Merge remote-tracking branch 'origin/develop'

ObservationSim/_util.py → observation_sim/_util.py

@@ -4,7 +4,8 @@ from datetime import datetime
 import argparse
 from astropy.time import Time
 
-from ObservationSim.Config import Pointing
+from observation_sim.config import Pointing
+
 
 def parse_args():
     '''
@@ -12,19 +13,25 @@ def parse_args():
     can be set in the .yaml config file as well.
     '''
     parser = argparse.ArgumentParser()
-    parser.add_argument('--config_file', type=str, required=True, help='.yaml config file for simulation settings.')
-    parser.add_argument('--catalog', type=str, help='name of the catalog interface class to be loaded.')
-    parser.add_argument('-c', '--config_dir', type=str, help='Directory that houses the .yaml config file.')
-    parser.add_argument('-d', '--data_dir', type=str, help='Directory that houses the input data.')
-    parser.add_argument('-w', '--work_dir', type=str, help='The path for output.')
+    parser.add_argument('--config_file', type=str, required=True,
+                        help='.yaml config file for simulation settings.')
+    parser.add_argument('--catalog', type=str,
+                        help='name of the catalog interface class to be loaded.')
+    parser.add_argument('-c', '--config_dir', type=str,
+                        help='Directory that houses the .yaml config file.')
+    parser.add_argument('-d', '--data_dir', type=str,
+                        help='Directory that houses the input data.')
+    parser.add_argument('-w', '--work_dir', type=str,
+                        help='The path for output.')
     return parser.parse_args()
 
+
 def generate_pointing_list(config, pointing_filename=None, data_dir=None):
     pointing_list = []
 
     # Only valid when the pointing list does not contain time stamp column
     t0 = datetime(2021, 5, 25, 12, 0, 0)
-    delta_t = 10. # Time elapsed between exposures (minutes)
+    delta_t = 10.  # Time elapsed between exposures (minutes)
 
     # Calculate starting time(s) for CAL exposures
     # NOTE: temporary implementation
@@ -36,7 +43,7 @@ def generate_pointing_list(config, pointing_filename=None, data_dir=None):
         obs_config_file = config['obs_setting']["obs_config_file"]
     else:
         obs_config_file = None
-    
+
     # if pointing_filename and data_dir:
     if pointing_filename:
         if data_dir:
@@ -48,7 +55,7 @@ def generate_pointing_list(config, pointing_filename=None, data_dir=None):
         #     header = f.readline()
         iline = 0
         for line in f:
-            if len(line.strip()) == 0 or line[0]=='#':
+            if len(line.strip()) == 0 or line[0] == '#':
                 continue
             if run_pointings and iline not in run_pointings:
                 iline += 1
@@ -77,12 +84,13 @@ def generate_pointing_list(config, pointing_filename=None, data_dir=None):
             exp_time=exp_time,
             pointing_type='SCI',
             obs_config_file=obs_config_file
-            )
+        )
         t += delta_t * 60.
         pointing_list.append(pointing)
         ipoint += 1
     return pointing_list
 
+
 def make_run_dirs(work_dir, run_name, pointing_list):
     if not os.path.exists(work_dir):
         try:
@@ -97,6 +105,7 @@ def make_run_dirs(work_dir, run_name, pointing_list):
             pass
     return imgDir
 
+
 def make_output_pointing_dir(path_dict, config, pointing_ID=0):
     imgDir = os.path.join(path_dict["work_dir"], config["run_name"])
     if not os.path.exists(imgDir):
@@ -113,6 +122,7 @@ def make_output_pointing_dir(path_dict, config, pointing_ID=0):
             pass
     return subImgdir, prefix
 
+
 def get_shear_field(config):
     if not config["shear_setting"]["shear_type"] in ["constant", "catalog"]:
         raise ValueError("Please set a right 'shear_method' parameter.")
@@ -125,4 +135,4 @@ def get_shear_field(config):
     else:
         g1, g2 = 0., 0.
         nshear = 0
-    return g1, g2, nshear
+    return g1, g2, nshear
\ No newline at end of file

