* unified the naming of .cat and .log files.

* Changed the name of output folder of pointing to corresponding pointing.obs_id.
* fixed the order .cat hdr updating and the creation of .cat file.
* Changed the naming of shutter and flat reference image: chip IDs now all in 2 digits.
* Updated the __init__ method of ChipOutput
* Removed Config.py from ObservationSim.Config
* Cleaned codes in ObservationSim.py, ChipOutput

Catalog/C6_50sqdeg.py

@@ -122,7 +122,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/C6_Catalog.py

@@ -99,7 +99,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/C6_fits_Catalog.py

@@ -113,7 +113,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/Calib_Catalog.py

@@ -106,7 +106,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/FGS_Catalog.py

@@ -100,7 +100,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/NGPCatalog.py

@@ -65,7 +65,7 @@ class Catalog(CatalogBase):
     def _add_output_columns_header(self):
         self.add_hdr = " model_tag teff logg feh"
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/fd_test_C6.py

@@ -99,7 +99,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/testCat_fits.py

@@ -77,7 +77,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/testCat_galaxy.py

@@ -97,7 +97,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/testCat_star.py

@@ -124,7 +124,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

Catalog/wcs_test_C6.py

@@ -99,7 +99,7 @@ class Catalog(CatalogBase):
 
         self.add_fmt = " %10s %8.4f %8.4f %8.4f"
         self.add_fmt += " %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %8.4f %4d %8.4f "
-        self.chip_output.update_ouptut_header(additional_column_names=self.add_hdr)
+        self.chip_output.update_output_header(additional_column_names=self.add_hdr)
 
     def _get_healpix_list(self):
         self.sky_coverage = self.chip.getSkyCoverageEnlarged(self.chip.img.wcs, margin=0.2)

ObservationSim/Config/ChipOutput.py

 import os
 import logging
 import ObservationSim.Config._util as _util
+from ObservationSim.Config.Header import generatePrimaryHeader
 
 class ChipOutput(object):
-    def __init__(self, config, focal_plane, chip, filt, imgKey0="", imgKey1="", imgKey2="", exptime=150., mjdTime="", ra_cen=None, dec_cen=None, pointing_type='SCI', pointing_ID='0',pointing_type_code='101', subdir="./", prefix=""):
-        self.focal_plane = focal_plane
+    def __init__(self, config, chip, filt, pointing):
+        self.config = config
         self.chip = chip
         self.filt = filt
-        self.imgKey0 = imgKey0
-        self.imgKey1 = imgKey1
-        self.imgKey2 = imgKey2
-        self.exptime = exptime
-        self.mjdTime = mjdTime
-        self.pointing_type = pointing_type
-        if (ra_cen is not None) and (dec_cen is not None):
-            self.ra_cen = ra_cen
-            self.dec_cen = dec_cen
-        else:
-            self.ra_cen = config["obs_setting"]["ra_center"]
-            self.dec_cen = config["obs_setting"]["dec_center"]
+        self.pointing_type = pointing.pointing_type
+        self.chip_label = str(chip.chipID).rjust(2, '0')
 
-        self.chipLabel = focal_plane.getChipLabel(chip.chipID)
-        obs_id = _util.get_obs_id(img_type=pointing_type, project_cycle=config["project_cycle"], run_counter=config["run_counter"], pointing_id=pointing_ID, pointing_type_code = pointing_type_code)
-        # self.cat_name = "MSC_1%s_chip_%s_filt_%s"%(str(pointing_ID).rjust(8, '0'), self.chipLabel, filt.filter_type) + ".cat"
-        self.cat_name = "MSC_%s_chip_%s_filt_%s"%(obs_id, self.chipLabel, filt.filter_type) + ".cat"
+        # Get primary header based on chip and pointing
+        self.h_prim = generatePrimaryHeader(
+            xlen=chip.npix_x, 
+            ylen=chip.npix_y, 
+            pointing_id = pointing.obs_id,
+            pointing_type_code = pointing.pointing_type_code, 
+            ra=pointing.ra, 
+            dec=pointing.dec, 
+            pixel_scale=chip.pix_scale,
+            time_pt = pointing.timestamp,
+            exptime=pointing.exp_time,
+            im_type=pointing.pointing_type,
+            sat_pos=[pointing.sat_x, pointing.sat_y, pointing.sat_z],
+            sat_vel=[pointing.sat_vx, pointing.sat_vy, pointing.sat_vz],
+            project_cycle=self.config["project_cycle"],
+            run_counter=self.config["run_counter"],
+            chip_name=self.chip_label)
 
