Implemented image compression via JPEG-LS

environment.yml

@@ -18,5 +18,6 @@ dependencies:
   - netCDF4=1.6.0
   - h5netcdf=1.1.0
   - bottleneck=1.3.7
+  - pillow-jpls=1.2.0
 
 prefix: ~/anaconda3

requirements.txt

@@ -10,4 +10,5 @@ seaborn==0.11
 xarray==2022.6.0
 netCDF4==1.6.0
 h5netcdf==1.1.0
-bottleneck==1.3.7
+bottleneck==1.3.7
+pillow-jpls==1.2.0

suncet_instrument_simulator/config_files/config_default.ini

@@ -7,11 +7,13 @@ apply_psf = True
 apply_scattered_light_psf = False
 # Subtract a dark frame with onboard software
 subtract_dark_onboard = True
+# Compress images or not (uses JPEG-LS)
+compress_image = True
 # Select timesteps to work on [first, last, step]
 timesteps_to_process = [1, 500, 1]
 # Directory name for simulator run
-model_directory_name = /mhd/bright_fast/
-# Director for EM Maps
+model_directory_name = /mhd/bright_fast/ # TODO: Move these to the "structure" section
+# Directory for EM Maps
 em_directory_name = /em_maps/
 # Directory name for saved maps
 map_directory_name = /rendered_euv_maps/

suncet_instrument_simulator/config_parser.py

@@ -19,6 +19,7 @@ def __init__(self, filename):
         self.apply_psf = config['behavior'].getboolean('apply_psf')
         self.apply_scattered_light_psf = config['behavior'].getboolean('apply_scattered_light_psf')
         self.subtract_dark = config['behavior'].getboolean('subtract_dark_onboard')
+        self.compress_image = config['behavior'].getboolean('compress_image')
         self.timesteps_to_process = json.loads(config.get('behavior', 'timesteps_to_process'))
         self.model_directory_name = config['behavior']['model_directory_name']
         self.em_directory_name = config['behavior']['em_directory_name']

suncet_instrument_simulator/instrument.py

@@ -11,6 +11,7 @@
 from astropy.coordinates import SkyCoord
 from astropy import constants as const
 import sunpy.map
+from pillow_jpls import Image
 from sunpy.coordinates import frames
 from suncet_instrument_simulator import config_parser # This is just for running as a script -- should delete when done testing
 
@@ -451,6 +452,26 @@ def bin_image(self, onboard_processed_images, xbin=None, ybin=None):
             onboard_processed_images.meta['cdelt2'] = self.config.plate_scale.value * ybin # Note 2: there is also risk here because a) the user must be responsible in the config file to ensure the image_dimensions and plate_scale are compatible, and b) the units they input for plate_scale must be the same as those already in the map
 
         return onboard_processed_images
+
+    def compress_image(self, onboard_processed_images): 
+        normalized_data = (onboard_processed_images.data - np.min(onboard_processed_images.data)) / (np.max(onboard_processed_images.data) - np.min(onboard_processed_images.data))
+        max_value = 2**self.config.readout_bits.value - 1
+
+        if self.config.readout_bits <= (8 * u.bit):
+            dtype = np.uint8
+            mode = 'L'
+        elif self.config.readout_bits <= (16 * u.bit): # if readout_bits is, e.g., 12 or 14, we've scaling accordingly and just won't use the excess bits in these standard numpy containers (8, 16, 32)
+            dtype = np.uint16
+            mode = 'I;16'
+        elif self.config.readout_bits <= (32 * u.bit):
+            dtype = np.uint32
+            mode = 'I'
+        else:
+            raise ValueError("Unsupported bit depth")
+
+        scaled_data = (normalized_data * max_value).astype(dtype)
+        image = Image.fromarray(scaled_data, mode=mode)
+        return sunpy.map.Map(np.array(image), onboard_processed_images.meta)
 
 
 

suncet_instrument_simulator/simulator.py

@@ -105,6 +105,8 @@ def __apply_camera_software(self):
         self.onboard_processed_images = self.onboard_software.filter_out_particle_hits(self.onboard_processed_images)
         self.onboard_processed_images = self.onboard_software.create_composite(self.onboard_processed_images)
         self.onboard_processed_images = self.onboard_software.bin_image(self.onboard_processed_images)
+        if self.config.compress_image:
+            self.onboard_processed_images = self.onboard_software.compress_image(self.onboard_processed_images)
 
 
     def __calculate_snr(self):