Merge remote-tracking branch 'origin/develop'

ObservationSim/Instrument/Filter.py → observation_sim/instruments/Filter.py

@@ -4,9 +4,9 @@ import os
 import numpy as np
 import gc
 
-import ObservationSim.Instrument._util as _util
-from ObservationSim.Instrument.FilterParam import FilterParam
-from ObservationSim.Straylight import Straylight
+import observation_sim.instruments._util as _util
+from observation_sim.instruments.FilterParam import FilterParam
+from observation_sim.sky_background import Straylight
 
 try:
     import importlib.resources as pkg_resources
@@ -14,6 +14,7 @@ except ImportError:
     # Try backported to PY<37 'importlib_resources'
     import importlib_resources as pkg_resources
 
+
 class Filter(object):
     def __init__(self, filter_id, filter_type, filter_param, ccd_bandpass=None):
         self.filter_id = filter_id
@@ -52,57 +53,67 @@ class Filter(object):
     def _get_bandpasses(self, filter_dir=None, unit='A'):
         if self.filter_id < 7:  # Photometric
             try:
-                with pkg_resources.files('ObservationSim.Instrument.data.filters').joinpath(self.filter_type.lower() + '.txt') as filter_file:
-                    self.filter_bandpass = galsim.Bandpass(str(filter_file), wave_type=unit)
+                with pkg_resources.files('observation_sim.instruments.data.filters').joinpath(self.filter_type.lower() + '.txt') as filter_file:
+                    self.filter_bandpass = galsim.Bandpass(
+                        str(filter_file), wave_type=unit)
             except AttributeError:
-                with pkg_resources.path('ObservationSim.Instrument.data.filters', self.filter_type.lower() + '.txt') as filter_file:
-                    self.filter_bandpass = galsim.Bandpass(str(filter_file), wave_type=unit)
+                with pkg_resources.path('observation_sim.instruments.data.filters', self.filter_type.lower() + '.txt') as filter_file:
+                    self.filter_bandpass = galsim.Bandpass(
+                        str(filter_file), wave_type=unit)
             try:
-                with pkg_resources.files('ObservationSim.Instrument.data.throughputs').joinpath(self.filter_type.lower() + '_throughput.txt') as filter_file:
-                    bandpass_full = galsim.Bandpass(str(filter_file), wave_type=unit)
+                with pkg_resources.files('observation_sim.instruments.data.throughputs').joinpath(self.filter_type.lower() + '_throughput.txt') as filter_file:
+                    bandpass_full = galsim.Bandpass(
+                        str(filter_file), wave_type=unit)
             except AttributeError:
-                with pkg_resources.path('ObservationSim.Instrument.data.throughputs', self.filter_type.lower() + '_throughput.txt') as filter_file:
-                    bandpass_full = galsim.Bandpass(str(filter_file), wave_type=unit)
+                with pkg_resources.path('observation_sim.instruments.data.throughputs', self.filter_type.lower() + '_throughput.txt') as filter_file:
+                    bandpass_full = galsim.Bandpass(
+                        str(filter_file), wave_type=unit)
             # bandpass_full = bandpass_full * self.ccd_bandpass
 
             # Get sub-bandpasses
             bandpass_sub_list = []
             try:
-                with pkg_resources.files('ObservationSim.Instrument.data.filters').joinpath(self.filter_type.lower() + "_sub.list") as wave_bin_file:
+                with pkg_resources.files('observation_sim.instruments.data.filters').joinpath(self.filter_type.lower() + "_sub.list") as wave_bin_file:
                     wave_points = open(wave_bin_file).read().splitlines()
             except AttributeError:
-                with pkg_resources.path('ObservationSim.Instrument.data.filters', self.filter_type.lower() + "_sub.list") as wave_bin_file:
+                with pkg_resources.path('observation_sim.instruments.data.filters', self.filter_type.lower() + "_sub.list") as wave_bin_file:
                     wave_points = open(wave_bin_file).read().splitlines()
 
