use .ini instead of.yml instrument files

maoppy/data/muse_nfm.ini

 [metadata]
 ; Tag
-tag = "muse_nfm"
+tag = muse_nfm
 ; Human readable name
-name = "VLT MUSE (NFM)"
+name = VLT MUSE (NFM)
 
 [telescope]
 ; Primary diameter [m]

maoppy/data/muse_nfm.yml

-d: 8.0
-filters: {}
-fullname: VLT MUSE (NFM)
-gain: 5.0
-nact: 34
-name: MUSE_NFM
-occ: 0.14
-phasemask_path: null
-phasemask_shift: !!python/tuple
-- 0.0
-- 0.0
-res: 1.1977272727272726e-07
-ron: 15.0

maoppy/data/muse_wfm.ini

 [metadata]
 ; Tag
-tag = "muse_wfm"
+tag = muse_wfm
 ; Human readable name
-name = "VLT MUSE (WFM)"
+name = VLT MUSE (WFM)
 
 [telescope]
 ; Primary diameter [m]

maoppy/data/muse_wfm.yml

-d: 8.0
-filters: {}
-fullname: VLT MUSE (WFM)
-gain: 5.0
-nact: 34
-name: MUSE_WFM
-occ: 0.14
-phasemask_path: null
-phasemask_shift: !!python/tuple
-- 0.0
-- 0.0
-res: 9.698196540301804e-07
-ron: 15.0

maoppy/data/zimpol.ini

 [metadata]
 ; Tag
-tag = "zimpol"
+tag = zimpol
 ; Human readable name
-name = "VLT SPHERE/Zimpol"
+name = VLT SPHERE/Zimpol
 
 [telescope]
 ; Primary diameter [m]

maoppy/data/zimpol.yml

-d: 8.0
-filters:
-  N_R: !!python/tuple
-  - 6.459e-07
-  - 5.6700000000000005e-08
-  V: !!python/tuple
-  - 5.54e-07
-  - 8.06e-08
-fullname: VLT SPHERE/ZIMPOL
-gain: 10.5
-nact: 40
-name: ZIMPOL
-occ: 0.14
-phasemask_path: null
-phasemask_shift: !!python/tuple
-- 0.0
-- 0.0
-res: 1.69683257918552e-08
-ron: 20.0

maoppy/example/fit_muse_simulated_psf.py

@@ -24,7 +24,7 @@ from maoppy.instrument import muse_nfm
 npix = 128 # pixel size of PSF
 wvl = 600*1e-9 # wavelength [m]
 
-flux = 1e5
+flux = 1e4
 ron = muse_nfm.ron
 bckgd = 1.0
 
@@ -34,8 +34,8 @@ Pmodel = Psfao((npix,npix),system=muse_nfm,samp=samp)
 
 #%% Generate a MUSE-NFM PSF
 r0 = 0.15 # Fried parameter [m]
-b = 1e-7 # Phase PSD background [rad² m²]
-amp = 1.4 # Phase PSD Moffat amplitude [rad²]
+b = 1e-2 # Phase PSD background [rad² m²]
+amp = 3.0 # Phase PSD Moffat amplitude [rad²]
 alpha = 0.1 # Phase PSD Moffat alpha [1/m]
 ratio = 1.0
 theta = 0.0
@@ -49,7 +49,7 @@ noise = ron*np.random.randn(npix,npix)
 image = flux*psf + bckgd + noise
 
 #%% Fit the PSF with Psfao
-guess = [0.145,2e-7,1.2,0.08,ratio,theta,1.5]
+guess = [0.145,2e-2,1.2,0.08,ratio,theta,1.5]
 w = np.ones_like(image)/ron**2.0
 fixed = [False,False,False,False,True,True,False]
 

maoppy/example/fit_muse_simulated_psf_small_fov.py

@@ -32,9 +32,9 @@ from maoppy.instrument import muse_nfm
 npix = 128 # pixel size of PSF
 wvl = 600*1e-9 # wavelength [m]
 
-flux = 1e6
+flux = 1e4
 ron = muse_nfm.ron
-bckgd = 10.0
+bckgd = 1.0
 
 #%% Initialize PSF model
 samp = muse_nfm.samp(wvl) # sampling (2.0 for Shannon-Nyquist)
@@ -42,8 +42,8 @@ Pmodel = Psfao((npix,npix),system=muse_nfm,samp=samp)
 
 #%% Generate a MUSE-NFM PSF
 r0 = 0.15 # Fried parameter [m]
-b = 1e-7 # Phase PSD background [rad² m²]
-amp = 1.4 # Phase PSD Moffat amplitude [rad²]
+b = 1e-2 # Phase PSD background [rad² m²]
+amp = 3.0 # Phase PSD Moffat amplitude [rad²]
 alpha = 0.1 # Phase PSD Moffat alpha [1/m]
 ratio = 1.0 # Phase PSD Moffat ellipticity
 theta = 0.0 # Phase PSD Moffat angle
@@ -57,12 +57,12 @@ noise = ron*np.random.randn(npix,npix)
 image = flux*psf + bckgd + noise
 
 #%% Crop the image
-ncrop = 32
+ncrop = 40
 im_crop = image[npix//2-ncrop//2:npix//2+ncrop//2,
                 npix//2-ncrop//2:npix//2+ncrop//2]
 
