NGSF 0.0.2
Next Generation SuperFit in Python
License: MIT
Requires Python: >=3.7

# Welcome to NGSF - Next Generation SuperFit in Python! :dizzy: :bomb: :boom:

Superfit in python is a software for the spectral classification of Supernovae of all major types accompanied by a host galaxy. The following list of versions are the minumum requierments for its use.

NOTE: this is just a fork! I do not claim any authorship for NGSF, just the script provided `run_ngsf.py`. Find the original repo at [https://github.com/oyaron/NGSF](https://github.com/oyaron/NGSF).

## Requierments

- `Python version: 3.7.1`
- `numpy version: 1.21.2`
- `scipy version: 1.7.1`
- `matplotlib version: 3.0.2`
- `astropy version: 3.1`
- `Pandas version: 0.23.4`
- `PyAstronomy version: 0.13.0`

# Installation

From pip NGSF:

```code
pip install NGSF
```

From source:

```code
git clone https://github.com/temuller/NGSF.git
cd NGSF
pip install .
```

# Easy run

You can used the script provided in this fork to avoid complexity:

```code
python run_ngsf.py

usage: run_ngsf <object_to_fit> [options]

Next Generation SuperFit script by T. Müller-Bravo

positional arguments:
  object_to_fit         The object to analyze.

options:
  -h, --help            show this help message and exit
  -z Z_EXACT, --z_exact Z_EXACT
                        Exact redshift value that will be used if different from '0'
                        (default: 0)
  --z_range_begin Z_RANGE_BEGIN
                        Redshift value to begin the redshift array to look for the best
                        fit. (default: 0)
  --z_range_end Z_RANGE_END
                        Redshift value to end the redshift array to look for the best
                        fit. (default: 0.1)
  --z_int Z_INT         Redshift step to create the redshift array to look for the best
                        fit. (default: 0.01)
  -r RESOLUTION, --resolution RESOLUTION
                        The resolution of the fit, the default is 10Å, however, if the
                        spectra is of lower quality then the fit will be performed
                        automatically at 30Å. (default: 10)
  --lower_lam LOWER_LAM
                        Lower bound for wavelength over which to perform the fit.
                        (default: 0)
  --upper_lam UPPER_LAM
                        Upper bound for wavelength over which to perform the fit, if
                        this is equal to 'lower_lam' then the wavelength range will be
                        chosen automatically as that of the object to fit ± 300Å
                        (default: 0)
  --error_spectrum ERROR_SPECTRUM
                        refers to the type of routine used to perform the calculation of
                        the error spectrum. The recommended one is sg Savitzky-Golay,
                        there is also the option of linear estimation and the option
                        included in which the user can use the error spectrum that comes
                        with an object if he wants to, however, this is not recommended.
                        (default: sg)
  -s SAVING_RESULTS_PATH, --saving_results_path SAVING_RESULTS_PATH
                        Path in which to save the performed fits, the default one is the
                        superfit folder. (default: )
  --minimum_overlap MINIMUM_OVERLAP
                        Minimum percentage overlap between the template and the object
                        of interest. Recommendation is for this to stay near 0.7
                        (default: 0.7)           
  -p {0,1}, --show_plot {0,1}   To show the plotted fit or no, the default being 1, to show.
                        (default: 1)
  --how_many_plots HOW_MANY_PLOTS
                        Number of plots to show if the user wants to show, if the 'show'
                        is zero then 'n' has no effect. (default: 5)
  --mask_galaxy_lines {0,1}
                        Either 1 or 0, masks the galaxy lines for both the template bank
                        and the object of interest. For this option to work the redshift
                        must be one defined values and not at array of values, meaning
                        'z_int' must be equal to zero and 'z_start' must be the redshift
                        of choice. (default: 1)
  --mask_telluric {0,1}
                        Either 1 or 0, masks the flux within the wavelength range from
                        7594 to 7680 in the observer's frame. (default: 1)
  --epoch_high EPOCH_HIGH
                        Upper bound epoch for phase truncation. If this equals the
                        'epoch_low' parameter then there is not phase truncation.
                        (default: 0)
  --epoch_low EPOCH_LOW
                        Lower bound epoch for phase truncation. (default: 0)
  --Alam_high ALAM_HIGH
                        High value for the extinction law constant. (default: 2)
  --Alam_low ALAM_LOW   Lower value for the extinction law constant. (default: -2)
  --Alam_interval ALAM_INTERVAL
                        Size of interval. (default: 0.2)

```

Example:

```code
python run_ngsf SN2021urb_2021-08-06_00-00-00_Keck1_LRIS_TNS.flm -z 0.127
```
The first time you run the `run_ngsf.py` script, it will download the WISeREP templates bank into your local installation of NGSF, which might take a minute or two.

