encapsulate instrumental data

Catalog/C3Catalog.py

@@ -14,6 +14,12 @@ from ObservationSim.MockObject import CatalogBase, Star, Galaxy, Quasar
 from ObservationSim.MockObject._util import seds, sed_assign, extAv, tag_sed, getObservedSED
 from ObservationSim.Astrometry.Astrometry_util import on_orbit_obs_position
 
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
 NSIDE = 128
 
 class C3Catalog(CatalogBase):
@@ -21,10 +27,14 @@ class C3Catalog(CatalogBase):
         super().__init__()
         self.cat_dir = os.path.join(config["data_dir"], config["input_path"]["cat_dir"])
         self.seed_Av = config["random_seeds"]["seed_Av"]
-        self.normalize_dir = os.path.join(config["data_dir"], config["SLS_path"]["SLS_norm"])
+        # self.normalize_dir = os.path.join(config["data_dir"], config["SLS_path"]["SLS_norm"])
 
-        self.normF_star = Table.read(os.path.join(self.normalize_dir, 'SLOAN_SDSS.g.fits'))
-        self.normF_galaxy = Table.read(os.path.join(self.normalize_dir, 'lsst_throuput_g.fits'))
+        # self.normF_star = Table.read(os.path.join(self.normalize_dir, 'SLOAN_SDSS.g.fits'))
+        # self.normF_galaxy = Table.read(os.path.join(self.normalize_dir, 'lsst_throuput_g.fits'))
+        with pkg_resources.path('Catalog.data', 'SLOAN_SDSS.g.fits') as filter_path:
+                self.normF_star = filter_path
+        with pkg_resources.path('Catalog.data', 'lsst_throuput_g.fits') as filter_path:
+                self.normF_star = filter_path
         
         self.config = config
         self.chip = chip
@@ -136,14 +146,15 @@ class C3Catalog(CatalogBase):
         # Apply astrometric modeling
         ra_arr = stars["RA"][:]
         dec_arr = stars["Dec"][:]
-        if "astrometric_lib" in self.config["obs_setting"] and self.config["obs_setting"]["enable_astrometric_model"]:
+        # if "astrometric_lib" in self.config["obs_setting"] and self.config["obs_setting"]["enable_astrometric_model"]:
+        if self.config["obs_setting"]["enable_astrometric_model"]:
             ra_list = ra_arr.tolist()
             dec_list = dec_arr.tolist()
             pmra_list = np.zeros(nstars).tolist()
             pmdec_list = np.zeros(nstars).tolist()
             rv_list = np.zeros(nstars).tolist()
             parallax_list = [1e-9] * nstars
-            lib_path = os.path.join(self.config["data_dir"], self.config["obs_setting"]["astrometric_lib"])
+            # lib_path = os.path.join(self.config["data_dir"], self.config["obs_setting"]["astrometric_lib"])
             dt = datetime.fromtimestamp(self.pointing.timestamp)
             date_str = dt.date().isoformat()
             time_str = dt.time().isoformat()
@@ -164,7 +175,7 @@ class C3Catalog(CatalogBase):
                 input_epoch="J2015.5",
                 input_date_str=date_str,
                 input_time_str=time_str,
-                lib_path=lib_path
+                # lib_path=lib_path
             )
         for istars in range(nstars):
             param = self.initialize_param()

ObservationSim/Astrometry/Astrometry_util.py

 from ctypes import *
 import numpy as np
 
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
 def checkInputList(input_list, n):
     if not isinstance(input_list, list):
         raise TypeError("Input type is not list!", input_list)
@@ -11,7 +17,7 @@ def checkInputList(input_list, n):
     if len(input_list) != n:
         raise RuntimeError("Length of input list is not equal to stars' number!", input_list)
             
