Merge branch 'master' into 'release_v3.0'

Release version v3.2.0

See merge request !33

observation_sim/instruments/chip/Chip.py

@@ -191,7 +191,7 @@ class Chip(FocalPlane):
         """Return the filter index and type for a given chip #(chipID)
         """
         filter_type_list = _util.ALL_FILTERS
-        if chipID == None:
+        if chipID is None:
             chipID = self.chipID
 
         # updated configurations

observation_sim/instruments/chip/chip_utils.py

@@ -173,6 +173,13 @@ def get_flat(img, seed):
     return flat_img, flat_normal
 
 
+def get_innerflat(chip=None, filt=None):
+    from observation_sim.mock_objects import FlatLED
+    led_obj = FlatLED(chip, filt)
+    flat_img = led_obj.getInnerFlat()
+    return flat_img
+
+
 def add_cosmic_rays(img, chip, exptime=150, seed=0):
     cr_map, cr_event_num = effects.produceCR_Map(
         xLen=chip.npix_x, yLen=chip.npix_y,
@@ -206,7 +213,7 @@ def get_poisson(seed=0, sky_level=0.):
 
 
 def get_base_img(img, chip, read_noise, readout_time, dark_noise, exptime=150., InputDark=None):
-    if InputDark == None:
+    if InputDark is None:
         # base_level = read_noise**2 + dark_noise*(exptime+0.5*readout_time)
         # base_level = dark_noise*(exptime+0.5*readout_time)
         base_level = dark_noise*(exptime)
@@ -237,7 +244,7 @@ def add_poisson(img, chip, exptime=150., seed=0, sky_level=0., poisson_noise=Non
     img.addNoise(poisson_noise)
     # img -= read_noise**2
 
-    if InputDark != None:
+    if InputDark is not None:
         # "Instrument/data/dark/dark_1000s_example_0.fits"
         hdu = fits.open(InputDark)
         img += hdu[0].data/hdu[0].header['exptime']*exptime

observation_sim/instruments/chip/libBF/diffusion_X1.c

@@ -37,7 +37,7 @@ void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bi
   {
     printf("Adding BF effect...\n");
     //setup BF correlation fliter
-    float neX;
+    float neX, neXtemp;
     float neP1 = 50000;
     float bfaP1[9]={0.9707182, 0.002143905, 0.004131103, 0.001149542, 0.0005501739, 0.0005469659, 0.0003726081, 0.0003795207, 0.0001633302};
     float neP2 = 10000;
@@ -56,15 +56,18 @@ void addEffects(int ngx_ima, int ngy_ima, float *arr_ima, float *arr_imc, int bi
         neX = arr_ima[j+i*ny];
         if(neX >= 10000)
         {
+          neXtemp = neX;
+          if(neXtemp > 100000)
+              neXtemp = 100000;
           bfa[0][0]=0; //linearInterp(neX, neP1, bfaP1[0], neP2, bfaP2[0]); //0;
-          bfa[0][1]=bfa[0][-1]=linearInterp(neX, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
-          bfa[-1][0]=bfa[1][0]=linearInterp(neX, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
-          bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neX, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
-          bfa[0][-2]=bfa[0][2]=linearInterp(neX, neP1, bfaP1[4], neP2, bfaP2[4]);
-          bfa[-2][0]=bfa[2][0]=linearInterp(neX, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
-          bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neX, neP1, bfaP1[6], neP2, bfaP2[6]);
-          bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neX, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
-          bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neX, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
+          bfa[0][1]=bfa[0][-1]=linearInterp(neXtemp, neP1, bfaP1[1], neP2, bfaP2[1]); //0.01575;
+          bfa[-1][0]=bfa[1][0]=linearInterp(neXtemp, neP1, bfaP1[2], neP2, bfaP2[2]); //0.00652;
+          bfa[-1][-1]=bfa[1][1]=bfa[-1][1]=bfa[1][-1]=linearInterp(neXtemp, neP1, bfaP1[3], neP2, bfaP2[3]); //0.00335;
+          bfa[0][-2]=bfa[0][2]=linearInterp(neXtemp, neP1, bfaP1[4], neP2, bfaP2[4]);
+          bfa[-2][0]=bfa[2][0]=linearInterp(neXtemp, neP1, bfaP1[5], neP2, bfaP2[5]); //0.00118;
+          bfa[-2][-1]=bfa[-2][1]=bfa[2][1]=bfa[2][-1]=linearInterp(neXtemp, neP1, bfaP1[6], neP2, bfaP2[6]);
+          bfa[-1][-2]=bfa[1][2]=bfa[-1][2]=bfa[1][-2]=linearInterp(neXtemp, neP1, bfaP1[7], neP2, bfaP2[7]); //0.00083;
+          bfa[-2][-2]=bfa[-2][2]=bfa[2][-2]=bfa[2][2]=linearInterp(neXtemp, neP1, bfaP1[8], neP2, bfaP2[8]); //0.00043;
         }
         else
         {