ObservationSim/Astrometry/Astrometry_util.py → observation_sim/astrometry/Astrometry_util.py

@@ -7,28 +7,32 @@ 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)
     for i in input_list:
         if type(i) != type(1.1):
             if type(i) != type(1):
-                raise TypeError("Input list's element is not float or int!", input_list)
+                raise TypeError(
+                    "Input list's element is not float or int!", input_list)
     if len(input_list) != n:
-        raise RuntimeError("Length of input list is not equal to stars' number!", input_list)
-            
+        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=None):
-    #Check input parameters
+    # Check input parameters
     if not isinstance(input_nstars, int):
         raise TypeError("Parameter 7 is not int!", input_nstars)
-    
+
     checkInputList(input_ra_list, input_nstars)
     checkInputList(input_dec_list, input_nstars)
     checkInputList(input_pmra_list, input_nstars)
     checkInputList(input_pmdec_list, input_nstars)
     checkInputList(input_rv_list, input_nstars)
     checkInputList(input_parallax_list, input_nstars)
-    
+
     if not isinstance(input_x, float):
         raise TypeError("Parameter 8 is not double!", input_x)
     if not isinstance(input_y, float):
@@ -41,69 +45,77 @@ def on_orbit_obs_position(input_ra_list, input_dec_list, input_pmra_list, input_
         raise TypeError("Parameter 12 is not double!", input_vy)
     if not isinstance(input_vz, float):
         raise TypeError("Parameter 13 is not double!", input_vz)
-    #Convert km -> m
-    input_x = input_x*1000.0 
-    input_y = input_y*1000.0 
+    # Convert km -> m
+    input_x = input_x*1000.0
+    input_y = input_y*1000.0
     input_z = input_z*1000.0
     input_vx = input_vx*1000.0
     input_vy = input_vy*1000.0
-    input_vz  = input_vz*1000.0
-    
+    input_vz = input_vz*1000.0
+
     if not isinstance(input_date_str, str):
         raise TypeError("Parameter 15 is not string!", input_date_str)
     else:
         input_date_str = input_date_str.strip()
-        if not (input_date_str[4]=="-" and input_date_str[7]=="-"):
+        if not (input_date_str[4] == "-" and input_date_str[7] == "-"):
             raise TypeError("Parameter 15 format error (1)!", input_date_str)
         else:
             tmp = input_date_str.split("-")
             if len(tmp) != 3:
-                raise TypeError("Parameter 15 format error (2)!", input_date_str)
+                raise TypeError(
+                    "Parameter 15 format error (2)!", input_date_str)
             input_year = int(tmp[0])
             input_month = int(tmp[1])
             input_day = int(tmp[2])
-            if not (input_year>=1900 and input_year<=2100):
-                raise TypeError("Parameter 15 year range error [1900 ~ 2100]!", input_year)
-            if not (input_month>=1 and input_month<=12):
-                raise TypeError("Parameter 15 month range error [1 ~ 12]!", input_month)
-            if not (input_day>=1 and input_day<=31):
-                raise TypeError("Parameter 15 day range error [1 ~ 31]!", input_day)
-    
+            if not (input_year >= 1900 and input_year <= 2100):
+                raise TypeError(
+                    "Parameter 15 year range error [1900 ~ 2100]!", input_year)
+            if not (input_month >= 1 and input_month <= 12):
+                raise TypeError(
+                    "Parameter 15 month range error [1 ~ 12]!", input_month)
+            if not (input_day >= 1 and input_day <= 31):
+                raise TypeError(
+                    "Parameter 15 day range error [1 ~ 31]!", input_day)
+
     if not isinstance(input_time_str, str):
         raise TypeError("Parameter 16 is not string!", input_time_str)
     else:
         input_time_str = input_time_str.strip()
-        if not (input_time_str[2]==":" and input_time_str[5]==":"):
+        if not (input_time_str[2] == ":" and input_time_str[5] == ":"):
             raise TypeError("Parameter 16 format error (1)!", input_time_str)
         else:
             tmp = input_time_str.split(":")
             if len(tmp) != 3:
-                raise TypeError("Parameter 16 format error (2)!", input_time_str)
