Merge branch 'master' into 'main'

build

See merge request shaosim/mci!1

LICENSE

+MIT License
+
+Copyright (c) 2022 CSST-L1
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

-# mci
+# csst_ifs_common
 
 
 
@@ -15,14 +15,14 @@ Already a pro? Just edit this README.md and make it your own. Want to make it ea
 
 ```
 cd existing_repo
-git remote add origin https://csst-tb.bao.ac.cn/code/shaosim/mci.git
+git remote add origin https://csst-tb.bao.ac.cn/code/csst-l1/ifs/csst_ifs_common.git
 git branch -M main
 git push -uf origin main
 ```
 
 ## Integrate with your tools
 
-- [ ] [Set up project integrations](https://csst-tb.bao.ac.cn/code/shaosim/mci/-/settings/integrations)
+- [ ] [Set up project integrations](http://10.3.10.28/code/csst-l1/ifs/csst_ifs_common/-/settings/integrations)
 
 ## Collaborate with your team
 

csst_mci_sim/mci_data/mci_sim_example.config

+[TEST]
+
+### user should define file path below
+inData_path =/home/yan/MCI_sim_Fabu/MCI_inputData
+
+result_path =/home/yan/MCI_sim_Fabu/mci_sim_result
+
+
+#size of the output image array, xsize is column, ysize is row, xsize = 9216,ysize = 9232
+xsize = 1000
+ysize = 1000 
+
+##prescan and overscan , do not change!!!
+prescan  = 27
+overscan = 320
+
+###sourcein = XDF, DARK, FLAT, BIAS
+
+sourcein=XDF
+
+##################################################
+####                                          ####    
+####Control flags (can be yes/no) ####
+##################################################
+
+cosmicRays     = yes
+
+darknoise      = yes 
+
+cosmetics      = yes
+
+radiationDamage= no
+
+bleeding       = yes
+
+overscans      = yes
+
+nonlinearity   = yes                           
+
+readoutNoise   = yes                             
+
+skyback        = yes
+
+TianceEffect   = yes
+
+intscale       = yes 
+
+ghosts         = yes
+
+shutterEffect      = yes                              
+
+flatfieldM         = yes 
+
+PRNUeffect         = yes 
+
+appFatt            = no 
+
+sky_shift_rot      = yes
+
+distortion         = no
+
+sim_star           = yes
+
+sim_galaxy         = yes   
+
+##############################################                             
+##############################################                            
+
+#CCD properties
+fullwellcapacity = 90000
+
+#dark noise in electrons per second
+dark = 0.001
+
+#exposure to simulate, exposure time
+exptime = 300.0
+
+###PNRU matrix sigma
+prnu_sigma=0.001
+
+### cosmicray coveringFraction
+coveringFraction=1.0
+
+
+#offset from the object, note that at the moment this is fixed, but in reality a focal plane position dependent.
+ghostOffsetX = 50
+ghostOffsetY = 50
+ghostRatio  = 1e-04
+
+
+
+####treering effect,bright fatter effect and difusion effect
+treering=0.1
+
+fatter=1.0
+
+difusion=0.1
+    
+### the choosen Filters in three CCDs   
+filter_g=u
+filter_r=F555W
+filter_i=F814W
+
+##['G_filters']=["F275W",  "F280N","NUV",   "WU",   "CBU",   "F343N",  "u",      "F373N", "F395N"," F336W"]
+##['R_filters']=["F487N", "F502N", "CBV",   "r",    "F656N", "F658N",  "F467M",  "F555W", "F606W",  "F673N"]        
+##['I_filters']=["z",      "y",    "F815N", "CBI",  "F925N", "F960M",  "F968N",  "F845M" ,"F850LP" ,"F814W"]
+
+####################
+g_gain1=1.53
+g_gain2=1.54
+g_gain3=1.55
+g_gain4=1.53
+g_gain5=1.51
+g_gain6=1.56
+g_gain7=1.58
+g_gain8=1.53
+g_gain9=1.54
+g_gain10=1.57
+g_gain11=1.51
+g_gain12=1.53
+g_gain13=1.55
+g_gain14=1.57
+g_gain15=1.53
+g_gain16=1.52
+
+#######################
+g_rdnois1=4.53
+g_rdnois2=4.54
+g_rdnois3=4.55
+g_rdnois4=4.53
+g_rdnois5=4.51
+g_rdnois6=4.56
+g_rdnois7=4.58
+g_rdnois8=4.53
+g_rdnois9=4.54
+g_rdnois10=4.57
+g_rdnois11=4.51
+g_rdnois12=4.53
+g_rdnois13=4.55
+g_rdnois14=4.57
+g_rdnois15=4.53
+g_rdnois16=4.52
+
+############################
+g_detbia1=500
+g_detbia2=510
+g_detbia3=514
+g_detbia4=520
+g_detbia5=524
+g_detbia6=540
+g_detbia7=530
+g_detbia8=532
+g_detbia9=534
+g_detbia10=526
+g_detbia11=532
+g_detbia12=516
+g_detbia13=540
+g_detbia14=560
+g_detbia15=536
+g_detbia16=528
+
+############################
+r_gain1=1.52
+r_gain2=1.54
+r_gain3=1.52
+r_gain4=1.55
+r_gain5=1.56
+r_gain6=1.52
+r_gain7=1.54
+r_gain8=1.6
+r_gain9=1.54
+r_gain10=1.52
+r_gain11=1.54
+r_gain12=1.57
+r_gain13=1.52
+r_gain14=1.55
+r_gain15=1.52
+r_gain16=1.55
+
+################################
+r_rdnois1=4.23
+r_rdnois2=4.24
+r_rdnois3=4.25
+r_rdnois4=4.23
+r_rdnois5=4.21
+r_rdnois6=4.26
+r_rdnois7=4.28
+r_rdnois8=4.23
+r_rdnois9=4.24
+r_rdnois10=4.27
+r_rdnois11=4.21
+r_rdnois12=4.23
+r_rdnois13=4.25
+r_rdnois14=4.27
+r_rdnois15=4.23
+r_rdnois16=4.22
+
+###################################
+r_detbia1=600
+r_detbia2=610
+r_detbia3=614
+r_detbia4=620
+r_detbia5=624
+r_detbia6=640
+r_detbia7=630
+r_detbia8=632
+r_detbia9=634
+r_detbia10=626
+r_detbia11=632
+r_detbia12=616
+r_detbia13=640
+r_detbia14=660
+r_detbia15=636
+r_detbia16=628
+
+###################################
+i_gain1=1.62
+i_gain2=1.64
+i_gain3=1.62
+i_gain4=1.65
+i_gain5=1.66
+i_gain6=1.62
+i_gain7=1.64
+i_gain8=1.6
+i_gain9=1.64
+i_gain10=1.62
+i_gain11=1.64
+i_gain12=1.67
+i_gain13=1.62
+i_gain14=1.65
+i_gain15=1.62
+i_gain16=1.65
+
+###################################
+i_rdnois1=4.63
+i_rdnois2=4.64
+i_rdnois3=4.65
+i_rdnois4=4.63
+i_rdnois5=4.61
+i_rdnois6=4.66
+i_rdnois7=4.68
+i_rdnois8=4.63
+i_rdnois9=4.64
+i_rdnois10=4.67
+i_rdnois11=4.61
+i_rdnois12=4.63
+i_rdnois13=4.65
+i_rdnois14=4.67
+i_rdnois15=4.63
+i_rdnois16=4.62
+
+#######################################
+i_detbia1=400
+i_detbia2=410
+i_detbia3=414
+i_detbia4=420
+i_detbia5=424
+i_detbia6=440
+i_detbia7=430
+i_detbia8=432
+i_detbia9=434
+i_detbia10=426
+i_detbia11=432
+i_detbia12=416
+i_detbia13=440
+i_detbia14=460
+i_detbia15=436
+i_detbia16=428
+
+####### end #######################
+
+
+
+
+
+        
+        
+
+
+
+
+

