ObservationSim.py

import os
import numpy as np
import mpi4py.MPI as MPI
import galsim
import psutil
import gc
from datetime import datetime

import traceback

from ObservationSim.Config import config_dir, ChipOutput
from ObservationSim.Instrument import Telescope, Filter, FilterParam, FocalPlane, Chip
from ObservationSim.Instrument.Chip import Effects
from ObservationSim.Instrument.Chip import ChipUtils as chip_utils
from ObservationSim._util import makeSubDir_PointingList
from ObservationSim.Astrometry.Astrometry_util import on_orbit_obs_position
from ObservationSim.sim_steps import SimSteps, SIM_STEP_TYPES

class Observation(object):
    def __init__(self, config, Catalog, work_dir=None, data_dir=None):
        self.path_dict = config_dir(config=config, work_dir=work_dir, data_dir=data_dir)
        self.config = config
        self.tel = Telescope()
        self.filter_param = FilterParam() 
        self.Catalog = Catalog

    def prepare_chip_for_exposure(self, chip, ra_cen, dec_cen, pointing, wcs_fp=None):
        # Get WCS for the focal plane
        if wcs_fp == None:
            wcs_fp = self.focal_plane.getTanWCS(ra_cen, dec_cen, pointing.img_pa, chip.pix_scale)

        # Create chip Image
        chip.img = galsim.ImageF(chip.npix_x, chip.npix_y)
        chip.img.setOrigin(chip.bound.xmin, chip.bound.ymin)
        chip.img.wcs = wcs_fp

        # Get random generators for this chip
        chip.rng_poisson, chip.poisson_noise = chip_utils.get_poisson(
            seed=int(self.config["random_seeds"]["seed_poisson"]) + pointing.id*30 + chip.chipID, sky_level=0.)
        
        # Get flat, shutter, and PRNU images
        chip.flat_img, _ = chip_utils.get_flat(img=chip.img, seed=int(self.config["random_seeds"]["seed_flat"]))
        if chip.chipID > 30:
            chip.shutter_img = np.ones_like(chip.img.array)
        else:
            chip.shutter_img = Effects.ShutterEffectArr(chip.img, t_shutter=1.3, dist_bearing=735, dt=1E-3)
        chip.prnu_img = Effects.PRNU_Img(xsize=chip.npix_x, ysize=chip.npix_y, sigma=0.01,
                                         seed=int(self.config["random_seeds"]["seed_prnu"]+chip.chipID))
        
        return chip

    def run_one_chip(self, chip, filt, pointing, chip_output, wcs_fp=None, psf_model=None, cat_dir=None, sed_dir=None):

        chip_output.Log_info(':::::::::::::::::::Current Pointing Information::::::::::::::::::')
        chip_output.Log_info("RA: %f, DEC; %f" % (pointing.ra, pointing.dec))
        chip_output.Log_info("Time: %s" % datetime.utcfromtimestamp(pointing.timestamp).isoformat())
        chip_output.Log_info("Exposure time: %f" % pointing.exp_time)
        chip_output.Log_info("Satellite Position (x, y, z): (%f, %f, %f)" % (pointing.sat_x, pointing.sat_y, pointing.sat_z))
        chip_output.Log_info("Satellite Velocity (x, y, z): (%f, %f, %f)" % (pointing.sat_vx, pointing.sat_vy, pointing.sat_vz))
        chip_output.Log_info("Position Angle: %f" % pointing.img_pa.deg)
        chip_output.Log_info('Chip : %d' % chip.chipID)
        chip_output.Log_info(':::::::::::::::::::::::::::END:::::::::::::::::::::::::::::::::::')

        # Apply astrometric simulation for pointing
        if self.config["obs_setting"]["enable_astrometric_model"]:
            dt = datetime.utcfromtimestamp(pointing.timestamp)
            date_str = dt.date().isoformat()
            time_str = dt.time().isoformat()
            ra_cen, dec_cen = on_orbit_obs_position(
                input_ra_list=[pointing.ra],
                input_dec_list=[pointing.dec],
                input_pmra_list=[0.],
                input_pmdec_list=[0.],
                input_rv_list=[0.],
                input_parallax_list=[1e-9],
                input_nstars=1,
                input_x=pointing.sat_x,
                input_y=pointing.sat_y,
                input_z=pointing.sat_z,
                input_vx=pointing.sat_vx,
                input_vy=pointing.sat_vy,
                input_vz=pointing.sat_vz,
                input_epoch="J2000",
                input_date_str=date_str,
                input_time_str=time_str
            )
            ra_cen, dec_cen = ra_cen[0], dec_cen[0]
        else:
            ra_cen = pointing.ra
            dec_cen = pointing.dec