+                raise TypeError(
+                    "Parameter 16 format error (2)!", input_time_str)
             input_hour = int(tmp[0])
             input_minute = int(tmp[1])
             input_second = float(tmp[2])
-            if not (input_hour>=0 and input_hour<=23):
-                raise TypeError("Parameter 16 hour range error [0 ~ 23]!", input_hour)
-            if not (input_minute>=0 and input_minute<=59):
-                raise TypeError("Parameter 16 minute range error [0 ~ 59]!", input_minute)
-            if not (input_second>=0 and input_second<60.0):
-                raise TypeError("Parameter 16 second range error [0 ~ 60)!", input_second)
-    
-    #Inital dynamic lib
+            if not (input_hour >= 0 and input_hour <= 23):
+                raise TypeError(
+                    "Parameter 16 hour range error [0 ~ 23]!", input_hour)
+            if not (input_minute >= 0 and input_minute <= 59):
+                raise TypeError(
+                    "Parameter 16 minute range error [0 ~ 59]!", input_minute)
+            if not (input_second >= 0 and input_second < 60.0):
+                raise TypeError(
+                    "Parameter 16 second range error [0 ~ 60)!", input_second)
+
+    # Inital dynamic lib
     try:
-        with pkg_resources.files('ObservationSim.Astrometry.lib').joinpath("libshao.so") as lib_path:
+        with pkg_resources.files('observation_sim.astrometry.lib').joinpath("libshao.so") as lib_path:
             shao = cdll.LoadLibrary(lib_path)
     except AttributeError:
-        with pkg_resources.path('ObservationSim.Astrometry.lib', "libshao.so") as lib_path:
+        with pkg_resources.path('observation_sim.astrometry.lib', "libshao.so") as lib_path:
             shao = cdll.LoadLibrary(lib_path)
     shao.onOrbitObs.restype = c_int
-    
+
     d3 = c_double * 3
-    shao.onOrbitObs.argtypes = [c_double, c_double, c_double, c_double, c_double, c_double, \
-                                c_int, c_int, c_int, c_int, c_int, c_double, \
-                                c_double, POINTER(d3), POINTER(d3), \
-                                c_int, c_int, c_int, c_int, c_int, c_double, \
-                                POINTER(c_double), POINTER(c_double) ]
+    shao.onOrbitObs.argtypes = [c_double, c_double, c_double, c_double, c_double, c_double,
+                                c_int, c_int, c_int, c_int, c_int, c_double,
+                                c_double, POINTER(d3), POINTER(d3),
+                                c_int, c_int, c_int, c_int, c_int, c_double,
+                                POINTER(c_double), POINTER(c_double)]
     output_ra_list = list()
     output_dec_list = list()
     for i in range(input_nstars):
@@ -118,17 +130,17 @@ def on_orbit_obs_position(input_ra_list, input_dec_list, input_pmra_list, input_
         v3 = d3(input_vx, input_vy, input_vz)
         input_year_c = c_int(input_year)
         input_month_c = c_int(input_month)
-        input_day_c = c_int(input_day) 
+        input_day_c = c_int(input_day)
         input_hour_c = c_int(input_hour)
         input_minute_c = c_int(input_minute)
-        input_second_c  = c_double(input_second)
+        input_second_c = c_double(input_second)
         DAT = c_double(37.0)
         output_ra = c_double(0.0)
         output_dec = c_double(0.0)
-        rs = shao.onOrbitObs(input_ra, input_dec, input_parallax, input_pmra, input_pmdec, input_rv, \
-                             input_year_c, input_month_c, input_day_c, input_hour_c, input_minute_c, input_second_c, \
-                             DAT, byref(p3), byref(v3), \
-                             input_year_c, input_month_c, input_day_c, input_hour_c, input_minute_c, input_second_c, \
+        rs = shao.onOrbitObs(input_ra, input_dec, input_parallax, input_pmra, input_pmdec, input_rv,
+                             input_year_c, input_month_c, input_day_c, input_hour_c, input_minute_c, input_second_c,
+                             DAT, byref(p3), byref(v3),
+                             input_year_c, input_month_c, input_day_c, input_hour_c, input_minute_c, input_second_c,
                              byref(output_ra), byref(output_dec))
         if rs != 0:
             raise RuntimeError("Calculate error!")