csst_mci_sim/support/MCIinstrumentModel.py

+"""
+VIS Instrument Model
+====================
+
+The file provides a function that returns VIS related information such as pixel
+size, dark current, gain, zeropoint, and sky background.
+
+:requires: NumPy
+:requires: numexpr
+
+:version: 0.7
+"""
+# import matplotlib
+# import matplotlib.pyplot as plt
+# import datetime, math
+# import numpy as np
+# import numexpr as ne
+
+
+def MCIinformation():
+    """
+    Returns a dictionary describing MCI CCD. The following information is provided (id: value - reference)::
+
+        
+         dob: 0 - CDM03 (Short et al. 2010)
+         fwc: 90000 - CCD spec EUCL-EST-RS-6-002 (for CDM03)      
+         rdose: 30000000000.0 - derived (above the PLM requirement)
+         sfwc: 730000.0 - CDM03 (Short et al. 2010), see also the CCD spec EUCL-EST-RS-6-002       
+         st: 5e-06 - CDM03 (Short et al. 2010)        
+         svg: 1e-10 - CDM03 (Short et al. 2010)
+         t: 0.01024 - CDM03 (Short et al. 2010)
+         trapfile: cdm_euclid.dat - CDM03 (derived, refitted to CCD204 data)
+         vg: 6e-11 - CDM03 (Short et al. 2010)
+         vth: 11680000.0 - CDM03 (Short et al. 2010)
+
+
+
+    :return: instrument model parameters
+    :rtype: dict
+    """
+
+    #########################################################################################################
+    out=dict()
+    out.update({'dob' : 0, 'rdose' : 8.0e9,
+                'parallelTrapfile' : 'cdm_euclid_parallel.dat', 'serialTrapfile' : 'cdm_euclid_serial.dat',
+                'beta_s' : 0.6, 'beta_p': 0.6, 'fwc' : 90000, 'vth' : 1.168e7, 't' : 20.48e-3, 'vg' : 6.e-11,
+                'st' : 5.0e-6, 'sfwc' : 730000., 'svg' : 1.0e-10})
+
+    return out
+
+
+def CCDnonLinearityModel(data, beta=6e-7):
+    """   
+
+    The non-linearity is modelled based on the results presented. 
+    :param data: data to which the non-linearity model is being applied to
+    :type data: ndarray
+
+    :return: input data after conversion with the non-linearity model
+    :rtype: float or ndarray
+    """
+    out = data-beta*data**2
+    
+    return out
+###################################################################
+
+if __name__ == '__main__':
+    print()

csst_mci_sim/support/logger.py

+"""
+These functions can be used for logging information.
+
+.. Warning:: logger is not multiprocessing safe.
+
+:version: 0.3
+"""
+import logging
+import logging.handlers
+
+
+def setUpLogger(log_filename, loggername='logger'):
+    """
+    Sets up a logger.
+
+    :param: log_filename: name of the file to save the log.
+    :param: loggername: name of the logger
+
+    :return: logger instance
+    """
+    # create logger
+    logger = logging.getLogger(loggername)
+    logger.setLevel(logging.DEBUG)
+    # Add the log message handler to the logger
+    handler = logging.handlers.RotatingFileHandler(log_filename)
+    #maxBytes=20, backupCount=5)
+    # create formatter
+    formatter = logging.Formatter('%(asctime)s - %(module)s - %(funcName)s - %(levelname)s - %(message)s')
+    # add formatter to ch
+    handler.setFormatter(formatter)
+    # add handler to logger 
+    
+    if (logger.hasHandlers()):
+        logger.handlers.clear()
+        
+    logger.addHandler(handler)
+
+    return logger
+
+
+class SimpleLogger(object):
+    """
+    A simple class to create a log file or print the information on screen.
+    """
+
+    def __init__(self, filename, verbose=False):
+        self.file = open(filename, 'w')
+        self.verbose = verbose
+
+    def write(self, text):
+        """
+        Writes text either to file or screen.
+        """
+        print >> self.file, text
+        if self.verbose: print( text)

