modified to absolute import, change location of runExposure.py and run.pbs

ObservationSim/Instrument/Chip/Chip.py

 import galsim
 import os
 import numpy as np
-import Instrument.Chip.Effects as effects
-from Instrument.FocalPlane import FocalPlane
 from astropy.table import Table
 from numpy.random import Generator, PCG64
-from Config.Header import generatePrimaryHeader, generateExtensionHeader
 from astropy.io import fits
 from datetime import datetime
 
+from ObservationSim.Instrument.Chip import Effects as effects
+from ObservationSim.Instrument.FocalPlane import FocalPlane
+from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader
+
 class Chip(FocalPlane):
     def __init__(self, chipID, ccdEffCurve_dir, CRdata_dir, normalize_dir=None, sls_dir=None, config=None, treering_func=None):
         # Get focal plane (instance of paraent class) info
         # TODO: use chipID to config individual chip?
         super().__init__()
-        # if config is not None:
-        #     self.npix_x     = config["npix_x"]
-        #     self.npix_y     = config["npix_y"]
-        #     self.read_noise = config["read_noise"]
-        #     self.dark_noise = config["dark_noise"]
-        #     self.pix_scale  = config["pix_scale"]
-        #     self.gain       = config["gain"]
-        #     self.bias_level = config["bias_level"]
-        #     self.overscan   = config["overscan"]
-        # else:
-        # Default setting
         self.npix_x = 9216
         self.npix_y = 9232
         self.read_noise = 5.0   # e/pix

ObservationSim/Instrument/Filter.py

@@ -2,8 +2,9 @@ import galsim
 import pylab as pl
 import os
 import numpy as np
-from ._util import photonEnergy
-from .FilterParam import FilterParam
+
+from ObservationSim.Instrument._util import photonEnergy
+from ObservationSim.Instrument.FilterParam import FilterParam
 
 class Filter(object):
     def __init__(self, filter_id, filter_type, filter_param, ccd_bandpass):

ObservationSim/MockObject/Catalog.py

@@ -4,13 +4,14 @@ import random
 import galsim
 import h5py as h5
 import healpy as hp
-from .Star import Star
-from .Galaxy import Galaxy
-from .Quasar import Quasar
-from ._util import seds, sed_assign, extAv
 from astropy.table import Table
 from astropy.coordinates import spherical_to_cartesian
 
+from ObservationSim.MockObject.Star import Star
+from ObservationSim.MockObject.Galaxy import Galaxy
+from ObservationSim.MockObject.Quasar import Quasar
+from ObservationSim.MockObject._util import seds, sed_assign, extAv
+
 NSIDE = 128
 
 class Catalog(object):

ObservationSim/MockObject/CosmicRay.py

-import MockObject
+from ObservationSim.MockObject.MockObject import MockObject
 
 class CosmicRay(MockObject):
 	pass
\ No newline at end of file

ObservationSim/MockObject/Galaxy.py

@@ -3,11 +3,12 @@ import galsim
 import os, sys
 import astropy.constants as cons
 from astropy.table import Table
-from ._util import eObs, integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG,convolveGaussXorders
-from .SpecDisperser import SpecDisperser
-from .MockObject import MockObject
 from scipy import interpolate
 
+from ObservationSim.MockObject._util import eObs, integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG,convolveGaussXorders
+from ObservationSim.MockObject.SpecDisperser import SpecDisperser
+from ObservationSim.MockObject.MockObject import MockObject
+
 class Galaxy(MockObject):
     def __init__(self, param, rotation=None):
         super().__init__(param)

ObservationSim/MockObject/MockObject.py

@@ -2,9 +2,10 @@ import galsim
 import numpy as np
 import astropy.constants as cons
 from astropy.table import Table
-from ._util import magToFlux, vc_A, convolveGaussXorders
-from ._util import integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG
-from .SpecDisperser import SpecDisperser
+
+from ObservationSim.MockObject._util import magToFlux, vc_A, convolveGaussXorders
+from ObservationSim.MockObject._util import integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG
+from ObservationSim.MockObject.SpecDisperser import SpecDisperser
 
 class MockObject(object):
     def __init__(self, param):