        # Prepare necessary chip properties for simulation
        chip = self.prepare_chip_for_exposure(chip, ra_cen, dec_cen, pointing)

        # Load catalogues
        self.cat = self.Catalog(config=self.config, chip=chip, pointing=pointing, cat_dir=cat_dir, sed_dir=sed_dir, chip_output=chip_output, filt=filt)

        # Initialize SimSteps
        sim_steps = SimSteps(overall_config=self.config, chip_output=chip_output, all_filters=self.all_filters)

        for step in pointing.obs_param["call_sequence"]:
            if self.config["run_option"]["out_cat_only"]:
                if step != "scie_obs":
                    continue
            chip_output.Log_info("Starting simulation step: %s, calling function: %s"%(step, SIM_STEP_TYPES[step]))
            obs_param = pointing.obs_param["call_sequence"][step]
            step_name = SIM_STEP_TYPES[step]
            try:
                step_func = getattr(sim_steps, step_name)
                chip, filt, tel, pointing = step_func(
                    chip=chip, 
                    filt=filt, 
                    tel=self.tel,
                    pointing=pointing, 
                    catalog=self.cat, 
                    obs_param=obs_param)
                chip_output.Log_info("Finished simulation step: %s"%(step))
            except Exception as e:
                traceback.print_exc()
                chip_output.Log_error(e)
                chip_output.Log_error("Failed simulation on step: %s"%(step))
                break

        chip_output.Log_info("check running:1: pointing-%d chip-%d pid-%d memory-%6.2fGB"%(pointing.id, chip.chipID, os.getpid(), (psutil.Process(os.getpid()).memory_info().rss / 1024 / 1024 / 1024) ))
        del chip.img

    # def run_one_chip_calibration(self, chip, filt, pointing, chip_output, skyback_level = 20000, sky_level_filt = 'g', wcs_fp=None, psf_model=None, cat_dir=None, sed_dir=None):




    #     # # Get WCS for the focal plane
    #     # if wcs_fp == None:
    #     # wcs_fp = self.focal_plane.getTanWCS(ra_cen, dec_cen, pointing.img_pa, chip.pix_scale)

    #     # Create chip Image
    #     chip.img = galsim.ImageF(chip.npix_x, chip.npix_y)
    #     chip.img.setOrigin(chip.bound.xmin, chip.bound.ymin)
    #     # chip.img.wcs = wcs_fp
    #     pf_map = np.zeros_like(chip.img.array)
    #     if self.config["obs_setting"]["LED_TYPE"] is not None:
    #         if len(self.config["obs_setting"]["LED_TYPE"]) != 0:
    #             print("LED OPEN--------")

    #             led_obj = FlatLED(chip, filt)

    #             led_flat = led_obj.drawObj_LEDFlat(led_type_list=self.config["obs_setting"]["LED_TYPE"], exp_t_list=self.config["obs_setting"]["LED_TIME"])
    #             pf_map = led_flat
    #     # whether to output zero, dark, flat calibration images.
    #     expTime = self.config["obs_setting"]["exp_time"]
    #     norm_scaler = skyback_level/expTime / self.filter_param.param[sky_level_filt][5]