csst_mci_sim/support/sed.py

+#!/usr/bin/env python
+# -*- coding:utf-8 -*-
+
+# @Author: Shuai Feng (hebtu.edu.cn)
+# @Time:   2022-09-25
+
+import numpy as np
+from scipy.interpolate import interp1d
+from astropy.io import fits
+from astropy.io import ascii
+from astropy import units as u
+
+# ----------------
+# Magnitude Module
+
+from scipy.interpolate import interp1d
+
+def Calzetti_Law(wave, Rv = 4.05):
+    """Dust Extinction Curve by Calzetti et al. (2000)
+
+    Args:
+        wave (float): Wavelength
+        Rv (float, optional): Extinction curve. Defaults to 4.05.
+
+    Returns:
+        float: Extinction value E(B-V)
+    """
+    
+    wave_number = 1./(wave * 1e-4)
+    reddening_curve = np.zeros(len(wave))
+    
+    idx = np.logical_and(wave >= 1200, wave <= 6300)
+    reddening_curve[idx] = 2.659 * ( -2.156 + 1.509 * wave_number[idx] - 0.198 * \
+                    (wave_number[idx] ** 2)) + 0.011 * (wave_number[idx] **3 ) + Rv
+                                    
+    idx = np.logical_and(wave >= 6300, wave <= 22000)
+    reddening_curve[idx] = 2.659 * ( -1.857 + 1.040 * wave_number[idx]) + Rv
+    return reddening_curve
+
+def reddening(wave, flux, ebv = 0.0, law = 'calzetti', Rv = 4.05):
+    """
+    Reddening an input spectra through a given reddening curve.
+
+    Args:
+        wave (float): Wavelength of input spectra
+        flux (float): Flux of input spectra
+        ebv (float, optional): Extinction value. Defaults to 0.
+        law (str, optional): Extinction curve. Defaults to 'calzetti'.
+        Rv (float, optional): _description_. Defaults to 4.05.
+
+    Returns:
+        float: Flux of spectra after reddening.
+    """
+    if law == 'calzetti':
+        curve = Calzetti_Law(wave, Rv = Rv)
+        fluxNew = flux / (10. ** (0.4 * ebv * curve))
+    return fluxNew
+
+def flux_to_mag(wave, flux, filepath, band='GAIA_bp'):
+    """Convert flux of given spectra to magnitude
+
+    Args:
+        wave (float): Wavelength
+        flux (float): Flux of spectra
+        band (str, optional): Filter band name. Defaults to 'GAIA_bp'.
+
+    Returns:
+        float: value of magnitude
+    """
+    # /home/yan/MCI_sim/MCI_input/SED_Code/data
+    import os
+    
+    #parent = os.path.dirname(os.path.realpath(__file__))
+    
+    parent=filepath
+    
+    band = ascii.read(parent+'/SED_Code/seddata/' + band + '.dat')
+    
+    wave0= band['col1']
+    curv0= band['col2']
+    
+    # Setting the response
+    func = interp1d(wave0, curv0)
+    response = np.copy(wave)
+    ind_extra = (wave > max(wave0)) | (wave < min(wave0))
+    response[ind_extra] = 0
+    ind_inside = (wave < max(wave0)) & (wave > min(wave0))
+    response[ind_inside] = func(wave[ind_inside])
+
+    # Total Flux
+    Tflux = np.trapz(flux * response, wave) / np.trapz(response, wave)
+    
+    return -2.5 * np.log10(Tflux)
+
+def calibrate(wave, flux, mag, filepath,band='GAIA_bp'):
+    """
+    Calibrate the spectra according to the magnitude.
+
+    Args:
+        wave (float): Wavelength
+        flux (float): Flux of spectra
+        mag (float): Input magnitude.
+        band (str, optional): Filter band name. Defaults to 'GAIA_bp'.
+
+    Returns:
+        float: Flux of calibrated spectra. Units: 1e-17 erg/s/A/cm^2
+    """
+    inst_mag = flux_to_mag(wave, flux,filepath ,band = band)
+    instflux = 10 ** (-0.4 * inst_mag)
+    realflux = (mag * u.STmag).to(u.erg/u.s/u.cm**2/u.AA).value
+
+    # Normalization
+    flux_ratio = realflux / instflux
+    flux_calibrate = flux * flux_ratio * 1e17                        # Units: 10^-17 erg/s/A/cm^2
+    
+    return flux_calibrate
+
+# ------------
+# SED Template
+
+class Gal_Temp():
+    """
+    Template of Galaxy SED
+    """
+    
+    def __init__(self,parent):
+        import os
+        
+        self.parent = parent
+        
