Add Defects method for reading defects from text file

python/lsst/meas/algorithms/defects.py

@@ -256,3 +256,42 @@ def readFits(cls, *args):
         """
         table = lsst.afw.table.BaseCatalog.readFits(*args)
         return cls.fromTable(table)
+
+    @classmethod
+    def readLsstDefectsFile(cls, filename):
+        """Read defects information from an LSST format text file.
+
+        Parameters
+        ----------
+        filename : `str`
+            Name of text file containing the defect information.
+
+        Returns
+        -------
+        defects : `Defects`
+            The defects.
+
+        Notes
+        -----
+        These defect text files are used as the human readable definitions
+        of defects in calibration data definition repositories.  The format
+        is to use four columns defined as follows:
+
+        x0 : `int`
+            X coordinate of bottom left corner of box.
+        y0 : `int`
+            Y coordinate of bottom left corner of box.
+        width : `int`
+            X extent of the box.
+        height : `int`
+            Y extent of the box.
+        """
+        # Use loadtxt so that ValueError is thrown if the file contains a
+        # non-integer value. genfromtxt converts bad values to -1.
+        defect_array = np.loadtxt(filename,
+                                  dtype=[("x0", "int"), ("y0", "int"),
+                                         ('x_extent', '<i8'), ('y_extent', '<i8')])
+
+        return Defects(lsst.geom.Box2I(lsst.geom.Point2I(row["x0"], row["y0"]),
+                                       lsst.geom.Extent2I(row["x_extent"], row["y_extent"]))
+                       for row in defect_array)

tests/test_interp.py

@@ -80,6 +80,28 @@ def test_defects(self):
         with self.assertRaises(ValueError):
             defects.append("defect")
 
+    def testLsstTextfile(self):
+        with lsst.utils.tests.getTempFilePath(".txt") as tmpFile:
+            with open(tmpFile, "w") as fh:
+                print("""# X0  Y0  width height
+     996        0       56       24
+       0     4156     2048       20
+       0        0       17     4176
+    1998     4035       50      141
+    1023        0        2     4176
+    2027        0       21     4176
+       0     4047       37      129
+# Some rows without fixed column widths
+14 20 2000 50
+10 10 10 10
+""", file=fh)
+
+            defects = algorithms.Defects.readLsstDefectsFile(tmpFile)
+
+            self.assertEqual(len(defects), 9)
+            self.assertEqual(defects[3].getBBox(), lsst.geom.Box2I(lsst.geom.Point2I(1998, 4035),
+                                                                   lsst.geom.Extent2I(50, 141)))
+
 
 class InterpolationTestCase(lsst.utils.tests.TestCase):
     """A test case for interpolation."""