observation_sim/instruments/chip/libCTI/CTI_modeling.py

@@ -31,7 +31,7 @@ def get_trap_map(seeds,nx,ny,nmax,rho_trap,beta,c,out_dir):
     get_trap_h(seeds_p,c_int(int(nsp)),c_int(int(nx)),c_int(int(ny)),\
             c_int(int(nmax)),rho_trap_p,c_float(beta),\
             c_float(c),filename)
-        
+
 def bin2fits(bin_file,fits_dir,nsp,nx,ny,nmax):
     data = np.fromfile(bin_file,dtype=np.float32)
     data = data.reshape(nx,nsp,ny,nmax).transpose(1,3,2,0)
@@ -101,6 +101,6 @@ if __name__ =='__main__':
     image = fits.getdata("inputdata/image.fits").astype(np.int32)
     get_trap_map(trap_seeds,nx,ny,nmax,rho_trap,beta,c,".")
     bin2fits("trap.bin",".",nsp,nx,ny,nmax)
-    image_cti = CTI_sim(image,nx,ny,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed)  
+    image_cti = CTI_sim(image,nx,ny,noverscan,nsp,nmax,beta,w,c,t,rho_trap,trap_seeds,release_seed)
     fits.writeto("output/image_CTI.fits",data=image_cti,overwrite=True)
 """

observation_sim/mock_objects/CatalogBase.py

@@ -12,6 +12,9 @@ class CatalogBase(metaclass=ABCMeta):
     def __init__(self):
         pass
 
+    def free_mem(self, **kward):
+        pass
+
     @abstractmethod
     def load_sed(self, obj, **kward):
         pass
@@ -29,8 +32,8 @@ class CatalogBase(metaclass=ABCMeta):
         param = {
             "star": -1,
             "id": -1,
-            "ra": 0,
-            "dec": 0.,
+            "ra": -999.,
+            "dec": -999.,
             "ra_orig": 0.,
             "dec_orig": 0.,
             "z": 0.,
@@ -44,15 +47,15 @@ class CatalogBase(metaclass=ABCMeta):
             "bfrac": 0.,
             "av": 0.,
             "redden": 0.,
-            "hlr_bulge": 0.,
-            "hlr_disk": 0.,
+            "hlr_bulge": -999.,
+            "hlr_disk": -999.,
             "ell_bulge": 0.,
             "ell_disk": 0.,
             "ell_tot": 0.,
-            "e1_disk": 0.,
-            "e2_disk": 0.,
-            "e1_bulge": 0.,
-            "e2_bulge": 0.,
+            "e1_disk": -999.,
+            "e2_disk": -999.,
+            "e1_bulge": -999.,
+            "e2_bulge": -999.,
             "teff": 0.,
             "logg": 0.,
             "feh": 0.,
@@ -91,6 +94,8 @@ class CatalogBase(metaclass=ABCMeta):
         bandpass = target_filt.bandpass_full
 
         if norm_filt is not None:
+            if hasattr(norm_filt, 'bandpass_full'):
+                norm_filt = Table(np.array(np.array([norm_filt.bandpass_full.wave_list*10.0, norm_filt.bandpass_full.func(norm_filt.bandpass_full.wave_list)])).T, names=(['WAVELENGTH', 'SENSITIVITY']))
             norm_thr_rang_ids = norm_filt['SENSITIVITY'] > 0.001
         else:
             norm_filt = Table(

observation_sim/mock_objects/FlatLED.py

@@ -50,6 +50,8 @@ fluxLED = {'LED1': 15, 'LED2': 15, 'LED3': 12.5, 'LED4': 9, 'LED5': 9,
 #            'LED14': 10}
 
 mirro_eff = {'GU': 0.61, 'GV': 0.8, 'GI': 0.8}
+
+bandtoLed = {'NUV': ['LED1', 'LED2'], 'u': ['LED13', 'LED14'], 'g': ['LED3', 'LED4', 'LED5'], 'r': ['LED6', 'LED7'], 'i': ['LED8'], 'z': ['LED9', 'LED10'], 'y': ['LED10'], 'GU': ['LED1', 'LED2', 'LED13', 'LED14'], 'GV': ['LED3', 'LED4', 'LED5', 'LED6'], 'GI': ['LED7', 'LED8', 'LED9', 'LED10']}
 # mirro_eff = {'GU':1, 'GV':1, 'GI':1}
 
 
@@ -69,10 +71,18 @@ class FlatLED(MockObject):
                 with pkg_resources.path('observation_sim.mock_objects.data.led', "") as ledDir:
                     self.flatDir = ledDir.as_posix()
 
+    def getInnerFlat(self):
+        ledflats = bandtoLed[self.chip.filter_type]
+        iFlat = np.zeros([self.chip.npix_y, self.chip.npix_x])
+        for nled in ledflats:
+            iFlat = iFlat + self.getLEDImage1(led_type=nled, LED_Img_flag=False)
+        iFlat = iFlat/len(ledflats)
+        return iFlat
+
     ###
     # return LED flat, e/s
     ###
-    def getLEDImage(self, led_type='LED1'):
+    def getLEDImage(self, led_type='LED1', LED_Img_flag=True):
         # cwave = cwaves[led_type]
         flat = fits.open(os.path.join(self.flatDir, 'model_' +
                          cwaves_name[led_type] + 'nm.fits'))
@@ -102,7 +112,10 @@ class FlatLED(MockObject):
             N[self.chip.npix_y * i:self.chip.npix_y * (i + 1), self.chip.npix_x * j:self.chip.npix_x * (j + 1)]),
             method='linear')
         U = U/np.mean(U)
-        flatImage = U*fluxLED[led_type]*1000
+
+        flatImage = U
+        if LED_Img_flag:
+            flatImage = flatImage*fluxLED[led_type]*1000
         gc.collect()
         return flatImage
 
