Merge branch 'release_v3.0' into 'master'

# Conflicts:
#   observation_sim/mock_objects/Galaxy.py
#   observation_sim/mock_objects/MockObject.py
#   observation_sim/psf/PSFInterpSLS.py

observation_sim/mock_objects/__init__.py

@@ -5,4 +5,3 @@ from .Quasar import Quasar
 from .Star import Star
 from .Stamp import Stamp
 from .FlatLED import FlatLED
-from .ExtinctionMW import ExtinctionMW

observation_sim/psf/PSFGauss.py

@@ -17,7 +17,7 @@ class PSFGauss(PSFModel):
             self.fwhm = self.fwhmGauss(r=psfRa)
             self.sigGauss = psfRa  # 80% light radius
         self.sigSpin = sigSpin
-        self.psf = galsim.Gaussian(flux=1.0, fwhm=self.fwhm)
+        self.psf = galsim.Gaussian(flux=1.0, fwhm=fwhm)
 
     def perfGauss(self, r, sig):
         """
@@ -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
+        return self.psf.shear(PSFshear), PSFshear
\ No newline at end of file

observation_sim/psf/PSFInterpSLS.py

@@ -435,16 +435,7 @@ class PSFInterpSLS(PSFModel):
         # PSF_int_trans[ids_szero] = 0
         # print(PSF_int_trans[ids_szero].shape[0],PSF_int_trans.shape)
         PSF_int_trans = PSF_int_trans/np.sum(PSF_int_trans)
-        ###DEBGU
-        ids_szero = PSF_int_trans<0
-        n01 = PSF_int_trans[ids_szero].shape[0]
 
-        n1 = np.sum(np.isinf(PSF_int_trans))
-        n2 = np.sum(np.isnan(PSF_int_trans))
-        if n1>0 or n2>0:
-            print("DEBUG: PSFInterpSLS, inf:%d, nan:%d, 0 num:%d"%(n1, n2, n01))
-
-        ####
         # from astropy.io import fits
         # fits.writeto(str(bandNo) + '_' + g_order+ '_psf_o.fits', PSF_int_trans)
 

observation_sim/sim_steps/__init__.py

 import os
 
-
 class SimSteps:
-    def __init__(self, overall_config, chip_output, all_filters, ra_offset=0., dec_offset=0.):
+    def __init__(self, overall_config, chip_output, all_filters):
         self.overall_config = overall_config
         self.chip_output = chip_output
         self.all_filters = all_filters
-        self.ra_offset = ra_offset
-        self.dec_offset = dec_offset
 
     from .prepare_headers import prepare_headers, updateHeaderInfo
     from .add_sky_background import add_sky_background_sci, add_sky_flat_calibration, add_sky_background
@@ -18,7 +15,6 @@ class SimSteps:
     from .readout_output import add_prescan_overscan, add_readout_noise, apply_gain, quantization_and_output
     from .add_LED_flat import add_LED_Flat
 
-
 SIM_STEP_TYPES = {
     "scie_obs": "add_objects",
     "sky_background": "add_sky_background",
@@ -35,6 +31,6 @@ SIM_STEP_TYPES = {
     "readout_noise": "add_readout_noise",
     "gain": "apply_gain",
     "quantization_and_output": "quantization_and_output",
-    "led_calib_model": "add_LED_Flat",
-    "sky_flatField": "add_sky_flat_calibration",
-}
+    "led_calib_model":"add_LED_Flat",
+    "sky_flatField":"add_sky_flat_calibration",
+}
\ No newline at end of file

observation_sim/sim_steps/add_objects.py

@@ -145,7 +145,7 @@ def add_objects(self, chip, filt, tel, pointing, catalog, obs_param):
 