    #     if skyback_level == 0:
    #         self.config["ins_effects"]["shutter_effect"] = False

    #     if chip.survey_type == "photometric":
    #         sky_map = np.ones_like(chip.img.array) * norm_scaler * self.filter_param.param[chip.filter_type][5] / self.tel.pupil_area
    #     elif chip.survey_type == "spectroscopic":
    #         flat_normal = np.ones_like(chip.img.array)
    #         if self.config["ins_effects"]["flat_fielding"] == True:
    #             chip_output.Log_info("SLS flat preprocess,CHIP %d : Creating and applying Flat-Fielding" % chip.chipID)
    #             msg = str(chip.img.bounds)
    #             chip_output.Log_info(msg)
    #             flat_img = Effects.MakeFlatSmooth(
    #                 chip.img.bounds,
    #                 int(self.config["random_seeds"]["seed_flat"]))
    #             flat_normal = flat_normal * flat_img.array / np.mean(flat_img.array)
    #         if self.config["ins_effects"]["shutter_effect"] == True:
    #             chip_output.Log_info("SLS flat preprocess,CHIP %d : Apply shutter effect" % chip.chipID)
    #             shuttimg = Effects.ShutterEffectArr(chip.img, t_shutter=1.3, dist_bearing=735,
    #                                                 dt=1E-3)  # shutter effect normalized image for this chip
    #             flat_normal = flat_normal * shuttimg
    #             flat_normal = np.array(flat_normal, dtype='float32')
    #         sky_map = calculateSkyMap_split_g(
    #             skyMap=flat_normal,
    #             blueLimit=filt.blue_limit,
    #             redLimit=filt.red_limit,
    #             conf=chip.sls_conf,
    #             pixelSize=chip.pix_scale,
    #             isAlongY=0,
    #             flat_cube=chip.flat_cube)
    #         sky_map = sky_map * norm_scaler

    #     chip.img = chip.addEffects(
    #         config=self.config,
    #         img=chip.img,
    #         chip_output=chip_output,
    #         filt=filt,
    #         ra_cen=pointing.ra,
    #         dec_cen=pointing.dec,
    #         img_rot=pointing.img_pa,
    #         exptime=self.config["obs_setting"]["exp_time"],
    #         pointing_ID=pointing.id,
    #         timestamp_obs=pointing.timestamp,
    #         pointing_type=pointing.pointing_type,
    #         sky_map=sky_map, tel=self.tel,
    #         post_flash_map=pf_map,
    #         logger=chip_output.logger)

    #     datetime_obs = datetime.utcfromtimestamp(pointing.timestamp)
    #     date_obs = datetime_obs.strftime("%y%m%d")
    #     time_obs = datetime_obs.strftime("%H%M%S")
    #     h_prim = generatePrimaryHeader(
    #         xlen=chip.npix_x,
    #         ylen=chip.npix_y,
    #         pointNum=str(pointing.id),
    #         ra=pointing.ra,
    #         dec=pointing.dec,
    #         pixel_scale=chip.pix_scale,
    #         date=date_obs,
    #         time_obs=time_obs,
    #         exptime=self.config["obs_setting"]["exp_time"],
    #         im_type='DARKPF',
    #         sat_pos=[pointing.sat_x, pointing.sat_y, pointing.sat_z],
    #         sat_vel=[pointing.sat_vx, pointing.sat_vy, pointing.sat_vz],
    #         chip_name=str(chip.chipID).rjust(2, '0'))
    #     h_ext = generateExtensionHeader(
    #         chip=chip,
    #         xlen=chip.npix_x,
    #         ylen=chip.npix_y,
    #         ra=pointing.ra,
    #         dec=pointing.dec,
    #         pa=pointing.img_pa.deg,
    #         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,
    #         extName='SCI',
    #         timestamp=pointing.timestamp,
    #         exptime=self.config["obs_setting"]["exp_time"],
    #         readoutTime=chip.readout_time)

    #     chip.img = galsim.Image(chip.img.array, dtype=np.uint16)
    #     hdu1 = fits.PrimaryHDU(header=h_prim)
    #     hdu1.add_checksum()
    #     hdu1.header.comments['CHECKSUM'] = 'HDU checksum'
    #     hdu1.header.comments['DATASUM'] = 'data unit checksum'
    #     hdu2 = fits.ImageHDU(chip.img.array, header=h_ext)
    #     hdu2.add_checksum()
    #     hdu2.header.comments['XTENSION'] = 'extension type'
    #     hdu2.header.comments['CHECKSUM'] = 'HDU checksum'
    #     hdu2.header.comments['DATASUM'] = 'data unit checksum'
    #     hdu1 = fits.HDUList([hdu1, hdu2])
    #     fname = os.path.join(chip_output.subdir, h_prim['FILENAME'] + '.fits')
    #     hdu1.writeto(fname, output_verify='ignore', overwrite=True)