You can also make the script executable from any path:

```code
chmod +x run_ngsf.py
```

# To run one object
The user must make sure to have a template bank to look at. The new template bank can be downloaded from WISeREP [here](https://www.wiserep.org/content/wiserep-getting-started#supyfit).


The user must download the full superfit folder and place the bank inside it, also any spectra to be analyzed. The user only changes the parameters from the json file already within the folder, the following is an explanation of the parameters.


## The parameters of the fit

The user must only change the parameters of the fit from the parameters.json file, the file looks like this (the template for this example is included in the git)


    "object_to_fit" : "SN2021urb_2021-08-06_00-00-00_Keck1_LRIS_TNS.flm",

    "use_exact_z": 1,
    "z_exact": 0.127,


    "z_range_begin": 0,
    "z_range_end": 0.13,
    "z_int": 0.01,


    "resolution":10,

    "temp_sn_tr"  : ["IIb-flash", "computed", "Ia 02es-like", "Ia-02cx like", "TDE He", "Ca-Ia",
                    "Ia-CSM-(ambigious)", "II", "super_chandra", "SLSN-II", "IIn", "FBOT", "Ibn",
                    "SLSN-IIn", "Ia 91T-like", "IIb", "TDE H", "SN - Imposter", "II-flash", "ILRT",
                    "Ia 99aa-like", "Ic", "SLSN-I", "Ia-pec", "Ib", "Ia-CSM", "Ia-norm", "SLSN-Ib",
                    "TDE H+He", "Ia 91bg-like", "Ca-Ib", "Ia-rapid", "Ic-BL", "Ic-pec", "SLSN-IIb"],

    "temp_gal_tr" : ["E","S0","Sa","Sb","SB1","SB2","SB3","SB4","SB5","SB6","Sc"],

    "lower_lam": 0,
    "upper_lam": 0,

    "error_spectrum" : "sg",
    "saving_results_path" : "",

    "show_plot" : 1,
    "how_many_plots" : 1,

    "mask_galaxy_lines":1,
    "mask_telluric":0,

    "minimum_overlap": 0.7,

    "epoch_high": 0,
    "epoch_low" : 0,

    "Alam_high": 2,
    "Alam_low": -2,
    "Alam_interval":0.2



`"object_to_fit"` : the object to analyze, should be located within the superfit folder.

`"use_exact_z"`: can be 1 (yes) or 0 (no). Determines wether the redshift will be an exact number or an array.

`"z_exact"`    : exact redshift value that will be used if `"use_exact_z"` = 1

`"z_range_begin"`, `"z_range_end"`, `"z_int"`: redshift values from which to build an array over which to look for the best fit.

`"resolution"`: the resolution of the fit, the default is 10Å, however, if the spectra is of lower quality then the fit will be performed automatically at 30Å.

`"temp_gal_tr"`, `"temp_sn_tr"`: template library folders over which to look in order to find the fit. It is recommended that the user uses the full library as is.

`"lower_lam"`: Lower bound for wavelength over which to perform the fit
`"upper_lam"`: Upper bound for wavelength over which to perform the fit, if this is equal to `"lower_lam"` then the wavelength range will be chosen automatically as that of the object to fit ± 300Å

`"error_spectrum"` : refers to the type of routine used to perform the calculation of the error spectrum. The recommended one is `sg` Savitzky-Golay, there is also the option of `linear` estimation and the option `included` in which the user can use the error spectrum that comes with an object if he wants to, however, this is not recommended.

`"saving_results_path"`: path in which to save the performed fits, the default one is the superfit folder.

`"show_plot"` : to show the plotted fit or no, the default being 1, to show.
`"how_many_plots"`: number of plots to show if the user wants to show, if the `"show"` is zero then `"n"` has no effect.

