plato-fits 2024.1.4__py3-none-any.whl

egse/plugins/storage/fits.py

@@ -0,0 +1,1221 @@
+import logging
+import warnings
+from pathlib import Path
+
+import numpy as np
+from astropy.io import fits
+from astropy.io.ascii.cparser import AstropyWarning
+from egse.settings import Settings
+from egse.setup import Setup
+from egse.setup import SetupError
+from egse.spw import DataPacket
+from egse.spw import DataPacketType
+from egse.state import GlobalState
+from egse.persistence import PersistenceLayer
+from egse.system import time_since_epoch_1958
+
+LOGGER = logging.getLogger(__name__)
+
+CCD_SETTINGS = Settings.load("CCD")
+
+
+class FITSPersistenceError(Exception):
+    """ Error for the FITS persistence layer."""
+    pass
+
+
+class FITS(PersistenceLayer):
+    """ Persistence layer that saves (image) data in a FITS file."""
+
+    extension = "fits"
+
+    warnings.simplefilter('ignore', category=AstropyWarning)
+
+    def __init__(self, filename: str, prep: dict):
+        """ Initialisation of the FITS persistence layer.
+
+        This consists of the following steps:
+
+            - Initialise the filepath (for the given filename);
+            - Fetch the register map from the DPU;
+            - Read all necessary data from that register map:
+                - Which CCD(s) will be read;
+                - Which side(s) of the CCD(s) will be read (E = left; F = right);
+                - Which rows and columns will be transmitted;
+                - How can we know whether all information has been received for a particular exposure;
+            - Initialisation of the (1D) arrays in which the received data will be stored;
+            - Initialisation of basic headers for the image, serial pre-scan(s), serial over-scan(s), and parallel
+              over-scan for any exposure.
+
+        Assumed is that the crucial parameters in the register map (N-FEE mode, v_start, v_end, h_end) will stay the
+        same throughout data acquisition and assembly of the FITS file.  It is not explicitly checked whether this is
+        indeed the case.
+
+        All information (image data, serial pre-scan, serial over-scan, and parallel over-scan) will be stored in the
+        same FITS file.  If the data of multiple CCDs would be transmitted, it is all stored in the same FITS file.  The
+        extension name will indicate which kind of data it contains (image data, serial pre-scan, serial over-scan, or
+        parallel over-scan), for which CCD.  In case of the serial scan maps, the extension will also indicate which
+        CCD side it applies to.
+
+        Args:
+             - filename: Name of the output FITS file.
+             - prep: Dictionary with the following information:
+                    * v_start (int) and v_end(int): index of the first and the last row being transmitted;
+                    * h_end (int): index of the last serial readout of the readout register;
+                    * rows_final_dump:
+                    * ccd_mode_config (egse.fee.n_fee_mode): readout mode;
+                    * ccd_readout_order (List[int]): CCDs that will be read out;
+                    * expected_last_packet_flags (List[bool]): expected last packet flags;
+                    * obsid: observation identifier;
+                    * cycle_time: image cycle time [s];
+                    * cgse_version: version of the Common EGSE;
+                    * setup: setup;
+                    * register_map: FEE register map;
+                    * vgd: configured VGD;
+                    * in case of windowing mode or windowing pattern mode: dictionary with one window list for each CCD.
+        """
+
+        self.fee_side = GlobalState.setup.camera.fee.ccd_sides.enum
+
+        self._filepath = Path(filename)
+
+        # Which side(s) of which CCD(s) will be transmitted?
+        # (initialise the data arrays for each of these)
+
+        self.ccd_readout_order = prep["ccd_readout_order"]  # CCD numbering [1-4]
+        self.selected_ccds = np.unique(self.ccd_readout_order)
+        LOGGER.debug(f"Selected CCDs: {self.selected_ccds}")
+
+        self.data_arrays = {}
+        self.init_data_arrays()
+
+        self.frame_number = {ccd: {self.fee_side.LEFT_SIDE: 0, self.fee_side.RIGHT_SIDE: 0} for ccd in self.selected_ccds}
+        self.timestamp = None
+        self.finetime = None
+
+        # How can you know whether or not all data for a given CCD has been received?
+        # (this depends on whether or not there is parallel over-scan data and on which CCD side(s) will be transmitted)
+
+        self.expected_last_packet_flags = prep["expected_last_packet_flags"]                    # To be received
+        self.received_last_packet_flags = {ccd: [False] * 4 for ccd in self.selected_ccds}      # Actually received
+
+        LOGGER.debug(f"Init last packets flag: {self.received_last_packet_flags}")
+
+        # Readout mode
+
+        self.ccd_mode_config = prep["ccd_mode_config"]
+        self.is_windowing_mode = self.check_readout_mode()
+
+        # if self.is_windowing_mode:
+        #
+        #     self.windows = self.init_window_list(prep["window_list"])
+
+        # Define the values of the WCS keywords
+
+
+        self.v_start = prep["v_start"]                              # First transmitted row
+        self.v_end = prep["v_end"]                                  # Last transmitted row
+        self.h_end = prep["h_end"]                                  # Last transmitted column
+        self.rows_final_dump = prep["rows_final_dump"]              # Number of rows to be dumped after readout
+        self.cycle_time = prep["cycle_time"]                        # Image cycle time [s]
+        self.cgse_version = prep["cgse_version"]                    # Version of the Common EGSE
+        self.obsid = prep["obsid"]
+
+        self.register_map = prep["register_map"]                    # Register map
+
+        # Read information from the setup
+
+        self.setup: Setup = prep["setup"]
+
+        self.site_name = self.setup["site_id"]           # Site ID
+        self.setup_id = self.setup.get_id()              # Setup ID
+        self.camera_id = self.setup.camera.get("ID")     # Camera ID (None if not present in the setup)
+
+        self.readout_time = self.calculate_readout_time(self.setup)      # Readout time [s]
+        try:
+            self.exposure_time = self.cycle_time - self.readout_time    # Exposure time [s]
+        except TypeError:
+            # Image cycle time is unknown (None)
+            self.exposure_time = None
+
+        self.has_serial_overscan = self.h_end >= CCD_SETTINGS.LENGTH_SERIAL_PRESCAN + CCD_SETTINGS.NUM_COLUMNS / 2
+        self.has_parallel_overscan = self.v_end >= CCD_SETTINGS.NUM_ROWS
+
+        # Create basic WCS
+        # (part of the information can only be determined when the data is assembled)
+
+        self.image_header = self.create_base_image_wcs()
+        self.serial_prescan_header = self.create_base_serial_prescan_wcs()
+        self.serial_overscan_header = self.create_base_serial_overscan_wcs()
+        self.parallel_overscan_header = self.create_base_parallel_overscan_wcs()
+
+        self.is_fits_file_open = False
+
+    def calculate_readout_time(self, setup: Setup):
+        """ Calculate the readout time.
+
+        The readout time consists of:
+
+            - clearout for the rows up to v_start;
+            - reading (i.e. parallel transfer of the row + serial transfer of all its pixels up to h_end) rows v_start
+              to v_end;
+            - dumping rows_final_dump.
+
+        Returns: Readout time for the requested part of a single CCD side [s].
+        """
+
+        time_row_parallel = setup.camera.fee.time_row_parallel
+        time_row_clearout = setup.camera.fee.time_row_clearout
+        time_pixel_readout = setup.camera.fee.time_pixel_readout
+
+        time_read_rows = (self.v_end - self.v_start + 1) * (time_row_parallel + (self.h_end + 1) * time_pixel_readout)
+        time_dump_rows = (self.v_start + self.rows_final_dump) * time_row_clearout
+
+        return time_read_rows + time_dump_rows
+
+    def get_vgd(self):
+        """ Extract the VGD voltage from the register map.