ObservationSim/Config/ChipOutput.py → observation_sim/config/ChipOutput.py

 import os
 import logging
-import ObservationSim.Config._util as _util
-from ObservationSim.Config.Header import generatePrimaryHeader
+import observation_sim.config._util as _util
+from observation_sim.config.header import generatePrimaryHeader
 
 
 class ChipOutput(object):

ObservationSim/Config/Pointing.py → observation_sim/config/Pointing.py

@@ -5,11 +5,12 @@ import galsim
 import numpy as np
 from astropy.time import Time
 
-from ObservationSim.Config._util import get_obs_id
-import ObservationSim.Instrument._util as _util
+from observation_sim.config._util import get_obs_id
+import observation_sim.instruments._util as _util
+
 
 class Pointing(object):
-    def __init__(self, id=0, ra=0., dec=0., img_pa=0., timestamp=1621915200, sat_x=0., sat_y=0., sat_z=0., sun_x=0., sun_y=0., sun_z=0., sat_vx=0., sat_vy=0., sat_vz=0., exp_time=150., pointing_type='SCI', pointing_type_code='101', pointing_id = '00000001', obs_config_file=None, t_shutter_open = 1.3, t_shutter_close = 1.3):
+    def __init__(self, id=0, ra=0., dec=0., img_pa=0., timestamp=1621915200, sat_x=0., sat_y=0., sat_z=0., sun_x=0., sun_y=0., sun_z=0., sat_vx=0., sat_vy=0., sat_vz=0., exp_time=150., pointing_type='SCI', pointing_type_code='101', pointing_id='00000001', obs_config_file=None, t_shutter_open=1.3, t_shutter_close=1.3):
         self.id = id
         self.ra = ra
         self.dec = dec
@@ -23,7 +24,7 @@ class Pointing(object):
         self.pointing_type_code = pointing_type_code
         self.obs_id = pointing_id
         self.survey_field_type = 'WIDE'
-        self.jdt = 0. 
+        self.jdt = 0.
         self.obs_config_file = obs_config_file
         self.t_shutter_open = t_shutter_open
         self.t_shutter_close = t_shutter_close
@@ -41,7 +42,6 @@ class Pointing(object):
             if self.obs_param["obs_id"]:
                 self.obs_id = str(self.obs_param["obs_id"])
 
-    
     def get_full_depth_exptime(self, filter_type):
         if self.survey_field_type == 'WIDE':
             if filter_type in _util.SPEC_FILTERS:
@@ -52,7 +52,7 @@ class Pointing(object):
                 elif filter_type.lower() in ['u', 'g', 'r', 'i', 'z']:
                     return 150. * 2
                 else:
-                    return max(150., self.exp_time) # [TODO] for FGS
+                    return max(150., self.exp_time)  # [TODO] for FGS
         elif self.survey_field_type == 'DEEP':
             if filter_type in _util.SPEC_FILTERS:
                 return 250. * 4 * 4
@@ -62,8 +62,7 @@ class Pointing(object):
                 elif filter_type.lower() in ['u', 'g', 'r', 'i', 'z']:
                     return 250. * 2 * 4
                 else:
-                    return max(150., self.exp_time) # [TODO] for FGS
-
+                    return max(150., self.exp_time)  # [TODO] for FGS
 