-        self.subdir = subdir
+        obs_id = _util.get_obs_id(img_type=self.pointing_type, project_cycle=config["project_cycle"], run_counter=config["run_counter"], pointing_id=pointing.obs_id, pointing_type_code = pointing.pointing_type_code)
+        
+        self.subdir = pointing.output_dir
+        self.cat_name = self.h_prim['FILENAME'] + '.cat'
+        logger_filename = self.h_prim['FILENAME'] + '.log'
 
-        # Setup logger for each chip
-        # logger_filename = "MSC_1%s_chip_%s_filt_%s"%(str(pointing_ID).rjust(8, '0'), self.chipLabel, filt.filter_type) + ".log"
-        logger_filename = "MSC_%s_chip_%s_filt_%s"%(obs_id, self.chipLabel, filt.filter_type) + ".log"
         self.logger = logging.getLogger()
         fh = logging.FileHandler(os.path.join(self.subdir, logger_filename), mode='w+', encoding='utf-8')
         fh.setLevel(logging.DEBUG)
@@ -46,7 +51,7 @@ class ChipOutput(object):
         self.hdr = hdr1 + hdr2
         self.fmt = fmt1 + fmt2
 
-        self.logger.info("pointing_type = %s\n"%(pointing_type))
+        self.logger.info("pointing_type = %s\n"%(self.pointing_type))
     
     def Log_info(self, message):
         print(message)
@@ -56,7 +61,7 @@ class ChipOutput(object):
         print(message)
         self.logger.error(message)
     
-    def update_ouptut_header(self, additional_column_names=""):
+    def update_output_header(self, additional_column_names=""):
         self.hdr += additional_column_names
     
     def create_output_file(self):
@@ -68,14 +73,11 @@ class ChipOutput(object):
             self.cat.write(self.hdr)
 
     def cat_add_obj(self, obj, pos_img, pos_shear):
-        # self.logger.info('-------------debug-----------------')
-        # self.logger.info('from global',ximg, yimg)
         ximg = obj.real_pos.x + 1.0
         yimg = obj.real_pos.y + 1.0
-        # self.logger.info('from loacl',ximg, yimg)
         
         line = self.fmt%(
-            obj.id, int(self.chipLabel), self.filt.filter_type, ximg, yimg, obj.ra, obj.dec, obj.ra_orig, obj.dec_orig, obj.z, obj.getMagFilter(self.filt), obj.type, 
+            obj.id, int(self.chip_label), self.filt.filter_type, ximg, yimg, obj.ra, obj.dec, obj.ra_orig, obj.dec_orig, obj.z, obj.getMagFilter(self.filt), obj.type, 
             obj.pmra, obj.pmdec, obj.rv, obj.parallax)
         line += obj.additional_output_str
         if not line.endswith("\n"):