+
+        Return: Configured VGD voltage [V].
+        """
+
+        vgd_19 = self.register_map[('reg_19_config', 'ccd_vgd_config')]
+        vgd_20 = self.register_map[('reg_20_config', 'ccd_vgd_config')]
+
+        return ((vgd_20 << 4) + vgd_19) / 1000 * 5.983
+
+    def get_ccd2_vrd(self):
+        """
+        Extract the VRD voltage for CCD2 from the register map.
+
+        NOTE: Use this function only for the FM cameras.
+
+        Return: Configured VRD voltage.
+        """
+        vrd_18 = self.register_map[('reg_18_config', 'ccd2_vrd_config')]
+        vrd_19 = self.register_map[('reg_19_config', 'ccd2_vrd_config')]
+
+        return int(f'0x{vrd_19:x}{vrd_18:x}', 16)
+
+
+    def get_ccd3_vrd(self):
+        """
+        Extract the VRD voltage for CCD3 from the register map.
+
+        NOTE: Use this function only for the EM camera.
+
+        Return: Configured VRD voltage.
+        """
+        vrd_18 = self.register_map[('reg_18_config', 'ccd3_vrd_config')]
+        vrd_19 = self.register_map[('reg_19_config', 'ccd3_vrd_config')]
+
+        return int(f'0x{vrd_19:x}{vrd_18:x}', 16)
+
+
+    def init_data_arrays(self):
+        """ Initialise data arrays in which the data content of the SpW packets will be dumped.
+
+        At this point, we have already determined which side(s) of which CCD(s) will be read out.  For each of them,
+        a placeholder will be foreseen in a dedicated dictionary.  The structure of this dictionary is the following,
+        in case both sides of all CCDs will be read:
+
+            data_arrays[fee_side.LEFT_SIDE][1] # left side of CCD1
+            data_arrays[fee_side.LEFT_SIDE][2] # left side of CCD2
+            data_arrays[fee_side.LEFT_SIDE][3] # left side of CCD3
+            data_arrays[fee_side.LEFT_SIDE][4] # left side of CCD4
+            data_arrays[fee_side.RIGHT_SIDE][1] # right side of CCD1
+            data_arrays[fee_side.RIGHT_SIDE][2] # right side of CCD2
+            data_arrays[fee_side.RIGHT_SIDE][3] # right side of CCD3
+            data_arrays[fee_side.RIGHT_SIDE][4] # right side of CCD4
+
+        In case not all CCDs will be read out and/or only one side, placeholders will only be foreseen for the relevant
+        CCD data.
+
+        Returns: Dictionary with placeholders for the data arrays of the selected CCD sides.
+        """
+
+        left_side_arrays = {ccd: np.array([], dtype=np.uint16) for ccd in self.selected_ccds}
+        self.data_arrays[self.fee_side.LEFT_SIDE] = left_side_arrays
+
+        right_side_arrays = {ccd: np.array([], dtype=np.uint16) for ccd in self.selected_ccds}
+        self.data_arrays[self.fee_side.RIGHT_SIDE] = right_side_arrays
+
+    def clear_for_next_exposure(self, ccd_number: int, ccd_side):
+        """ Indicate that no data has been received yet for the next exposure of the given CCD.
+
+        At the end of an exposure, when the data have been assembled and written to FITS:
+
+            - clear the data arrays for the next exposure;
+            - indicate that the last packet has not been received yet for the next exposure;
+            - clear the timestamp for the next exposure.
+
+        Args:
+            - ccd_number: CCD identifier (1/2/3/4).
+            - ccd_side: CCD side from which the last received data originates.
+        """
+
+        for ccd_side in self.fee_side:
+            self.clear_data_arrays(ccd_number, ccd_side)
+
+        self.clear_last_packet_received(ccd_number)
+
+    def clear_data_arrays(self, ccd_number: int, ccd_side):
+        """ Clear the data arrays for the given CCD.
+
+        At the end of an exposure, when the data have been assembled and written to FITS, the data arrays must be
+        cleared for the next exposure.
+
+        Args:
+            - ccd_number: CCD identifier (1/2/3/4).
+        """
+
+        self.data_arrays[ccd_side][ccd_number] = np.array([], dtype=np.uint16)
+
+    def clear_last_packet_received(self, ccd_number: int):
+        """ Clear the information about the last packet being received for the given CCD.
+
+        At the end of an exposure, when the data have been assembled and written to FITS, it must be indicated that the
+        last packet has not been received for the next exposure for the given CCD.
+
+        Args:
+            - ccd_number: CCD identifier (1/2/3/4).
+        """
+
+        self.received_last_packet_flags[ccd_number] = [False for el in self.received_last_packet_flags[ccd_number]]
+
+    # def get_data_array(self, ccd_number: int, ccd_side: fee_side):
+    #     """ Return the data array for the given side of the given CCD.
+    #
+    #     In this array all SpW data concerning the serial pre-scan, image, serial over-scan, and parallel over-scan
+    #     will be dumped (in 1D).  If the last data packet has been received, the different parts will be extracted and
+    #     written to FITS.
+    #
+    #     Args:
+    #         - ccd_number: CCD identifier (1/2/3/4).
+    #         - ccd_side: CCD side.
+    #
+    #     Returns: Data array for the given side of the given CCD.
+    #     """
+    #
+    #     return self.data_arrays[ccd_side][ccd_number]
+
+    def check_readout_mode(self):
+        """ For now only checks whether the N-FEE is in the correct mode, i.e. full-image (pattern) mode.
+
+        In the future, if deemed necessary, windowing (pattern) mode may be implemented as well.
+        """
+
+        if self.ccd_mode_config in [n_fee_mode.FULL_IMAGE_MODE, n_fee_mode.FULL_IMAGE_PATTERN_MODE,
+                                    n_fee_mode.PARALLEL_TRAP_PUMPING_1_MODE, n_fee_mode.PARALLEL_TRAP_PUMPING_2_MODE,
+                                    n_fee_mode.SERIAL_TRAP_PUMPING_1_MODE, n_fee_mode.SERIAL_TRAP_PUMPING_2_MODE]:
+
+            return False
+
+        if self.ccd_mode_config in [n_fee_mode.WINDOWING_PATTERN_MODE, n_fee_mode.WINDOWING_MODE]:
+
+            return True
+
+        else:
+
+            raise FITSPersistenceError("Construction of FITS files from SpW packets only implemented for full-image "
+                                       "(pattern) mode, windowing (pattern) mode, and parallel/serial trap pumping 1/2 "
+                                       "mode")
+
+    # def init_window_list(self, window_list: dict):
+    #     """ Compile the window list.
+    #
+    #     For each of the CCDs that will be read out, execute the following steps:
+    #
+    #         - For each of the CCD sides that will be transmitted, identify which pixels in the compound 2D array (i.e.
+    #           in which the image and the scan maps are still glued together) will be transmitted.  Store their index
+    #           in the corresponding 1D array in a dictionary.
+    #         - Store the pixel coordinates of the lower left corner of the window (in the CCD reference frame) of all
+    #           windows in the image area.
