From 882b7820fc4b59da36ace51189901696558b4a7a Mon Sep 17 00:00:00 2001
From: Romain Fetick <rfetick@OSU.PYTHEAS>
Date: Tue, 9 Jul 2024 15:47:12 +0200
Subject: [PATCH] simplify file headers, update FITS functions
---
maoppy/__init__.py | 26 +++----------
maoppy/instrument.py | 4 +-
maoppy/psffit.py | 3 +-
maoppy/psfmodel.py | 90 +++++++++++++++++++++++++++-----------------
maoppy/psfutils.py | 23 +----------
maoppy/utils.py | 4 +-
setup.py | 9 +----
7 files changed, 67 insertions(+), 92 deletions(-)
diff --git a/maoppy/__init__.py b/maoppy/__init__.py
index dfc7ad7..eed7660 100644
--- a/maoppy/__init__.py
+++ b/maoppy/__init__.py
@@ -1,21 +1,7 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Mon May 27 17:15:07 2019
+"""MAOPPY library"""
-@author: rfetick
-"""
-
-import sys as _sys
-import warnings as _warnings
-
-if _sys.version_info[0]<3:
- _warnings.warn("MAOPPY was developped on Python 3, but your Python version is anterior. We hope everything will be fine")
-
-# MAOPPY release version
-__version__ = "1.6.0"
-__author__ = "Romain JL. Fétick (LAM, France)"
-__date__ = "January 18th, 2022"
-
-from . import utils, instrument, psfutils, psfmodel, psffit
-# from maoppy import utils, instrument, psfmodel
+from . import utils
+from . import instrument
+from . import psfutils
+from . import psfmodel
+from . import psffit
diff --git a/maoppy/instrument.py b/maoppy/instrument.py
index 6888d7e..0ff45a8 100644
--- a/maoppy/instrument.py
+++ b/maoppy/instrument.py
@@ -1,7 +1,5 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
"""
-Created on Mon May 27 17:30:51 2019
+List of all available instruments loaded from the <data> folder.
@author: rfetick
"""
diff --git a/maoppy/psffit.py b/maoppy/psffit.py
index a723afd..d3c2b1b 100644
--- a/maoppy/psffit.py
+++ b/maoppy/psffit.py
@@ -1,6 +1,5 @@
-# -*- coding: utf-8 -*-
"""
-Created on Wed Nov 17 19:39:53 2021
+Methods to fit a PSF model on data.
@author: rfetick
"""
diff --git a/maoppy/psfmodel.py b/maoppy/psfmodel.py
index 96ece54..ca4345d 100644
--- a/maoppy/psfmodel.py
+++ b/maoppy/psfmodel.py
@@ -1,7 +1,5 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
"""
-Created on Mon May 27 17:31:18 2019
+All PSF models available in this library.
@author: rfetick
"""
@@ -11,7 +9,7 @@ import numpy as np
from scipy.fft import fft2, ifft2, fftshift, ifftshift
from astropy.io import fits
from maoppy.utils import binning, random_sample
-from maoppy.psfutils import moffat, gauss, oversample, moffat_center, make_fits_hdr
+from maoppy.psfutils import moffat, gauss, oversample, moffat_center
import warnings
__all__ = ["ParametricPSF", "ConstantPSF", "Moffat", "Gaussian",
@@ -53,6 +51,11 @@ class ParametricPSF:
"""Ordered list of the parameters names"""
return ["param_%u"%i for i in range(self._nparam)]
+ @property
+ def param_comment(self):
+ """Comment on the parameters (self.param_name)"""
+ return ["default name" for i in range(self._nparam)]
+
def dict2list(self, dctnry):
"""Transform a dictionary of parameters into a list"""
return [dctnry[k] for k in self.param_name]
@@ -73,12 +76,32 @@ class ParametricPSF:
"""Return the Modulation Transfer Function (MTF)"""
return np.abs(self.otf(args,kwargs))
- def tofits(self, param, filename, *args, **kwargs):
- """Save PSF as FITS data"""
+ def fits_header_read(self, hdr):
+ """Read a FITS header and return PSF parameters.
+ Also accepts a path to the FITS file."""
+ if type(hdr)==str:
+ fts = fits.open(hdr)
+ hdr = fts[0].header
+ fts.close()
+ param = [0]*len(self.param_name)
+ for i in range(len(self.param_name)):
+ param[i] = float(hdr[self.param_name[i]])
+ return param
+
+ def fits_header_make(self, param):
+ """Generate a FITS header and fill it with the given PSF parameters"""
+ hdr = fits.Header()
+ hdr['ORIGIN'] = 'MAOPPY automatic header'
+ for i in range(len(param)):
+ hdr[self.param_name[i]] = (param[i], self.param_comment[i])
+ return hdr
+
+ def fits_psf_write(self, param, filename, *args, **kwargs):
+ """Write PSF into a FITS file"""
psf = self.__call__(param, *args, **kwargs)
- hdr = make_fits_hdr(param, keys=self.param_name)
+ hdr = self.fits_header_make(param)
hdu = fits.PrimaryHDU(psf, hdr)
- hdu.writeto(filename) # overwrite ?