    #         # chip_output.Log_info("# objects that are too bright %d out of %d" % (bright_obj, self.nobj))
    #         # chip_output.Log_info("# objects that are too dim %d out of %d" % (dim_obj, self.nobj))
    #         # chip_output.Log_info("# objects that are missed %d out of %d" % (missed_obj, self.nobj))
    #     del chip.img

    #     chip_output.Log_info("check running:2: pointing-%d chip-%d pid-%d memory-%6.2fGB" % (
    #     pointing.id, chip.chipID, os.getpid(), (psutil.Process(os.getpid()).memory_info().rss / 1024 / 1024 / 1024)))

    def runExposure_MPI_PointingList(self, pointing_list, chips=None, use_mpi=False):
        if use_mpi:
            comm = MPI.COMM_WORLD
            ind_thread = comm.Get_rank()
            num_thread = comm.Get_size()

        process_counter = 0
        for ipoint in range(len(pointing_list)):
            # Construct chips & filters:
            pointing = pointing_list[ipoint]
            pointing_ID = pointing.id
            self.focal_plane = FocalPlane(chip_list=pointing.obs_param["run_chips"])
            # Make Chip & Filter lists
            self.chip_list = []
            self.filter_list = []
            self.all_filters = []
            for i in range(self.focal_plane.nchips):
                chipID = i + 1
                chip = Chip(chipID=chipID, config=self.config)
                filter_id, filter_type = chip.getChipFilter()
                filt = Filter(
                    filter_id=filter_id,
                    filter_type=filter_type,
                    filter_param=self.filter_param)
                if not self.focal_plane.isIgnored(chipID=chipID):
                    self.chip_list.append(chip)
                    self.filter_list.append(filt)
                self.all_filters.append(filt)

            if chips is None:
                # Run all chips defined in configuration of this pointing
                run_chips = self.chip_list
                run_filts = self.filter_list
                nchips_per_fp = len(self.chip_list)
            else:
                # Only run a particular set of chips (defined in the overall config file)
                run_chips = []
                run_filts = []
                for ichip in range(len(self.chip_list)):
                    chip = self.chip_list[ichip]
                    filt = self.filter_list[ichip]
                    if chip.chipID in chips:
                        run_chips.append(chip)
                        run_filts.append(filt)
                nchips_per_fp = len(chips)
            
            for ichip in range(nchips_per_fp):
                i_process = process_counter + ichip
                if use_mpi:
                    if i_process % num_thread != ind_thread:
                        continue
                pid = os.getpid()

                sub_img_dir, prefix = makeSubDir_PointingList(path_dict=self.path_dict, config=self.config, pointing_ID=pointing_ID)

                chip = run_chips[ichip]
                filt = run_filts[ichip]
                # chip_output.Log_info("running pointing#%d, chip#%d, at PID#%d..."%(pointing_ID, chip.chipID, pid))
                chip_output = ChipOutput(
                    config=self.config, 
                    focal_plane=self.focal_plane, 
                    chip=chip, 
                    filt=filt,  
                    exptime=pointing.exp_time,
                    pointing_type=pointing.pointing_type,
                    pointing_ID=pointing_ID,  
                    subdir=sub_img_dir,
                    prefix=prefix,
                    ra_cen=pointing.ra,
                    dec_cen=pointing.dec)
                chip_output.Log_info("running pointing#%d, chip#%d, at PID#%d..."%(pointing_ID, chip.chipID, pid))
                self.run_one_chip(
                    chip=chip,
                    filt=filt,
                    chip_output=chip_output,
                    pointing=pointing)
                # if self.config["obs_setting"]["survey_type"] == "CALIBRATION":
                #     self.run_one_chip_calibration(chip=chip,
                #                                filt=filt,
                #                                chip_output=chip_output,
                #                                pointing=pointing,
                #                                skyback_level = self.config["obs_setting"]["FLAT_LEVEL"],
                #                                sky_level_filt = self.config["obs_setting"]["FLAT_LEVEL_FIL"])
                # else:
                #     self.run_one_chip(
                #         chip=chip,
                #         filt=filt,
                #         chip_output=chip_output,
                #         pointing=pointing)
                chip_output.Log_info("finished running chip#%d..."%(chip.chipID))
                for handler in chip_output.logger.handlers[:]:
                    chip_output.logger.removeHandler(handler)
                gc.collect()
            process_counter += nchips_per_fp