+    #     """
+    #
+    #     window_indices = {ccd_side: {} for ccd_side in self.selected_ccd_side}
+    #
+    #     for ccd_number in self.selected_ccds:
+    #
+    #         # Get the window information for the current CCD
+    #
+    #         ccd_window_list_obj: WindowList = window_list[ccd_number]
+    #         ccd_window_list = ccd_window_list_obj.get_window_list()     # Ordered set of windows
+    #         ccd_window_num_columns, ccd_window_num_rows = ccd_window_list_obj.get_window_size()     # Window size
+    #
+    #         ccd_window_x_array = np.array([])
+    #         ccd_window_y_array = np.array([])
+    #
+    #         ccd_window_indices = {ccd_side: np.array([]) for ccd_side in self.selected_ccd_side}
+    #
+    #         for (x_window, y_window, ccd_side_window) in ccd_window_list:
+    #
+    #             # Calculate the index in the 1D array
+    #
+    #             for row in range(y_window, y_window + ccd_window_num_rows + 1):
+    #
+    #                 for column in range(x_window, x_window + ccd_window_num_columns + 1):
+    #
+    #                     index = row * (self.v_end - self.v_start + 1) + column
+    #                     ccd_window_indices[ccd_side_window] = np.append(ccd_window_indices[ccd_side_window], index)
+    #
+    #             # Store the coordinates of the lower left corner of the windows in the CCD reference frame
+    #             # (only for the windows in the image area)
+    #
+    #             x_to_append = x_window - CCD_SETTINGS.LENGTH_SERIAL_PRESCAN
+    #
+    #             # TODO Should we check that the window is on the image area?
+    #
+    #             if ccd_side_window == fee_side.F_SIDE:
+    #
+    #                 x_to_append = CCD_SETTINGS.NUM_COLUMNS / 2 - 1 - x_to_append
+    #
+    #                 if fee_side.E_SIDE in self.selected_ccd_side:
+    #
+    #                     x_to_append += CCD_SETTINGS.NUM_COLUMNS / 2
+    #
+    #             ccd_window_x_array = np.append(ccd_window_x_array, x_to_append)
+    #             ccd_window_y_array = np.append(ccd_window_y_array, y_window)
+    #
+    #         for ccd_side in self.selected_ccd_side:
+    #
+    #             window_indices[ccd_side][ccd_number] = np.sort(np.unique(ccd_window_indices[ccd_side]))
+    #
+    #         rows = fits.Column("Rows", format="I", array=ccd_window_y_array)
+    #         columns = fits.Column("Columns", format="I", array=ccd_window_x_array)
+    #         table = fits.BinTableHDU.from_columns([rows, columns])
+    #         table.header["EXTNAME"] = f"Windows"
+    #         table.header["EXTVER"] = ccd_number
+    #         table.header["CCD_ID"] = (ccd_number, "CCD identifier",)
+    #
+    #         # TODO
+    #
+    #         # fits.append(table)
+    #
+    #         # with fits.open(self._filepath, mode="append") as hdul:
+    #         #
+    #         #     hdul.append(table)
+    #
+    #     return window_indices
+
+    def create_primary_header(self):
+        """ Creates the primary header (i.e. the header of the primary HDU).
+
+        This contains information that is specific for the camera.
+        """
+
+        primary_header = fits.PrimaryHDU().header
+
+        primary_header["LEVEL"] = 1     # Flat structure
+
+        primary_header["V_START"] = (self.v_start, "Index of 1st row that is transmitted (counting starts at 0)")
+        primary_header["V_END"] = (self.v_end, "Index of last row that is transmitted (counting starts at 0)")
+        primary_header["H_END"] = (self.h_end, "Number of serial register transfers")
+        primary_header["ROWS_FINAL_DUMP"] = (self.rows_final_dump, "Number of rows for clearout after readout")
+        primary_header["READ_MODE"] = (n_fee_mode(self.ccd_mode_config).name, "N-FEE operating mode")
+
+        primary_header["CI_WIDTH"] = (self.register_map["charge_injection_width"],
+                                      "Number of rows in each charge injection region")
+        primary_header["CI_GAP"] = (self.register_map["charge_injection_gap"],
+                                    "Number of rows between charge injection regions")
+        primary_header["PARALLEL_TOI_PERIOD"] = (self.register_map["parallel_toi_period"],
+                                                 "Duration of a parallel  overlap period (TOI) [us]")
+        primary_header["PARALLEL_CLK_OVERLAP"] = (self.register_map["parallel_clk_overlap"],
+                                                  "Extra parallel clock overlap [us]")
+        primary_header["CI_EN"] = (self.register_map["charge_injection_width"],
+                                   "Charge injection enabled (1) / disabled (0)")
+        primary_header["TRI_LEVEL_CLK_EN"] = (self.register_map["tri_level_clk_en"],
+                                              "Generating bi-level parallel clocks (0) / tri-level parallel clocks (1)")
+        primary_header["IMG_CLK_DIR"] = (self.register_map["img_clk_dir"],
+                                         "Generating reverse parallel clocks (1) / normal forward parallel clocks (0)")
+        primary_header["REG_CLK_DIR"] = (self.register_map["reg_clk_dir"],
+                                         "Generating reverse serial clocks (1) / normal forward serial clocks (0)")
+        primary_header["PACKET_SIZE"] = (self.register_map["packet_size"],
+                                         "Packet size = load bytes + 10 (header bytes)")
+
+        primary_header["TRAP_PUMP_DWELL_CTR"] = (self.register_map["Trap_Pumping_Dwell_counter"],
+                                                 "Dwell timer for trap pumping [ns]")
+        primary_header["SENSOR_SEL"] = (self.register_map["sensor_sel"], "CCD port data transmission selection control")
+        primary_header["SYNC_SEL"] = (self.register_map["sync_sel"], "Internal (1) / external (0) sync")
+        primary_header["DIGITISE_EN"] = (self.register_map["digitise_en"],
+                                         "Digitised data transferred to the N-DPU (1) or not (0) during image mode")
+        primary_header["DG_EN"] = (self.register_map["DG_en"], "Dump gate high (1) / low (0)")
+        primary_header["CCD_READ_EN"] = (self.register_map["ccd_read_en"], "CCD readout enabled (1) / disabled (0)")
+        primary_header["CONV_DLY"] = (self.register_map["conv_dly"],
+                                      "Delay value from rising edge of CCD_R_EF_DRV (where ADC convert pulse "
+                                      "is generated) [ns]")
+        primary_header["HIGH_PRECISION_HK_EN"] = (self.register_map["High_precision_HK_en"],
+                                                  "Sending high-precision HK (1) / pixel data (0)")
+
+        primary_header["CCD_VOD"] = (self.register_map["ccd_vod_config"], "Configured VOD")
+
+        primary_header["CCD1_VRD"] = (self.register_map["ccd1_vrd_config"], "Configured VRD for CCD1")
+        if PLATO_CAMERA_IS_EM:
+            primary_header["CCD2_VRD"] = (self.register_map["ccd2_vrd_config"], "Configured VRD for CCD2")
+            primary_header["CCD3_VRD"] = (self.get_ccd3_vrd(), "Configured VRD for CCD3")
+        else:
+            primary_header["CCD2_VRD"] = (self.get_ccd2_vrd(), "Configured VRD for CCD2")
+            primary_header["CCD3_VRD"] = (self.register_map["ccd3_vrd_config"], "Configured VRD for CCD3")
+
+        primary_header["CCD4_VRD"] = (self.register_map["ccd4_vrd_config"], "Configured VRD for CCD4")
+        primary_header["CCD_VOG"] = (self.register_map["ccd_vog_config"], "Configured VOG")
+        primary_header["CCD_VGD"] = (self.get_vgd(), "Configured VGD [V]")