             for i in range(2, len(wave_points), 2):
-                blim = max(float(wave_points[i-2])*0.1, bandpass_full.blue_limit)
+                blim = max(float(wave_points[i-2])
+                           * 0.1, bandpass_full.blue_limit)
                 rlim = min(float(wave_points[i])*0.1, bandpass_full.red_limit)
                 if blim >= rlim:
                     continue
-                bandpass = bandpass_full.truncate(blue_limit=blim, red_limit=rlim)
+                bandpass = bandpass_full.truncate(
+                    blue_limit=blim, red_limit=rlim)
                 bandpass_sub_list.append(bandpass)
             # print("num of sub-bandpasses for filter#%d(%s) = "%(self.filter_id, self.filter_type), len(bandpass_sub_list), flush=True)
         else:   # Spectroscopic
             sls_lamb = np.linspace(self.blue_limit, self.red_limit, 100)
             sls_flux = np.ones_like(sls_lamb)
-            con_spec = galsim.LookupTable(sls_lamb, sls_flux, interpolant='nearest')
+            con_spec = galsim.LookupTable(
+                sls_lamb, sls_flux, interpolant='nearest')
             bandpass_full = galsim.Bandpass(con_spec, wave_type=unit)
             bandpass_sub_list = []
             try:
-                with pkg_resources.files('ObservationSim.Instrument.data.filters').joinpath(self.filter_type.lower() + "_sub.list") as wave_bin_file:
+                with pkg_resources.files('observation_sim.instruments.data.filters').joinpath(self.filter_type.lower() + "_sub.list") as wave_bin_file:
                     wave_points = open(wave_bin_file).read().splitlines()
             except AttributeError:
-                with pkg_resources.path('ObservationSim.Instrument.data.filters', self.filter_type.lower() + "_sub.list") as wave_bin_file:
+                with pkg_resources.path('observation_sim.instruments.data.filters', self.filter_type.lower() + "_sub.list") as wave_bin_file:
                     wave_points = open(wave_bin_file).read().splitlines()
             for i in range(2, len(wave_points), 2):
-                blim = max(float(wave_points[i - 2]) * 0.1, bandpass_full.blue_limit)
-                rlim = min(float(wave_points[i]) * 0.1, bandpass_full.red_limit)
+                blim = max(float(wave_points[i - 2])
+                           * 0.1, bandpass_full.blue_limit)
+                rlim = min(float(wave_points[i])
+                           * 0.1, bandpass_full.red_limit)
                 if blim >= rlim:
                     continue
-                bandpass = bandpass_full.truncate(blue_limit=blim, red_limit=rlim)
+                bandpass = bandpass_full.truncate(
+                    blue_limit=blim, red_limit=rlim)
                 bandpass_sub_list.append(bandpass)
             # print("num of sub-bandpasses for filter#%d(%s) = " % (self.filter_id, self.filter_type), len(bandpass_sub_list), flush=True)
-            
+
         return bandpass_full, bandpass_sub_list
 
     def getPhotonE(self):
@@ -111,17 +122,20 @@ class Filter(object):
     def getSkyNoise(self, exptime, gain=1.):
         return self.sky_background * exptime / gain
 
-    def setFilterStrayLightPixel(self,jtime = 2460843., sat_pos = np.array([0,0,0]), pointing_radec = np.array([0,0]), sun_pos = np.array([0,0,0])):
-        sl = Straylight(jtime=jtime, sat_pos=sat_pos, pointing_radec=pointing_radec,sun_pos=sun_pos)
+    def setFilterStrayLightPixel(self, jtime=2460843., sat_pos=np.array([0, 0, 0]), pointing_radec=np.array([0, 0]), sun_pos=np.array([0, 0, 0])):
+        sl = Straylight(jtime=jtime, sat_pos=sat_pos,
+                        pointing_radec=pointing_radec, sun_pos=sun_pos)
         if self.filter_type in _util.SPEC_FILTERS:
-            s_pix, spec = sl.calculateStrayLightGrating(grating = self.filter_type.upper())
-            if s_pix>0.8:
+            s_pix, spec = sl.calculateStrayLightGrating(
+                grating=self.filter_type.upper())
+            if s_pix > 0.8:
                 s_pix = 0.8
             self.sky_background = s_pix
             self.zodical_spec = spec
         elif self.filter_type.lower() in [x.lower for x in _util.PHOT_FILTERS]:
-            s_pix = sl.calculateStrayLightFilter(filter=self.filter_type.lower())
-            if s_pix>1:
+            s_pix = sl.calculateStrayLightFilter(
+                filter=self.filter_type.lower())
+            if s_pix > 1:
                 s_pix = 1
             self.sky_background = s_pix
             self.zodical_spec = None
@@ -144,6 +158,8 @@ class Filter(object):
             full_well = 90000
         throughput_file = self.filter_type.lower() + '_throughput.txt'
 
