FITS Overwrite

scripts/python/merge_star_cat_mccd.py

@@ -210,8 +210,10 @@ def create_full_cat(input_dir, input_file_pattern, output_path, verbose=False):
         ccd_nb = list(starcat_j[1].data['CCD_ID_LIST'])
 
     # Prepare output FITS catalogue
-    output = sc.FITSCatalog(output_path,
-                            open_mode=sc.BaseCatalog.OpenMode.ReadWrite)
+    output = sc.FITSCatalog(
+        output_path,
+        open_mode=sc.BaseCatalog.OpenMode.ReadWrite
+    )
 
     # Collect columns
     # convert back to sigma for consistency
@@ -234,7 +236,7 @@ def create_full_cat(input_dir, input_file_pattern, output_path, verbose=False):
     # Write file
     if verbose:
         print('Writing full PSF catalog file {}...'.format(output_path))
-    output.save_as_fits(data)
+    output.save_as_fits(data, overwrite=True)
 
 
 def log_command(argv, name=None, close_no_return=True):

scripts/python/merge_star_cat_psfex.py

@@ -201,8 +201,10 @@ def create_full_cat(input_dir, input_file_pattern, output_path, verbose=False):
         ccd_nb += [re.split(r"\-([0-9]*)\-([0-9]+)\.", name)[-2]]*len(starcat_j[2].data['RA'])
 
     # Prepare output FITS catalogue
-    output = sc.FITSCatalog(output_path,
-                            open_mode=sc.BaseCatalog.OpenMode.ReadWrite)
+    output = sc.FITSCatalog(
+        output_path,
+        open_mode=sc.BaseCatalog.OpenMode.ReadWrite
+    )
 
     # Collect columns
     # convert back to sigma for consistency
@@ -216,7 +218,7 @@ def create_full_cat(input_dir, input_file_pattern, output_path, verbose=False):
     # Write file
     if verbose:
         print('Writing full PSF catalog file {}...'.format(output_path))
-    output.save_as_fits(data)
+    output.save_as_fits(data, overwrite=True)
 
 
 def main(argv=None):

scripts/python/stats_global.py

@@ -23,7 +23,7 @@
 
 from optparse import OptionParser
 
-import cfis
+import shapepipe.utilities.cfis as cfis
 
 
 def params_default():

shapepipe/modules/find_exposures_package/__init__.py

@@ -9,4 +9,3 @@
 """
 
 __all__ = ['find_exposures.py']
-

shapepipe/modules/split_exp_package/__init__.py

@@ -9,4 +9,3 @@
 """
 
 __all__ = ['split_exp_script.py']
-

shapepipe/modules/spread_model_package/spread_model.py

@@ -205,7 +205,7 @@ def process(self):
         skip_obj = False
         spread_model_final = []
         spread_model_err_final = []
-        for idx id_tmp in enumerate(obj_id):
+        for idx, id_tmp in enumerate(obj_id):
             sigma_list = []
 
             if psf_cat[str(id_tmp)] == 'empty':

shapepipe/pipeline/file_io.py

@@ -451,7 +451,7 @@ def open(self):
 
    # ------------------------------------------------------------------------------------------------
    # MODIFIED
-   def create(self, ext_name=None, overwrite=True, s_hdu=True, sex_cat_path=None):
+   def create(self, ext_name=None, s_hdu=True, sex_cat_path=None):
       """!
          Create an empty catalog with a FITS format
          @param ext_name extension name or number
@@ -468,7 +468,7 @@ def create(self, ext_name=None, overwrite=True, s_hdu=True, sex_cat_path=None):
                   sex_cat.open()
                   secondary_hdu = sex_cat._cat_data[1]
                   self._cat_data = fits.HDUList([primary_hdu, secondary_hdu])
-                  self._cat_data.writeto(self.fullpath, overwrite=overwrite)
+                  self._cat_data.writeto(self.fullpath, overwrite=True)
                   sex_cat.close()
                   del(sex_cat)
               else:
@@ -478,10 +478,10 @@ def create(self, ext_name=None, overwrite=True, s_hdu=True, sex_cat_path=None):
       elif s_hdu:
           secondary_hdu = fits.BinTableHDU(data=None, header=None, name=ext_name)
           self._cat_data = fits.HDUList([primary_hdu, secondary_hdu])
-          self._cat_data.writeto(self.fullpath, overwrite=overwrite)
+          self._cat_data.writeto(self.fullpath, overwrite=True)
       else:
           self._cat_data = fits.HDUList([primary_hdu])
-          self._cat_data.writeto(self.fullpath, overwrite=overwrite)
+          self._cat_data.writeto(self.fullpath, overwrite=True)
 
