utils and baselines

utils/__init__.py

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+from .create_splits import *

utils/eval_baselines.py

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+"""
+Runs several baseline compression algorithms and stores results for each FITS file in a csv.
+This code is written functionality-only and cleaning it up is a TODO.
+"""
+
+
+import os
+import re
+from pathlib import Path
+import argparse
+import os.path
+from astropy.io import fits
+import numpy as np
+from time import time
+import pandas as pd
+from tqdm import tqdm
+
+from astropy.io.fits import CompImageHDU
+from imagecodecs import (
+    jpeg2k_encode, 
+    jpeg2k_decode, 
+    jpegls_encode, 
+    jpegls_decode, 
+    jpegxl_encode,
+    jpegxl_decode,
+    rcomp_encode,
+    rcomp_decode,
+)
+
+# Functions that require some preset parameters. All others default to lossless.
+
+jpegxl_encode_max_effort_preset = lambda x: jpegxl_encode(x, lossless=True, effort=9)
+jpegxl_encode_preset = lambda x: jpegxl_encode(x, lossless=True)
+
+def find_matching_files():
+    """
+    Returns list of test set file paths.
+    """
+    df = pd.read_json("./splits/full_test.jsonl", lines=True)
+    return list(df['image'])
+
+def benchmark_imagecodecs_compression_algos(arr, compression_type):
+
+    encoder, decoder = ALL_CODECS[compression_type]
+
+    write_start_time = time()
+    encoded = encoder(arr)
+    write_time = time() - write_start_time
+
+    read_start_time = time()
+    if compression_type == "RICE":
+        decoded = decoder(encoded, shape=arr.shape, dtype=np.uint16)
+    else:
+        decoded = decoder(encoded)
+    read_time = time() - read_start_time
+
+    assert np.array_equal(arr, decoded)
+
+    buflength = len(encoded)
+
+    return {compression_type + "_BPD": buflength / arr.size,
+            compression_type + "_WRITE_RUNTIME": write_time,
+            compression_type + "_READ_RUNTIME": read_time,
+            #compression_type + "_TILE_DIVISOR": np.nan,
+           }
+
+def main(dim):
+
+    save_path = f"baseline_results_{dim}.csv"
+
+    file_paths = find_matching_files()
+    
+    df = pd.DataFrame(columns=columns, index=[str(p) for p in file_paths])
+    
+    print(f"Number of files to be tested: {len(file_paths)}")
+    
+    ct = 0
+
+    for path in tqdm(file_paths):
+        for hdu_idx in [1, 4]:
+            with fits.open(path) as hdul:
+                if dim == '2d':
+                    arr = hdul[hdu_idx].data
+                else:
+                    raise RuntimeError(f"{dim} not applicable.")
+
+            ct += 1
+            if ct % 10 == 0:
+                print(df.mean())
+                df.to_csv(save_path)
+
+            for algo in ALL_CODECS.keys():
+                try:
+                    if algo == "JPEG_2K" and dim != '2d':
+                        test_results = benchmark_imagecodecs_compression_algos(arr.transpose(1, 2, 0), algo)
+                    else:
+                        test_results = benchmark_imagecodecs_compression_algos(arr, algo)
+
+                    for column, value in test_results.items():
+                        if column in df.columns:
+                            df.at[path + f"_hdu{hdu_idx}", column] = value
+
+                except Exception as e:
+                    print(f"Failed at {path} under exception {e}.")
+            
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Process some 2D or 3D data.")
+    parser.add_argument(
+        "dimension", 
+        choices=['2d'],
+        help="Specify whether the data is 2d, or; not applicable here: 3dt (3d time dimension), or 3dw (3d wavelength dimension)."
+    )
+    args = parser.parse_args()
+    dim = args.dimension.lower()
+    
+    # RICE REQUIRES UNIQUE INPUT OF ARR SHAPE AND DTYPE INTO DECODER
+
+    ALL_CODECS = {
+        "JPEG_XL_MAX_EFFORT": [jpegxl_encode_max_effort_preset, jpegxl_decode],
+        "JPEG_XL": [jpegxl_encode_preset, jpegxl_decode],
+        "JPEG_2K": [jpeg2k_encode, jpeg2k_decode], 
+        "JPEG_LS": [jpegls_encode, jpegls_decode],
+        "RICE": [rcomp_encode, rcomp_decode],
+    }
+
+    columns = []
+    for algo in ALL_CODECS.keys():
+        columns.append(algo + "_BPD")
+        columns.append(algo + "_WRITE_RUNTIME")
+        columns.append(algo + "_READ_RUNTIME")
+        #columns.append(algo + "_TILE_DIVISOR")
+        
+    main(dim)