Merge pull request #201 from simontorres/add_gracefull_exit__fix_keyw…

…ords

Add gracefull exit  fix keywords

environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - pandas
   - matplotlib
   - scipy
-  - cython
+  - cython=0.26.1
   - astropy>3
   - pip
   - pip:

pipeline/core/__init__.py

@@ -21,6 +21,7 @@
                    extraction,
                    extract_fractional_pixel,
                    extract_optimal,
+                   fix_keywords,
                    fractional_sum,
                    get_best_flat,
                    get_central_wavelength,

pipeline/core/core.py

@@ -853,6 +853,26 @@ def extract_optimal():
     raise NotImplementedError
 
 
+def fix_keywords(path, pattern='*.fits'):
+    """Fix FITS uncompliance of some keywords
+
+    Uses automatic header fixing by :class:`~astropy.nddata.CCDData`. Note that
+    this only fixes FITS compliance.
+
+    Args:
+        path (str): Path to raw data
+        pattern (str): Search pattern for listing file in path.
+
+    """
+    file_list = glob.glob(os.path.join(path, pattern))
+    for _file in file_list:
+        log.info("Fixing file {:s}".format(_file))
+        ccd = CCDData.read(_file, unit='adu')
+
+        ccd.write(_file, overwrite=True)
+        log.info("Fix succeeded!")
+
+
 def fractional_sum(data, index, low_limit, high_limit):
     """Performs a fractional pixels sum
 

pipeline/images/data_classifier.py

@@ -1,8 +1,12 @@
 from __future__ import (absolute_import, division, print_function,
                         unicode_literals)
 import os
+import sys
 import logging
+
+from astropy.io.fits.verify import VerifyError
 from ccdproc import ImageFileCollection
+from ..core import fix_keywords
 
 
 class DataClassifier(object):
@@ -50,8 +54,20 @@ def __call__(self, raw_path):
         self.raw_path = raw_path
 
         # define the ImageFileCollection instance right away.
-        # todo add try/except astropy.io.fits.verify.VerifyError: clean exit
-        ifc = ImageFileCollection(self.raw_path)
+
+        try:
+            ifc = ImageFileCollection(self.raw_path)
+
+        except VerifyError as error:
+            self.log.error("Raised VerifyError: {:}".format(error))
+            self.log.critical("Some keywords are not FITS compliant. Trying "
+                              "to fix the headers.")
+
+            fix_keywords(path=self.raw_path)
+
+            self.log.info("Headers have been fixed, please rerun the pipeline!")
+            sys.exit()
+
         self.image_collection = ifc.summary.to_pandas()
 
         self.objects_collection = self.image_collection[

pipeline/version.py

@@ -1,2 +1,2 @@
 # This is an automatic generated file please do not edit
-__version__ = '1.1.0'
+__version__ = '1.1.1.dev1'

setup.cfg

@@ -24,4 +24,4 @@ edit_on_github = False
 github_project = soar-telescope/goodman
 # install_requires = astropy six gwcs scipy
 # version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
-version = 1.1.0
+version = 1.1.1.dev1