-        self.mag_limiting, self.mag_saturation = _util.calculateLimitMag(psf_fwhm=psf_fwhm, pixelSize=pix_scale, throughputFn=throughput_file, readout=5.0, skyFn=skyFn, darknoise=dark_noise, exTime=exptime, fw=full_well)
+        self.mag_limiting, self.mag_saturation = _util.calculateLimitMag(
+            psf_fwhm=psf_fwhm, pixelSize=pix_scale, throughputFn=throughput_file, readout=5.0, skyFn=skyFn, darknoise=dark_noise, exTime=exptime, fw=full_well)
 
-        print("for filter %s: mag_limiting: %.3f, mag_saturation: %.3f"%(self.filter_type, self.mag_limiting, self.mag_saturation))
+        print("for filter %s: mag_limiting: %.3f, mag_saturation: %.3f" %
+              (self.filter_type, self.mag_limiting, self.mag_saturation))

ObservationSim/Instrument/FilterParam.py → observation_sim/instruments/FilterParam.py

 import galsim
 import numpy as np
 
+
 class FilterParam(object):
     def __init__(self, filter_dir=None, filter_param=None):
         self.param = self._filtParam(filter_param)
@@ -14,7 +15,7 @@ class FilterParam(object):
         TODO: subject to change
         Basic parameters of the CSSOS filters.
         """
-        # filter parameters: name: 
+        # filter parameters: name:
         # 1) effective wavelength
         # 2) effective width
         # 3) blue end
@@ -26,19 +27,20 @@ class FilterParam(object):
         # 8) dim end magnitude
         if filter_param == None:
             filtP = {
-                    "NUV":   [2867.7,   705.4,  2470.0,   3270.0,  0.1404, 0.004, 15.7, 25.4],
-                    "u":     [3601.1,   852.1,  3120.0,   4090.0,  0.2176, 0.021, 16.1, 25.4],
-                    "g":     [4754.5,  1569.8,  3900.0,   5620.0,  0.4640, 0.164, 17.2, 26.3],
-                    "r":     [6199.8,  1481.2,  5370.0,   7030.0,  0.5040, 0.207, 17.0, 26.0],
-                    "i":     [7653.2,  1588.1,  6760.0,   8550.0,  0.4960, 0.212, 16.7, 25.9],
-                    "z":     [9600.6,  2490.5,  8240.0,  11000.0,  0.2000, 0.123, 15.7, 25.2],
-                    "y":     [10051.0, 1590.6,  9130.0,  11000.0,  0.0960, 0.037, 14.4, 24.4],
-                    "FGS":   [5000.0,  8000.0,  3000.0,  11000.0,  0.6500, 0.164, 0., 30.], # [TODO]
-                    
-                    "GU":    [0.0,        0.0,  2550.0,   4200.0,     1.0, 0.037, 14.0, 26.0],
-                    "GV":    [0.0,        0.0,  4000.0,   6500.0,     1.0, 0.037, 14.0, 26.0],
-                    "GI":    [0.0,        0.0,  6200.0,  10000.0,     1.0, 0.037, 14.0, 26.0],
-                    }
+                "NUV":   [2867.7,   705.4,  2470.0,   3270.0,  0.1404, 0.004, 15.7, 25.4],
+                "u":     [3601.1,   852.1,  3120.0,   4090.0,  0.2176, 0.021, 16.1, 25.4],
+                "g":     [4754.5,  1569.8,  3900.0,   5620.0,  0.4640, 0.164, 17.2, 26.3],
+                "r":     [6199.8,  1481.2,  5370.0,   7030.0,  0.5040, 0.207, 17.0, 26.0],
+                "i":     [7653.2,  1588.1,  6760.0,   8550.0,  0.4960, 0.212, 16.7, 25.9],
+                "z":     [9600.6,  2490.5,  8240.0,  11000.0,  0.2000, 0.123, 15.7, 25.2],
+                "y":     [10051.0, 1590.6,  9130.0,  11000.0,  0.0960, 0.037, 14.4, 24.4],
+                # [TODO]
+                "FGS":   [5000.0,  8000.0,  3000.0,  11000.0,  0.6500, 0.164, 0., 30.],
+
+                "GU":    [0.0,        0.0,  2550.0,   4200.0,     1.0, 0.037, 14.0, 26.0],
+                "GV":    [0.0,        0.0,  4000.0,   6500.0,     1.0, 0.037, 14.0, 26.0],
+                "GI":    [0.0,        0.0,  6200.0,  10000.0,     1.0, 0.037, 14.0, 26.0],
+            }
         else:
             filtP = filter_param
 