         # Get position of object on the focal plane
         pos_img, _, _, _, fd_shear = obj.getPosImg_Offset_WCS(
-            img=chip.img, fdmodel=fd_model, chip=chip, verbose=False, chip_wcs=chip_wcs, img_header=self.h_ext, ra_offset=self.ra_offset, dec_offset=self.dec_offset)
+            img=chip.img, fdmodel=fd_model, chip=chip, verbose=False, chip_wcs=chip_wcs, img_header=self.h_ext)
 
         # [TODO] For now, only consider objects which their centers (after field distortion) are projected within the focal plane
         # Otherwise they will be considered missed objects
@@ -194,8 +194,7 @@ def add_objects(self, chip, filt, tel, pointing, catalog, obs_param):
 
             if isUpdated == 1:
                 # TODO: add up stats
-                self.chip_output.cat_add_obj(
-                    obj, pos_img, pos_shear, ra_offset=self.ra_offset, dec_offset=self.dec_offset)
+                self.chip_output.cat_add_obj(obj, pos_img, pos_shear)
                 pass
             elif isUpdated == 0:
                 missed_obj += 1
@@ -217,27 +216,7 @@ def add_objects(self, chip, filt, tel, pointing, catalog, obs_param):
         # Unload SED:
         obj.unload_SED()
         del obj
-        # gc.collect()
-
-    if chip.survey_type == "spectroscopic" and not self.overall_config["run_option"]["out_cat_only"] and chip.slsPSFOptim:
-        # from observation_sim.instruments.chip import chip_utils as chip_utils
-        # gn = chip_utils.getChipSLSGratingID(chip.chipID)[0]
-        # img1 = np.zeros([2,chip.img.array.shape[0],chip.img.array.shape[1]])
-
-        # for id1 in np.arange(2):
-        #     gn = chip_utils.getChipSLSGratingID(chip.chipID)[id1]
-        #     img_i = 0
-        #     for id2 in ['0','1']:
-        #         o_n = "order"+id2
-        #         for id3 in ['1','2','3','4']:
-        #             w_n = "w"+id3
-        #             img1[img_i] = img1[img_i] + chip.img_stack[gn][o_n][w_n].array
-        #         img_i = img_i + 1
-        # from astropy.io import fits
-        # fits.writeto('order0.fits',img1[0],overwrite=True)
-        # fits.writeto('order1.fits',img1[1],overwrite=True)
-
-        psf_model.convolveFullImgWithPCAPSF(chip)
+        gc.collect()
     del psf_model
     gc.collect()
 

observation_sim/sim_steps/add_pattern_noise.py

@@ -27,7 +27,7 @@ def add_poisson_and_dark(self, chip, filt, tel, pointing, catalog, obs_param):
                                              InputDark=None)
     else:
         chip.img, _ = chip_utils.add_poisson(img=chip.img,
-                                             chip=chip,
+                                             chip=self,
                                              exptime=exptime,
                                              poisson_noise=chip.poisson_noise,
                                              dark_noise=0.)
@@ -81,5 +81,5 @@ def add_bias(self, chip, filt, tel, pointing, catalog, obs_param):
                                                nsecx=chip.nsecx,
                                                seed=self.overall_config["random_seeds"]["seed_biasNonUniform"]+chip.chipID)
     elif obs_param["bias_16channel"] == False:
-        chip.img += chip.bias_level
+        chip.img += self.bias_level
     return chip, filt, tel, pointing

observation_sim/sim_steps/readout_output.py

@@ -87,10 +87,10 @@ def quantization_and_output(self, chip, filt, tel, pointing, catalog, obs_param)
     fname = os.path.join(self.chip_output.subdir,
                          self.h_prim['FILENAME'] + '.fits')
 