+        hdulist = fits.open(self.parent+'/SED_Code/seddata/galaxy_temp.fits')
+        self.wave = hdulist[1].data['wave']
+        self.flux = hdulist[2].data
+        self.age_grid = hdulist[3].data['logAge']
+        self.feh_grid = hdulist[3].data['FeH']
+        
+    def toMag(self, redshift = 0):
+        """Calculating magnitude
+
+        Args:
+            redshift (float, optional): redshift of spectra. Defaults to 0.
+        """
+        wave = self.wave * (1 + redshift)
+        self.umag = flux_to_mag(wave, self.flux, self.parent,band='SDSS_u')
+        self.gmag = flux_to_mag(wave, self.flux, self.parent,band='SDSS_g')
+        self.rmag = flux_to_mag(wave, self.flux, self.parent,band='SDSS_r')
+        self.imag = flux_to_mag(wave, self.flux, self.parent,band='SDSS_i')
+        self.zmag = flux_to_mag(wave, self.flux, self.parent,band='SDSS_z')
+        
+class Star_Temp():
+    """
+    Template of Stellar SED
+    """
+    
+    def __init__(self, parent):
+        
+        #import os
+        
+        #parent = os.path.dirname(os.path.realpath(__file__))
+
+        ##/home/yan/MCI_sim_Fabu/MCI_inputData/SED_Code
+        
+        self.parent = parent
+        
+        hdulist = fits.open(parent+'/SED_Code/seddata/stellar_temp.fits')
+        
+        self.wave = hdulist[1].data['wave']
+        self.flux = hdulist[2].data
+        self.Teff_grid = hdulist[3].data['Teff']
+        self.FeH_grid = hdulist[3].data['FeH']
+        
+    def toMag(self):
+        wave = self.wave
+        self.bpmag = flux_to_mag(wave, self.flux, self.parent,band='GAIA_bp')
+        self.rpmag = flux_to_mag(wave, self.flux, self.parent,band='GAIA_rp')
+        
+# -------------
+# SED Modelling
+
+def Model_Stellar_SED(wave, bp, rp, temp, filepath):
+    """Modelling stellar SED based on bp, rp magnitude
+
+    Args:
+        wave (float): Wavelength
+        bp (float): Magnitude of GAIA BP band
+        rp (float): Magnitude of GAIA RP band
+        temp (class): Class of stellar template
+
+    Returns:
+        float array: Spectral energy distribution of stellar SED, 
+        which have the same length to the input wave
+    """
+
+    color0 = bp - rp
+    colors = temp.bpmag - temp.rpmag
+    
+    idx = np.argmin(np.abs(colors - color0))
+    flux0 = temp.flux[idx]
+    flux1 = np.interp(wave, temp.wave, flux0)
+    flux  = calibrate(wave, flux1, rp, filepath, band = 'GAIA_rp')
+    return flux
+
+def Model_Galaxy_SED(wave, ugriz, z, temp):
+    """Modelling galaxy SED based on u,g,r,i,z magnitude
+
+    Args:
+        wave (float): Wavelength
+        ugriz (float, array): The array of magnitude of SDSS ugriz band
+        z (float): Redshift
+        temp (class): Class of gaalxy template
+
+    Returns:
+        float array: Spectral energy distribution of stellar SED, 
+        which have the same length to the input wave
+    """
+    sed = 10. ** (-0.4 * ugriz)
+    sed = sed / sed[2]
+    ntemp = len(temp.rmag)
+    dmag  = np.zeros(ntemp)
+    for j in range(ntemp):
+        ugriz0 = np.array([temp.umag[j], temp.gmag[j], temp.rmag[j], 
+                           temp.imag[j], temp.zmag[j]])
+        sed0 = 10. ** (-0.4 * ugriz0)
+        sed0 = sed0 / sed0[2]
+        dmag[j] = np.sum(np.abs(sed - sed0))
+    
+    idx = np.argmin(dmag)
+    flux0 = temp.flux[idx]
+    
+    # Effect of E(B-V)
+    ri0 = ugriz[2] - ugriz[3]
+    ri  = temp.rmag - temp.imag
+    dri = ri0 - ri[idx]
+    Alambda = Calzetti_Law(np.array([6213 / (1 + z), 7625 / (1 + z)]))
+    eri0 = (Alambda[0] - Alambda[1])
+    ebv = dri/eri0
+    if ebv<0:
+        ebv=0
+    if ebv>0.5:
+        ebv=0.5
+    flux1 = reddening(temp.wave, flux0, ebv = ebv)
+    
+    flux2 = np.interp(wave, temp.wave * (1 + z), flux1)
+    flux  = calibrate(wave, flux2, ugriz[2], band = 'SDSS_r')
+    return flux
\ No newline at end of file