@@ -48,10 +50,10 @@ class FilterParam(object):
         """
         read filters and save into Python dictionary
         NOTE: the wavelength unit must be in "Angstrom"
-        
+
         Parameters:
         Same as function 'seds'
-        
+
         Return:
         Same as function 'seds'
         """
@@ -65,9 +67,10 @@ class FilterParam(object):
             ifiltn = filtdir+itype+".dat"
             iblim = filtParams[itype][2]
             irlim = filtParams[itype][3]
-            ifilt =  galsim.Bandpass(ifiltn,wave_type=unit,blue_limit=iblim,red_limit=irlim)
-            wave  = ifilt.wave_list
+            ifilt = galsim.Bandpass(
+                ifiltn, wave_type=unit, blue_limit=iblim, red_limit=irlim)
+            wave = ifilt.wave_list
             ifilt = ifilt.func(wave)
-            filts[itype] = np.transpose(np.array([wave*10.0,ifilt]))
+            filts[itype] = np.transpose(np.array([wave*10.0, ifilt]))
 
-        return filtype, filts
+        return filtype, filts
\ No newline at end of file

ObservationSim/Instrument/FocalPlane.py → observation_sim/instruments/FocalPlane.py

@@ -40,18 +40,6 @@ class FocalPlane(object):
             for i in range(1, 31):
                 self.ignore_chips.append(i)
 
-        # if config is not None:
-        #     self.nchip_x    = config["nchip_x"]
-        #     self.nchip_y    = config["nchip_y"]
-        #     self.npix_tot_x = config["npix_tot_x"]
-        #     self.npix_tot_y = config["npix_tot_y"]
-        #     self.npix_gap_x = config["npix_gap_x"]
-        #     self.npix_gap_y = config["npix_gap_y"]
-        #     if "chipLabelIDs" in config:
-        #         self.chipLabelIDs = config["chipLabelIDs"]
-        #     if "bad_chips" in config:
-        #         self.bad_chips = config["bad_chips"]
-        # else:
         self.nchip_x = 6
         self.nchip_y = 5
         self.npix_tot_x = 59516
@@ -95,10 +83,6 @@ class FocalPlane(object):
         if (xcen == None) or (ycen == None):
             xcen = self.cen_pix_x
             ycen = self.cen_pix_y
-        # dudx =  -np.cos(img_rot.rad) * pix_scale
-        # dudy =  -np.sin(img_rot.rad) * pix_scale
-        # dvdx =  -np.sin(img_rot.rad) * pix_scale
-        # dvdy =  +np.cos(img_rot.rad) * pix_scale
 
         dudx = -np.cos(img_rot.rad) * pix_scale
         dudy = +np.sin(img_rot.rad) * pix_scale