-    # f_name_size = 68
-    # if (len(self.h_prim['FILENAME']) > f_name_size):
-    #     self.updateHeaderInfo(header_flag='prim', keys=['FILENAME'], values=[
-    #                           self.h_prim['FILENAME'][0:f_name_size]])
+    f_name_size = 68
+    if (len(self.h_prim['FILENAME']) > f_name_size):
+        self.updateHeaderInfo(header_flag='prim', keys=['FILENAME'], values=[
+                              self.h_prim['FILENAME'][0:f_name_size]])
 
     hdu1 = fits.PrimaryHDU(header=self.h_prim)
 

submit_jobs.slurm

 #!/bin/bash
 
 #SBATCH -J CSSTSim
-#SBATCH -N 2
+#SBATCH -N 1
 #SBATCH --ntasks-per-node=6
 #SBATCH -p debug
-#SBATCH --mem=96G
+#SBATCH --mem=60G
 
 module load mpi/hpcx/2.4.1/gcc-7.3.1
 date
@@ -12,4 +12,4 @@ date
 #限定单节点任务数
 srun hostname -s | sort -n | awk -F"-" '{print $2}' | uniq > pnodes
 
-mpirun -mca pml ucx -x  UCX_NET_DEVICES=mlx5_0:1 -machinefile pnodes -np 12 --map-by node python3 /public/home/fangyuedong/project/csst_msc_sim/run_sim.py  --config_file config_overall.yaml --catalog C9_Catalog -c /public/home/fangyuedong/project/csst_msc_sim/config
+mpirun -mca pml ucx -x  UCX_NET_DEVICES=mlx5_0:1 -machinefile pnodes -np 6 --map-by node python3 /public/home/fangyuedong/project/csst_msc_sim/run_sim.py  --config_file config_overall.yaml --catalog C9_Catalog -c /public/home/fangyuedong/project/csst_msc_sim/config
\ No newline at end of file

tools/get_pointing.py

@@ -63,15 +63,10 @@ class Chip(object):
             ycen = self.cen_pix_y
         if pix_scale == None:
             pix_scale = self.pix_scale
-        # 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
-        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
+        dvdx =  -np.sin(img_rot.rad) * pix_scale
+        dvdy =  +np.cos(img_rot.rad) * pix_scale
         
         # dudx =  +np.sin(img_rot.rad) * pix_scale
         # dudy =  +np.cos(img_rot.rad) * pix_scale
@@ -144,11 +139,12 @@ def getobsPA(ra, dec):
     angle = math.acos(np.dot(l1l2cross,pdl2cross)/(np.linalg.norm(l1l2cross)*np.linalg.norm(pdl2cross)))
 
     angle = (angle)/math.pi*180
-    angle = angle + 90
-    if (ra<90 or ra> 270):
-        angle=-angle
+
+    # if (ra>90 and ra< 270):
+    #     angle=-angle
     return angle
 
+
 # @jit()
 def getSelectPointingList(center = [60,-40], radius = 2):
     points = np.loadtxt('sky.dat')
@@ -265,7 +261,7 @@ def findPointingbyChipID(chipID = 8, ra = 60., dec = -40.):
 
 
 if __name__ == "__main__":
-    tchip, tra, tdec = 13, 60., -40.
+    tchip, tra, tdec = 8, 60., -40.
     pointing = findPointingbyChipID(chipID=tchip, ra=tra, dec=tdec)
     print("[ra_center, dec_center, image_rot]: ", pointing)
 

