Merge pull request #4 from a-griffiths/v1.1.2

v1.1.2

AutoSpec

@@ -3,8 +3,8 @@
 """
 AutoSpec: Automated Datacube Spectrum Extractor
 @author: Alex Griffiths
-v 1.1.0
-05-09-2018
+v 1.1.2
+20-09-2018
 """
 # Import dependencies.
 from __future__ import absolute_import, division, print_function
@@ -59,16 +59,16 @@ def create_source(ID, ra, dec, size, ref):
     if ref == '':
         ext_mode = 'IMG'
         refspec = 'MUSE_WHITE'
-    elif ref not in imgs.keys():
-        print('Reference not in images or apertures, using white light.')
+    elif ref.replace('.', '').isdigit() is False:
         ext_mode = 'IMG'
-        refspec = 'MUSE_WHITE'
+        refspec = ref
     elif ref.replace('.', '').isdigit() is True:
         ext_mode = 'APER'
         refspec = 'MUSE_APER_%.1f' % float(ref)
-    elif ref.replace('.', '').isdigit() is False:
+    elif ref not in imgs.keys():
+        print('Reference not in images or apertures, using white light.')
         ext_mode = 'IMG'
-        refspec = ref
+        refspec = 'MUSE_WHITE'
 
     # This creates the source object (see MPDAF for more details).
     s = Source.from_data(ID=ID, ra=ra, dec=dec, extras=extra,
@@ -108,10 +108,11 @@ def create_source(ID, ra, dec, size, ref):
 
     # Extract all spectra set by user.
     tags = [i for i in s.images.keys() if 'SEG_' not in i and 'MASK_' not in i]
+    aps = params.APER if isinstance(params.APER, tuple) else [params.APER]
 
     s.extract_spectra(s.cubes['MUSE'], obj_mask=mask,
                       sky_mask='MASK_SKY', skysub=params.SKY_SUB,
-                      tags_to_try=tags, apertures=params.APER)
+                      tags_to_try=tags, apertures=aps)
 
     # Set up naming convention based on if the user has sky-subtraction set.
     if params.SKY_SUB is True:
@@ -186,8 +187,10 @@ def create_masks(src):
     src.add_seg_images(del_sex=False)
     seg = [i for i in src.images.keys() if 'SEG_' in i]
     # Do not use the white light image not set.
-    if params.USE_WHITE is False:
+    if params.USE_IMGS is False:
         seg.remove('SEG_MUSE_WHITE')
+        for key in imgs:
+            seg.remove('SEG_'+key)
     src.find_sky_mask(seg)
     src.find_union_mask(seg)
     # Check if any maps are empty before creating intersection mask.

catalog_format.txt

@@ -1,5 +1,5 @@
-# Example catalog file for AutoSpec v 1.1.0
-# DATE: 05-09-2018
+# Example catalog file for AutoSpec v 1.1.2
+# DATE: 20-09-2018
 
 # Parameter mode catalog format [id ra dec].
 #

param_format.py

@@ -1,5 +1,5 @@
-# Default configuration file for AutoSpec v 1.1.0
-# DATE: 05-09-2018
+# Default configuration file for AutoSpec v 1.1.2
+# DATE: 20-09-2018
 
 # ----------- Operating Mode -------------------------------------------------------------------------------------------------------------------------------------------------------------
 
@@ -25,7 +25,7 @@
 
 # ----------- Object Masks ----------------------------------------------------------------------------------------------------------------------------------------------------------------
 
-USE_WHITE      =  True                         # if AutoSpec should also use the MUSE_WHITE segmentation map to create masks (True or False).
+USE_IMGS       =  True                         # if AutoSpec should also use the segmentation maps created from the images in IMG parameter to create final masks (True or False).
 OBJ_MASK       = 'INTER'                       # object mask from union (UNION) or intersection (INTER) of segmentation maps (string).
 SEG            = ''                            # name of additional segmentation maps files to be used (string or comma seperated list of strings).
 

test/catalog.txt

@@ -1,5 +1,5 @@
-# Example catalog file for AutoSpec v 1.1.0
-# DATE: 05-09-2018
+# Example catalog file for AutoSpec v 1.1.2
+# DATE: 20-09-2018
 
 # Parameter mode catalog format [id ra dec].
 #

test/param.py

@@ -1,5 +1,5 @@
-# Default configuration file for AutoSpec v 1.1.0
-# DATE: 05-09-2018
+# Default configuration file for AutoSpec v 1.1.2
+# DATE: 20-09-2018
 
 # ----------- Operating Mode -------------------------------------------------------------------------------------------------------------------------------------------------------------
 
@@ -20,14 +20,14 @@
 
 # ----------- Spectral Extractions --------------------------------------------------------------------------------------------------------------------------------------------------------
 
-APER           = 1.0, 2.0                      # aperture sizes (in arcseconds) for spectrum extraction (float or array or floats).
-IMG            = 'g-band.fits', 'r-band.fits'  # name of additional image files for weighted spectra and segmentation extractions (string or comma seperated list of strings), '' if none.
+APER           = 2.0                           # aperture sizes (in arcseconds) for spectrum extraction (float or array or floats).
+IMG            = 'g-band.fits','r-band.fits'   # name of additional image files for weighted spectra and segmentation extractions (string or comma seperated list of strings), '' if none.
 
 # ----------- Object Masks ----------------------------------------------------------------------------------------------------------------------------------------------------------------
 
-USE_WHITE      =  True                         # if AutoSpec should also use the MUSE_WHITE segmentation map to create masks (True or False).
+USE_IMGS       =  True                         # if AutoSpec should also use the segmentation maps created from the images in IMG parameter to create final masks (True or False).
 OBJ_MASK       = 'INTER'                       # object mask from union (UNION) or intersection (INTER) of segmentation maps (string).
-SEG            = 'g-seg.fits', 'r-seg.fits'    # name of additional segmentation maps files to be used (string or comma seperated list of strings).
+SEG            = 'g-seg.fits'                  # name of additional segmentation maps files to be used (string or comma seperated list of strings).
 
 # ----------- Output Formatting -----------------------------------------------------------------------------------------------------------------------------------------------------------