-def on_orbit_obs_position(input_ra_list, input_dec_list, input_pmra_list, input_pmdec_list, input_rv_list, input_parallax_list, input_nstars, input_x, input_y, input_z, input_vx, input_vy, input_vz, input_epoch, input_date_str, input_time_str, lib_path):
+def on_orbit_obs_position(input_ra_list, input_dec_list, input_pmra_list, input_pmdec_list, input_rv_list, input_parallax_list, input_nstars, input_x, input_y, input_z, input_vx, input_vy, input_vz, input_epoch, input_date_str, input_time_str, lib_path=None):
     #Check input parameters
     if not isinstance(input_nstars, int):
         raise TypeError("Parameter 7 is not int!", input_nstars)
@@ -83,6 +89,8 @@ def on_orbit_obs_position(input_ra_list, input_dec_list, input_pmra_list, input_
             if not (input_second>=0 and input_second<60.0):
                 raise TypeError("Parameter 16 second range error [0 ~ 60)!", input_second)
     #Inital dynamic lib
+    # shao = cdll.LoadLibrary(lib_path)
+    with pkg_resources.path('ObservationSim.Astrometry.lib', "libshao.so") as lib_path:
         shao = cdll.LoadLibrary(lib_path)
     shao.onOrbitObs.restype = c_int
     

ObservationSim/Config/Config.py

@@ -26,18 +26,24 @@ def config_dir(config, work_dir=None, data_dir=None):
     # SED catalog directory
     # TODO: SED_dir is deprecated
     path_dict["SED_dir"] = os.path.join(path_dict["data_dir"], "imageSims/Catalog/SEDObject")
+    
     # Directories/files for instrument parameters, e.g. efficiency curves.
-    path_dict["filter_dir"] = os.path.join(path_dict["data_dir"], config["Efficiency_curve_path"]["filter_eff"])
-    path_dict["ccd_dir"] = os.path.join(path_dict["data_dir"], config["Efficiency_curve_path"]["ccd_eff"])
-    path_dict["mirror_file"] = os.path.join(path_dict["data_dir"], config["Efficiency_curve_path"]["mirror_eff"])
+    # path_dict["filter_dir"] = os.path.join(path_dict["data_dir"], config["Efficiency_curve_path"]["filter_eff"])
+    # path_dict["ccd_dir"] = os.path.join(path_dict["data_dir"], config["Efficiency_curve_path"]["ccd_eff"])
+    # path_dict["mirror_file"] = os.path.join(path_dict["data_dir"], config["Efficiency_curve_path"]["mirror_eff"])
 
     # Cosmic-ray data directory:
-    path_dict["CRdata_dir"] = os.path.join(path_dict["data_dir"], config["CR_data_path"])
-    path_dict["sky_file"] = os.path.join(path_dict["data_dir"], config["sky_data_path"])
+    # path_dict["CRdata_dir"] = os.path.join(path_dict["data_dir"], config["CR_data_path"])
+    
+    # if "sky_file" in config:
+    #     path_dict["sky_file"] = os.path.join(path_dict["data_dir"], config["sky_file"])
+    # else:
+    #     path_dict["sky_file"] = 'sky_emiss_hubble_50_50_A.dat'
+    # path_dict["sky_file"] = os.path.join(path_dict["data_dir"], config["sky_data_path"])
 
     # Slitless spectroscopy realted
-    path_dict["sls_dir"] = os.path.join(path_dict["data_dir"], config["SLS_path"]["SLS_conf"])
-    path_dict["normalize_dir"] = os.path.join(path_dict["data_dir"], config["SLS_path"]["SLS_norm"])
+    # path_dict["sls_dir"] = os.path.join(path_dict["data_dir"], config["SLS_path"]["SLS_conf"])
+    # path_dict["normalize_dir"] = os.path.join(path_dict["data_dir"], config["SLS_path"]["SLS_norm"])
 
     return path_dict
 

ObservationSim/Instrument/Chip/Chip.py

@@ -10,8 +10,14 @@ from ObservationSim.Instrument.Chip import Effects as effects
 from ObservationSim.Instrument.FocalPlane import FocalPlane
 from ObservationSim.Config.Header import generatePrimaryHeader, generateExtensionHeader
 