`"mask_galaxy_lines"` : Either 1 or 0, masks the galaxy lines for both the template bank and the object of interest. For this option to work the redshift must be one defined values and not at array of values, meaning `"z_int"` must be equal to zero and `"z_start"` must be the redshift of choice.
`"mask_telluric"`: Either 1 or 0, masks the flux within the wavelength range from 7594 to 7680 in the observer's frame.

`"minimum_overlap"`: minimum percentage overlap between the template and the object of interest. Recommendation is for this to stay near 0.7

`"epoch_high"`: Upper bound epoch for phase truncation. If this equals the `"epoch_low"` parameter then there is not phase truncation.
`"epoch_low"`: Lower bound epoch for phase truncation.

`"Alam_high"`: High value for the extinction law constant
`"Alam_low"`: Lower value for the extinction law constant
`"Alam_interval"`: size of interval


## To Run

Once the parameters have been updated in the `parameters.json` file the user simply needs to run the script from the `run.py` file.

It is important to note that the file of the object to be analyzed should be within the superfit folder.




# Further details about the code


## New template bank

The improved Superfit template bank contains major subclasses such as: calcium rich supernovae, type II flashers, TDEs, SLSN-I and II, among others, separated in different folders for more accurate classification. The default option for binning in 10A.
The user must make sure to have this template bank or some alternative template bank of his own in order to run pySF, and please be mindful that pySF is only as good as the template bank it uses.


The user has the option to create a bank with masked lines, meaning to mask host galaxy lines that could be in the templates, this option is default to False. If the user is interested in seeing which lines are being masked he can access the `mask_lines_bank` function within the `Header_binnings.py` file.

It is important to note that when you open the folder of the bank there are two main subfolders, one named "original_resolution" and one named "binnings".
The "original_resolution" folder contains the raw spectra from the bank, with the wavelengths in observed frame. In the "binnings" folder we have the binned and redshift-corrected spectra from the "original_resolution" folder, and so the fits are done using the "binnings" folder.
Within the object subfolders inside the "original_resolution" folder we will find the wiserep files containing the metadata for each object (name,redshift, observational date, etc.) we use this metadata during the fit, and so we keep the folder.


## Main NGSF Function

In the `sf_class.py` file we find the main function which looks like this:


```python
all_parameter_space(self.int_obj,Parameters.redshift,Parameters.extconstant,Parameters.templates_sn_trunc,
                    Parameters.templates_gal_trunc, Parameters.lam, Parameters.resolution,Parameters.iterations,
                    kind=Parameters.kind, original= self.binned_name, save=self.results_name, show=show,
                    minimum_overlap=Parameters.minimum_overlap)
```



The inputs of the function are called from the Parameters class within the `params.py` file, and are as follow:

- `self.int_obj:` interpolated object to fit
- `redshift:` Can be an array or an individual number. These are the redshift values over which to optimize.
- `extconstant:` Array of values over which to optimize for the extinction constant. The user does not change this.
- `templates_sn_trunc:`  Truncated library of supernovae, aka: which SN types to look at when optimizing.
- `templates_gal_trunc:` Truncated library of host galaxies, aka: which HG types to look at when optimizing.
- `lam:` Lambda array over which to perform the fit. The default is from 3000 A to 10500 A.
- `resolution:` Resolution at which to bin and perform the fit. The default is 10 A.
- `kind:` Corresponds to the type of error spectrum the user prefers, the options are `SG`:Savitsky Golay, `linear`: for obtaining the error of the spectrum by making linear fit every 10 points, and `included`: if the user wants to use the error that comes with the object itself. The default is `sg`
- `save:` Name of results file
- `minimum_overlap:` Corresponds to minimum percentage overlap between the template and the object of interest


# Results

The results are: an astropy table that is saved as a csv file, and the best fit plots saved as pdf files (they both save to the superfit folder or to the specified `saving_results_path`)


## The output graphs look like this


![Output](ZTF18abokyfk_20180925_P60_v1_10_0.png)


The plot shows the input object in red, the SN and Host Galaxy combined templates in green. The legend shows the SN type, HG type and percentage contribution from the SN template to the fit. On top of the plot the redshift value is indicated.