    # ------------------------------------------------------------------------------------------------
    # ADDED
@@ -581,12 +581,12 @@ def save_as_fits(self, data=None, names=None, ext_name=None, sex_cat_path=None,
                   data = np.array(data[names[0]])
                else:
                   data = [np.array(data[i]) for i in names]
-               self._save_to_fits(data, names, it, ext_name, sex_cat_path)
+               self._save_to_fits(data, names, it, ext_name, sex_cat_path, overwrite=overwrite)
 
            elif type(data) is np.recarray:
                names = list(data.dtype.names)
                it = names
-               self._save_to_fits(data, names, it, ext_name, sex_cat_path)
+               self._save_to_fits(data, names, it, ext_name, sex_cat_path, overwrite=overwrite)
 
            elif type(data) is fits.fitsrec.FITS_rec:
                self._save_from_recarray(data, ext_name, sex_cat_path)
@@ -600,20 +600,20 @@ def save_as_fits(self, data=None, names=None, ext_name=None, sex_cat_path=None,
                      raise ValueError('Names not provided')
                else:
                   it = range(len(names))
-               self._save_to_fits(data, names, it, ext_name, sex_cat_path)
+               self._save_to_fits(data, names, it, ext_name, sex_cat_path, overwrite=overwrite)
 
            elif type(data) is list:
                if names is None:
                    raise ValueError('Names not provided')
                it = range(len(names))
                data = np.asarray(data)
-               self._save_to_fits(data, names, it, ext_name, sex_cat_path)
+               self._save_to_fits(data, names, it, ext_name, sex_cat_path, overwrite=overwrite)
 
            elif type(data) is Table:
                if names is None:
                    raise ValueError('Names not provided')
                it = names
-               self._save_to_fits(data, names, it, ext_name, sex_cat_path)
+               self._save_to_fits(data, names, it, ext_name, sex_cat_path, overwrite=overwrite)
 
        else:
            if type(data) is np.ndarray:
@@ -1169,7 +1169,7 @@ def _get_python_col_type(self, col_type):
 
    # ------------------------------------------------------------------------------------------------
    # ADDED
-   def _save_to_fits(self, data, names, it, ext_name=None, sex_cat_path=None):
+   def _save_to_fits(self, data, names, it, ext_name=None, sex_cat_path=None, overwrite=False):
       """!
             Save array of data as fits with their associated column names.
             @param data array withe the data
@@ -1182,7 +1182,7 @@ def _save_to_fits(self, data, names, it, ext_name=None, sex_cat_path=None):
       if data is None:
          raise ValueError('Data not provided')
 
-      if self._file_exists(self.fullpath):
+      if self._file_exists(self.fullpath) and not overwrite:
           if self._cat_data is None:
               self.open()
           if ext_name is None:
@@ -1229,7 +1229,7 @@ def _save_to_fits(self, data, names, it, ext_name=None, sex_cat_path=None):
 
    # ------------------------------------------------------------------------------------------------
    # ADDED
-   def _save_from_recarray(self, data=None, ext_name=None, sex_cat_path=None):
+   def _save_from_recarray(self, data=None, ext_name=None, sex_cat_path=None, overwrite=False):
        """!
             Save a numpy.recarray or astropy.io.fits.fitsrec.FITS_rec into a fits.
             @param data data to store
@@ -1241,7 +1241,7 @@ def _save_from_recarray(self, data=None, ext_name=None, sex_cat_path=None):
        if data is None:
            raise ValueError('Data not provided')
 
-       if self._file_exists(self.fullpath):
+       if self._file_exists(self.fullpath) and not overwrite:
            if self._cat_data is None:
                self.open()
            if ext_name is None:

shapepipe/utilities/canfar.py

@@ -74,8 +74,9 @@ def command(self):
     def command(self, value):
 
         if value not in self._avail_commands:
-            raise ValueError('vos command must be one of {}'
-                             ''.format(self._avail_commands))
+            raise ValueError(
+                f'vos command must be one of {self._avail_commands}'
+            )
 
         self._command = getattr(vosc, value)
 
@@ -88,18 +89,20 @@ def __call__(self, *args, **kwargs):
         try:
             self._command()
 
-        except Exception:
-            raise vosError(f'Error in VOs command: {self._command.__name__}')
+        except:
+            raise vosError(
+                f'Error in VOs command: {self._command.__name__}'
+            )
 
 
 def download(source, target, verbose=False):
     """Download file from vos.
 
     Parameters
     ----------
-    source : string
+    source : str
         source path on vos
-    target : string
+    target : str
         target path
     verbose : bool, optional, default=False
         verbose output if True
@@ -108,21 +111,22 @@ def download(source, target, verbose=False):
     -------
     status : bool
         status, True/False or success/failure
+    """
 
     cmd = 'vcp'
 
     if not os.path.exists(target):
         sys.argv = [cmd, source, target]
         if verbose:
-            print('Downloading file {} to {}...'.format(source, target))
+            print(f'Downloading file {source} to {target}...')
         vcp = vosHandler(cmd)
 
         vcp()
         if verbose:
             print('Download finished.')
     else:
         if verbose:
-            print('Target file {} exists, skipping download.'.format(target))
+            print(f'Target file {target} exists, skipping download.')
 
 
 def dir_list(path, verbose=False):
@@ -132,7 +136,7 @@ def dir_list(path, verbose=False):
 
     Parameters
     ----------
-    path : string
+    path : str
         path on vos, starts with 'vos:cfis/...'
     verbose : bool, optional, default=False
         verbose output if True
@@ -143,7 +147,7 @@ def dir_list(path, verbose=False):
 
     Returns
     -------
-    vls_out : array of string
+    vls_out : array of str
         file or directory at path
     """