@@ -110,39 +123,42 @@ class FlatLED(MockObject):
     # return LED flat, e/s
     ###
 
-    def getLEDImage1(self, led_type='LED1'):
+    def getLEDImage1(self, led_type='LED1', LED_Img_flag=True):
         # cwave = cwaves[led_type]
         flat = fits.open(os.path.join(self.flatDir, 'model_' +
                          cwaves_name[led_type] + 'nm.fits'))
         xlen = flat[0].header['NAXIS1']
         ylen = 601
-
         i = self.chip.rowID - 1
         j = self.chip.colID - 1
-
         x = np.linspace(0, self.chip.npix_x, int(xlen/6.))
         y = np.linspace(0, self.chip.npix_y, int(ylen/5.))
         xx, yy = np.meshgrid(x, y)
-
         a1 = flat[0].data[int(ylen*i/5.):int(ylen*i/5.)+int(ylen/5.),
                           int(xlen*j/6.):int(xlen*j/6.)+int(xlen/6.)]
         # z = np.sin((xx+yy+xx**2+yy**2))
         # fInterp = interp2d(xx, yy, z, kind='linear')
-
         X_ = np.hstack((xx.flatten()[:, None], yy.flatten()[:, None]))
         Z_ = a1.flatten()
-
         n_x = np.arange(0, self.chip.npix_x, 1)
         n_y = np.arange(0, self.chip.npix_y, 1)
-
         M, N = np.meshgrid(n_x, n_y)
-
-        U = griddata(X_, Z_, (
-            M[0:self.chip.npix_y, 0:self.chip.npix_x],
-            N[0:self.chip.npix_y, 0:self.chip.npix_x]),
-            method='linear')
+        x_seg_len = 4
+        y_seg_len = 8
+        x_seg = int(self.chip.npix_x/x_seg_len)
+        y_seg = int(self.chip.npix_y/y_seg_len)
+        U = np.zeros([self.chip.npix_y, self.chip.npix_x], dtype=np.float32)
+        for y_seg_i in np.arange(y_seg_len):
+            for x_seg_i in np.arange(x_seg_len):
+                U[y_seg_i*y_seg:(y_seg_i+1)*y_seg, x_seg_i*x_seg:(x_seg_i+1)*x_seg] = griddata(X_, Z_, (M[y_seg_i*y_seg:(y_seg_i+1)*y_seg, x_seg_i*x_seg:(x_seg_i+1)*x_seg], N[y_seg_i*y_seg:(y_seg_i+1)*y_seg, x_seg_i*x_seg:(x_seg_i+1)*x_seg]), method='linear')
+        # U = griddata(X_, Z_, (
+        #     M[0:self.chip.npix_y, 0:self.chip.npix_x],
+        #     N[0:self.chip.npix_y, 0:self.chip.npix_x]),
+        #     method='nearest').astype(np.float32)
         U = U/np.mean(U)
-        flatImage = U*fluxLED[led_type]*1000
+        flatImage = U
+        if LED_Img_flag:
+            flatImage = U*fluxLED[led_type]*1000
         gc.collect()
         return flatImage
 

observation_sim/mock_objects/Galaxy.py

@@ -33,7 +33,7 @@ class Galaxy(MockObject):
             raise ValueError(
                 "!!!The number of PSF profiles and the number of bandpasses must be equal.")
         objs = []
-        if nphotons_tot == None:
+        if nphotons_tot is None:
             nphotons_tot = self.getElectronFluxFilt(filt, tel, exptime)
         # print("nphotons_tot = ", nphotons_tot)
 
@@ -92,7 +92,7 @@ class Galaxy(MockObject):
         return final
 
     def drawObj_multiband(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0, exptime=150., fd_shear=None):
-        if nphotons_tot == None:
+        if nphotons_tot is None:
             nphotons_tot = self.getElectronFluxFilt(filt, tel, exptime)
         # print("nphotons_tot = ", nphotons_tot)
 
@@ -115,7 +115,7 @@ class Galaxy(MockObject):
 
         # Set Galsim Parameters
         if self.getMagFilter(filt) <= 15 and (not big_galaxy):
-            folding_threshold = 5.e-4
+            folding_threshold = 5.e-8
         else:
             folding_threshold = 5.e-3
         gsp = galsim.GSParams(folding_threshold=folding_threshold)
@@ -170,8 +170,11 @@ class Galaxy(MockObject):
             # print("nphotons_sub-band_%d = %.2f"%(i, nphotons))
 