tools/get_pointing_accuracy.py

-
-from pylab import *
-import math, sys, numpy as np
-import astropy.coordinates as coord
-from astropy.coordinates import SkyCoord
-from astropy import wcs, units as u
-from observation_sim.config.header import ImageHeader
-from observation_sim.instruments import Telescope, Chip, FilterParam, Filter, FocalPlane
-
-
-def transRaDec2D(ra, dec):
-    x1 = np.cos(dec / 57.2957795) * np.cos(ra / 57.2957795)
-    y1 = np.cos(dec / 57.2957795) * np.sin(ra / 57.2957795)
-    z1 = np.sin(dec / 57.2957795)
-    return np.array([x1, y1, z1])
-
-def ecl2radec(lon_ecl, lat_ecl):
-    ## convert from ecliptic coordinates to equatorial coordinates
-    c_ecl = SkyCoord(
-        lon=lon_ecl * u.degree, lat=lat_ecl * u.degree, frame="barycentrictrueecliptic"
-    )
-    c_eq = c_ecl.transform_to("icrs")
-    ra_eq, dec_eq = c_eq.ra.degree, c_eq.dec.degree
-    return ra_eq, dec_eq
-
-
-def radec2ecl(ra, dec):
-    ## convert from equatorial coordinates to ecliptic coordinates
-    c_eq = SkyCoord(ra=ra * u.degree, dec=dec * u.degree, frame="icrs")
-    c_ecl = c_eq.transform_to("barycentrictrueecliptic")
-    lon_ecl, lat_ecl = c_ecl.lon.degree, c_ecl.lat.degree
-    return lon_ecl, lat_ecl
-
-def cal_FoVcenter_1P_equatorial(ra_FieldCenter, dec_FieldCenter, chipID = 1, pa = -23.5):
-
-    ### [ra_FieldCenter, dec_FieldCenter] is the center ra, dec of calibration fileds, such as: NEP, NGC 6397, etc.
-    ### [ra_ChipCenter, dec_ChipCenter] is the center ra, dec of the Chip center.
-    ### [ra_PointCenter, dec_PointCenter] is the telescope pointing center.
-    ## Calculate PA angle
-    chip = Chip(chipID)
-
-    h_ext = ImageHeader.generateExtensionHeader(
-        chip=chip,
-        xlen=chip.npix_x,
-        ylen=chip.npix_y,
-        ra=(ra_FieldCenter * u.degree).value, 
-        dec=(dec_FieldCenter * u.degree).value,
-        pa=pa,
-        gain=chip.gain,
-        readout=chip.read_noise,
-        dark=chip.dark_noise,
-        saturation=90000,
-        pixel_scale=chip.pix_scale,
-        pixel_size=chip.pix_size,
-        xcen=chip.x_cen,
-        ycen=chip.y_cen,
-        )
-
-    # assume that the telescope point to the sky center; then abtain the chip center under this situation; then calculate the differenc between the assumed telescope center and chip center; then add this difference to the sky center
-
-    wcs_h = wcs.WCS(h_ext)
-    pixs = np.array([[4608, 4616]])
-    world_point = wcs_h.wcs_pix2world(pixs, 0)
-    ra_ChipCenter, dec_ChipCenter = world_point[0][0], world_point[0][1]
-
-    d_ra = ra_FieldCenter - ra_ChipCenter
-    d_dec = dec_FieldCenter - dec_ChipCenter
-
-    ra_PointCenter = ra_FieldCenter + d_ra
-    dec_PointCenter = dec_FieldCenter + d_dec
-
-    lon_ecl_PointCenter, lat_ecl_PointCenter = radec2ecl(
-        ra_PointCenter, dec_PointCenter
-    )
-
-    return ra_PointCenter, dec_PointCenter, lon_ecl_PointCenter, lat_ecl_PointCenter
-
-def cal_FoVcenter_1P_ecliptic(lon_ecl_FieldCenter, lat_ecl_FieldCenter, chipID = 1, pa = -23.5):
-
-    ### [ra_FieldCenter, dec_FieldCenter] is the center ra, dec of calibration fileds, such as: NEP, NGC 6397, etc.
-    ### [ra_ChipCenter, dec_ChipCenter] is the center ra, dec of the Chip center.
-    ### [ra_PointCenter, dec_PointCenter] is the telescope pointing center.
-