+ hdu.writeto(filename)
class ConstantPSF(ParametricPSF):
@@ -650,8 +673,8 @@ class Psfao(ParametricPSFfromPSD):
#bounds_down = [_EPSILON,0,0,_EPSILON,_EPSILON,-np.inf,1+_EPSILON]
#bounds_up = [np.inf for i in range(7)]
### Physical bounds
- bounds_down = [1e-3,0,0,1e-3,1e-2,-np.inf,1.01]
- bounds_up = [np.inf]*4 + [1e2,np.inf,5]
+ bounds_down = [1e-3, 0, 0, 1e-5, 1e-2, -np.inf, 1.01]
+ bounds_up = [np.inf]*4 + [1e2, np.inf, 5]
self.bounds = (bounds_down,bounds_up)
@@ -678,6 +701,17 @@ class Psfao(ParametricPSFfromPSD):
"""Ordered list of the parameters names"""
return ["r0","bck","amp","alpha","ratio","theta","beta"]
+ @property
+ def param_comment(self):
+ """Comment on the parameters (self.param_name)"""
+ comments = ["Fried parameter [m]",
+ "AO background [rad2 m2]",
+ "AO Moffat variance [rad2]",
+ "AO Moffat alpha [1/m]",
+ "AO Moffat sqrt(ax/ay) ratio",
+ "AO Moffat theta [rad]",
+ "AO Moffat beta"]
+ return comments
def var_corr(self, parampsd):
"""Return the numerical variance on the corrected area"""
@@ -802,31 +836,17 @@ class Psfao(ParametricPSFfromPSD):
return psd, integral
- def tofits(self, param, filename, *args, **kwargs):
- keys_comment = ["Fried parameter [m]",
- "AO background [rad2 m2]",
- "AO Moffat variance A [rad2]",
- "AO Moffat alpha [1/m]",
- "AO Moffat sqrt(ax/ay) ratio",
- "AO Moffat theta [rad]",
- "AO Moffat beta"]
-
- # redefine tofits() because extra hdr is required
- psf = self.__call__(param, *args, **kwargs)
- hdr = make_fits_hdr(param, keys=self.param_name, keys_comment=keys_comment)
-
- hdr['CDELT1'] = (self.system.resolution_mas,"pixel size")
- hdr['CUNIT1'] = ("mas","pixel size unit unit")
- hdr['CDELT2'] = (self.system.resolution_mas,"pixel size")
- hdr['CUNIT2'] = ("mas","pixel size unit unit")
- hdr["HIERARCH SYSTEM"] = (self.system.name,"System name")
- hdr["HIERARCH SYSTEM D"] = (self.system.D,"Primary mirror diameter")
- hdr["HIERARCH SYSTEM NACT"] = (self.system.Nact,"Linear number of AO actuators")
- hdr["HIERARCH SAMP"] = (self.samp,"Sampling (eg. 2 for Shannon)")
- hdr["HIERARCH lext"] = (self.lext,"Von-Karman outer scale")
-
- hdu = fits.PrimaryHDU(psf, hdr)
- hdu.writeto(filename)
+ def fits_header_make(self, param):
+ """Generate a FITS header and fill it with the given PSF parameters"""
+ hdr = super().fits_header_make(param)
+ # hdr['CDELT1'] = (self.system.resolution_mas,"pixel size")
+ # hdr['CUNIT1'] = ("mas","pixel size unit unit")
+ # hdr['CDELT2'] = (self.system.resolution_mas,"pixel size")
+ # hdr['CUNIT2'] = ("mas","pixel size unit unit")
+ hdr["SYSTEM"] = (self.system.name,"System name")
+ hdr["SAMP"] = (self.samp,"Sampling (eg. 2 for Shannon)")
+ hdr["LEXT"] = (self.lext,"Von-Karman outer scale")
+ return hdr
diff --git a/maoppy/psfutils.py b/maoppy/psfutils.py
index 20015d0..c5216f4 100644
--- a/maoppy/psfutils.py
+++ b/maoppy/psfutils.py
@@ -1,15 +1,13 @@
-# -*- coding: utf-8 -*-
"""
-Created on Tue Jan 18 12:02:10 2022
+List of useful functions to generate PSF.
@author: rfetick
"""
import numpy as np
-from astropy.io import fits
__all__ = ["oversample", "reduced_coord", "reduced_center_coord", "moffat",
- "moffat_center", "gauss", "make_fits_hdr"]
+ "moffat_center", "gauss"]
def oversample(samp, fixed_k = None):
@@ -216,20 +214,3 @@ def gauss(xxyy,param):
uu = reduced_coord(xxyy,ax,ay,param[2],param[3],param[4])
return np.exp(-uu) / (2*np.pi*param[0]*param[1])
-
-def make_fits_hdr(param, keys=None, keys_comment=None):
- """Define a header to save a .fits file"""
- if len(keys)!=len(param):
- raise ValueError("`keys` must be same size as `param`")
- if keys_comment is not None:
- if len(keys_comment)!=len(param):
- raise ValueError("When defined, `keys_comment` must be same size as `param`")
- hdr = fits.Header()
-
- hdr["HIERARCH ORIGIN"] = "MAOPPY automatic header"
- for i in range(len(param)):
- if keys_comment is None:
- hdr["HIERARCH PARAM "+keys[i]] = param[i]
- else:
- hdr["HIERARCH PARAM "+keys[i]] = (param[i],keys_comment[i])
- return hdr
diff --git a/maoppy/utils.py b/maoppy/utils.py
index e9c22aa..d096b11 100644
--- a/maoppy/utils.py
+++ b/maoppy/utils.py
@@ -1,7 +1,5 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
"""
-Created on Mon May 27 17:27:44 2019
+List of useful functions.
@author: rfetick
"""
diff --git a/setup.py b/setup.py
index a35bfbd..d1b052f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,13 +1,6 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Mon May 27 17:11:01 2019
-
-@author: rfetick
-"""
from setuptools import setup, find_packages
-
+
setup(name='maoppy',
version='1.6.0',
url='https://gitlab.lam.fr/lam-grd-public/maoppy.git',
--
GitLab