chunking bug fix

fits_helpers/crop_nan_boundaries.py

@@ -0,0 +1,56 @@
+import numpy as np
+from astropy.io import fits
+from argparse import ArgumentParser
+
+def crop_nan_boundaries(fits_in, fits_out):
+    """
+    Crop nan boundaries
+
+    input:
+        - fits_in: input fits file
+        - fits_out: output fits file
+    """
+
+    with fits.open(fits_in) as hdul:
+        image_data = hdul[0].data
+        header = hdul[0].header
+
+    mask = ~np.isnan(image_data)
+    non_nan_indices = np.where(mask)
+
+    ymin, ymax = non_nan_indices[0].min(), non_nan_indices[0].max()
+    xmin, xmax = non_nan_indices[1].min(), non_nan_indices[1].max()
+
+    print(f"Original shape {image_data.shape}")
+    print(ymin, ymax)
+    print(xmin, xmax)
+
+    cropped_image = image_data[ymin:ymax + 1, xmin:xmax + 1]
+
+    header['NAXIS1'] = cropped_image.shape[1]
+    header['NAXIS2'] = cropped_image.shape[0]
+    header['CRPIX1'] -= xmin
+    header['CRPIX2'] -= ymin
+
+    print(f"New shape {cropped_image.shape}")
+
+    hdu = fits.PrimaryHDU(cropped_image, header=header)
+    hdu.writeto(fits_out, overwrite=True)
+
+def parse_args():
+    """
+    Command line argument parser
+    :return: parsed arguments
+    """
+    parser = ArgumentParser(description='Crop fits file with nan boundaries')
+    parser.add_argument('--fits_input', help='fits input file', required=True, type=str)
+    parser.add_argument('--fits_output', help='fits output file', required=True, type=str)
+    return parser.parse_args()
+
+def main():
+    """ Main function"""
+    args = parse_args()
+    crop_nan_boundaries(args.fits_input, args.fits_output)
+
+if __name__ == '__main__':
+    main()