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# Table of Contents

* [swmfpy](#.swmfpy)
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  * [write\_imf\_from\_omni](#.swmfpy.write_imf_from_omni)
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* [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)
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* [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)
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* [swmfpy.paramin](#.swmfpy.paramin)
  * [replace\_command](#.swmfpy.paramin.replace_command)
  * [read\_command](#.swmfpy.paramin.read_command)
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* [swmfpy.tools](#.swmfpy.tools)
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<a name=".swmfpy"></a>
## swmfpy
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A collection of tools to read, write, visualize with the
Space Weather Modeling Framework (SWMF).
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### Modules
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These are automatically imported.
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- `swmfpy.io` Input/Output tools.
- `swmfpy.paramin` PARAM.in editing tools.
- `swmfpy.web` Internet data downloading/uploading tools.
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### Extra Modules
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These are not automatically imported. Might have extra dependancies.
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*None yet.*
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<a name=".swmfpy.write_imf_from_omni"></a>
#### write\_imf\_from\_omni
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```python
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write_imf_from_omni(time_from, time_to, filename='IMF.dat', **kwargs)
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```

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Writes an IMF.dat file for the geospace model runs for a specific time
period.
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**Arguments**:

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- `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'.
  **kwargs:
  see `swmfpy.io.write_imf_input()` and `swmfpy.web.get_omni_data()`
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**Examples**:

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  Using this function is simple:
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  ```python
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  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')
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  ```

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

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### Tools to download/upload data on the web
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Here are a collection of tools to work with data on the internet. Thus,
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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.
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<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.
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  **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.
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**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)
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  # or for low res
  data = swmfpy.web.get_omni_data(time_from=storm_start,
  time_to=storm_end,
  resolution='low')
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  ```

<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/')
  ```

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<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'])
  ```

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<a name=".swmfpy.paramin"></a>
## swmfpy.paramin
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### Editing PARAM.in files

These tools are to help script the editing and reading of PARAM.in files.
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<a name=".swmfpy.paramin.replace_command"></a>
#### replace\_command
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```python
replace_command(parameters, input_file, output_file='PARAM.in')
```
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Replace values for the parameters in a PARAM.in file.

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

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**Arguments**:
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- `parameters` _dict_ - Dictionary of strs with format
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  replace = '\#COMMAND': ['value', 'comments', ...]
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  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.
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**Returns**:
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  A list of lines of the PARAM.in file that would be outputted.
  
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**Raises**:
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- `TypeError` - If a value given couldn't be converted to string.
  
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**Examples**:
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  ```python
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  change['\#SOLARWINDFILE'] = [['T', 'UseSolarWindFile'],
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  ['new_imf.dat', 'NameSolarWindFile']]
  # This will overwrite PARAM.in
  swmfpy.paramin.replace('PARAM.in.template', change)
  ```
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<a name=".swmfpy.paramin.read_command"></a>
#### read\_command
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```python
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read_command(command, paramin_file='PARAM.in', **kwargs)
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```

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Get parameters of a certain command in PARAM.in file.
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This will find the \#COMMAND and return a list of
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values for the parameters.
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**Arguments**:
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- `command` _str_ - This is the \#COMMAND you're looking for.
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- `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.
  
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**Returns**:
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- `list` - Values found for the \#COMMAND in file. Index 0 is
  \#COMMAND and the values follow (1 for first argument...)
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**Raises**:
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- `ValueError` - When the \#COMMAND is not found.
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**Examples**:
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  ```python
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  start_time = swmfpy.paramin.read_command('\#STARTTIME')
  end_time = swmfpy.paramin.read_command('\#ENDTIME')
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  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.
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<a name=".swmfpy.tools"></a>
## swmfpy.tools

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