Make purpose of fix_file clearer

README.md

@@ -11,17 +11,24 @@ Processing scripts for Apertif Radio Transient System data
 `pip install arts_tools`
 
 ## Fixing archival FITS files
-FITS files retrieved from the Apertif Long-Term Archive (ALTA) from before 2020/04/08 can be made readable with `arts_fix_fits file.fits`. These fixes are applied:
+FITS files retrieved from the Apertif Long-Term Archive (ALTA) from before 2020/04/08 can be made readable with 
+`arts_fix_fits_from_before_20200408 file.fits`. These fixes are applied:
 1. The NAXIS2 value in the header is changed from zero to the correct value
 2. The data size is expressed in bytes instead of bits
-2. The frequency and time axes of the data are swapped
-3. The frequency order of the data and weights, scales, offsets, and frequencies columns is flipped
+3. The frequency and time axes of the data are swapped
+4. The frequency order of the data and weights, scales, offsets, and frequencies columns is flipped
 
-By default, the script appends `_fixed` to the filename. Run `arts_fix_fits -h` for more options.
+By default, the script appends `_fixed` to the filename. Run `arts_fix_fits_from_before_20200408 -h` for more options.
+
+#### Note for Science Verification Campaign data
+Data from the SVC has a correct NAXIS2 value in some cases. However, the other fixes do need to be applied. 
+This can be forced by running `arts_fix_fits_from_before_20200408 --force file.fits`.
 
 ## Reading parametersets
-The FITS headers contain an encoded observation parameterset. To print the parameterset, use `arts_read_parameterset file.fits`. It can also be loaded in python as a dictionary with:
+The FITS headers contain an encoded observation parameterset. To print the parameterset, use 
+`arts_read_parameterset file.fits`. It can also be loaded in python as a dictionary with:
 ```python
 from arts_tools.fits.reader import read_parameterset
 parset = read_parameterset('/path/to/file.fits')
 ```
+Note that all values are read as strings.

arts_tools/fits/fix_file.py → arts_tools/fits/fix_file_from_before_20200408.py

@@ -144,9 +144,9 @@ def fix_header(header, naxis2, force=False):
     logging.debug("New header line: {}".format(new_line))
 
     # bit to bytes fix
-    # assume the old value is unique enough to appear anywhere else in the header
+    # assume the old value is unique enough to not appear anywhere else in the header
     old_value = '{}X'.format(NSAMP * NCHAN)
-    # new value has one space to make length the same as old value
+    # new value has a space at the end to make length the same as old value
     new_value = '{}B '.format(int((NCHAN * NSAMP) / 8))
     logging.debug("Replacing {} by {} in header".format(old_value, new_value))
     header_fixed = header_fixed.replace(old_value, new_value)
@@ -224,7 +224,14 @@ def write_file(fname, *args):
 
 def main():
     parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
-                                     description="Repair ARTS 1-bit FITS files")
+                                     description="Repair ARTS 1-bit FITS files. "
+                                     "These fixes are applied:\n"
+                                     "1. The NAXIS2 value in the header is changed from zero to the correct value\n"
+                                     "2. The data size is expressed in bytes instead of bits\n"
+                                     "3. The frequency and time axes of the data are swapped\n"
+                                     "4. The frequency order of the data and weights, scales, offsets, "
+                                     "and frequencies columns is flipped"
+                                     )
     parser.add_argument('--output', help="Output file "
                                          "(Default: input.fits -> input_fixed.fits)")
     parser.add_argument('--force', action='store_true', help="Apply fix even if FITS file seems good")

setup.py

@@ -21,7 +21,7 @@
       packages=find_packages(),
       install_requires=['numpy>=1.17',
                         'astropy'],
-      entry_points={'console_scripts': ['arts_fix_fits=arts_tools.fits.fix_file:main']},
+      entry_points={'console_scripts': ['arts_fix_fits_from_before_20200408=arts_tools.fits.fix_file_from_before_20200408:main']},
       scripts=scripts,
       classifiers=['License :: OSI Approved :: Apache Software License',
                    'Programming Language :: Python :: 3',