setup.py

+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name='csst_mci_sim',
+    version='2.0.0-MCI1.0.0',
+    author='CSST Team',
+    author_email='zhaojunyan@shao.ac.cn',
+    description='The CSST - mci - sim',  # short description
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url='https://csst-tb.bao.ac.cn/',
+    # project_urls={
+    #     'Source': 'https://csst-tb.bao.ac.cn/code/csst-l1/ifs/csst_mci_sim',
+    # },
+    packages=setuptools.find_packages(),
+    license='MIT',
+    classifiers=["Development Status :: 5 - Production/Stable",
+                 "Intended Audience :: Science/Research",
+                 "License :: OSI Approved :: MIT License",
+                 "Operating System :: OS Independent",
+                 "Programming Language :: Python :: 3.8",
+                 "Topic :: Scientific/Engineering :: Physics",
+                 "Topic :: Scientific/Engineering :: Astronomy"],
+    package_dir={'csst_mci_sim': 'csst_mci_sim'},
+    # include_package_data=True,
+    package_data={"": ["LICENSE", "README.md"],
+                  "csst_mci_sim": ["mci_so/*", "mci_data/*"]},
+    # install_requires=['sphinx',
+    #                   'numpy',
+    #                   'scipy', 'matplotlib',
+    #                   'astropy', 'healpy', 'ccdproc', 'deepCR', 'photutils'],
+    python_requires='>=3.8',
+)