Merge pull request #29 from jurjen93/refactor

Refactor
jurjen93 · Oct 17, 2024 · b7420d6 · b7420d6
2 parents 9401361 + 9da7124
commit b7420d6
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Showing 39 changed files with 693 additions and 3,351 deletions.
diff --git a/__init__.py b/__init__.py
diff --git a/catalogue_helpers/__init__.py b/catalogue_helpers/__init__.py
diff --git a/catalogue_helpers/find_sources.py b/catalogue_helpers/find_sources.py
diff --git a/catalogue_helpers/run_pybdsf.py → ..._helpers/pybdsf_experiments/run_pybdsf.py b/catalogue_helpers/run_pybdsf.py → ..._helpers/pybdsf_experiments/run_pybdsf.py
diff --git a/ds9_helpers/__init__.py b/ds9_helpers/__init__.py
diff --git a/ds9_helpers/select_facets.py b/ds9_helpers/select_facets.py
diff --git a/ds9_helpers/split_polygon_facets.py b/ds9_helpers/split_polygon_facets.py
@@ -143,9 +143,9 @@ def main():
     H.close()
 
     #TODO: dangerous! Convert to degrees
-    if np.all(np.abs(dirs)<2*np.pi):
-        dirs %= (2*np.pi)
-        dirs *= 360/(2*np.pi)
+    if np.all(np.abs(dirs) < 2 * np.pi):
+        # Converting radians to degrees
+        dirs = np.degrees(dirs)
 
     f = open('polygon_info.csv', 'w')
     writer = csv.writer(f)

diff --git a/fits_helpers/__init__.py b/fits_helpers/__init__.py
diff --git a/fits_helpers/crop_nan_boundaries.py b/fits_helpers/crop_nan_boundaries.py
@@ -43,14 +43,18 @@ def parse_args():
     :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)
+    parser.add_argument('fits_in', help='fits input file', type=str)
+    parser.add_argument('--output_name', help='fits output file', type=str)
     return parser.parse_args()
 
 def main():
     """ Main function"""
     args = parse_args()
-    crop_nan_boundaries(args.fits_input, args.fits_output)
+    if args.output_name is None:
+        outname = args.fits_in
+    else:
+        outname = args.output_name
+    crop_nan_boundaries(args.fits_in, outname)
 
 if __name__ == '__main__':
     main()
diff --git a/fits_helpers/cropy_2048.py b/fits_helpers/cropy_2048.py
@@ -1,5 +1,10 @@
+"""
+Crop image to 2048x2048 (for neural network)
+"""
+
 from astropy.io import fits
 import numpy as np
+from argparse import ArgumentParser
 
 
 def crop_fits_image(input_filename, output_filename, center=None):
@@ -55,3 +60,22 @@ def crop_fits_image(input_filename, output_filename, center=None):
         # Write the cropped image to the output file
         hdu = fits.PrimaryHDU(data=np.array([[cropped_data]]), header=header)
         hdu.writeto(output_filename, overwrite=True)
+
+
+def parse_args():
+    """
+    Command line argument parser
+    :return: parsed arguments
+    """
+    parser = ArgumentParser(description='Crop image to 2048x2048')
+    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_fits_image(args.fits_input, args.fits_output)
+
+if __name__ == '__main__':
+    main()
diff --git a/fits_helpers/cut_fitsfile.py → fits_helpers/cut_fits_with_region.py b/fits_helpers/cut_fitsfile.py → fits_helpers/cut_fits_with_region.py
@@ -12,8 +12,8 @@ def parse_args():
     :return: parsed arguments
     """
     parser = ArgumentParser(description='Cut fits file with region file')
-    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)
+    parser.add_argument('fits_input', help='fits input file', type=str)
+    parser.add_argument('--output_name', help='fits output file', type=str)
     parser.add_argument('--region', help='region file', required=True, type=str)
     return parser.parse_args()
 
@@ -24,7 +24,9 @@ def main():
 
     fitsfile = args.fits_input
     regionfile = args.region
-    outputfits = args.fits_output
+    outputfits = args.output_name
+    if outputfits is None:
+        outputfits = fitsfile
 
     hdu = fits.open(fitsfile)
 

diff --git a/fits_helpers/get_beam_rms_facet.py b/fits_helpers/get_beam_rms_facet.py
diff --git a/fits_helpers/make_cutouts.py → fits_helpers/image_utils/make_cutouts.py b/fits_helpers/make_cutouts.py → fits_helpers/image_utils/make_cutouts.py
diff --git a/fits_helpers/power_spec_simple.py → ..._helpers/image_utils/power_spec_simple.py b/fits_helpers/power_spec_simple.py → ..._helpers/image_utils/power_spec_simple.py
diff --git a/fits_helpers/plot_baseline_track.py b/fits_helpers/plot_baseline_track.py
diff --git a/h5_helpers/__init__.py b/h5_helpers/__init__.py