugi.kyoto-u.ac.jp/aeasy/index.html
and puts it into a dictionary.

**Arguments**:

- `wdc_filename` _str_ - Relative filename (or file handle no.) to read.
  

**Returns**:

- `dict` - of values. {'[ASY-SYM]-[D-H]': 'times': [], 'values': []}
  

**Examples**:

  ```python
  indeces = swmfpy.io.read_wdc_asy_sym('wdc.dat')
  # Plot data
  plt.plot(indeces['SYM-H']['times'],
  indeces['SYM-H']['values'],
  label='SYM-H [nT]'
  )
  plt.xlabel('Time [UT]')
  ```
  
  Important to note if there is bad data it will be filled as None.

<a name=".swmfpy.io.read_gm_log"></a>
#### read\_gm\_log

```python
read_gm_log(filename, colnames=None, dtypes=None, index_time=True)
```

Make a dictionary out of the indeces outputted
from the GM model log.

**Arguments**:

- `filename` _str_ - The relative filename as a string. (or file handle no.)
- `colnames` _[str]_ - (default: None) Supply the name of the columns.
  If None it will use second line
  of log file.
- `dtypes` _[types]_ - (default: None) Provide types for the columns, if
  None then all will be float.
- `index_time` _bool_ - (default: True) Make a column of dt.datetime objects
  in dictionary key 'Time [UT]'.
  

**Returns**:

- `dict` - Dictionary of the log file
  

**Examples**:

  To plot AL and Dst get the log files
  ```python
  geo = swmfpy.io.read_gm_log('run/GM/IO2/geoindex_e20140215-100500.log')
  dst = swmfpy.io.read_gm_log('run/GM/IO2/log_e20140215-100500.log')
  
  # Plot AL indeces
  plt.plot(geo['times', geo['AL'])
  ```

Qusai Al Shidi's avatar
Qusai Al Shidi committed
395
396
<a name=".swmfpy.paramin"></a>
## swmfpy.paramin
397

398
399
400
### Editing PARAM.in files

These tools are to help script the editing and reading of PARAM.in files.
401

Qusai Al Shidi's avatar
Qusai Al Shidi committed
402
403
<a name=".swmfpy.paramin.replace_command"></a>
#### replace\_command
404

Qusai Al Shidi's avatar
Autodoc    
Qusai Al Shidi committed
405
406
407
```python
replace_command(parameters, input_file, output_file='PARAM.in')
```
Qusai Al Shidi's avatar
Qusai Al Shidi committed
408

409
410
411
412
Replace values for the parameters in a PARAM.in file.

Note, if you have repeat commands this will replace all the repeats.

Qusai Al Shidi's avatar
Qusai Al Shidi committed
413
**Arguments**:
414

Qusai Al Shidi's avatar
Qusai Al Shidi committed
415
- `parameters` _dict_ - Dictionary of strs with format
416
  replace = '#COMMAND': ['value', 'comments', ...]
Qusai Al Shidi's avatar
Qusai Al Shidi committed
417
418
419
420
  This is case sensitive.
- `input_file` _str_ - String of PARAM.in file name.
- `output_file` _str_ - (default 'PARAM.in') The output file to write to.
  A value of None will not output a file.
421

Qusai Al Shidi's avatar
Qusai Al Shidi committed
422
**Returns**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
423

Qusai Al Shidi's avatar
Qusai Al Shidi committed
424
425
  A list of lines of the PARAM.in file that would be outputted.
  
426

Qusai Al Shidi's avatar
Qusai Al Shidi committed
427
**Raises**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
428

Qusai Al Shidi's avatar
Qusai Al Shidi committed
429
430
- `TypeError` - If a value given couldn't be converted to string.
  
431

Qusai Al Shidi's avatar
Qusai Al Shidi committed
432
**Examples**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
433

Qusai Al Shidi's avatar
Qusai Al Shidi committed
434
  ```python
435
  change['#SOLARWINDFILE'] = [['T', 'UseSolarWindFile'],
Qusai Al Shidi's avatar
Qusai Al Shidi committed
436
437
438
439
  ['new_imf.dat', 'NameSolarWindFile']]
  # This will overwrite PARAM.in
  swmfpy.paramin.replace('PARAM.in.template', change)
  ```
Qusai Al Shidi's avatar
Qusai Al Shidi committed
440

Qusai Al Shidi's avatar
Qusai Al Shidi committed
441
442
<a name=".swmfpy.paramin.read_command"></a>
#### read\_command
Qusai Al Shidi's avatar
Qusai Al Shidi committed
443
444

```python
Qusai Al Shidi's avatar
Qusai Al Shidi committed
445
read_command(command, paramin_file='PARAM.in', **kwargs)
Qusai Al Shidi's avatar
Qusai Al Shidi committed
446
447
```

Qusai Al Shidi's avatar
Qusai Al Shidi committed
448
Get parameters of a certain command in PARAM.in file.
Qusai Al Shidi's avatar
Qusai Al Shidi committed
449

450
This will find the #COMMAND and return a list of
451
values for the parameters.
Qusai Al Shidi's avatar
Qusai Al Shidi committed
452

Qusai Al Shidi's avatar
Qusai Al Shidi committed
453
**Arguments**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
454

455
- `command` _str_ - This is the #COMMAND you're looking for.
Qusai Al Shidi's avatar
Qusai Al Shidi committed
456
457
458
459
460
461
- `paramin_file` _str_ - (default: 'PARAM.in') The file in which you're
  looking for the command values.
  **kwargs:
- `num_of_values` _int_ - (default: None) Number of values to take from
  command.
  
Qusai Al Shidi's avatar
Qusai Al Shidi committed
462

Qusai Al Shidi's avatar
Qusai Al Shidi committed
463
**Returns**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
464

465
466
- `list` - Values found for the #COMMAND in file. Index 0 is
  #COMMAND and the values follow (1 for first argument...)
Qusai Al Shidi's avatar
Qusai Al Shidi committed
467
  
Qusai Al Shidi's avatar
Qusai Al Shidi committed
468

Qusai Al Shidi's avatar
Qusai Al Shidi committed
469
**Raises**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
470

471
- `ValueError` - When the #COMMAND is not found.
Qusai Al Shidi's avatar
Qusai Al Shidi committed
472
  
Qusai Al Shidi's avatar
Qusai Al Shidi committed
473

Qusai Al Shidi's avatar
Qusai Al Shidi committed
474
**Examples**:
Qusai Al Shidi's avatar
Qusai Al Shidi committed
475

Qusai Al Shidi's avatar
Qusai Al Shidi committed
476
  ```python
477
478
  start_time = swmfpy.paramin.read_command('#STARTTIME')
  end_time = swmfpy.paramin.read_command('#ENDTIME')
Qusai Al Shidi's avatar
Qusai Al Shidi committed
479
480
481
482
483
484
485
  print('Starting month is ', start_time[1])
  print('Ending month is ', end_time[1])
  ```
  
  This will treat all following lines as values for the command. To suppress
  this, try using the `num_of_values` keyword. This is helpful if your
  PARAM.in is comment heavy.
Qusai Al Shidi's avatar
Qusai Al Shidi committed
486

487
488
489
490
491
492
<a name=".swmfpy.tools"></a>
## swmfpy.tools

Tools to be used in swmfpy functions and classes. Some of the functions are
*hidden functions*.