 #%% Fit the cropped image with Psfao
-guess = [0.145,2e-7,1.2,0.08,ratio,theta,1.5]
+guess = [0.145,2e-2,1.2,0.08,ratio,theta,1.5]
 w = np.ones_like(im_crop)/ron**2.0
 fixed = [False,False,False,False,True,True,False]
 

maoppy/instrument.py

@@ -8,8 +8,7 @@ Created on Mon May 27 17:30:51 2019
 
 import sys
 import os
-
-import yaml
+from configparser import ConfigParser
 from astropy.io import fits
 import numpy as np
 from scipy.interpolate import interp2d
@@ -17,13 +16,6 @@ from scipy.interpolate import interp2d
 from maoppy.utils import circarr as _circarr
 from maoppy.utils import RAD2ARCSEC as _RAD2ARCSEC
 
-
-def _get_data_folder():
-    folder = os.path.abspath(__file__)
-    folder = os.sep.join(folder.split(os.sep)[0:-1])+os.sep+'data'+os.sep
-    return folder
-
-
 #%% INSTRUMENT CLASS
 class Instrument:
     """Represents an optical system (telescope to detector)
@@ -48,7 +40,7 @@ class Instrument:
         Pixel binning factor (default=1)
     """
 
-    def __init__(self, D=None, occ=0., res=None, Nact=0, gain=1., ron=0.):
+    def __init__(self, D=None, occ=0., res=None, Nact=0, gain=1., ron=1.):
         
         if D is None:
             raise ValueError("Please enter keyword `D` to set Instrument's aperture diameter")
@@ -136,42 +128,63 @@ class Instrument:
         """Returns wavelength for the given sampling"""
         return samp*(self.resolution_rad*self.D)
 
-    def to_yaml(self,filename):
-        """Save current instrument as YAML"""
-        data = {}
-        data['name'] = self.name
-        data['fullname'] = self.fullname
-        data['d'] = self.D
-        data['occ'] = self.occ
-        data['res'] = self.resolution_rad
-        data['gain'] = self.gain
-        data['ron'] = self.ron
-        data['nact'] = self.Nact
-        data['filters'] = self.filters
-        data['phasemask_path'] = self.phasemask_path
-        data['phasemask_shift'] = self.phasemask_shift
-        with open(filename,'w') as f:
-            yaml.dump(data,f)
 
 #%% LOAD INSTRUMENT INSTANCES (make them attributes of this module)
 # this might be clumsy, should I make something like this:
 # from maoppy.instrument import load_instrument
 # zimpol = load_instrument("zimpol")
 
+def _get_data_folder():
+    folder = os.path.abspath(__file__)
+    folder = os.sep.join(folder.split(os.sep)[0:-1])+os.sep+'data'+os.sep
+    return folder
+
+
+def _get_all_ini(pth):
+    return [f for f in os.listdir(pth) if f.endswith('.ini')]
+
+
+def load_ini(pth):
+    """Create an Instrument instance from a path to a .ini file"""
+    config = ConfigParser()
+    config.optionxform = str
+    try:
+        config.read(pth)
+    except:
+        raise FileNotFoundError("The instrument file has not been found")
+    # [metadata]
+    tag = config['metadata']['tag']
+    name = config['metadata']['name']
+    # [telescope]
+    d = float(config['telescope']['d'])
+    occ = float(config['telescope']['occ'])
+    # [ao]
+    nact = int(config['ao']['nact'])
+    # [camera]
+    res_mas = float(config['camera']['res_mas'])
+    # [filters]
+    filters = {}
+    if 'filters' in config.keys():
+        for filt in config['filters']:
+            s = config['filters'][filt]
+            wvl_central,width = s[1:-1].split(',')
+            filters[filt] = (float(wvl_central)*1e-9,float(width)*1e-9)
+    # Make instrument
+    res_rad = res_mas*1e-3 / _RAD2ARCSEC
+    instru = Instrument(D=d,occ=occ,res=res_rad,Nact=nact)
+    instru.name = tag
+    instru.fullname = name
+    instru.filters = filters
+    return instru
+    
+
+
 _this_module = sys.modules[__name__]
 _d = _get_data_folder()
-_l = [_f for _f in os.listdir(_d) if _f.endswith('.yml')]
-for _f in _l:
-    with open(_d+_f,'r') as _fi:
-        _i = yaml.full_load(_fi)
-    _instru = Instrument(D=_i['d'],occ=_i['occ'],res=_i['res'],gain=_i['gain'],ron=_i['ron'],Nact=_i['nact'])
-    _instru.name = _i['name']
-    _instru.fullname = _i['fullname']
-    _instru.filters = _i['filters']
-    _instru.phasemask_path = _i['phasemask_path']
-    _instru.phasemask_shift = _i['phasemask_shift']
-    _n = _i['name'].lower().replace(" ","_") # format name
+for _f in _get_all_ini(_d):
+    _instru = load_ini(_d+_f)
+    _n = _instru.name.lower().replace(" ","_") # format name
     setattr(_this_module, _n, _instru)
     
-del _this_module, _d, _l, _f, _instru, _fi, _i, _n
+del _this_module, _d, _f, _instru, _n
 

setup.py

@@ -15,8 +15,8 @@ setup(name='maoppy',
       author='Romain JL Fetick (LAM, Marseille, France)',
       author_email='romain.fetick@lam.fr',
       description='Modelization of the Adaptive Optics Psf in PYthon (MAOPPY)',
-      package_data={'maoppy': ['data/*.yml']},
+      package_data={'maoppy': ['data/*.ini']},
       include_package_data=True,
       packages=find_packages(exclude=['example','test']),
-      requires=['numpy','scipy','astropy','pyyaml'],
+      requires=['numpy','scipy','astropy'],
       zip_safe=False)