+        primary_header["CCD_IG_HI"] = (self.register_map["ccd_ig_hi_config"], "Configured IG-high")
+        primary_header["CCD_IG_LO"] = (self.register_map["ccd_ig_lo_config"], "Configured IG-high")
+        primary_header["TRK_HLD_HI"] = (self.register_map["trk_hld_hi"], "Track and hold high")
+        primary_header["TRK_HLD_LO"] = (self.register_map["trk_hld_lo"], "Track and hold low")
+        primary_header["CONT_RST_ON"] = (self.register_map["cont_rst_on"],
+                                         "When 1, FPGA generates continuous reset clock during readout")
+        if not PLATO_CAMERA_IS_EM:
+            primary_header["CONT_CDSCLP_ON"] = (self.register_map["cont_cdsclp_on"],
+                                                "When 1, FPGA generates continuous CDS clamp during readout")
+            primary_header["CONT_ROWCLP_ON"] = (self.register_map["cont_rowclp_on"],
+                                                "When 1, FPGA generates continuous row clamp during readout")
+        primary_header["R_CFG1"] = (self.register_map["r_cfg1"], "Clock cycle for Rph3-low, Rph1-high")
+        primary_header["R_CFG2"] = (self.register_map["r_cfg2"], "Clock cycle for Rph1-low, Rph2-high")
+        primary_header["CDSCLP_LO"] = (self.register_map["cdsclp_lo"], "Clock cycle for cdsclp low")
+        if not PLATO_CAMERA_IS_EM:
+            primary_header["ADC_PWRDN_EN"] = (self.register_map["adc_pwrdn_en"],
+                                              "ADC power-down enabled (0) / disabled (1)")
+            primary_header["CDSCLP_HI"] = (self.register_map["cdsclp_hi"], "Clock cycle for cdsclp high")
+            primary_header["ROWCLP_HI"] = (self.register_map["rowclp_hi"], "Clock cycle for rowclp high")
+            primary_header["ROWCLP_LO"] = (self.register_map["rowclp_lo"], "Clock cycle for rowclp low")
+        # primary_header["SURFACE_INV_CTR"] = (self.register_map["Surface_Inversion_counter"],
+        #                                      "Surface inversion counter")
+        primary_header["READOUT_PAUSE_CTR"] = (self.register_map["Readout_pause_counter"], "Readout pause counter")
+        primary_header["TRAP_PUMP_SHUFFLE_CTR"] = (self.register_map["Trap_Pumping_Shuffle_counter"],
+                                                   "Trap pumping shuffle counter")
+
+        # primary_header["FOCALLEN"] = (FOV_SETTINGS["FOCAL_LENGTH"], "Focal length [mm]")
+
+        # Additional keywords
+
+        primary_header["TELESCOP"] = "PLATO"
+        if self.camera_id:
+            primary_header["INSTRUME"] = (self.camera_id, "Camera ID")
+        primary_header["SITENAME"] = (self.site_name, "Name of the test site")
+        primary_header["SETUP"] = (self.setup_id, "Setup ID")
+        primary_header["CCD_READOUT_ORDER"] = (str(self.ccd_readout_order), "Transmitted CCDs")
+        primary_header["CYCLETIME"] = (self.cycle_time, "Image cycle time [s]")
+        primary_header["READTIME"] = (self.readout_time,
+                                      "Time needed to read out the requested part for a single CCD side [s]")
+
+        if self.register_map["sync_sel"] == 1:  # See https://github.com/IvS-KULeuven/plato-common-egse/issues/2475
+            primary_header["READPERIOD"] = (self.cycle_time + INT_SYNC_TIMING_OFFSET, "Time between frames [s] "
+                                                                                       "(internal sync)")
+            texp_cmd = self.cycle_time - self.readout_time
+            primary_header["TEXP_CMD"] = (texp_cmd, "Commanded exposure time [s] (internal sync)")
+            primary_header["TEXP_EFF"] = (texp_cmd + INT_SYNC_TIMING_OFFSET, "Effective exposure time [s] (internal "
+                                                                              "sync)")
+
+        primary_header["CGSE"] = (self.cgse_version, "Version of the Common EGSE")
+
+        LOGGER.info(f"Obsid in FITS persistence layer: {self.obsid}")
+
+        if self.obsid is not None:
+
+            LOGGER.debug(f"{self.obsid = }")
+
+            primary_header["OBSID"] = (self.obsid, "Observation identifier")
+
+        primary_header["PRE_SC_N"] = (CCD_SETTINGS.LENGTH_SERIAL_PRESCAN,
+                                      "Number of pixels/columns in the serial pre-scan")
+        primary_header["OVR_SC_N"] = (max(0, self.h_end + 1
+                                          - CCD_SETTINGS.LENGTH_SERIAL_PRESCAN - CCD_SETTINGS.NUM_COLUMNS // 2),
+                                      "Number of virtual pixels / columns in the serial over-scan")
+        primary_header["OVR_SC_R"] = (max(0, self.v_end + 1 - CCD_SETTINGS.NUM_ROWS),
+                                      "Number of rows in the parallel over-scan")
+        primary_header["IMG_REPR"] = ("FOV_IMG", "Right CCD side flipped w.r.t. readout direction")
+
+        return primary_header
+
+    def create_base_image_wcs(self):
+        """ Create a basic FITS header for the image.
+
+        Not all information can be filled out at this point (i.c. extension, CCD identifier, number of columns,
+        rotation, reference pixel).  This will be done at the moment the serial pre-scan will be written to file.
+
+        Note that, if both CCD sides will be transmitted, the image of both sides will be glued together (the E-side
+        must be flipped horizontally first).  If only the E-side will be transmitted, its image must be flipped
+        horizontally.
+
+        Returns: Basic FITS header for the image.
+        """
+
+        image_header = fits.ImageHDU().header
+
+        # Make sure the data is saved as 16-bit
+
+        image_header["BITPIX"] = 16
+        image_header["BZERO"] = 32768
+
+        # Dimensionality
+
+        num_rows = min(CCD_SETTINGS["NUM_ROWS"] - 1, self.v_end) - self.v_start + 1
+
+        image_header["NAXIS"] = (2, "Dimensionality of the image",)
+        image_header["NAXIS2"] = (num_rows, "Number of rows in the image",)
+
+
+        # Focal length (this is needed for the conversion to field angles)
+
+        image_header["FOCALLEN"] = (FOV_SETTINGS["FOCAL_LENGTH"], "Focal length [mm]",) # TODO
+
+        # Linear coordinate transformation from sub-field to focal-plane coordinates
+
+        image_header["ctype1"] = ("LINEAR", "Linear coordinate transformation",)
+        image_header["ctype2"] = ("LINEAR", "Linear coordinate transformation",)
+
+        # Focal-plane coordinates are expressed in mm
+
+        image_header["CUNIT1"] = ("MM", "Target unit in the column direction (mm)",)
+        image_header["CUNIT2"] = ("MM", "Target unit in the row direction (mm)",)
+
+        # Pixel size
+
+        cdelt = CCD_SETTINGS["PIXEL_SIZE"] / 1000.0  # Pixel size [mm]
+        image_header["CDELT1"] = (cdelt, "Pixel size in the x-direction [mm]",)
+        image_header["CDELT2"] = (cdelt, "Pixel size in the y-direction [mm]",)
+
+        # Additional keywords
+
+        # image_header["TELESCOP"] = (setup["camera_id"], "Camera ID")
+        # image_header["INSTRUME"] = (setup["camera_id"], "Camera ID")
+
+        image_header["TELESCOP"] = "PLATO"
+        if self.camera_id:
+            image_header["INSTRUME"] = (self.camera_id, "Camera ID")
+        image_header["SITENAME"] = (self.site_name, "Name of the test site")
+        image_header["SETUP"] = (self.setup_id, "Setup ID")
+        if self.obsid is not None:
+            image_header["OBSID"] = (self.obsid, "Observation identifier")
+
+        return image_header
+
+    def create_base_serial_prescan_wcs(self):
+        """ Create a basic FITS header for the serial pre-scan.