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
 class Chip(FocalPlane):
-    def __init__(self, chipID, ccdEffCurve_dir, CRdata_dir, normalize_dir=None, sls_dir=None, config=None, treering_func=None):
+    def __init__(self, chipID, ccdEffCurve_dir=None, CRdata_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__()
@@ -40,17 +46,21 @@ class Chip(FocalPlane):
         self.bound = self.getChipLim()
         self.ccdEffCurve_dir = ccdEffCurve_dir
         self.CRdata_dir = CRdata_dir
-        self.normalize_dir = normalize_dir
-        self.sls_dir=sls_dir
+        # self.sls_dir=sls_dir
         # self.sls_conf = os.path.join(self.sls_dir, self.getChipSLSConf())
         slsconfs = self.getChipSLSConf()
         if np.size(slsconfs) == 1:
-            self.sls_conf = [os.path.join(self.sls_dir, slsconfs)]
+            # self.sls_conf = [os.path.join(self.sls_dir, slsconfs)]
+            with pkg_resources.path('ObservationSim.Instrument.data.sls_conf', slsconfs) as conf_path:
+                self.sls_conf = str(conf_path)
         else:
-            self.sls_conf = [os.path.join(self.sls_dir, slsconfs[0]), os.path.join(self.sls_dir, slsconfs[1])]
+            # self.sls_conf = [os.path.join(self.sls_dir, slsconfs[0]), os.path.join(self.sls_dir, slsconfs[1])]
+            self.sls_conf = []
+            with pkg_resources.path('ObservationSim.Instrument.data.sls_conf', slsconfs[0]) as conf_path:
+                self.sls_conf.append(str(conf_path))
+            with pkg_resources.path('ObservationSim.Instrument.data.sls_conf', slsconfs[1]) as conf_path:
+                self.sls_conf.append(str(conf_path))
         
-        if self.normalize_dir is not None:
-            self._getNormF()
         self.effCurve = self._getChipEffCurve(self.filter_type)
         self._getCRdata()
 
@@ -77,10 +87,6 @@ class Chip(FocalPlane):
         else:
             return "photometric"
 
-    def _getNormF(self):
-        self.normF_star = Table.read(os.path.join(self.normalize_dir, 'SLOAN_SDSS.g.fits'))
-        self.normF_galaxy = Table.read(os.path.join(self.normalize_dir, 'lsst_throuput_g.fits'))
-
     def _getChipEffCurve(self, filter_type):
         # CCD efficiency curves
         if filter_type in ['nuv', 'u', 'GU']: filename = 'UV0.txt'
@@ -92,15 +98,19 @@ class Chip(FocalPlane):
         if filter_type in ['g', 'r', 'i', 'z', 'y']: mirror_eff = 0.8
         if filter_type in ['GU', 'GV', 'GI']: mirror_eff = 1. # Not sure if this is right
         
-        path = os.path.join(self.ccdEffCurve_dir, filename)
-        table = Table.read(path, format='ascii')
+        # path = os.path.join(self.ccdEffCurve_dir, filename)
+        # table = Table.read(path, format='ascii')
+        with pkg_resources.path('ObservationSim.Instrument.data.ccd', filename) as ccd_path:
+            table = Table.read(ccd_path, format='ascii')
         throughput = galsim.LookupTable(x=table['col1'], f=table['col2']*mirror_eff, interpolant='linear')
         bandpass = galsim.Bandpass(throughput, wave_type='nm')
         return bandpass
 
     def _getCRdata(self):
-        path = os.path.join(self.CRdata_dir, 'wfc-cr-attachpixel.dat')
-        self.attachedSizes = np.loadtxt(path)
+        # path = os.path.join(self.CRdata_dir, 'wfc-cr-attachpixel.dat')
+        # self.attachedSizes = np.loadtxt(path)
+        with pkg_resources.path('ObservationSim.Instrument.data', "wfc-cr-attachpixel.dat") as cr_path:
+            self.attachedSizes = np.loadtxt(cr_path)
 
     def getChipFilter(self, chipID=None, filter_layout=None):
         """Return the filter index and type for a given chip #(chipID)

ObservationSim/Instrument/Filter.py

@@ -6,14 +6,20 @@ import numpy as np
 from ObservationSim.Instrument._util import photonEnergy
 from ObservationSim.Instrument.FilterParam import FilterParam
 
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
 class Filter(object):
     def __init__(self, filter_id, filter_type, filter_param, ccd_bandpass):
         self.filter_id = filter_id
         self.filter_type = filter_type
         self.ccd_bandpass = ccd_bandpass
         self._getParam(filter_param, filter_type)
-        if self.filter_dir is not None:
-            self.bandpass_full, self.bandpass_sub_list = self._get_bandpasses(self.filter_dir)
+        # if self.filter_dir is not None:
+        self.bandpass_full, self.bandpass_sub_list = self._get_bandpasses()
         self.survey_type = self._getSurveyType()
 
     def _getSurveyType(self):
@@ -31,7 +37,7 @@ class Filter(object):
         self.sky_background = filter_param.param[filter_type][5]
         self.mag_saturation = filter_param.param[filter_type][6]
         self.mag_dim = filter_param.param[filter_type][7]
-        self.filter_dir = filter_param.filter_dir
+        # self.filter_dir = filter_param.filter_dir
 
     def is_too_bright(self, mag):
         return mag <= self.mag_saturation - 1.0
@@ -39,16 +45,20 @@ class Filter(object):
     def is_too_dim(self, mag):
         return mag >= self.mag_dim + 1.0
 