             # Get PSF model
+            EXTRA = False
+            if self.getMagFilter(filt) <= filt.mag_saturation-1.:
+                EXTRA = True
             psf, pos_shear = psf_model.get_PSF(
-                chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold)
+                chip=chip, pos_img=pos_img, bandpass=bandpass, folding_threshold=folding_threshold, extrapolate=EXTRA)
 
             if self.bfrac == 0:
                 gal_temp = disk
@@ -325,23 +328,28 @@ class Galaxy(MockObject):
 
             galImg_List = []
             try:
-                pos_img_local = [0,0]
+                pos_img_local = [0, 0]
                 x_start = chip.x_cen/chip.pix_size - chip.npix_x / 2.
                 y_start = chip.y_cen/chip.pix_size - chip.npix_y / 2.
                 pos_img_local[0] = pos_img.x - x_start
                 pos_img_local[1] = pos_img.y - y_start
                 nnx = 0
                 nny = 0
-                for order in ["A","B"]:
+                for order in ["A", "B"]:
+                    EXTRA = False
+                    if self.getMagFilter(filt) <= filt.mag_saturation-2.:
+                        EXTRA = True
                     psf, pos_shear = psf_model.get_PSF(
-                        chip, pos_img_local=pos_img_local, bandNo=i+1, galsimGSObject=True, g_order=order, grating_split_pos=grating_split_pos)
+                        chip, pos_img_local=pos_img_local, bandNo=i+1, galsimGSObject=True, g_order=order, grating_split_pos=grating_split_pos, extrapolate=EXTRA, ngg=3072)
                     star_p = galsim.Convolve(psf, gal)
                     if nnx == 0:
-                        galImg = star_p.drawImage(wcs=chip_wcs_local, offset=offset)
+                        galImg = star_p.drawImage(
+                            wcs=chip_wcs_local, offset=offset, method='no_pixel')
                         nnx = galImg.xmax - galImg.xmin + 1
                         nny = galImg.ymax - galImg.ymin + 1
                     else:
-                        galImg = star_p.drawImage(nx = nnx, ny = nny, wcs=chip_wcs_local, offset=offset)
+                        galImg = star_p.drawImage(
+                            nx=nnx, ny=nny, wcs=chip_wcs_local, offset=offset, method='no_pixel')
                     galImg.setOrigin(0, 0)
                     # n1 = np.sum(np.isinf(galImg.array))
                     # n2 = np.sum(np.isnan(galImg.array))
@@ -351,19 +359,23 @@ class Galaxy(MockObject):
                         # ERROR happens
                         return 2, pos_shear
                     galImg_List.append(galImg)
-                for order in ["C","D","E"]:
+                for order in ["C", "D", "E"]:
                     galImg_List.append(galImg)
             except:
-                psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img)
-                star_p = galsim.Convolve(psf, gal)
-                galImg = star_p.drawImage(wcs=chip_wcs_local, offset=offset)
-                galImg.setOrigin(0, 0)
-                if np.sum(np.isnan(galImg.array)) > 0:
-                    # ERROR happens
-                    return 2, pos_shear
-                for order in ["A","B","C","D","E"]:
-                    galImg_List.append(galImg)
-
+                try:
+                    psf, pos_shear = psf_model.get_PSF(
+                        chip=chip, pos_img=pos_img)
+                    star_p = galsim.Convolve(psf, gal)
+                    galImg = star_p.drawImage(
+                        wcs=chip_wcs_local, offset=offset)
+                    galImg.setOrigin(0, 0)
+                    if np.sum(np.isnan(galImg.array)) > 0:
+                        # ERROR happens
+                        return 2, pos_shear
+                    for order in ["A", "B", "C", "D", "E"]:
+                        galImg_List.append(galImg)
+                except Exception as e:
+                    continue
             # starImg = gal.drawImage(
             #     wcs=chip_wcs_local, offset=offset, method='real_space')
 
@@ -378,7 +390,7 @@ class Galaxy(MockObject):
                 subSlitPos = int(grating_split_pos_chip - gal_origin[1])
                 # part img disperse
 
-                star_p1s=[]
+                star_p1s = []
                 for galImg in galImg_List:
 
                     subImg_p1 = galImg.array[:, 0:subSlitPos]
@@ -397,17 +409,18 @@ class Galaxy(MockObject):
                                        isAlongY=0,
                                        flat_cube=flat_cube)
 
-                self.addSLStoChipImage(sdp=sdp_p1, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp_p1, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp_p1, chip=chip, pos_img_local=[xcenter_p1, ycenter_p1],
                 #                                           psf_model=psf_model, bandNo=i + 1,
                 #                                           grating_split_pos=grating_split_pos,
                 #                                           local_wcs=chip_wcs_local, pos_img=pos_img)
 
-                star_p2s=[]
+                star_p2s = []
                 for galImg in galImg_List:
 
                     subImg_p2 = galImg.array[:,
-                                          subSlitPos:galImg.array.shape[1]]
+                                             subSlitPos:galImg.array.shape[1]]
                     star_p2 = galsim.Image(subImg_p2)
                     star_p2.setOrigin(0, 0)
                     star_p2s.append(star_p2)
@@ -423,7 +436,8 @@ class Galaxy(MockObject):
                                        isAlongY=0,
                                        flat_cube=flat_cube)
 