ObservationSim/Config/Config.py

-import galsim
-import os
-from astropy.time import Time as asTime
-
-def config_dir(config, work_dir=None, data_dir=None):
-    path_dict = {}
-    # Working directory
-    if work_dir == None:
-        dirname, _ = os.path.split(os.path.abspath(__file__))
-        path_dict["work_dir"] = "/".join(dirname.split("/")[:-1]) + "/"
-    else:
-        path_dict["work_dir"] = work_dir
-    
-    # Data directory
-    # if data_dir == None:
-    #     # Assume all input datasets are in the work directory
-    #     path_dict["data_dir"] =os.path.join(path_dict["work_dir"], "data/")
-    # else:
-    #     path_dict["data_dir"] = data_dir
-    
-    # PSF data directory
-    # if config["psf_setting"]["psf_model"] == "Interp":
-    #     path_dict["psf_pho_dir"] = os.path.join(path_dict["data_dir"], config["psf_setting"]["psf_pho_dir"])
-    #     path_dict["psf_sls_dir"] = os.path.join(path_dict["data_dir"], config["psf_setting"]["psf_sls_dir"])
-    if config["psf_setting"]["psf_model"] == "Interp":
-        path_dict["psf_pho_dir"] = config["psf_setting"]["psf_pho_dir"]
-        path_dict["psf_sls_dir"] = config["psf_setting"]["psf_sls_dir"]
-
-    return path_dict
-
-def read_config(config_filename):
-    """Read in a configuration file and return the corresponding dict(s).
-
-    Parameters:
-        config_filename:    The name of the configuration file to read.
-    Returns:
-        (list) of config dicts
-    """
-    config = {}
-    config_file = open(config_filename).readlines()
-    nlines = len(config_file)
-    for i in range(nlines):
-        row = config_file[i].split()
-        if len(row) <= 1: continue # blank row
-        if not "#" in row:
-            if len(row) == 2:
-                key, val = row[0:2]
-                config.update({key:val})
-            else:
-                print("!! Something is wrong with parameter '%s'."%row[0])
-                return
-        elif row.index("#") == 2:
-            key, val = row[0:2]
-            config.update({key:val})
-        elif row.index("#") == 0:
-            continue # annotation
-        else:
-            print("!! Something is wrong with parameter '%s'."%row[0])
-            return
-    config = parse_config(config)
-    return config
-
-def parse_config(config):
-    """Parse the config values to the right type
-
-    Parameters:
-        config:     raw config dict 
-    Returns:
-        Parsed config dict
-    """
-    config["ra_center"]     = float(config["ra_center"])
-    config["dec_center"]    = float(config["dec_center"])
-    config["psf_rcont"]     = config["psf_rcont"].split(",")
-    config["psfRa"]         = float(config["psf_rcont"][0])
-    config["psfCont"]       = float(config["psf_rcont"][1])
-    config["image_rot"]     = float(config["image_rot"])*galsim.degrees
-    config["sigma_spin"]    = float(config["sigma_spin"])
-    config["reduced_g1"]    = float(config["reduced_g1"])
-    config["reduced_g2"]    = float(config["reduced_g2"])
-    config["rotateEll"]     = float(config["rotateEll"])
-    config["reEll"]         = int(config["rotateEll"]/45.0)
-    if config["reEll"]==0: config["reIndex"] = "P"
-    if config["reEll"]==1: config["reIndex"] = "X"
-    if config["reEll"]==2: config["reIndex"] = "N"
-    if config["reEll"]==3: config["reIndex"] = "Y"
-    config["seed_flat"]     = int(config["seed_flat"])
-    config["seed_prnu"]     = int(config["seed_prnu"])
-    config["seed_star"]     = int(config["seed_star"])
-    config["seed_gal"]      = int(config["seed_gal"])
-    config["seed_Av"]       = int(config["seed_Av"])
-    config["bias_level"]    = int(config["bias_level"])
-    config["df_strength"]   = float(config["df_strength"])
-    return config

ObservationSim/Config/Pointing.py

@@ -27,6 +27,7 @@ class Pointing(object):
         self.obs_config_file = obs_config_file
         self.t_shutter_open = t_shutter_open
         self.t_shutter_close = t_shutter_close
+        self.output_dir = "."
         if self.obs_config_file is not None:
             with open(self.obs_config_file, "r") as stream:
                 try:
@@ -107,7 +108,7 @@ class Pointing(object):
         else:
             self.timestamp = t
 
-    def make_output_pointing_dir(self, overall_config, pointing_ID=0, copy_obs_config=False):
+    def make_output_pointing_dir(self, overall_config, copy_obs_config=False):
         run_dir = os.path.join(overall_config["work_dir"], overall_config["run_name"])
         if not os.path.exists(run_dir):
             try:
@@ -131,7 +132,7 @@ class Pointing(object):
             obs_config_output_path = os.path.join(self.output_dir, os.path.basename(self.obs_config_file))
             if not os.path.exists(obs_config_output_path):
                 try:
-                    shutil.copy(args.obs_config_file, self.output_dir)
+                    shutil.copy(self.obs_config_file, self.output_dir)
                 except OSError:
                     pass
 

ObservationSim/Config/__init__.py

-from .Config import *
 from .ChipOutput import ChipOutput
 from .Pointing import Pointing
\ No newline at end of file

ObservationSim/ObservationSim.py

@@ -8,17 +8,15 @@ from datetime import datetime
 
 import traceback
 
-from ObservationSim.Config import config_dir, ChipOutput
+from ObservationSim.Config import 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 make_output_pointing_dir
 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() 
@@ -92,9 +90,6 @@ class Observation(object):
         # 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)
 
@@ -124,138 +119,6 @@ class Observation(object):
         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
@@ -266,9 +129,10 @@ class Observation(object):
         for ipoint in range(len(pointing_list)):
             # Construct chips & filters:
             pointing = pointing_list[ipoint]
-            pointing_ID = pointing.id
+            # pointing_ID = pointing.id
+            pointing_ID = pointing.obs_id
 