+
+        Not all information can be filled out at this point (i.c. extension, CCD identifier).  This will be
+        done at the moment the serial pre-scan will be written to file.
+
+        Note that, if both CCD sides will be transmitted, you will end up having to serial pre-scan maps per exposures
+        (one for each side).
+
+        Returns: Basic FITS header for the serial pre-scan.
+        """
+
+        serial_prescan_wcs = fits.ImageHDU().header
+
+        # Make sure the data is saved as 16-bit
+
+        serial_prescan_wcs["BITPIX"] = 16
+        serial_prescan_wcs["BZERO"] = 32768
+
+        # Dimensionality
+
+        num_rows = self.v_end - self.v_start + 1
+        num_columns = CCD_SETTINGS.LENGTH_SERIAL_PRESCAN
+
+        serial_prescan_wcs["NAXIS"] = (2, "Dimensionality of the serial pre-scan",)
+        serial_prescan_wcs["NAXIS1"] = (num_columns, "Number of columns in the serial pre-scan",)
+        serial_prescan_wcs["NAXIS2"] = (num_rows, "Number of rows in the serial pre-scan",)
+
+        serial_prescan_wcs["TELESCOP"] = "PLATO"
+        if self.camera_id:
+            serial_prescan_wcs["INSTRUME"] = (self.camera_id, "Camera ID")
+        serial_prescan_wcs["SITENAME"] = (self.site_name, "Name of the test site")
+        serial_prescan_wcs["SETUP"] = (self.setup_id, "Setup ID")
+        if self.obsid is not None:
+            serial_prescan_wcs["OBSID"] = (self.obsid, "Observation identifier")
+
+        return serial_prescan_wcs
+
+    def create_base_serial_overscan_wcs(self):
+        """ Create a basic FITS header for the serial over-scan.
+
+        Not all information can be filled out at this point (i.c. extension, CCD identifier).  This will be
+        done at the moment the serial over-scan will be written to file.
+
+        Note that, if both CCD sides will be transmitted, you will end up having to serial over-scan maps per exposures
+        (one for each side).
+
+        Returns: Basic FITS header for the serial over-scan.
+        """
+
+        serial_overscan_wcs = fits.ImageHDU().header
+
+        # Make sure the data is saved as 16-bit
+
+        serial_overscan_wcs["BITPIX"] = 16
+        serial_overscan_wcs["BZERO"] = 32768
+
+        # Dimensionality
+
+        num_rows = self.v_end - self.v_start + 1
+        num_columns = self.v_end + 1 - CCD_SETTINGS.LENGTH_SERIAL_PRESCAN - CCD_SETTINGS.NUM_COLUMNS / 2
+
+        serial_overscan_wcs["NAXIS"] = (2, "Dimensionality of the serial over-scan",)
+        serial_overscan_wcs["NAXIS1"] = (num_columns, "Number of columns in the serial over-scan",)
+        serial_overscan_wcs["NAXIS2"] = (num_rows, "Number of rows in the serial over-scan",)
+
+        # Site name
+
+        serial_overscan_wcs["TELESCOP"] = "PLATO"
+        if self.camera_id:
+            serial_overscan_wcs["INSTRUME"] = (self.camera_id, "Camera ID")
+        serial_overscan_wcs["SITENAME"] = (self.site_name, "Name of the test site")
+        serial_overscan_wcs["SETUP"] = (self.setup_id, "Setup ID")
+        if self.obsid is not None:
+            serial_overscan_wcs["OBSID"] = (self.obsid, "Observation identifier")
+
+        return serial_overscan_wcs
+
+    def create_base_parallel_overscan_wcs(self):
+        """ Create a basic FITS header for the parallel over-scan.
+
+        Not all information can be filled out at this point (i.c. extension, CCD identifier, number of columns).  This
+        will be done at the moment the parallel over-scan will be written to file.
+
+        Note that, if both CCD sides will be transmitted, the parallel over-scan of both sides will be glued together
+        (the E-side must be flipped horizontally first).  If only the E-side will be transmitted, its parallel
+        over-scan must be flipped horizontally.
+
+        Returns: Basic FITS header for the parallel over-scan.
+        """
+
+        parallel_overscan_wcs = fits.ImageHDU().header
+
+        # Make sure the data is saved as 16-bit
+
+        parallel_overscan_wcs["BITPIX"] = 16
+        parallel_overscan_wcs["BZERO"] = 32768
+
+        # Dimensionality
+
+        num_rows_parallel_overscan = max(0, self.v_end - CCD_SETTINGS.NUM_ROWS + 1)
+
+        parallel_overscan_wcs["NAXIS"] = (2, "Dimensionality of the parallel over-scan",)
+        parallel_overscan_wcs["NAXIS2"] = (num_rows_parallel_overscan, "Number of rows in the parallel over-scan",)
+
+        # Site name
+
+        parallel_overscan_wcs["TELESCOP"] = "PLATO"
+        if self.camera_id:
+            parallel_overscan_wcs["INSTRUME"] = (self.camera_id, "Camera ID")
+        parallel_overscan_wcs["SITENAME"] = (self.site_name, "Name of the test site")
+        parallel_overscan_wcs["SETUP"] = (self.setup_id, "Setup ID")
+        if self.obsid is not None:
+            parallel_overscan_wcs["OBSID"] = (self.obsid, "Observation identifier")
+
+        return parallel_overscan_wcs
+
+    def open(self, mode=None):
+
+        primary_header = self.create_primary_header()
+
+        # The primary HDU contains only this header and no image data
+
+        primary_hdu = fits.PrimaryHDU()
+        primary_hdu.header = primary_header
+
+        # The FITS file is created.  If the filename is already in use, and exception
+        # will be thrown.
+
+        primary_hdu.writeto(self._filepath)
+
+        self.is_fits_file_open = True
+
+    def close(self):
+        """Closes the resource."""
+
+        self.is_fits_file_open = False
+
+    def exists(self):
+
+        return self._filepath.exists()
+
+    def create(self, data: dict):
+        """Add the given data to the FITS file.
+
+        The given data is a stream of SpW packets, only part of which contains information should go in the FITS file:
+
+            - Image (and over-scan) data contain the transmitted readout of the CCD(s);
+            - Timecode and housekeeping packets are not needed for this purpose.
+        """
+
+        for key, spw_packet in data.items():
+
+            # if isinstance(spw_packet, TimecodePacket):
+            #
+            #     self.timestamp = spw_packet.
+
+            if key == "Timestamp":
+
+                self.timestamp = spw_packet
+                self.finetime = time_since_epoch_1958(self.timestamp)
+
+            elif isinstance(spw_packet, DataPacket):
+
+                try:
+                    ccd_bin_to_id = self.setup.camera.fee.ccd_numbering.CCD_BIN_TO_ID
+                except AttributeError:
+                    raise SetupError("No entry in the setup for camera.fee.ccd_numbering.CCD_BIN_TO_ID")
+                spw_packet_data_type = spw_packet.type
+                ccd_number = ccd_bin_to_id[spw_packet_data_type.ccd_number] # 1-4
+                ccd_side = self.fee_side(spw_packet_data_type.ccd_side)
+                data_array = spw_packet.data_as_ndarray
+
+                self.data_arrays[ccd_side][ccd_number] = np.append(self.data_arrays[ccd_side][ccd_number], data_array)
+
+                # If all data has been received for the current exposure of this CCD, the following steps must be
+                # performed:
+                #   - re-shape the 1D data arrays to 2D data arrays;
+                #   - extract the different pieces of the 2D data arrays (image + scan maps);
+                #   - for the F-side: flip the image and parallel over-scan horizontally;
+                #   - if both CCD sides are transmitted, stitch them together (for the image and parallel
+                #     over-scan);
+                #   - update the WCS of the different regions;
+                #   - add to the FITS file.