observation_sim/instruments/Telescope.py

+import numpy as np
+
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
+
+class Telescope(object):
+    def __init__(self, param=None, optEffCurve_path=None):
+        self.diameter = 2.0  # in unit of meter
+        if param is not None:
+            self.diameter = param["diameter"]
+        self.pupil_area = np.pi * (0.5 * self.diameter)**2
+        if optEffCurve_path is not None:
+            self.efficiency = self._get_efficiency(optEffCurve_path)
+        else:
+            try:
+                with pkg_resources.files('observation_sim.instruments.data').joinpath('mirror_ccdnote.txt') as optEffCurve_path:
+                    self.efficiency = self._get_efficiency(optEffCurve_path)
+            except AttributeError:
+                with pkg_resources.path('observation_sim.instruments.data', 'mirror_ccdnote.txt') as optEffCurve_path:
+                    self.efficiency = self._get_efficiency(optEffCurve_path)
+
+    def _get_efficiency(self, effCurve_path):
+        """ Read in the efficiency of optics
+                for each band
+        Parameters:
+                effCurve_path:	the path for efficiency file
+        Returns:
+                opticsEff:		a dictionary of efficiency (a scalar) for each band
+        """
+        f = open(effCurve_path, 'r')
+        for _ in range(2):
+            header = f.readline()
+
+        iline = 0
+        opticsEff = {}
+        for line in f:
+            line = line.strip()
+            columns = line.split()
+            opticsEff[str(columns[0])] = float(columns[2])
+        f.close()
+        return opticsEff

ObservationSim/Instrument/__init__.py → observation_sim/instruments/__init__.py

@@ -2,4 +2,4 @@ from .Telescope import Telescope
 from .Filter import Filter
 from .FilterParam import FilterParam
 from .FocalPlane import FocalPlane
-from .Chip import Chip
+from .chip import Chip
\ No newline at end of file