ObservationSim/MockObject/Quasar.py

@@ -2,11 +2,11 @@ import galsim
 import os, sys
 import numpy as np
 import astropy.constants as cons
-from .MockObject import MockObject
 from astropy.table import Table
 from scipy import interpolate
-from ._util import integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG
-from .MockObject import MockObject
+
+from ObservationSim.MockObject.MockObject import MockObject
+from ObservationSim.MockObject._util import integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG
 
 class Quasar(MockObject):
     def __init__(self, param):

ObservationSim/MockObject/SkybackgroundMap.py

-from .SpecDisperser import SpecDisperser
-
-from .SpecDisperser import rotate90
+from ObservationSim.MockObject.SpecDisperser import SpecDisperser
+from ObservationSim.MockObject.SpecDisperser import rotate90
 
 import galsim
 import numpy as np

ObservationSim/MockObject/Star.py

@@ -3,11 +3,11 @@ import os, sys
 import numpy as np
 import astropy.constants as cons
 from astropy.table import Table
-from ._util import integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG, tag_sed
-from .SpecDisperser import SpecDisperser
-from .MockObject import MockObject
 from scipy import interpolate
 
+from ObservationSim.MockObject._util import integrate_sed_bandpass, getNormFactorForSpecWithABMAG, getObservedSED, getABMAG, tag_sed
+from ObservationSim.MockObject.MockObject import MockObject
+
 class Star(MockObject):
     def __init__(self, param):
         super().__init__(param)

ObservationSim/ObservationSim.py

-from Config import ConfigDir, ChipOutput
-from Config.Header import generatePrimaryHeader, generateExtensionHeader
-from Instrument import Telescope, Filter, FilterParam, FocalPlane, Chip
-from MockObject import Catalog, MockObject, Star, Galaxy, Quasar, calculateSkyMap_split_g
-from PSF import PSFGauss, FieldDistortion, PSFInterp
-from _util import getShearFiled, makeSubDir_PointingList
+import sys
+import os
+
+from ObservationSim.Config import ConfigDir, ChipOutput
+from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader
+from ObservationSim.Instrument import Telescope, Filter, FilterParam, FocalPlane, Chip
+from ObservationSim.MockObject import Catalog, MockObject, Star, Galaxy, Quasar, calculateSkyMap_split_g
+from ObservationSim.PSF import PSFGauss, FieldDistortion, PSFInterp
+from ObservationSim._util import getShearFiled, makeSubDir_PointingList
+
 from astropy.io import fits
 from datetime import datetime
 import numpy as np
 import mpi4py.MPI as MPI
 import galsim
-import os, sys
 import logging
 import psutil
 
@@ -345,6 +348,7 @@ class Observation(object):
             timestamp_obs = np.tile(timestamp_obs, len(ra_cen))
             pointing_type = np.tile(pointing_type, len(ra_cen))
         
+        if pRange is not None:
             timestamp_obs = timestamp_obs[pRange]
             pointing_type = pointing_type[pRange]
             ra_cen = ra_cen[pRange]

ObservationSim/PSF/PSFGauss.py

@@ -2,8 +2,8 @@ import galsim
 import sep
 import numpy as np
 from scipy.interpolate import interp1d
-from .PSFModel import PSFModel
-import os, sys
+
+from ObservationSim.PSF.PSFModel import PSFModel
 
 class PSFGauss(PSFModel):
 	def __init__(self, chip, fwhm=0.187, sigSpin=0., psfRa=0.15):

ObservationSim/PSF/PSFInterp/PSFInterp.py

@@ -6,14 +6,13 @@ NOTE: [iccd, iwave, ipsf] are counted from 1 to n, but [tccd, twave, tpsf] are c
 
 import galsim
 import numpy as np
-
 import os
 import time
 import copy
 
-from . import PSFConfig as myConfig
-from . import PSFUtil as myUtil
-from ..PSFModel import PSFModel
+from ObservationSim.PSF.PSFInterp import PSFConfig as myConfig
+from ObservationSim.PSF.PSFInterp import PSFUtil as myUtil
+from ObservationSim.PSF.PSFModel import PSFModel
 