-    def _get_bandpasses(self, filter_dir, unit='A'):
+    def _get_bandpasses(self, filter_dir=None, unit='A'):
         if self.filter_id < 7:  # Photometric
             # Get full-bandpass
-            filter_file = os.path.join(filter_dir, self.filter_type+".dat")
-            bandpass_full = galsim.Bandpass(filter_file, wave_type=unit)
+            # filter_file = os.path.join(filter_dir, self.filter_type+".dat")
+            # bandpass_full = galsim.Bandpass(filter_file, wave_type=unit)
+            with pkg_resources.path('ObservationSim.Instrument.data.filters', self.filter_type.lower() + '.txt') as filter_file:
+                bandpass_full = galsim.Bandpass(str(filter_file), wave_type=unit)
             bandpass_full = bandpass_full * self.ccd_bandpass
 
             # Get sub-bandpasses
             bandpass_sub_list = []
-            wave_bin_file = os.path.join(filter_dir, self.filter_type.lower() + "_sub.list")
+            # wave_bin_file = os.path.join(filter_dir, self.filter_type.lower() + "_sub.list")
+            # wave_points = open(wave_bin_file).read().splitlines()
+            with pkg_resources.path('ObservationSim.Instrument.data.filters', self.filter_type.lower() + "_sub.list") as wave_bin_file:
                 wave_points = open(wave_bin_file).read().splitlines()
 
             for i in range(2, len(wave_points), 2):
@@ -65,7 +75,9 @@ class Filter(object):
             con_spec = galsim.LookupTable(sls_lamb, sls_lamb, interpolant='nearest')
             bandpass_full = galsim.Bandpass(con_spec, wave_type=unit)
             bandpass_sub_list = []
-            wave_bin_file = os.path.join(filter_dir, self.filter_type.lower() + "_sub.list")
+            # wave_bin_file = os.path.join(filter_dir, self.filter_type.lower() + "_sub.list")
+            # wave_points = open(wave_bin_file).read().splitlines()
+            with pkg_resources.path('ObservationSim.Instrument.data.filters', self.filter_type.lower() + "_sub.list") as wave_bin_file:
                 wave_points = open(wave_bin_file).read().splitlines()
             for i in range(2, len(wave_points), 2):
                 blim = max(float(wave_points[i - 2]) * 0.1, bandpass_full.blue_limit)

ObservationSim/Instrument/Telescope.py

 import numpy as np
 
+try:
+    import importlib.resources as pkg_resources
+except ImportError:
+    # Try backported to PY<37 'importlib_resources'
+    import importlib_resources as pkg_resources
+
 class Telescope(object):
 	def __init__(self, param=None, optEffCurve_path=None):
 		self.diameter = 2.0 # in unit of meter
@@ -8,6 +14,9 @@ class Telescope(object):
 		self.pupil_area = np.pi * (0.5 * self.diameter)**2
 		if optEffCurve_path is not None:
 			self.efficiency = self._get_efficiency(optEffCurve_path)
+		else:
+			with pkg_resources.path('ObservationSim.Instrument.data', 'mirror_ccdnote.txt') as optEffCurve_path:
+				self.efficiency = self._get_efficiency(optEffCurve_path)
 
 	def _get_efficiency(self, effCurve_path):
 		""" Read in the efficiency of optics