-                self.addSLStoChipImage(sdp=sdp_p2, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp_p2, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp_p2, chip=chip, pos_img_local=[xcenter_p2, ycenter_p2],
                 #                                           psf_model=psf_model, bandNo=i + 1,
                 #                                           grating_split_pos=grating_split_pos,
@@ -439,7 +453,8 @@ class Galaxy(MockObject):
                                     conf=chip.sls_conf[1],
                                     isAlongY=0,
                                     flat_cube=flat_cube)
-                self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp, chip=chip, pos_img_local=[x_nominal, y_nominal],
                 #                                           psf_model=psf_model, bandNo=i + 1,
                 #                                           grating_split_pos=grating_split_pos,
@@ -453,7 +468,8 @@ class Galaxy(MockObject):
                                     conf=chip.sls_conf[0],
                                     isAlongY=0,
                                     flat_cube=flat_cube)
-                self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus = xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp, chip=chip, pos_img_local=[x_nominal, y_nominal],
                 #                                           psf_model=psf_model, bandNo=i + 1,
                 #                                           grating_split_pos=grating_split_pos,
@@ -465,7 +481,7 @@ class Galaxy(MockObject):
         return 1, pos_shear
 
     def getGSObj(self, psf, g1=0, g2=0, flux=None, filt=None, tel=None, exptime=150.):
-        if flux == None:
+        if flux is None:
             flux = self.getElectronFluxFilt(filt, tel, exptime)
         disk = galsim.Sersic(n=self.disk_sersic_idx,
                              half_light_radius=self.hlr_disk, flux=1.0)

observation_sim/mock_objects/MockObject.py

@@ -78,6 +78,8 @@ class MockObject(object):
                       (self.posImg.x, self.posImg.y), flush=True)
             self.posImg, self.fd_shear = fdmodel.get_distorted(
                 chip=chip, pos_img=self.posImg)
+            if self.posImg is None:
+                return None, None, None, None, None
             if verbose:
                 print("After field distortion:\n")
                 print("x = %.2f, y = %.2f\n" %
@@ -108,7 +110,7 @@ class MockObject(object):
 
     def drawObj_multiband(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0,
                           exptime=150., fd_shear=None):
-        if nphotons_tot == None:
+        if nphotons_tot is None:
             nphotons_tot = self.getElectronFluxFilt(filt, tel, exptime)
         # print("nphotons_tot = ", nphotons_tot)
 
@@ -122,7 +124,7 @@ class MockObject(object):
             return 2, None
         # Set Galsim Parameters
         if self.getMagFilter(filt) <= 15:
-            folding_threshold = 5.e-4
+            folding_threshold = 5.e-8
         else:
             folding_threshold = 5.e-3
         gsp = galsim.GSParams(folding_threshold=folding_threshold)
@@ -160,14 +162,17 @@ class MockObject(object):
             # print("nphotons_sub-band_%d = %.2f"%(i, nphotons))
 
             # Get PSF model
+            EXTRA = False
+            if self.getMagFilter(filt) <= filt.mag_saturation-1.:
+                EXTRA = True
             psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img, bandpass=bandpass,
-                                               folding_threshold=folding_threshold)
+                                               folding_threshold=folding_threshold, extrapolate=EXTRA)
             # star = galsim.DeltaFunction(gsparams=gsp)
             # star = star.withFlux(nphotons)
             # star = galsim.Convolve(psf, star)
             star = psf.withFlux(nphotons)
 
-            stamp = star.drawImage(wcs=chip_wcs_local, offset=offset)
+            stamp = star.drawImage(method='no_pixel', wcs=chip_wcs_local, offset=offset)
             if np.sum(np.isnan(stamp.array)) > 0:
                 continue
             stamp.setCenter(x_nominal, y_nominal)
@@ -235,14 +240,14 @@ class MockObject(object):
         if chip.slsPSFOptim:
             for k, v in spec_orders.items():
                 img_s = v[0]
-                            
+
                 nan_ids = np.isnan(img_s)
                 if img_s[nan_ids].shape[0] > 0:
                     img_s[nan_ids] = 0
                     print("DEBUG: specImg nan num is", img_s[nan_ids].shape[0])
                 #########################################################
                 # img_s, orig_off = convolveImg(img_s, psf_img_m)
-                orig_off = [0,0]
+                orig_off = [0, 0]
                 origin_order_x = v[1] - orig_off[0]
                 origin_order_y = v[2] - orig_off[1]
 
@@ -257,15 +262,18 @@ class MockObject(object):
                     continue
 
                 # orders = {'A': 'order1', 'B': 'order0', 'C': 'order2', 'D': 'order-1', 'E': 'order-2'}
-                orders = {'A': 'order1', 'B': 'order0', 'C': 'order0', 'D': 'order0', 'E': 'order0'}
+                orders = {'A': 'order1', 'B': 'order0',
+                          'C': 'order0', 'D': 'order0', 'E': 'order0'}
                 gratingN = chip_utils.getChipSLSGratingID(chip.chipID)[1]
                 if pos_img_local[0] < grating_split_pos:
                     gratingN = chip_utils.getChipSLSGratingID(chip.chipID)[0]
-                
 
-                chip.img_stack[gratingN][orders[k]]['w' + str(bandNo)].setOrigin(0, 0)
-                chip.img_stack[gratingN][orders[k]]['w' + str(bandNo)][bounds] = chip.img_stack[gratingN][orders[k]]['w' + str(bandNo)][bounds] + specImg[bounds]
-                chip.img_stack[gratingN][orders[k]]['w' + str(bandNo)].setOrigin(chip.bound.xmin, chip.bound.ymin)
+                chip.img_stack[gratingN][orders[k]
+                                         ]['w' + str(bandNo)].setOrigin(0, 0)
+                chip.img_stack[gratingN][orders[k]]['w' + str(
+                    bandNo)][bounds] = chip.img_stack[gratingN][orders[k]]['w' + str(bandNo)][bounds] + specImg[bounds]
+                chip.img_stack[gratingN][orders[k]]['w' +
+                                                    str(bandNo)].setOrigin(chip.bound.xmin, chip.bound.ymin)
 
         else:
             for k, v in spec_orders.items():
@@ -313,11 +321,11 @@ class MockObject(object):
 