 LOG_DEBUG = False  #***#
 NPSF      = 900    #***# 30*30

ObservationSim/PSF/PSFInterp/PSFProcess.py

@@ -3,13 +3,8 @@ import numpy as np
 import scipy.io
 import mpi4py.MPI as MPI
 
-
-
-#sys.path.append("/public/home/weichengliang/lnData/CSST_new_framwork/csstPSF_20201222")
-# import PSFConfig as myConfig
-# import PSFUtil as myUtil
-import PSFConfig
-import PSFUtil
+import ObservationSim.PSF.PSFInterp.PSFConfig as PSFConfig
+import ObservationSim.PSF.PSFInterp.PSFUtil as PSFUtil
 
 def mkdir(path):
     isExists = os.path.exists(path)

ObservationSim/__init__.py

-import numpy as np
-import galsim
\ No newline at end of file

ObservationSim/_util.py

@@ -36,18 +36,6 @@ def imgName(tt=0):
 
     return namekey
 
-# def makeSubDir(path_dict, config):
-#   subImgdir = path_dict["output_img_dir"] + config["mockImgDir"] + '/'
-#   if not os.path.exists(subImgdir):
-#       os.system("mkdir %s"%subImgdir)
-#   imgKey0 = imgName(tt=0)
-#   imgKey1 = imgName(tt=1)
-#   imgKey2 = imgName(tt=2)
-#   subImgdir = subImgdir + imgKey0 + config["reIndex"] + config["reShear"] + "/"
-#   if not os.path.exists(subImgdir):
-#       os.system("mkdir %s"%subImgdir)
-#   return subImgdir, imgKey0, imgKey1, imgKey2
-
 def makeSubDir_PointingList(path_dict, config, pointing_ID=0):
     imgDir = os.path.join(path_dict["work_dir"], config["run_name"])
     if not os.path.exists(imgDir):

config/config_sim.yaml

@@ -10,11 +10,15 @@
 # Can add some of the command-line arguments here as well;
 # OK to pass either way or both, as long as they are consistent
 # work_dir: "/public/home/fangyuedong/sim_code_release/CSST/test/"
-work_dir: "/public/home/fangyuedong/test_release/CSST/workplace/"
+work_dir: "/public/home/fangyuedong/20211203/CSST/workplace/"
 data_dir: "/data/simudata/CSSOSDataProductsSims/data/"
 run_name: "TEST"
 
 # (Optional) a file of point list 
+# if you just want to run default pointing:
+# - pointing_dir: null
+# - pointing_file: null
+pointing_dir: "/data/simudata/CSSOSDataProductsSims/data/"
 pointing_file: "pointing10_20210202.dat"
 
 # Whether to use MPI
@@ -63,13 +67,17 @@ obs_setting:
   # Note: only valid when a pointing list is specified
   np_cal: 0
 
-  # (Optional) only run specific pointing(s).
+  # Run specific pointing(s):
+  # - give a list of indexes of pointings: [ip_1, ip_2...]
+  # - run all pointings: null
   # Note: only valid when a pointing list is specified
   run_pointings: [5, 6]
   
-  # (Optional) only run specific chip(s)
+  # Run specific chip(s):
+  # - give a list of indexes of chips: [ip_1, ip_2...]
+  # - run all chips: null
   # Note: for all pointings
-  # run_chips: [6, 25]
+  run_chips: [1, 25]
 
 ###############################################
 # Input path setting

ObservationSim/run.pbs → run.pbs

@@ -16,4 +16,4 @@ NP=40
 date
 echo $NP
 
-mpirun -np $NP python /public/home/fangyuedong/test_release/CSST/ObservationSim/runExposure.py config_sim.yaml -c /public/home/fangyuedong/test_release/CSST/config
+mpirun -np $NP python /public/home/fangyuedong/20211203/CSST/runExposure.py config_sim.yaml -c /public/home/fangyuedong/20211203/CSST/config

ObservationSim/runExposure.py → runExposure.py

-from ObservationSim import Observation
-from _util import parse_args
+from ObservationSim.ObservationSim import Observation
+from ObservationSim._util import parse_args
 from datetime import datetime
 import os
 import numpy as np
@@ -9,20 +9,24 @@ import yaml
 import gc
 gc.enable()
 