ObservationSim/Instrument/data/ccd/Astro_MB.txt

+# Graph from Astro&MB, page 1
+251.4	0.5285
+254.2	0.4885
+257.0	0.4485
+259.9	0.4085
+264.1	0.3428
+269.8	0.2828
+272.6	0.2657
+276.9	0.2542
+281.1	0.2542
+285.3	0.2657
+291.0	0.2771
+299.5	0.2828
+316.5	0.3028
+329.2	0.3200
+349.1	0.3428
+366.1	0.3828
+371.7	0.4142
+371.7	0.4142
+376.0	0.4542
+383.0	0.4971
+390.1	0.5485
+398.6	0.6000
+405.7	0.6400
+412.8	0.6771
+424.1	0.7171
+438.3	0.7628
+448.2	0.7942
+448.2	0.7942
+448.2	0.7942
+448.2	0.7942
+469.4	0.8400
+490.7	0.8800
+490.7	0.8800
+511.9	0.9057
+541.6	0.9228
+565.7	0.9285
+586.9	0.9285
+620.9	0.9200
+647.8	0.9028
+680.4	0.8714
+721.5	0.8114
+741.3	0.7800
+758.3	0.7428
+771.0	0.7114
+786.6	0.6685
+800.7	0.6314
+813.5	0.5942
+822.0	0.5657
+836.1	0.5228
+850.3	0.4714
+860.2	0.4400
+860.2	0.4400
+868.7	0.4114
+877.2	0.3771
+887.1	0.3485
+901.3	0.3000
+915.4	0.2571
+926.8	0.2257
+938.1	0.1914
+955.1	0.1485
+976.3	0.1000
+997.6	0.06000
+1016	0.03714
+1033	0.02000
+1040	0.01428
+1050	0.01142

ObservationSim/Instrument/data/ccd/Basic_NIR.txt

+# Graph from Basic&NIR, page 1
+250.0	0.06837
+258.5	0.05973
+265.6	0.05681
+275.5	0.07380
+281.2	0.1050
+286.9	0.1363
+294.0	0.1704
+303.9	0.2102
+313.9	0.2443
+323.8	0.2641
+336.6	0.2754
+352.3	0.2838
+367.9	0.2836
+376.4	0.3091
+389.2	0.3432
+399.2	0.3801
+413.4	0.4170
+430.4	0.4539
+444.6	0.4794
+458.8	0.5077
+477.3	0.5502
+494.4	0.5871
+508.6	0.6154
+525.6	0.6466
+539.8	0.6721
+549.8	0.6891
+566.8	0.7145
+586.7	0.7456
+603.8	0.7711
+603.8	0.7711
+603.8	0.7711
+618.0	0.7937
+639.3	0.8220
+656.3	0.8418
+673.4	0.8587
+690.4	0.8756
+701.8	0.8840
+720.3	0.8924
+740.2	0.9007
+762.9	0.9062
+792.8	0.8944
+812.6	0.8743
+825.4	0.8570
+841.1	0.8255
+841.1	0.8255
+855.3	0.7855
+866.6	0.7540
+876.6	0.7226
+889.4	0.6712
+897.9	0.6341
+906.4	0.5969
+913.5	0.5655
+919.2	0.5370
+924.9	0.5084
+933.4	0.4684
+940.5	0.4256
+949.1	0.3856
+957.6	0.3428
+966.1	0.3000
+974.6	0.2572
+983.2	0.2200
+993.1	0.1772
+1004	0.1343
+1011	0.1058
+1024	0.07149
+1032	0.04861
+1042	0.03141
+1051	0.01992
+1059	0.01128

ObservationSim/Instrument/data/ccd/UV0.txt

+# Graph from UV0, page 1
+251.4	0.4900
+264.2	0.5041
+274.1	0.5268
+278.4	0.5609
+286.9	0.5864
+296.8	0.5949
+308.2	0.5919
+322.4	0.5861
+336.6	0.5717
+352.3	0.5516
+360.8	0.5401
+367.9	0.5229
+375.0	0.5342
+383.5	0.5541
+394.9	0.5767
+409.1	0.6108
+421.9	0.6220
+433.3	0.6333
+447.5	0.6389
+465.9	0.6444
+485.8	0.6555
+504.3	0.6582
+522.8	0.6552
+544.1	0.6578
+572.5	0.6546
+592.4	0.6516
+620.8	0.6484
+640.7	0.6396
+660.6	0.6280
+680.5	0.6136
+693.3	0.6021
+710.3	0.5876
+726.0	0.5647
+738.8	0.5474
+757.2	0.5216
+781.4	0.4729
+812.6	0.4127
+828.3	0.3755
+845.3	0.3355
+858.1	0.3040
+872.3	0.2725
+892.2	0.2324
+905.0	0.2009
+923.5	0.1551
+939.1	0.1265
+970.4	0.07207
+1003	0.03184
+1025	0.01450
+1038	0.008668
+1050	0.00000