Chip.py

import galsim
import os
import numpy as np
import pickle
import json
import ObservationSim.Instrument._util as _util
from astropy.table import Table
from numpy.random import Generator, PCG64
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
from ObservationSim.Instrument._util import rotate_conterclockwise
from ObservationSim.Instrument.Chip import ChipUtils as chip_utils

from ObservationSim.Instrument.Chip.libCTI.CTI_modeling import CTI_sim

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=None, CRdata_dir=None, sls_dir=None, config=None, treering_func=None, logger=None):
        # Get focal plane (instance of paraent class) info
        super().__init__()
        self.nsecy = 2
        self.nsecx = 8
        self.gain_channel = np.ones(self.nsecy * self.nsecx)
        self._set_attributes_from_config(config)

        self.logger = logger

        # A chip ID must be assigned
        self.chipID = int(chipID)
        self.chip_name = str(chipID).rjust(2, '0')

        # Get corresponding filter info
        self.filter_id, self.filter_type = self.getChipFilter()
        self.survey_type = self._getSurveyType()

        if self.filter_type != "FGS":
            self._getChipRowCol()

        # Set the relavent specs for detectors
        try:
            with pkg_resources.files('ObservationSim.Instrument.data.ccd').joinpath("chip_definition.json") as chip_definition:
                with open(chip_definition, "r") as f:
                    chip_dict = json.load(f)[str(self.chipID)]
        except AttributeError:
            with pkg_resources.path('ObservationSim.Instrument.data.ccd', "chip_definition.json") as chip_definition:
                with open(chip_definition, "r") as f:
                    chip_dict = json.load(f)[str(self.chipID)]
        for key in chip_dict:
            setattr(self, key, chip_dict[key])

        self.fdModel = None
        if self.filter_type == "FGS":
            fgs_name = self.chip_name[0:4]
            try:
                with pkg_resources.files('ObservationSim.Instrument.data.field_distortion').joinpath("FieldDistModelGlobal_pr4_%s.pickle" % (fgs_name.lower())) as field_distortion:
                    with open(field_distortion, "rb") as f:
                        self.fdModel = pickle.load(f)
            except AttributeError:
                with pkg_resources.path('ObservationSim.Instrument.data.field_distortion', "FieldDistModelGlobal_pr4_%s.pickle" % (fgs_name.lower())) as field_distortion:
                    with open(field_distortion, "rb") as f:
                        self.fdModel = pickle.load(f)
        else:
            # Get the corresponding field distortion model
            try:
                with pkg_resources.files('ObservationSim.Instrument.data.field_distortion').joinpath("FieldDistModel_v2.0.pickle") as field_distortion:
                    with open(field_distortion, "rb") as f:
                        self.fdModel = pickle.load(f)
            except AttributeError:
                with pkg_resources.path('ObservationSim.Instrument.data.field_distortion', "FieldDistModelGlobal_mainFP_v1.0.pickle") as field_distortion:
                    with open(field_distortion, "rb") as f:
                        self.fdModel = pickle.load(f)

        # Get boundary (in pix)
        self.bound = self.getChipLim()

        self.ccdEffCurve_dir = ccdEffCurve_dir
        self.CRdata_dir = CRdata_dir

        slsconfs = chip_utils.getChipSLSConf(chipID=self.chipID)
        if np.size(slsconfs) == 1:
            try:
                with pkg_resources.files('ObservationSim.Instrument.data.sls_conf').joinpath(slsconfs) as conf_path:
                    self.sls_conf = str(conf_path)
            except AttributeError:
                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 = []
            try:
                with pkg_resources.files('ObservationSim.Instrument.data.sls_conf').joinpath(slsconfs[0]) as conf_path:
                    self.sls_conf.append(str(conf_path))
            except AttributeError:
                with pkg_resources.path('ObservationSim.Instrument.data.sls_conf', slsconfs[0]) as conf_path:
                    self.sls_conf.append(str(conf_path))
            try:
                with pkg_resources.files('ObservationSim.Instrument.data.sls_conf').joinpath(slsconfs[1]) as conf_path:
                    self.sls_conf.append(str(conf_path))
            except AttributeError:
                with pkg_resources.path('ObservationSim.Instrument.data.sls_conf', slsconfs[1]) as conf_path:
                    self.sls_conf.append(str(conf_path))

        self.effCurve = self._getChipEffCurve(self.filter_type)
        self._getCRdata()

