CRL simulator

## Project description

### bnlcrl

Simulator of the compound refractive lenses (CRL).

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----
The code is written in Python, tested to be working under Linux and Windows with Python 2.7/3.5. There is no required NumPy dependency, but it still can be used for operations with matrices, etc. (see the `Usage` section below).

Determine Delta/Attenuation length:
-
To create a `.dat` file with the refractive index decrement or the attenuation length, use the following commands respectively:
```bash
bnlcrl simulate find-delta --characteristic delta -f Al -o Al_delta.dat 30
```

```bash
bnlcrl simulate find-delta --characteristic atten -f Al -o Al_atten.dat 30
```

Usage:
-
```
\$ bnlcrl simulate find-delta -h
usage: bnlcrl simulate find-delta [-h] [--calc-delta]
[--characteristic {transmission,atten,delta}]
[-d DATA_FILE] [--e-max E_MAX]
[--e-min E_MIN] [--e-step E_STEP]
[-f FORMULA] [-n N_POINTS] [-o OUTFILE]
[--plot] [--precise] [--save]
[--save-output] [--show-plot] [-t THICKNESS]
[-u] [-v]
energy

Determine the Index of Refraction (delta).

The index of refraction can be defined by three different methods/approaches:

1) Get delta for the closest energy from the saved *.dat files (see ``bnlcrl/package_data/dat/``).

2) Get delta from http://henke.lbl.gov/optical_constants/getdb2.html.

3) Calculate delta analytically (requires ``periodictable`` package installed).

Args:
calc_delta (bool): a flag to calculate delta analytically.
characteristic (str): characteristic to be extracted (``atten`` - attenuation length, ``delta`` - index of refraction, ``transmission`` - filter transmission).
data_file (str): a *.dat data file in ``bnlcrl/package_data/dat/`` directory with delta values for the material of the CRL (e.g., Be).
e_max (float): the highest available energy [eV].
e_min (float): the lowest available energy [eV].
e_step (float): energy step size used for saving data to a file [eV].
energy (float): photon energy [eV].
formula (str): material's formula of the interest.
n_points (int): number of points to get from the server.
outfile (str): optional output file.
plot (bool): a flag to plot the obtained data.
precise (bool): a flag to find delta within the energy interval +/- 1 eV from the specified energy.
save (bool): a flag to save the obtained data.
save_output (bool): a flag to save the output dictionary in JSON format.
show_plot (bool): a flag to show the show the plot.
thickness (float): thickness of the material.
use_numpy (bool): a flag to use NumPy.
verbose (bool): a flag to print output to console.

Returns:
dict: dictionary with the result.

positional arguments:
energy -

optional arguments:
-h, --help show this help message and exit
--calc-delta False
--characteristic {transmission,atten,delta}
'delta'
-d DATA_FILE, --data-file DATA_FILE
''
--e-max E_MAX 30000.0
--e-min E_MIN 30.0
--e-step E_STEP 10.0
-f FORMULA, --formula FORMULA
'Be'
-n N_POINTS, --n-points N_POINTS
500
-o OUTFILE, --outfile OUTFILE
''
--plot False
--precise False
--save False
--save-output False
--show-plot False
-t THICKNESS, --thickness THICKNESS
0.1
-u, --use-numpy False
-v, --verbose False
```

Examples of execution:
-
```bash
\$ bnlcrl simulate simulate-crl -p 6.52 -v --output-format json 2 4 6 7 8 21500
{
"d": 0.0012016728926447229,
"d_ideal": -0.06613035908221399,
"f": 1.0480597834969956,
"p0": 6.52,
"p1": 1.2487983271073553,
"p1_ideal": 1.3161303590822135
}
```

```bash
\$ bnlcrl simulate simulate-crl -p 6.52 -v --output-format csv 2 4 6 7 8 21500
"d","d_ideal","f","p0","p1","p1_ideal"
0.00120167289264,-0.0661303590822,1.0480597835,6.52,1.24879832711,1.31613035908
```

```bash
\$ bnlcrl simulate simulate-crl -p 6.52 -v --output-format txt 2 4 6 7 8 21500
d: 0.00120167289264, d_ideal: -0.0661303590822, f: 1.0480597835, p0: 6.52, p1: 1.24879832711, p1_ideal: 1.31613035908
```

```
\$ bnlcrl simulate simulate-crl -p 6.52 21500 -v
"d","d_ideal","f","p0","p1","p1_ideal"
0,0,0,6.52,0,0
```

This library is used on the SMI beamline at NSLS-II:
![transfocator](docs/transfocator.png)

![attenuation filters](docs/attenuation_filters.png)

## Project details

This version 20180115.183948 20171007.55002 20170614.123305 20170613.191338 20170531.195009 20170531.193959 20170529.215428 20170529.213346 20170524.205552 20170315.214808 20161108.183133 20161108.182933 20160912.35008 20160912.24109 20160912.23733 20160912.21244 20160912.14142 20160912.2706 20160912.857 20160831.212001 20160831.210458 20160812.184118 20160804.225043 20160725.40445 20160722.213330 20160722.205509 20160722.180155 20160721.233144 20160721.225654 20160720.154153 20160720.70806 20160720.65434 20160720.51011 20160720.50216 20160720.44628 20160719.193909 20160719.163315 20160719.3 20160718.235828 20160718.235044 20160718.234731 20160718.234503 20160718.233740 20160718.34538 20160715.152024 20160714.223307 20160714.200205 20160714.195854 20160714.173121 20160713.155519 20160713.535