Merge branch 'fix_concat' into 'master'

Fix bug in concat when order of spectral index differs

See merge request !35

lsmtool/tableio.py

@@ -29,6 +29,7 @@ import numpy.ma as ma
 import re
 import logging
 import os
+from copy import deepcopy
 
 # Python 3 compatibility
 try:
@@ -401,7 +402,9 @@ def processFormatString(formatString):
                 colDefaults[i] = defaultVal
                 metaDict[colNames[i]] = defaultVal
             elif allowedColumnDefaults[colName] is not None:
-                colDefaults[i] = allowedColumnDefaults[colName]
+                # Note: we used deepcopy() here to ensure that the original
+                # is not altered by later changes to colDefaults
+                colDefaults[i] = deepcopy(allowedColumnDefaults)[colName]
 
     # Check for required columns
     for reqCol in requiredColumnNames:
@@ -1124,7 +1127,9 @@ def convertExternalTable(table, columnMapping, fluxUnits='mJy'):
             table.columns[colName].unit = allowedColumnUnits[colName.lower()]
 
         if hasattr(table.columns[colName], 'filled') and allowedColumnDefaults[colName.lower()] is not None:
-            fillVal = allowedColumnDefaults[colName.lower()]
+            # Note: we used deepcopy() here to ensure that the original
+            # is not altered by later changes to fillVal
+            fillVal = deepcopy(allowedColumnDefaults)[colName.lower()]
             if colName == 'SpectralIndex':
                 while len(fillVal) < 1:
                     fillVal.append(0.0)
@@ -1280,4 +1285,3 @@ registry.register_writer('ds9', Table, ds9RegionWriter)
 registry.register_writer('kvis', Table, kvisAnnWriter)
 registry.register_writer('casa', Table, casaRegionWriter)
 registry.register_writer('factor', Table, factorDirectionsWriter)
-

tests/single_spectralindx.sky

+FORMAT = Name, Type, Ra, Dec, I, Q, U, V, ReferenceFrequency='60e6', SpectralIndex='[0.0]', MajorAxis, MinorAxis, Orientation
+
+# the next lines define the sources
+1553.9+5220, POINT, 15:53:56.76000000, +52.20.49.41600000, 2.5599, , , , , [-0.2648]
+1555.2+5517, POINT, 15:55:12.73920000, +55.17.12.30000000, 0.7088, , , , , [-0.3858]
+1556.2+5348, POINT, 15:56:15.38880000, +53.48.11.30400000, 0.7697, , , , , [-0.4379]
+1556.4+5539, POINT, 15:56:26.76960000, +55.39.01.80000000, 0.9, , , , , [-0.7]
+1556.7+5705, POINT, 15:56:42.78000000, +57.05.39.01200000, 1.1941, , , , , [-0.3247]
+1556.7+5558, POINT, 15:56:45.23040000, +55.58.31.11600000, 0.9446, , , , , [-0.0414]

tests/test_lsmtool.py

@@ -38,6 +38,13 @@ def test_concatenate():
     assert len(s) == 2165
 
 
+def test_concatenate_differing_spectral_index():
+    print('Concatenate with single_spectralindx.sky')
+    s4 = lsmtool.load('tests/no_patches.sky')
+    s4.concatenate('tests/single_spectralindx.sky', matchBy = 'position', radius = '30 arcsec', keep = 'from2')
+    assert len(s) == 2165
+
+
 def test_compare():
     print('Compare to concat.sky')
     if os.path.exists('tests/flux_ratio_vs_distance.sky'):