        # # Define the sensor model
        self.sensor = galsim.Sensor()

        self.flat_cube = None  # for spectroscopic flat field cube simulation

    def _set_attributes_from_config(self, config):
        # Default setting
        self.read_noise = 5.0   # e/pix
        self.dark_noise = 0.02  # e/pix/s
        self.rotate_angle = 0.
        self.overscan = 1000
        # Override default values
        # for key in ["gain", "bias_level, dark_exptime", "flat_exptime", "readout_time", "full_well", "read_noise", "dark_noise", "overscan"]:
        #     if key in config["ins_effects"]:
        #         setattr(self, key, config["ins_effects"][key])

    def _getChipRowCol(self):
        self.rowID, self.colID = self.getChipRowCol(self.chipID)

    def getChipRowCol(self, chipID):
        rowID = ((chipID - 1) % 5) + 1
        colID = 6 - ((chipID - 1) // 5)
        return rowID, colID

    def _getSurveyType(self):
        if self.filter_type in _util.SPEC_FILTERS:
            return "spectroscopic"
        elif self.filter_type in _util.PHOT_FILTERS:
            return "photometric"
        # elif self.filter_type in ["FGS"]:
        #     return "FGS"

    def _getChipEffCurve(self, filter_type):
        # CCD efficiency curves
        if filter_type in ['NUV', 'u', 'GU']:
            filename = 'UV0.txt'
        if filter_type in ['g', 'r', 'GV', 'FGS']:
            # TODO, need to switch to the right efficiency curvey for FGS CMOS
            filename = 'Astro_MB.txt'
        if filter_type in ['i', 'z', 'y', 'GI']:
            filename = 'Basic_NIR.txt'
        try:
            with pkg_resources.files('ObservationSim.Instrument.data.ccd').joinpath(filename) as ccd_path:
                table = Table.read(ccd_path, format='ascii')
        except AttributeError:
            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'], interpolant='linear')
        bandpass = galsim.Bandpass(throughput, wave_type='nm')
        return bandpass

    def _getCRdata(self):
        try:
            with pkg_resources.files('ObservationSim.Instrument.data').joinpath("wfc-cr-attachpixel.dat") as cr_path:
                self.attachedSizes = np.loadtxt(cr_path)
        except AttributeError:
            with pkg_resources.path('ObservationSim.Instrument.data', "wfc-cr-attachpixel.dat") as cr_path:
                self.attachedSizes = np.loadtxt(cr_path)

    # def loadSLSFLATCUBE(self, flat_fn='flat_cube.fits'):
    #     try:
    #         with pkg_resources.files('ObservationSim.Instrument.data').joinpath(flat_fn) as data_path:
    #             flat_fits = fits.open(data_path, ignore_missing_simple=True)
    #     except AttributeError:
    #         with pkg_resources.path('ObservationSim.Instrument.data', flat_fn) as data_path:
    #             flat_fits = fits.open(data_path, ignore_missing_simple=True)

    #     fl = len(flat_fits)
    #     fl_sh = flat_fits[0].data.shape
    #     assert fl == 4, 'FLAT Field Cube is Not 4 layess!!!!!!!'
    #     self.flat_cube = np.zeros([fl, fl_sh[0], fl_sh[1]])
    #     for i in np.arange(0, fl, 1):
    #         self.flat_cube[i] = flat_fits[i].data

    def getChipFilter(self, chipID=None):
        """Return the filter index and type for a given chip #(chipID)
        """
        filter_type_list = _util.ALL_FILTERS
        if chipID == None:
            chipID = self.chipID

        # updated configurations
        if chipID > 42 or chipID < 1:
            raise ValueError("!!! Chip ID: [1,42]")