-    ra_FieldCenter, dec_FieldCenter = ecl2radec(
-        lon_ecl_FieldCenter, lat_ecl_FieldCenter
-    )
-
-    ## Calculate PA angle
-    chip = Chip(chipID)
-
-    h_ext = ImageHeader.generateExtensionHeader(
-        chip=chip,
-        xlen=chip.npix_x,
-        ylen=chip.npix_y,
-        ra=(ra_FieldCenter * u.degree).value, 
-        dec=(dec_FieldCenter * u.degree).value,
-        pa=pa,
-        gain=chip.gain,
-        readout=chip.read_noise,
-        dark=chip.dark_noise,
-        saturation=90000,
-        pixel_scale=chip.pix_scale,
-        pixel_size=chip.pix_size,
-        xcen=chip.x_cen,
-        ycen=chip.y_cen,
-        )
-
-    # assume that the telescope point to the sky center; then abtain the chip center under this situation; then calculate the differenc between the assumed telescope center and chip center; then add this difference to the sky center
-
-    wcs_h = wcs.WCS(h_ext)
-    pixs = np.array([[4608, 4616]])
-    world_point = wcs_h.wcs_pix2world(pixs, 0)
-    ra_ChipCenter, dec_ChipCenter = world_point[0][0], world_point[0][1]
-
-    d_ra = ra_FieldCenter - ra_ChipCenter
-    d_dec = dec_FieldCenter - dec_ChipCenter
-
-    ra_PointCenter = ra_FieldCenter + d_ra
-    dec_PointCenter = dec_FieldCenter + d_dec
-
-    lon_ecl_PointCenter, lat_ecl_PointCenter = radec2ecl(
-        ra_PointCenter, dec_PointCenter
-    )
-
-    return ra_PointCenter, dec_PointCenter, lon_ecl_PointCenter, lat_ecl_PointCenter
-
-def getChipCenterRaDec(chipID = 1, p_ra = 60., p_dec = -40.):
-    chip = Chip(chipID)
-
-    h_ext = ImageHeader.generateExtensionHeader(
-        chip=chip,
-        xlen=chip.npix_x,
-        ylen=chip.npix_y,
-        ra=(p_ra * u.degree).value, 
-        dec=(p_dec * u.degree).value,
-        pa=pa,
-        gain=chip.gain,
-        readout=chip.read_noise,
-        dark=chip.dark_noise,
-        saturation=90000,
-        pixel_scale=chip.pix_scale,
-        pixel_size=chip.pix_size,
-        xcen=chip.x_cen,
-        ycen=chip.y_cen,
-        )
-    wcs_h = wcs.WCS(h_ext)
-    pixs = np.array([[4608, 4616]])
-    world_point = wcs_h.wcs_pix2world(pixs, 0)
-    RA_chip, Dec_chip = world_point[0][0], world_point[0][1]
-    return RA_chip, Dec_chip
-
-if __name__ == '__main__':
-    ra_input, dec_input = 270.00000, 66.56000  # NEP
-    pa = 23.5
-    # chipid = 2
-
-    for chipid in np.arange(1,31,1):
-        ra, dec, lon_ecl, lat_ecl = cal_FoVcenter_1P_equatorial(
-                    ra_input, dec_input,chipID=chipid, pa=pa)
-
-        print("chip id is %d, chip center [ra,dec] is [%f, %f], pointing center calculated [ra,dec] is [%f, %f]"%(chipid, ra_input, dec_input, ra, dec))
-        #for check the result
-        # testRA, testDec = getChipCenterRaDec(chipID = chipid, p_ra = ra, p_dec = dec)
-        # print(ra_input-testRA, dec_input-testDec)
-

tools/target_location_check.py

@@ -119,15 +119,10 @@ def getTanWCS(ra, dec, img_rot, pix_scale=0.074):
     """
     xcen, ycen = 0, 0
     img_rot = img_rot * galsim.degrees
-    # 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
+    dudy = -np.sin(img_rot.rad) * pix_scale
     dvdx = -np.sin(img_rot.rad) * pix_scale
-    dvdy = -np.cos(img_rot.rad) * pix_scale
+    dvdy = +np.cos(img_rot.rad) * pix_scale
 
     moscen = galsim.PositionD(x=xcen, y=ycen)
     sky_center = galsim.CelestialCoord(