observation_sim/instruments/_util.py

+import numpy as np
+import os
+import math
+from pylab import *
+from scipy import interpolate
+
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
+VC_A = 2.99792458e+18  # speed of light: A/s
+VC_M = 2.99792458e+8   # speed of light: m/s
+H_PLANK = 6.626196e-27  # Plank constant: erg s
+
+ALL_FILTERS = ["NUV", "u", "g", "r", "i", "z", "y", "GU", "GV", "GI", "FGS"]
+PHOT_FILTERS = ["NUV", "u", "g", 'r', 'i', 'z', 'y', 'FGS']
+SPEC_FILTERS = ["GI", "GV", "GU"]
+
+
+def rotate_conterclockwise(x0, y0, x, y, angle):
+    """
+Rotate a point counterclockwise by a given angle around a given origin.
+
+The angle should be given in radians.
+"""
+    angle = np.deg2rad(angle)
+    qx = x0 + np.cos(angle)*(x - x0) - np.sin(angle) * (y - y0)
+    qy = y0 + np.sin(angle)*(x - x0) + np.cos(angle) * (y - y0)
+    return qx, qy
+
+
+def photonEnergy(lambd):
+    """ The energy of photon at a given wavelength
+
+    Parameter:
+            lambd: the wavelength in unit of Angstrom
+    Return:
+            eph: energy of photon in unit of erg
+    """
+    nu = VC_A / lambd
+    eph = H_PLANK * nu
+    return eph
+
+
+def calculateLimitMag(aperture=2.0, psf_fwhm=0.1969, pixelSize=0.074, pmRation=0.8, throughputFn='i_throughput.txt', readout=5.0, skyFn='sky_emiss_hubble_50_50_A.dat', darknoise=0.02, exTime=150, exNum=1, fw=90000):
+    '''
+    description: 
+    param {*} aperture: unit m, default 2 m
+    param {*} psf_fwhm: psf fwhm, default 0.1969"
+    param {*} pixelSize: pixel size, default 0.074"
+    param {*} pmRation: the ratio of souce flux in the limit mag calculation
+    param {*} throughputFn: throuput file name
+    param {*} readout: unit, e-/pixel
+    param {*} skyFn: sky sed file name, average of hst, 'sky_emiss_hubble_50_50_A.dat'
+    param {*} darknoise: unit, e-/pixel/s
+    param {*} exTime: exposure time one time, default 150s
+    param {*} exNum: exposure number, defautl 1
+    param {*} fw, full well value( or saturation value),default 90000e-/pixel
+    return {*} limit mag and saturation mag
+    '''
+    try:
+        with pkg_resources.files('observation_sim.instruments.data.throughputs').joinpath(throughputFn) as data_file:
+            throughput_f = np.loadtxt(data_file)
+    except AttributeError:
+        with pkg_resources.path('observation_sim.instruments.data.throughputs', throughputFn) as data_file:
+            throughput_f = np.loadtxt(data_file)
+    thr_i = interpolate.interp1d(
+        throughput_f[:, 0]/10, throughput_f[:, 1])  # wavelength in anstrom
+    f_s = 200
+    f_e = 1100
+    delt_f = 0.5
+
+    data_num = int((f_e-f_s)/delt_f+1)
+
+    eff = np.zeros([data_num, 2])
+    eff[:, 0] = np.arange(f_s, f_e+delt_f, delt_f)
+    eff[:, 1] = thr_i(eff[:, 0])
+
+    wave = np.arange(f_s, f_e+delt_f, delt_f)
+    wavey = np.ones(wave.shape[0])
+
+    try:
+        with pkg_resources.files('observation_sim.instruments.data.throughputs').joinpath(skyFn) as data_file:
+            skydata = np.loadtxt(data_file)
+    except AttributeError:
+        with pkg_resources.path('observation_sim.instruments.data.throughputs', skyFn) as data_file:
+            skydata = np.loadtxt(data_file)
+    skydatai = interpolate.interp1d(skydata[:, 0]/10, skydata[:, 1]*10)
+
+    sky_data = np.zeros([data_num, 2])
+    sky_data[:, 0] = np.arange(f_s, f_e+delt_f, delt_f)
+    sky_data[:, 1] = skydatai(sky_data[:, 0])
+
+    flux_sky = trapz((sky_data[:, 1])*eff[:, 1], sky_data[:, 0])
+    skyPix = flux_sky*pixelSize*pixelSize*pi*(aperture*aperture/4)
+
+    # limit mag
+
+    r_pix = psf_fwhm*0.7618080243778568/pixelSize  # radius RE80, pixel
+    cnum = math.pi * r_pix * r_pix
+    sn = 5
+
+    d = skyPix*exTime*exNum*cnum + darknoise * \
+        exTime*exNum*cnum+readout*readout*cnum*exNum
+    a = 1
+    b = -sn*sn
+    c = -sn*sn*d
+
+    flux = (-b+sqrt(b*b-4*a*c))/(2*a)/pmRation
+    limitMag = -2.5*log10(flux/(54799275581.04437 * trapz(wavey *
+                          eff[:, 1]/wave, wave, 0.1)*exTime*exNum*pi*(aperture/2)*(aperture/2)))
+
+    # saturation mag
+
+    from astropy.modeling.models import Gaussian2D
+    m_size = int(20 * psf_fwhm/pixelSize)
+    if m_size % 2 == 0:
+        m_size + 1
+    m_cen = m_size//2
+    psf_sigma = psf_fwhm/2.355/pixelSize
+
+    gaussShape = Gaussian2D(1, m_cen, m_cen, psf_sigma, psf_sigma)
+    yp, xp = np.mgrid[0:m_size, 0:m_size]
+    psfMap = gaussShape(xp, yp)
+    maxRatio = np.amax(psfMap)/np.sum(psfMap)
+    # print(maxRatio)
+
+    flux_sat = fw/maxRatio*exNum
+    satMag = -2.5*log10(flux_sat/(54799275581.04437 * trapz(wavey *
+                        eff[:, 1]/wave, wave, 0.1)*exTime*exNum*pi*(aperture/2)*(aperture/2)))
+
+    return limitMag, satMag

ObservationSim/Instrument/Chip/libCTI/CTI_modeling.py → observation_sim/instruments/chip/libCTI/CTI_modeling.py

-from ctypes import CDLL, POINTER, c_int, c_double,c_float,c_long,c_char_p
+from ctypes import CDLL, POINTER, c_int, c_double, c_float, c_long, c_char_p
 from numpy.ctypeslib import ndpointer
 import numpy.ctypeslib as clb
 import numpy as np
@@ -10,12 +10,12 @@ import os
 
 lib_path = os.path.dirname(os.path.realpath(__file__))
 