-            sub_img_dir, prefix = make_output_pointing_dir(path_dict=self.path_dict, config=self.config, pointing_ID=pointing_ID)
+            pointing.make_output_pointing_dir(overall_config=self.config, copy_obs_config=True)
 
             self.focal_plane = FocalPlane(chip_list=pointing.obs_param["run_chips"])
             # Make Chip & Filter lists
@@ -314,39 +178,19 @@ class Observation(object):
 
                 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.obs_id,
-                    pointing_type_code = pointing.pointing_type_code,  
-                    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))
+                    config = self.config,
+                    chip = chip,
+                    filt = filt,
+                    pointing = pointing
+                )
+                chip_output.Log_info("running pointing#%d, chip#%d, at PID#%d..."%(int(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)

ObservationSim/sim_steps/add_objects.py

@@ -9,9 +9,6 @@ from ObservationSim.PSF import PSFGauss, FieldDistortion, PSFInterp, PSFInterpSL
 
 def add_objects(self, chip, filt, tel, pointing, catalog, obs_param):
 
-    # Prepare output file(s) for this chip
-    self.chip_output.create_output_file()
-
     # Get exposure time
     if (obs_param) and ("exptime" in obs_param) and (obs_param["exptime"] is not None):
         exptime = obs_param["exptime"]
@@ -24,6 +21,11 @@ def add_objects(self, chip, filt, tel, pointing, catalog, obs_param):
         raise ValueError("Catalog interface class must be specified for SCIE-OBS")
     cat = catalog(config=self.overall_config, chip=chip, pointing=pointing, chip_output=self.chip_output, filt=filt)
 
+    # Prepare output file(s) for this chip
+    # [NOTE] Headers of output .cat file may be updated by Catalog instance
+    # this should be called after the creation of Catalog instance
+    self.chip_output.create_output_file()
+
     # Prepare the PSF model
     if self.overall_config["psf_setting"]["psf_model"] == "Gauss":
         psf_model = PSFGauss(chip=chip, psfRa=self.overall_config["psf_setting"]["psf_rcont"])

ObservationSim/sim_steps/add_pattern_noise.py

@@ -5,7 +5,7 @@ from ObservationSim.Instrument.Chip import Effects
 def apply_PRNU(self, chip, filt, tel, pointing, catalog, obs_param):
     chip.img *= chip.prnu_img
     if self.overall_config["output_setting"]["prnu_output"] == True:
-        chip.prnu_img.write("%s/FlatImg_PRNU_%s.fits" % (self.chip_output.subdir, chip.chipID))
+        chip.prnu_img.write("%s/FlatImg_PRNU_%s.fits" % (self.chip_output.subdir, str(chip.chipID).rjust(2, '0')))
     return chip, filt, tel, pointing
 
 def add_poisson_and_dark(self, chip, filt, tel, pointing, catalog, obs_param):

ObservationSim/sim_steps/add_sky_background.py

@@ -78,7 +78,7 @@ def add_sky_flat_calibration(self, chip, filt, tel, pointing, catalog, obs_param
         flat_normal = np.array(flat_normal, dtype='float32')
         if self.overall_config["output_setting"]["shutter_output"] == True:    # output 16-bit shutter effect image with pixel value <=65535
             shutt_gsimg = galsim.ImageUS(chip.shutter_img*6E4)
-            shutt_gsimg.write("%s/ShutterEffect_%s_1.fits" % (self.chip_output.subdir, chip.chipID))
+            shutt_gsimg.write("%s/ShutterEffect_%s_1.fits" % (self.chip_output.subdir, str(chip.chipID).rjust(2, '0')))
         self.updateHeaderInfo(header_flag='ext', keys = ['SHTSTAT'], values = [True])
     else:
         self.updateHeaderInfo(header_flag='ext', keys = ['SHTSTAT','SHTOPEN0','SHTOPEN1','SHTCLOS0','SHTCLOS1'], values = [False,'','','',''])

config/obs_config_SCI_WIDE_phot.yaml

@@ -14,8 +14,9 @@ obs_type_code: "101"
 obs_id: "00000001" # this setting will only be used if pointing list file is not given
 
 # Define list of chips
-run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25]
+# run_chips: [6,7,8,9,11,12,13,14,15,16,17,18,19,20,22,23,24,25]
 #run_chips: [1,2,3,4,5,10,21,26,27,28,29,30]
+run_chips: [8]
 
 # Define observation sequence
 call_sequence:
@@ -65,7 +66,7 @@ call_sequence:
   # Apply CCD Saturation & Blooming
   blooming: {}
   # Run CTE simulation
-  CTE_effect: {}
+  # CTE_effect: {}
   # Add prescan and overscan
   prescan_overscan:
     add_dark: YES