     def read_pointing_columns(self, columns, id=0, t=1621915200, pointing_type='SCI'):
         self.id = id
@@ -91,7 +90,7 @@ class Pointing(object):
             # [TODO] Can also define other survey types
             if is_deep != -1.0:
                 self.survey_field_type = "DEEP"
-            
+
             if not self.obs_config_file:
                 self.obs_config_file = str(columns[20])
                 with open(self.obs_config_file, "r") as stream:
@@ -99,7 +98,7 @@ class Pointing(object):
                         self.obs_param = yaml.safe_load(stream)
                     except yaml.YAMLError as exc:
                         print(exc)
-            
+
             self.pointing_type_code = columns[21][0:3]
             self.obs_id = columns[21][3:]
 
@@ -108,18 +107,19 @@ class Pointing(object):
             self.timestamp = t
 
     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"])
+        run_dir = os.path.join(
+            overall_config["work_dir"], overall_config["run_name"])
         if not os.path.exists(run_dir):
             try:
                 os.makedirs(run_dir, exist_ok=True)
             except OSError:
                 pass
         self.output_prefix = get_obs_id(
-            img_type=self.pointing_type, 
-            project_cycle=overall_config["project_cycle"], 
-            run_counter=overall_config["run_counter"], 
-            pointing_id=self.obs_id, 
-            pointing_type_code = self.pointing_type_code)
+            img_type=self.pointing_type,
+            project_cycle=overall_config["project_cycle"],
+            run_counter=overall_config["run_counter"],
+            pointing_id=self.obs_id,
+            pointing_type_code=self.pointing_type_code)
         self.output_dir = os.path.join(run_dir, self.output_prefix)
         if not os.path.exists(self.output_dir):
             try:
@@ -127,10 +127,10 @@ class Pointing(object):
             except OSError:
                 pass
         if copy_obs_config and self.obs_config_file:
-            obs_config_output_path = os.path.join(self.output_dir, os.path.basename(self.obs_config_file))
+            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(self.obs_config_file, self.output_dir)
                 except OSError:
                     pass
-

ObservationSim/Config/_util.py → observation_sim/config/_util.py

 
-def get_obs_id(img_type='SCI', project_cycle=6, run_counter=0, pointing_id='00000001',pointing_type_code='101'):
+def get_obs_id(img_type='SCI', project_cycle=6, run_counter=0, pointing_id='00000001', pointing_type_code='101'):
     # obs_type = {'SCI': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99'}
     # obs_type = {'SCIE': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99', 'CAL': '01'}
-    obs_id = pointing_type_code + str(int(project_cycle)).rjust(2, '0') + str(int(run_counter)) + pointing_id
+    obs_id = pointing_type_code + \
+        str(int(project_cycle)).rjust(2, '0') + \
+        str(int(run_counter)) + pointing_id
     return obs_id
 
-# def get_obs_id(img_type='SCI', project_cycle=6, run_counter=0, pointing_num=0):
-#     # obs_type = {'SCI': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99'}
-#     obs_type = {'SCIE': '01', 'BIAS': '03', 'DARK': '07', 'FLAT': '11', 'CRS': '98', 'CRD': '99', 'CAL': '01'}
-#     obs_id = '1'+ obs_type[img_type] + str(int(project_cycle)).rjust(2, '0') + str(int(run_counter)) + str(pointing_num).rjust(8,'0')
-#     return obs_id
 
 def get_file_type(img_type='SCI'):
-    file_type = {'SCI':'SCI', 'BIAS':'BIAS', 'DARK':'DARK', 'FLAT':'FLAT', 'CRS':'CRS', 'CRD':'CRD','CALS':'CALS','CALF':'CALF'}
-    return file_type[img_type]
+    file_type = {'SCI': 'SCI', 'BIAS': 'BIAS', 'DARK': 'DARK', 'FLAT': 'FLAT',
+                 'CRS': 'CRS', 'CRD': 'CRD', 'CALS': 'CALS', 'CALF': 'CALF'}
\ No newline at end of file
+    return file_type[img_type]