                 # specImg.wcs = local_wcs
                 # specImg.setOrigin(origin_order_x, origin_order_y)
-                
+
                 # print('DEBUG: BEGIN -----------',bandNo,k)
-                
+
                 img_s = v[0]
-            
+
                 nan_ids = np.isnan(img_s)
                 if img_s[nan_ids].shape[0] > 0:
                     img_s[nan_ids] = 0
@@ -330,9 +338,11 @@ class MockObject(object):
                 specImg.wcs = local_wcs
                 specImg.setOrigin(origin_order_x, origin_order_y)
                 try:
-                    specImg = psf_model.get_PSF_AND_convolve_withsubImg(chip, cutImg=specImg, pos_img_local=pos_img_local, bandNo=bandNo, g_order=k, grating_split_pos=grating_split_pos)
+                    specImg = psf_model.get_PSF_AND_convolve_withsubImg(
+                        chip, cutImg=specImg, pos_img_local=pos_img_local, bandNo=bandNo, g_order=k, grating_split_pos=grating_split_pos)
                 except:
-                    psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img)
+                    psf, pos_shear = psf_model.get_PSF(
+                        chip=chip, pos_img=pos_img)
 
                     psf_img = psf.drawImage(nx=100, ny=100, wcs=local_wcs)
 
@@ -376,7 +386,7 @@ class MockObject(object):
             sedNormFactor = 1.
 
         if self.getMagFilter(filt) <= 15:
-            folding_threshold = 5.e-4
+            folding_threshold = 5.e-8
         else:
             folding_threshold = 5.e-3
         gsp = galsim.GSParams(folding_threshold=folding_threshold)
@@ -425,45 +435,51 @@ class MockObject(object):
             # star = galsim.DeltaFunction(gsparams=gsp)
             # star = star.withFlux(tel.pupil_area * exptime)
 
-            #psf list :["A","B","C","D","E"]
+            # psf list :["A","B","C","D","E"]
             starImg_List = []
             try:
-                pos_img_local = [0,0]
+                pos_img_local = [0, 0]
                 x_start = chip.x_cen/chip.pix_size - chip.npix_x / 2.
                 y_start = chip.y_cen/chip.pix_size - chip.npix_y / 2.
                 pos_img_local[0] = pos_img.x - x_start
                 pos_img_local[1] = pos_img.y - y_start
                 nnx = 0
                 nny = 0
-                for order in ["A","B"]:
+                for order in ["A", "B"]:
+                    EXTRA = False
+                    if self.getMagFilter(filt) <= filt.mag_saturation-2.:
+                        EXTRA = True
+                        nnx = 2048
+                        nny = 2048
                     psf, pos_shear = psf_model.get_PSF(
-                        chip, pos_img_local=pos_img_local, bandNo=i+1, galsimGSObject=True, g_order=order, grating_split_pos=grating_split_pos)
+                        chip, pos_img_local=pos_img_local, bandNo=i+1, galsimGSObject=True, g_order=order, grating_split_pos=grating_split_pos, extrapolate=EXTRA, ngg=3072)
                     # star_p = galsim.Convolve(psf, star)
-                    star_p =  psf.withFlux(tel.pupil_area * exptime)
+                    star_p = psf.withFlux(tel.pupil_area * exptime)
                     if nnx == 0:
-                        starImg = star_p.drawImage(wcs=chip_wcs_local, offset=offset)
+                        starImg = star_p.drawImage(
+                            wcs=chip_wcs_local, offset=offset, method='no_pixel')
                         nnx = starImg.xmax - starImg.xmin + 1
                         nny = starImg.ymax - starImg.ymin + 1
                     else:
-                        starImg = star_p.drawImage(nx = nnx, ny = nny, wcs=chip_wcs_local, offset=offset)
+                        starImg = star_p.drawImage(
+                            nx=nnx, ny=nny, wcs=chip_wcs_local, offset=offset, method='no_pixel')
                     # n1 = np.sum(np.isinf(starImg.array))
                     # n2 = np.sum(np.isnan(starImg.array))
                     # if n1>0 or n2 > 0:
                     #     print("DEBUG: MockObject, inf:%d, nan:%d"%(n1, n2))
                     starImg.setOrigin(0, 0)
                     starImg_List.append(starImg)
-                for order in ["C","D","E"]:
+                for order in ["C", "D", "E"]:
                     starImg_List.append(starImg)
             except:
                 psf, pos_shear = psf_model.get_PSF(chip=chip, pos_img=pos_img)
                 # star_p = galsim.Convolve(psf, star)
-                star_p =  psf.withFlux(tel.pupil_area * exptime)
-                starImg = star_p.drawImage(wcs=chip_wcs_local, offset=offset)
+                star_p = psf.withFlux(tel.pupil_area * exptime)
+                starImg = star_p.drawImage(wcs=chip_wcs_local, offset=offset, method='no_pixel')
                 starImg.setOrigin(0, 0)
-                for order in ["A","B","C","D","E"]:
+                for order in ["A", "B", "C", "D", "E"]:
                     starImg_List.append(starImg)
 
