From c9a94e2f96c54fcf4348b05dae37c2e672feab47 Mon Sep 17 00:00:00 2001
From: PaulHancock <paul.hancock@curtin.edu.au>
Date: Sun, 7 Jun 2020 20:40:26 +0800
Subject: [PATCH 1/4] create test for #117

---
 tests/test_source_finder.py | 32 +++++++++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 5 deletions(-)

diff --git a/tests/test_source_finder.py b/tests/test_source_finder.py
index a9e68e6c..6b89042f 100755
--- a/tests/test_source_finder.py
+++ b/tests/test_source_finder.py
@@ -9,6 +9,7 @@
 from AegeanTools import source_finder as sf
 from AegeanTools.wcs_helpers import Beam, WCSHelper
 from AegeanTools import models, flags
+from AegeanTools.models import classify_catalog
 from copy import deepcopy
 import numpy as np
 import logging
@@ -46,7 +47,6 @@ def test_psf_with_nans():
     return
 
 
-
 def test_misc():
     """Test some random things"""
     sf.IslandFittingData()
@@ -258,8 +258,31 @@ def test_esimate_lmfit_parinfo():
     return
 
 
+def test_island_contours():
+    """Test that island contours are correct"""
+    log = logging.getLogger("Aegean")
+    sfinder = sf.SourceFinder(log=log)
+    filename = 'tests/test_files/synthetic_test.fits'
+    nsrc = 98
+    nisl = 97
+    ntot = nsrc+nisl
+
+    # vanilla source finding
+    found = sfinder.find_sources_in_image(filename, cores=1, rms=0.5, bkg=0, doislandflux=True)
+
+    components, islands, simples = classify_catalog(found)
+    isle_0_contour = np.array([(41, 405), (41, 406), (41, 407), (42, 407), (42, 408), (42, 409), (43, 409), (43, 410),
+                       (44, 410), (45, 410), (46, 410), (47, 410), (47, 409), (48, 409), (48, 408), (49, 408),
+                       (49, 407), (49, 406), (49, 405), (48, 405), (48, 404), (48, 403), (47, 403), (46, 403),
+                       (45, 403), (44, 403), (43, 403), (43, 404), (42, 404), (42, 405)])
+    if not np.all(np.array(islands[0].contour) == isle_0_contour):
+        raise AssertionError("Island contour for island 0 is incoorect")
+    return
+
+
 # for 3.0 functionality
 
+
 def test_find_islands():
     im = np.ones((10,12), dtype=np.float32)
     bkg = np.zeros_like(im)
@@ -351,10 +374,9 @@ def test_estimate_parinfo_image():
 
 
 if __name__ == "__main__":
-    #test_psf_with_nans()
-    #test_estimate_parinfo_image()
-    #import sys
-    #sys.exit()
+    test_island_contours()
+    import sys
+    sys.exit()
     # introspect and run all the functions starting with 'test'
     for f in  dir(): #['test_find_islands', 'test_estimate_parinfo_image', 'test_find_and_prior_sources']:
         if f.startswith('test'):

From 4523f4ed1a6d8bbf44d97944f04cfd6dd0658191 Mon Sep 17 00:00:00 2001
From: PaulHancock <paul.hancock@curtin.edu.au>
Date: Sun, 7 Jun 2020 20:41:13 +0800
Subject: [PATCH 2/4] fix bug #117

---
 AegeanTools/source_finder.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/AegeanTools/source_finder.py b/AegeanTools/source_finder.py
index 50c003c6..c4014030 100755
--- a/AegeanTools/source_finder.py
+++ b/AegeanTools/source_finder.py
@@ -1008,8 +1008,8 @@ def result_to_components(self, result, model, island_data, isflags):
             area = height * width
             source.area = area * source.pixels / source.x_width / source.y_width  # area is in deg^2
 
-            # create contours
-            msq = MarchingSquares(idata)
+            # create contours around the data which was used in fitting
+            msq = MarchingSquares(kappa_sigma)
             source.contour = [(a[0] + xmin, a[1] + ymin) for a in msq.perimeter]
             # calculate the maximum angular size of this island, brute force method
             source.max_angular_size = 0

From 93fd5b5a1e375c08d31d73b8a35caba65e868235 Mon Sep 17 00:00:00 2001
From: PaulHancock <paul.hancock@curtin.edu.au>
Date: Sun, 7 Jun 2020 20:42:29 +0800
Subject: [PATCH 3/4] update date

---
 AegeanTools/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/AegeanTools/__init__.py b/AegeanTools/__init__.py
index eca9e3dd..07768bb4 100755
--- a/AegeanTools/__init__.py
+++ b/AegeanTools/__init__.py
@@ -11,7 +11,7 @@
 """
 __author__ = 'Paul Hancock'
 __version__ = '2.2.2'
-__date__ = '2020-06-06'
+__date__ = '2020-06-07'
 __citation__ = """
 % If your work makes use of AegeanTools please cite the following papers as appropriate:
 

From cb9e0b2ed70dfe9dad819a2d8f23c613eada38bc Mon Sep 17 00:00:00 2001
From: PaulHancock <paul.hancock@curtin.edu.au>
Date: Sun, 7 Jun 2020 20:42:45 +0800
Subject: [PATCH 4/4] include bugfix for #117

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d1ed4db2..c4b35625 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@ v 2.2.2
 =======
 Aegean
 - Fixed a bug that could cause a crash if the psf map had nan values
+- Fixed a bug that caused island contours to just be boxes.
 
 MIMAS
 - added new functionality, `--mask2mim`, which will convert a fits file into a region file.