+
+                if self.is_all_data_received(spw_packet_data_type, ccd_number, ccd_side):
+
+                    # Write the information to FITS
+
+                    for ccd_side in self.fee_side:
+
+                        try:
+                            if self.data_arrays[ccd_side][ccd_number].size > 0:
+                                self.assemble_slice(ccd_number, ccd_side)
+                                self.frame_number[ccd_number][ccd_side] += 1
+                        except MissingSpWPacketsError as exc:
+                            LOGGER.info(exc)
+
+                    # Get ready for the next exposure
+
+                    self.clear_for_next_exposure(ccd_number, ccd_side)
+
+    def is_all_data_received(self, spw_packet_data_type: DataPacketType, ccd_number: int, ccd_side):
+        """ Check if all data has been received for the current exposure.
+
+        Args:
+            - spw_packet_data_type: Last received data packet type.
+            - ccd_number: CCD from which the last received data originates (1-4).
+            - ccd_side: CCD side from which the last received data originates.
+
+        Returns: True if all data for the current exposure has been received; False otherwise.
+        """
+
+        from egse.dpu import got_all_last_packets
+
+        if spw_packet_data_type.last_packet:
+
+            packet_type = spw_packet_data_type.packet_type
+
+            if packet_type == PacketType.DATA_PACKET:
+
+                if ccd_side == self.fee_side.E_SIDE:
+
+                    self.received_last_packet_flags[ccd_number][0] = True
+
+                elif ccd_side == self.fee_side.F_SIDE:
+
+                    self.received_last_packet_flags[ccd_number][1] = True
+
+            elif packet_type == PacketType.OVERSCAN_DATA:
+
+                if ccd_side == self.fee_side.E_SIDE:
+
+                    self.received_last_packet_flags[ccd_number][2] = True
+
+                elif ccd_side == self.fee_side.F_SIDE:
+
+                    self.received_last_packet_flags[ccd_number][3] = True
+
+        return got_all_last_packets(self.received_last_packet_flags[ccd_number], self.expected_last_packet_flags)
+
+    def got_all_last_packets(self, ccd_number: int, ccd_side):
+        """ Check whether all the expected last-packet  flags have been seen for the given CCD side.
+
+        Args:
+            - ccd_number: CCD from which the last received data originates (1-4).
+            - ccd_side: CCD side from which the last received data originates.
+
+        Returns: True if the actual and the expected last-packet flags match for the given CCD side of the given CCD;
+                 False otherwise.
+        """
+
+        received_last_packet_flags = self.received_last_packet_flags[ccd_number]
+
+        if ccd_side == self.fee_side.E_SIDE:
+
+            return received_last_packet_flags[0] == self.expected_last_packet_flags[0] \
+                   and received_last_packet_flags[2] == self.expected_last_packet_flags[2]
+
+        elif ccd_side == self.fee_side.F_SIDE:
+
+            return received_last_packet_flags[1] == self.expected_last_packet_flags[1] \
+                   and received_last_packet_flags[3] == self.expected_last_packet_flags[3]
+
+        return False
+
+    def assemble_slice(self, ccd_number: int, ccd_side):
+        """ Assemble the data for the given CCD and write it to FITS.
+
+        Args:
+            - ccd_number: CCD identifier (1/2/3/4).
+        """
+
+        # Windowing (pattern) mode
+
+        if self.is_windowing_mode:
+
+            # self.assemble_slice_windowing_mode(ccd_number, ccd_side)
+            pass
+
+        # Full-image (pattern) mode
+
+        else:
+
+            self.assemble_slice_full_image_mode(ccd_number, ccd_side)
+
+    # def assemble_slice_windowing_mode(self, ccd_number: int):
+    #     """ Assemble the data for the given CCD and write it to FITS, for windowing mode or windowing pattern mode.
+    #
+    #     This consists of the following steps:
+    #
+    #         - Create a 1D array, filled with NaNs, exactly big enough to fit the image and scan maps;
+    #         - Insert the data that was acquired (i.e. coming from the windows);
+    #         - Convert the 1D data arrays to a 2D data array, in which the image and the scan maps are still glued
+    #           together (do this for each transmitted CCD side);
+    #         - Extract for each transmitted CCD side the different regions from the 2D array (image, serial pre-scan,
+    #           serial over-scan, and parallel over-scan);
+    #         - Append the serial pre-scan of the transmitted CCD side(s) to the FITS file (after completing its header);
+    #         - Append the serial over-scan of the transmitted CCD side(s) to the FITS file (after completing its header),
+    #           if present;
+    #         - In case the F-side is transmitted, flips its image and parallel over-scan horizontally;
+    #         - In case both sides are transmitted, stitch the two sides together for the image and the parallel
+    #           over-scan;
+    #         - Append the parallel over-scan to the FITS file (after completing its header), if present;
+    #         - Append the image to the FITS file (after completing its header).
+    #
+    #     Args:
+    #         - ccd_number: CCD identifier (1/2/3/4).
+    #     """
+    #
+    #     num_rows = self.v_end - self.v_start + 1
+    #     num_columns = self.h_end + 1
+    #
+    #     num_rows_image = min(CCD_SETTINGS.NUM_ROWS - 1, self.v_end) - self.v_start + 1
+    #     num_rows_parallel_overscan = max(0, num_rows - num_rows_image)
+    #
+    #     image = np.array([]).reshape(num_rows_image, 0)
+    #     parallel_overscan = np.array([]).reshape(num_rows_parallel_overscan, 0)
+    #
+    #     for ccd_side in fee_side:
+    #
+    #         if ccd_side in self.data_arrays:
+    #
+    #             data_array = np.array([float("nan")] * (num_rows * num_columns))
+    #             data_array[self.windows[ccd_side][ccd_number]] = self.data_arrays[ccd_side][ccd_number]
+    #
+    #             side_image, side_serial_prescan, side_serial_overscan, side_parallel_overscan = \
+    #                 self.extract_full_image_mode(data_array)
+    #
+    #             # Serial pre-scan
+    #
+    #             self.append_serial_prescan(side_serial_prescan, ccd_number, ccd_side)
+    #
+    #             # Serial over-scan
+    #
+    #             if self.has_serial_overscan:
+    #
+    #                 self.append_serial_overscan(side_serial_overscan, ccd_number, ccd_side)
+    #
+    #             # For the F-side, the image and parallel over-scan must be flipped horizontally
+    #
+    #             if ccd_side == fee_side.F_SIDE:
+    #
+    #                 side_image, side_parallel_overscan = self.flip_f_side_full_image_mode(side_image,
+    #                                                                                       side_parallel_overscan)
+    #
+    #             # Image (the part that is on this side)
+    #
+    #             image = np.hstack([image, side_image])
+    #
+    #             # Parallel over-scan (the part that is on this side)
+    #
+    #             if self.has_parallel_overscan:
+    #
+    #                 parallel_overscan = np.hstack([parallel_overscan, side_parallel_overscan])
+    #
+    #     # Parallel over-scan
+    #
+    #     if self.has_parallel_overscan:
+    #
+    #         self.append_parallel_overscan(parallel_overscan, ccd_number)
+    #
+    #     # Image
+    #
+    #     self.append_image(image, ccd_number)
+
+    def assemble_slice_full_image_mode(self, ccd_number: int, ccd_side):
+        """ Assemble the data for the given CCD and write it to FITS, for full-image mode or full-image pattern mode.
