sketch of spam-ldic with slicePadded but not yet working fine

tests/test_scripts.py

@@ -76,13 +76,16 @@ class testAll(unittest.TestCase):
             rm(testFolder+"zoom.tsv")
             rm(testFolder+"snow-ref-bin.tif")
             rm(testFolder+"snow-ref-watershed.tif")
+            rm(testFolder+"extreme-im1.tif")
+            rm(testFolder+"extreme-im1lab.tif")
+            rm(testFolder+"extreme-im2.tif")
             pass
         except OSError:
             pass
 
         pass
 
-    def _test_ldic_and_regularStrain(self):
+    def test_ldic_and_regularStrain(self):
         # Make test directory
         if not os.path.isdir(testFolder):
             os.mkdir(testFolder)
@@ -113,7 +116,7 @@ class testAll(unittest.TestCase):
         # Check output results with TSV output, bin1 registration + TIFFs
         # Decreasing node spacing in order to have more points for Geers strain calculation
         # exitCode = subprocess.call(["spam-ldic", "-Ffile", testFolder+"snow-ref-snow-def-bin2-registration.tsv", "-Ffb", "2", "-hws", "15", testFolder+"snow-ref.tif", testFolder+"snow-def.tif", "-od", testFolder+"", "-tsv"])
-        exitCode = subprocess.call(["spam-ldic", "-reg", "-regbb", "1", "-hws", "10", '-ns', '15', testFolder + "snow-ref.tif", testFolder + "snow-def.tif", "-od", testFolder + "", "-tsv", "-tif", '-vtk'])
+        exitCode = subprocess.call(["spam-ldic", "-ps", "off", "-reg", "-regbb", "2", "-regbe", "1", "-hws", "10", '-ns', '15', testFolder + "snow-ref.tif", testFolder + "snow-def.tif", "-od", testFolder + "", "-tsv", "-tif", '-vtk', '-gpmc', '1.0'])
         self.assertEqual(exitCode, 0)
 
         # Check registration
@@ -141,7 +144,7 @@ class testAll(unittest.TestCase):
         # There's Z-rotation so translations need to be decomposed properly... just check Z
         self.assertAlmostEqual(refTranslation[0], numpy.mean(Phis[converged,0,-1]), places=1)
         for i in range(3):
-            #self.assertAlmostEqual(refTranslation[i], numpy.mean(Phis[converged,i,-1]), places=1)
+            self.assertAlmostEqual(refTranslation[i], numpy.mean(Phis[converged,i,-1]), places=1)
             self.assertAlmostEqual(refRotation[i],    numpy.mean(decomposedPhisConverged['r'][converged, i]), places=1)
 
 
@@ -190,7 +193,7 @@ class testAll(unittest.TestCase):
         for component in ["U", "e", "vol", "volss", "dev", "devss"]:
             self.assertAlmostEqual(numpy.nanmean(strain[component]), numpy.nanmean(VTK[component]), places=3)
 
-    def _test_ITKwatershed(self):
+    def test_ITKwatershed(self):
         # make sure it runs the help without error
         exitCode = subprocess.call(["spam-ITKwatershed", "--help"],
                                    stdout=FNULL, stderr=FNULL)
@@ -212,12 +215,12 @@ class testAll(unittest.TestCase):
         lab = tifffile.imread(testFolder + "snow-ref-watershed.tif")
         self.assertEqual(lab.max()>10, True)
 
-    def _test_gdic(self):
+    def test_gdic(self):
         # make sure it runs the help without error
         exitCode = subprocess.call(["spam-gdic", "--help"], stdout=FNULL, stderr=FNULL)
         self.assertEqual(exitCode, 0)
 
-    def _test_deformImage(self):
+    def test_deformImage(self):
         # make sure it runs the help without error
         exitCode = subprocess.call(["spam-deformImageFromField", "--help"], stdout=FNULL, stderr=FNULL)
         self.assertEqual(exitCode, 0)
@@ -690,7 +693,7 @@ class testAll(unittest.TestCase):
             for label in [1,2]:
                 self.assertAlmostEqual(numpy.abs(TSVextreme['PhiField'][label, axis, -1] - 4.0), 0.0, places=1)
 
-    def _test_discreteStrain(self):
+    def test_discreteStrain(self):
         # make sure it runs the help without error
         exitCode = subprocess.call(["spam-discreteStrain", "--help"],
                                    stdout=FNULL,

tools/DIC/grid.py

@@ -460,7 +460,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
             if im1mask is not None:
                 # AND masks together, the one coming from the im1mask -- i.e., allowed correlation zones
                 # and the imagette1sliceMask indicating whether we've gone outside the volume
-                imagette1mask = numpy.logical_and(imagette1mask, spam.helpers.startStopIm1(im1mask, startStopIm1))
+                imagette1mask = numpy.logical_and(imagette1mask, spam.helpers.slicePadded(im1mask, startStopIm1))
             maskVolCondition = imagette1mask.sum() > minMaskVolume
 
             # Make sure imagette is not 0-dimensional in any dimension