-            
             # psf_tmp = galsim.Gaussian(sigma=0.002)
             # star = galsim.Convolve(psf_tmp, star)
 
@@ -472,14 +488,14 @@ class MockObject(object):
 
             origin_star = [y_nominal - (starImg.center.y - starImg.ymin),
                            x_nominal - (starImg.center.x - starImg.xmin)]
-            
+
             gal_origin = [origin_star[0], origin_star[1]]
             gal_end = [origin_star[0] + starImg.array.shape[0] -
                        1, origin_star[1] + starImg.array.shape[1] - 1]
             if gal_origin[1] < grating_split_pos_chip < gal_end[1]:
                 subSlitPos = int(grating_split_pos_chip - gal_origin[1])
                 # part img disperse
-                star_p1s=[]
+                star_p1s = []
                 for starImg in starImg_List:
 
                     subImg_p1 = starImg.array[:, 0:subSlitPos]
@@ -498,17 +514,17 @@ class MockObject(object):
                                        isAlongY=0,
                                        flat_cube=flat_cube)
 
-                self.addSLStoChipImage(sdp=sdp_p1, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp_p1, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp_p1, chip=chip, pos_img_local=[xcenter_p1, ycenter_p1],
                 #                                           psf_model=psf_model, bandNo=i+1, grating_split_pos=grating_split_pos,
                 #                                           local_wcs=chip_wcs_local, pos_img=pos_img)
 
-
-                star_p2s=[]
+                star_p2s = []
                 for starImg in starImg_List:
 
                     subImg_p2 = starImg.array[:,
-                                          subSlitPos:starImg.array.shape[1]]
+                                              subSlitPos:starImg.array.shape[1]]
                     star_p2 = galsim.Image(subImg_p2)
                     star_p2.setOrigin(0, 0)
                     star_p2s.append(star_p2)
@@ -524,7 +540,8 @@ class MockObject(object):
                                        isAlongY=0,
                                        flat_cube=flat_cube)
 
-                self.addSLStoChipImage(sdp=sdp_p2, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp_p2, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp_p2, chip=chip, pos_img_local=[xcenter_p2, ycenter_p2],
                 #                                           psf_model=psf_model, bandNo=i + 1, grating_split_pos=grating_split_pos,
                 #                                           local_wcs=chip_wcs_local, pos_img=pos_img)
@@ -539,7 +556,8 @@ class MockObject(object):
                                     conf=chip.sls_conf[1],
                                     isAlongY=0,
                                     flat_cube=flat_cube)
-                self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp, chip=chip, pos_img_local=[x_nominal, y_nominal],
                 #                                           psf_model=psf_model, bandNo=i + 1, grating_split_pos=grating_split_pos,
                 #                                           local_wcs=chip_wcs_local, pos_img=pos_img)
@@ -552,7 +570,8 @@ class MockObject(object):
                                     conf=chip.sls_conf[0],
                                     isAlongY=0,
                                     flat_cube=flat_cube)
-                self.addSLStoChipImage(sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
+                self.addSLStoChipImage(
+                    sdp=sdp, chip=chip, xOrderSigPlus=xOrderSigPlus, local_wcs=chip_wcs_local)
                 # pos_shear = self.addSLStoChipImageWithPSF(sdp=sdp, chip=chip, pos_img_local=[x_nominal, y_nominal],
                 #                                           psf_model=psf_model, bandNo=i + 1, grating_split_pos=grating_split_pos,
                 #                                           local_wcs=chip_wcs_local, pos_img=pos_img)
@@ -572,7 +591,7 @@ class MockObject(object):
 
     def drawObj_PSF(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0,
                     exptime=150., fd_shear=None, chip_output=None):
-        if nphotons_tot == None:
+        if nphotons_tot is None:
             nphotons_tot = self.getElectronFluxFilt(filt, tel, exptime)
         # print("nphotons_tot = ", nphotons_tot)
 
@@ -641,7 +660,7 @@ class MockObject(object):
         os.makedirs(fn, exist_ok=True)
         fn = fn + "/ccd_{:}".format(chip.chipID) + \
             "_psf_"+str(self.param['id'])+".fits"
-        if fn != None:
+        if fn is not None:
             if os.path.exists(fn):
                 os.remove(fn)
         hdu = fitsio.PrimaryHDU()

observation_sim/mock_objects/Quasar.py

@@ -98,7 +98,7 @@ class Quasar(MockObject):
         del self.sed
 
     def getGSObj(self, psf, g1=0, g2=0, flux=None, filt=None, tel=None, exptime=150.):
-        if flux == None:
+        if flux is None:
             flux = self.getElectronFluxFilt(filt, tel, exptime)
         qso = galsim.Gaussian(sigma=1.e-8, flux=1.)
         qso = qso.withFlux(flux)

observation_sim/mock_objects/SpecDisperser/__init__.py

 from .SpecDisperser import *
-from .disperse_c import disperse, interp
\ No newline at end of file
+from .disperse_c import disperse, interp