+
+        This consists of the following steps:
+
+            - Convert the 1D data arrays to a 2D data array, in which the image and the scan maps are still glued
+              together (do this for each transmitted CCD side);
+            - Extract for each transmitted CCD side the different regions from the 2D array (image, serial pre-scan,
+              serial over-scan, and parallel over-scan);
+            - Append the serial pre-scan of the transmitted CCD side(s) to the FITS file (after completing its header);
+            - Append the serial over-scan of the transmitted CCD side(s) to the FITS file (after completing its header),
+              if present;
+            - In case the F-side is transmitted, flips its image and parallel over-scan horizontally;
+            - In case both sides are transmitted, stitch the two sides together for the image and the parallel
+              over-scan;
+            - Append the parallel over-scan to the FITS file (after completing its header), if present;
+            - Append the image to the FITS file (after completing its header).
+
+        Args:
+            - ccd_number: CCD identifier (1/2/3/4).
+        """
+
+        num_rows = self.v_end - self.v_start + 1
+        num_columns = self.h_end + 1
+
+        # Re-shape the 1D array to a 2D array and extract the image and scan maps
+
+        try:
+            data_array = np.reshape(self.data_arrays[ccd_side][ccd_number], (num_rows, num_columns))    # 1D -> 2D
+        except ValueError as exc:
+            raise MissingSpWPacketsError(f"Incomplete SpW data for frame {self.frame_number[ccd_number][ccd_side]} "
+                                         f"for the {ccd_side.name[0]}-side off CCD{ccd_number}.  Check the DPU "
+                                         f"Processing logs for more information.") from exc
+        side_image, side_serial_prescan, side_serial_overscan, side_parallel_overscan = \
+            self.extract_full_image_mode(data_array)
+
+        # Serial pre-scan
+
+        self.append_serial_prescan(side_serial_prescan, ccd_number, ccd_side)
+
+        # Serial over-scan
+
+        if self.has_serial_overscan:
+
+            self.append_serial_overscan(side_serial_overscan, ccd_number, ccd_side)
+
+        # Parallel over-scan
+
+        if self.has_parallel_overscan:
+
+            self.append_parallel_overscan(side_parallel_overscan, ccd_number, ccd_side)
+
+        # Image
+
+        self.append_image(side_image, ccd_number, ccd_side)
+
+    def extract_full_image_mode(self, data_array):
+        """Extract the image and scan maps from the given data array.
+
+        For the F-side, the image and parallel over-scan still have to be flipped horizontally.
+
+        Args:
+            - data_array: 2D array in which the image data and scan maps are still glued together.
+
+        Returns:
+            - Image data;
+            - Serial pre-scan;
+            - Serial over-scan;
+            - Parallel over-scan.
+        """
+
+        # Calculate the following indices:
+        #   - Column index of the first transmitted image column;
+        #   - Column index of the last transmitted image column + 1 (if the serial over-scan is transmitted, this will
+        #     be the column index of the first transmitted serial over-scan column);
+        #   - Row index of the last transmitted image row + 1 (if the parallel over-scan is transmitted, this will be
+        #     the row index of the first transmitted parallel over-scan row).
+
+        start_column_image = CCD_SETTINGS.LENGTH_SERIAL_PRESCAN
+        end_column_image_plus_1 = min(CCD_SETTINGS.LENGTH_SERIAL_PRESCAN + CCD_SETTINGS.NUM_COLUMNS // 2, self.h_end + 1)
+        end_row_image_plus_1 = min(CCD_SETTINGS.NUM_ROWS - 1, self.v_end) - self.v_start + 1
+
+        # Serial pre-scan (all rows, but only the first couple of rows)
+
+        serial_prescan = data_array[:, 0: start_column_image]
+
+        # Serial over-scan (all rows, omit the columns from the serial pre-scan and the serial over-scan)
+
+        if self.has_serial_overscan:
+
+            serial_overscan = data_array[:, end_column_image_plus_1:]
+
+        else:
+
+            serial_overscan = None
+
+        # Image (omit the rows from the parallel over-scan
+        # and the columns from the serial pre-scan and the serial over-scan)
+
+        image = data_array[0: end_row_image_plus_1, start_column_image: end_column_image_plus_1]
+
+        # Parallel over-scan
+
+        if self.has_parallel_overscan:
+
+            parallel_overscan = data_array[end_row_image_plus_1:, start_column_image: end_column_image_plus_1]
+
+        else:
+
+            parallel_overscan = None
+
+        return image, serial_prescan, serial_overscan, parallel_overscan
+
+    def append_serial_prescan(self, serial_prescan, ccd_number: int, ccd_side: str):
+        """ Append the given serial pre-scan to the FITS file (after completing its header).
+
+        Args:
+            - serial_prescan: Serial pre-scan.
+            - ccd_number: CCD identifier.
+            - ccd_side: CCD side.
+        """
+
+        extension = f"SPRE_{ccd_number}_{self.fee_side(ccd_side).name[0]}"
+        self.serial_prescan_header["EXTNAME"] = extension
+        self.serial_prescan_header["EXTVER"] = self.frame_number[ccd_number][ccd_side]
+        self.serial_prescan_header["CCD_ID"] = (ccd_number, "CCD identifier",)
+        self.serial_prescan_header["SENSOR_SEL"] = (self.fee_side(ccd_side).name[0], "CCD side")
+        self.serial_prescan_header["DATE-OBS"] = (self.timestamp, "Timestamp for 1st frame",)
+        self.serial_prescan_header["FINETIME"] = (self.finetime, "Finetime representation of DATE-OBS",)
+
+        if ccd_side in [self.fee_side.RIGHT_SIDE.name, self.fee_side.RIGHT_SIDE]:
+            serial_prescan = np.fliplr(serial_prescan)
+
+        fits.append(str(self._filepath), serial_prescan, self.serial_prescan_header)
+
+    def append_serial_overscan(self, serial_overscan, ccd_number: int, ccd_side: str):
+        """ Append the given serial over-scan to the FITS file (after completing its header).
+
+        Args:
+            - serial_overscan: Serial over-scan.
+            - ccd_number: CCD identifier.
+            - ccd_side: CCD side.
+        """
+
+        extension = f"SOVER_{ccd_number}_{self.fee_side(ccd_side).name[0]}"
+        self.serial_overscan_header["EXTNAME"] = extension
+        self.serial_overscan_header["EXTVER"] = self.frame_number[ccd_number][ccd_side]
+        self.serial_overscan_header["CCD_ID"] = (ccd_number, "CCD identifier",)
+        self.serial_overscan_header["SENSOR_SEL"] = (self.fee_side(ccd_side).name[0], "CCD side")
+        self.serial_overscan_header["NAXIS1"] = (serial_overscan.shape[1], "Number of columns in the serial over-scan",)
+        self.serial_overscan_header["DATE-OBS"] = (self.timestamp, "Timestamp for 1st frame",)
+        self.serial_overscan_header["FINETIME"] = (self.finetime, "Finetime representation of DATE-OBS")
+
+        if ccd_side in [self.fee_side.RIGHT_SIDE.name, self.fee_side.RIGHT_SIDE]:
+            serial_overscan = np.fliplr(serial_overscan)
+
+        fits.append(str(self._filepath), serial_overscan, self.serial_overscan_header)
+
+    def append_parallel_overscan(self, parallel_overscan, ccd_number: int, ccd_side: str):
+        """ Append the given parallel over-scan to the FITS file (after completing its header).