-def Pointing(config, pointing_filename, data_dir):
+def Pointing(config, pointing_filename=None, data_dir=None):
+    pRA = []
+    pDEC = []
+    if pointing_filename and data_dir:
         pointing_file = os.path.join(data_dir, pointing_filename)
         f = open(pointing_file, 'r')
         for _ in range(1):
             header = f.readline()
         iline = 0
-    pRA = []
-    pDEC = []
         for line in f:
             line = line.strip()
             columns = line.split()
             pRA.append(float(columns[0]))
             pDEC.append(float(columns[1]))
         f.close()
+    else:
+        pRa.append(config["obs_setting"]["ra_center"])
+        pDec.append(config["obs_setting"]["dec_center"])
     pRA = np.array(pRA)
     pDEC = np.array(pDEC)
 
@@ -43,7 +47,7 @@ def Pointing(config, pointing_filename, data_dir):
     for i in range(len(pointing_type)):
         timestamp_obs.append(t)
         if pointing_type[i] == 'CAL':
-            t += 3 * delta_t * 60 # 3 calibration exposure
+            t += 3 * delta_t * 60 # 3 calibration exposures for each pointing
         elif pointing_type[i] == 'MS':
             t += delta_t * 60
     timestamp_obs = np.array(timestamp_obs)
@@ -98,22 +102,13 @@ def runSim():
     if args.work_dir is not None:
         config['work_dir'] = args.work_dir
 
-    pRA, pDEC, timestamp_obs, pointing_type = Pointing(config=config, pointing_filename=config['pointing_file'], data_dir=config['data_dir'])
+    pRA, pDEC, timestamp_obs, pointing_type = Pointing(config=config, pointing_filename=config['pointing_file'], data_dir=config['pointing_dir'])
 
     MakeDirectories(work_dir=config['work_dir'], run_name=config['run_name'], nPointings=len(pRA), pRange=config['obs_setting']['run_pointings'])
-    if "run_chips" in config["obs_setting"]:
-        run_chips = config["obs_setting"]["run_chips"]
-    else:
-        run_chips = None
-
-    # from Config import ConfigDir
-    # path_dict = ConfigDir(config=config, work_dir=config["work_dir"], data_dir=config["data_dir"])
-    # for key, value in path_dict.items():
-    #     print (key + " : " + str(value))
 
     obs = Observation(config=config, work_dir=config['work_dir'], data_dir=config['data_dir'])
     if config["pointing_file"] is None:
-        obs.runExposure(chips=run_chips)
+        obs.runExposure(chips=config["obs_setting"]["run_chips"])
     else:
         obs.runExposure_MPI_PointingList(
             ra_cen=pRA, 
@@ -123,24 +118,8 @@ def runSim():
             pointing_type=pointing_type,
             exptime=config["obs_setting"]["exp_time"],
             use_mpi=config["run_option"]["use_mpi"],
-            chips=run_chips
+            chips=config["obs_setting"]["run_chips"]
             )
-    print("run finished")
 
 if __name__=='__main__':
     runSim()
-
-#############################################
-# Testing run one exposure (NOT using MPI)
-# ipoint = 2
-# pointRa = float('{:8.4f}'.format(pRA[ipoint]))
-# pointDec = float('{:8.4f}'.format(pDEC[ipoint]))
-
-# obs = Observation(work_dir=work_dir, data_dir=data_dir)
-# obs.runExposure(ra_cen=pointRa, dec_cen=pointDec, pointing_ID=ipoint, oneChip=16)
-
-#############################################
-# Testing run pointing list (using MPI)
-# obs = Observation(work_dir=work_dir, data_dir=data_dir)
-# # obs.runExposure_MPI_PointingList(ra_cen=pRA, dec_cen=pDEC, pRange=pRange, timestamp_obs=timestamp_obs, pointing_type=pointing_type)
-# obs.runExposure_MPI_PointingList(ra_cen=pRA, dec_cen=pDEC, pRange=pRange, timestamp_obs=timestamp_obs, pointing_type=pointing_type, exptime=exp_time)