observation_sim/mock_objects/SpecDisperser/setup_c.py

@@ -8,16 +8,16 @@ import numpy
 
 extensions = [
     Extension("disperse_c.interp", ["disperse_c/interp.pyx"],
-        include_dirs = [numpy.get_include()],
-        libraries=["m"]),
-    
+              include_dirs=[numpy.get_include()],
+              libraries=["m"]),
+
     Extension("disperse_c.disperse", ["disperse_c/disperse.pyx"],
-        include_dirs = [numpy.get_include()],
-        libraries=["m"]),
+              include_dirs=[numpy.get_include()],
+              libraries=["m"]),
 ]
 
 
 setup(
-    name = "slssim_disperse",
-    ext_modules = cythonize(extensions),
+    name="slssim_disperse",
+    ext_modules=cythonize(extensions),
 )

observation_sim/mock_objects/Stamp.py

@@ -21,7 +21,7 @@ class Stamp(MockObject):
         del self.sed
 
     def drawObj_multiband(self, tel, pos_img, psf_model, bandpass_list, filt, chip, nphotons_tot=None, g1=0, g2=0, exptime=150., fd_shear=None):
-        if nphotons_tot == None:
+        if nphotons_tot is None:
             nphotons_tot = self.getElectronFluxFilt(filt, tel, exptime)
 
         try:
@@ -92,7 +92,7 @@ class Stamp(MockObject):
             else:
                 gal = gal + gal_temp
 
-        stamp = gal.drawImage(wcs=chip_wcs_local, offset=offset)
+        stamp = gal.drawImage(method='no_pixel', wcs=chip_wcs_local, offset=offset)
         if np.sum(np.isnan(stamp.array)) > 0:
             # ERROR happens
             return 2, pos_shear

observation_sim/mock_objects/Star.py

@@ -22,7 +22,7 @@ class Star(MockObject):
         del self.sed
 
     def getGSObj(self, psf, g1=0, g2=0, flux=None, filt=None, tel=None, exptime=150.):
-        if flux == None:
+        if flux is None:
             flux = self.getElectronFluxFilt(filt, tel, exptime)
         # star = galsim.Gaussian(sigma=1.e-8, flux=1.)
         star = galsim.DeltaFunction()
@@ -35,7 +35,7 @@ class Star(MockObject):
             raise ValueError(
                 "!!!The number of PSF profiles and the number of bandpasses must be equal.")
         objs = []
-        if nphotons_tot == None:
+        if nphotons_tot is None:
             nphotons_tot = self.getElectronFluxFilt(filt, tel, exptime)
 
         try:

observation_sim/mock_objects/_util.py

@@ -58,7 +58,7 @@ def seds(sedlistn, seddir="./", unit="A"):
     read SEDs and save into Python dictionary
 
     Parameters:
-    sedlistn: filename of the sed template list and corresponding intrinsic 
+    sedlistn: filename of the sed template list and corresponding intrinsic
               extinction model, see tmag_dz.py for detailes
     listdir:  directory of the list
     unit: wavelength unit of the input templates
@@ -420,7 +420,7 @@ def sed2mag(mag_i, sedCat, filter_list, redshift=0.0, av=0.0, redden=0):
 
 def eObs(e1, e2, g1, g2):
     """
-    Calculate the sheared (observed) ellipticity using the 
+    Calculate the sheared (observed) ellipticity using the
     intrinsic ellipticity and cosmic shear components.
 
     Parameters:
@@ -558,7 +558,7 @@ def getNormFactorForSpecWithABMAG(ABMag=20., spectrum=None, norm_thr=None, sWave
         eWave: the end of norm_thr
 
     Return:
-        the normalization factor   flux of AB system(fix a band  and magnitude ) /the flux of inpute spectrum(fix a band) 
+        the normalization factor   flux of AB system(fix a band  and magnitude ) /the flux of inpute spectrum(fix a band)
     """
     spectrumi = interpolate.interp1d(spectrum['WAVELENGTH'], spectrum['FLUX'])
     norm_thri = interpolate.interp1d(

observation_sim/psf/FieldDistortion.py

@@ -62,7 +62,8 @@ class FieldDistortion(object):
                                 the distored position.
         """
         if not self.isContainObj_FD(chip=chip, pos_img=pos_img):
-            return galsim.PositionD(-1, -1), None
+            # return galsim.PositionD(-1, -1), None
+            return None, None
         if not img_rot:
             img_rot = np.radians(self.img_rot)
         else:

observation_sim/psf/PSFGauss.py

@@ -50,7 +50,7 @@ class PSFGauss(PSFModel):
 
         Return: the flux ratio
         """
-        if pscale == None:
+        if pscale is None:
             pscale = self.pix_size
         gaussx = galsim.Gaussian(flux=1.0, sigma=sig)
         gaussImg = gaussx.drawImage(scale=pscale, method='no_pixel')
@@ -68,7 +68,7 @@ class PSFGauss(PSFModel):
 
         return the fwhm in arcsec
         """
-        if pscale == None:
+        if pscale is None:
             pscale = self.pix_size
         err = 1.0e-3
         nxx = 100
@@ -122,4 +122,4 @@ class PSFGauss(PSFModel):
 
         # return ell, beta, qr
         PSFshear = galsim.Shear(e=ell, beta=beta*galsim.radians)
-        return self.psf.shear(PSFshear), PSFshear
\ No newline at end of file
+        return self.psf.shear(PSFshear), PSFshear