+
+        Args:
+            - parallel_overscan: Parallel over-scan.
+            - ccd_number: CCD identifier.
+            - ccd_side: CCD side.
+        """
+
+        extension = f"POVER_{ccd_number}_{self.fee_side(ccd_side).name[0]}"
+        self.parallel_overscan_header["EXTNAME"] = extension
+        self.parallel_overscan_header["EXTVER"] = self.frame_number[ccd_number][ccd_side]
+        self.parallel_overscan_header["CCD_ID"] = (ccd_number, "CCD identifier",)
+        self.parallel_overscan_header["SENSOR_SEL"] = (self.fee_side(ccd_side).name[0], "CCD side")
+        self.parallel_overscan_header["NAXIS1"] = (parallel_overscan.shape[1],
+                                                   "Number of columns in the parallel over-scan",)
+        self.parallel_overscan_header["DATE-OBS"] = (self.timestamp, "Timestamp for 1st frame",)
+        self.parallel_overscan_header["FINETIME"] = (self.finetime, "Finetime representation of DATE-OBS",)
+
+        if ccd_side in [self.fee_side.RIGHT_SIDE.name, self.fee_side.RIGHT_SIDE]:
+            parallel_overscan = np.fliplr(parallel_overscan)
+
+        fits.append(str(self._filepath), parallel_overscan, self.parallel_overscan_header)
+
+    def append_image(self, image, ccd_number: int, ccd_side: str):
+        """ Append the given image to the FITS file (after completing its header).
+
+        Args:
+            - image: Image.
+            - ccd_number: CCD identifier (1/2/3/4).
+            - ccd_side: CCD side.
+        """
+
+        extension = f"IMAGE_{ccd_number}_{self.fee_side(ccd_side).name[0]}"
+        self.image_header["EXTNAME"] = extension
+        self.image_header["EXTVER"] = self.frame_number[ccd_number][ccd_side]
+        self.image_header["CCD_ID"] = (ccd_number, "CCD identifier",)
+        self.image_header["SENSOR_SEL"] = (self.fee_side(ccd_side).name[0], "CCD side")
+        self.image_header["NAXIS1"] = (image.shape[1], "Number of columns in the image",)
+
+        ccd_orientation_degrees = CCD_SETTINGS.ORIENTATION[ccd_number - 1]
+        ccd_orientation_radians = radians(ccd_orientation_degrees)
+
+        self.image_header["CROTA2"] = (ccd_orientation_degrees, "CCD orientation angle [degrees]",)
+
+        cdelt = CCD_SETTINGS["PIXEL_SIZE"] / 1000.0  # Pixel size [mm]
+
+        self.image_header["CD1_1"] = (cdelt * cos(ccd_orientation_radians),
+                                      "Pixel size x cos(CCD orientation angle)",)
+        self.image_header["CD1_2"] = (-cdelt * sin(ccd_orientation_radians),
+                                      "-Pixel size x sin(CCD orientation angle)",)
+        self.image_header["CD2_1"] = (cdelt * sin(ccd_orientation_radians),
+                                      "Pixel size x sin(CCD orientation angle)",)
+        self.image_header["CD2_2"] = (cdelt * cos(ccd_orientation_radians),
+                                      "Pixel size x cos(CCD orientation angle)",)
+
+        zeropoint_x, zeropoint_y = -np.array(CCD_SETTINGS.ZEROPOINT)
+        crval1 = zeropoint_x * cos(ccd_orientation_radians) - zeropoint_y * sin(ccd_orientation_radians)
+        crval2 = zeropoint_x * sin(ccd_orientation_radians) + zeropoint_y * cos(ccd_orientation_radians)
+
+        self.image_header["CRVAL1"] = (crval1, "FP x-coordinate of the CCD origin [mm]",)
+        self.image_header["CRVAL2"] = (crval2, "FP y-coordinate of the CCD origin [mm]",)
+
+        self.image_header["CRPIX2"] = (-self.v_start,
+                                       "CCD origin row wrt 1st transmitted row",)
+
+        if ccd_side in [self.fee_side.LEFT_SIDE.name, self.fee_side.LEFT_SIDE]:
+            self.image_header["CRPIX1"] = (0, "CCD origin column wrt lower left corner",)
+
+        if ccd_side in [self.fee_side.RIGHT_SIDE.name, self.fee_side.RIGHT_SIDE]:
+            image = np.fliplr(image)
+            self.image_header["CRPIX1"] = (-CCD_SETTINGS.NUM_ROWS + image.shape[1],
+                                           "CCD origin column wrt lower left corner")
+
+        self.image_header["DATE-OBS"] = (self.timestamp, "Timestamp for 1st frame",)
+        self.image_header["FINETIME"] = (self.finetime, "Finetime representation of DATE-OBS",)
+
+        fits.append(str(self._filepath), image, self.image_header)
+
+    def read(self, select=None):
+        """Returns a list of all entries in the persistence store.
+
+        The list can be filtered based on a selection from the `select` argument which
+        should be a Callable object.
+
+        Args:
+            - select (Callable): a filter function to narrow down the list of all entries.
+
+        Returns: List or generator for all entries in the persistence store.
+        """
+        raise NotImplementedError("Persistence layers must implement a read method")
+
+    def update(self, idx, data):
+
+        pass
+
+    def delete(self, idx):
+
+        LOGGER.warning("The delete functionality is not implemented for the CSV persistence layer.")
+
+    def get_filepath(self):
+
+        return self._filepath

plato_fits-2024.1.4.dist-info/METADATA

@@ -0,0 +1,20 @@
+Metadata-Version: 2.4
+Name: plato-fits
+Version: 2024.1.4
+Summary: FITS Persistence implementation for CGSE
+Author: IVS KU Leuven
+Maintainer-email: Rik Huygen <rik.huygen@kuleuven.be>, Sara Regibo <sara.regibo@kuleuven.be>
+License-Expression: MIT
+Keywords: CGSE,Common-EGSE,hardware testing,software framework
+Requires-Python: >=3.9
+Requires-Dist: astropy>=6.0.1
+Requires-Dist: cgse-common
+Requires-Dist: numpy==1.22.4
+Requires-Dist: plato-spw
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-mock; extra == 'test'
+Description-Content-Type: text/markdown
+
+# FITS plugin for the CGSE storage manager

plato_fits-2024.1.4.dist-info/RECORD

@@ -0,0 +1,5 @@
+egse/plugins/storage/fits.py,sha256=GlZSXCaFIihCKOj0dALcbzjeBcucxtImKGMtniFIvVk,56994
+plato_fits-2024.1.4.dist-info/METADATA,sha256=acPLE0vaArGKQCu0MH9JeA2_eUe1kpUK6OlO3J9xGDs,674
+plato_fits-2024.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+plato_fits-2024.1.4.dist-info/entry_points.txt,sha256=q-XB-6IMXSeoxPNRDU-EFHgAyI0K6GzujNAyEdrp3zM,115
+plato_fits-2024.1.4.dist-info/RECORD,,

plato_fits-2024.1.4.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

plato_fits-2024.1.4.dist-info/entry_points.txt

@@ -0,0 +1,5 @@
+[cgse.storage.persistence]
+FITS = egse.plugins.storage.fits:FITS
+
+[cgse.version]
+plato-fits = egse.storage.plugins