-#lib_path += "/add_CTI.so"
+# lib_path += "/add_CTI.so"
 lib_path += "/libmoduleCTI.so"
 lib = CDLL(lib_path)
 CTI_simul = lib.__getattr__('CTI_simul')
-CTI_simul.argtypes = [POINTER(POINTER(c_int)),c_int,c_int,c_int,c_int,POINTER(c_float),POINTER(c_float),\
-                    c_float,c_float,c_float,c_int,POINTER(c_int),c_int,POINTER(POINTER(c_int))]
+CTI_simul.argtypes = [POINTER(POINTER(c_int)), c_int, c_int, c_int, c_int, POINTER(c_float), POINTER(c_float),
+                      c_float, c_float, c_float, c_int, POINTER(c_int), c_int, POINTER(POINTER(c_int))]
 '''
 get_trap_h = lib.__getattr__('save_trap_map')
 get_trap_h.argtypes = [POINTER(c_int), c_int, c_int, c_int, c_int, POINTER(c_float), c_float, c_float, c_char_p]
@@ -45,42 +45,50 @@ def bin2fits(bin_file,fits_dir,nsp,nx,ny,nmax):
             datai[j+1,:,:] = h
         fits.writeto(fits_dir+"/trap_"+str(i+1)+".fits",datai,overwrite=True)
 '''
-        
+
+
 def numpy_matrix_to_int_pointer(arr):
     int_pointer_array = (POINTER(c_int)*arr.shape[0])()
     for i in range(arr.shape[0]):
-        arr1 = np.array(arr[i].copy().tolist(),dtype=np.int32)
+        arr1 = np.array(arr[i].copy().tolist(), dtype=np.int32)
         int_pointer_array[i] = np.ctypeslib.as_ctypes(arr1)
     return int_pointer_array
-def pointer_to_numpy_matrix(arr_pointer,row,col):
-    arr = np.zeros((row,col))
+
+
+def pointer_to_numpy_matrix(arr_pointer, row, col):
+    arr = np.zeros((row, col))
     for i in range(row):
         for j in range(col):
-            arr[i,j] = arr_pointer[i][j]
+            arr[i, j] = arr_pointer[i][j]
     return arr
-def CTI_sim(im,nx,ny,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed=0):
+
+
+def CTI_sim(im, nx, ny, noverscan, nsp, nmax, beta, w, c, t, rho_trap, trap_seeds, release_seed=0):
     image = im.T
-    nx_c,ny_c,noverscan_c,nsp_c,nmax_c = c_int(nx),c_int(ny),c_int(noverscan),c_int(nsp),c_int(nmax)
+    nx_c, ny_c, noverscan_c, nsp_c, nmax_c = c_int(nx), c_int(
+        ny), c_int(noverscan), c_int(nsp), c_int(nmax)
     ntotal = ny+noverscan
-    beta_c,w_c,c_c = c_float(beta),c_float(w),c_float(c)
+    beta_c, w_c, c_c = c_float(beta), c_float(w), c_float(c)
     t_p = np.ctypeslib.as_ctypes(t)
     rho_trap_p = np.ctypeslib.as_ctypes(rho_trap)
     image_p = numpy_matrix_to_int_pointer(image)
     trap_seeds1 = trap_seeds.astype(np.int32)
     trap_seeds_p = np.ctypeslib.as_ctypes(trap_seeds1)
     release_seed_c = c_int(release_seed)
-    image_cti = np.zeros((nx,ntotal))
+    image_cti = np.zeros((nx, ntotal))
     image_cti = image_cti.astype(np.int32)
     image_cti_p = numpy_matrix_to_int_pointer(image_cti)
     print(datetime.now())
-    CTI_simul(image_p,nx,ny,noverscan,nsp,rho_trap_p,t_p,beta,w,c,nmax,trap_seeds_p,release_seed_c,image_cti_p)
+    CTI_simul(image_p, nx, ny, noverscan, nsp, rho_trap_p, t_p, beta,
+              w, c, nmax, trap_seeds_p, release_seed_c, image_cti_p)
     print(datetime.now())
-    image_cti_result = np.zeros((nx,ntotal))
+    image_cti_result = np.zeros((nx, ntotal))
     for i in range(nx):
         for j in range(ntotal):
-            image_cti_result[i,j] = image_cti_p[i][j]
+            image_cti_result[i, j] = image_cti_p[i][j]
     return image_cti_result.T
 
+
 """
 if __name__ =='__main__':
     nx,ny,noverscan,nsp,nmax = 4608,4616,84,3,10