Refs #114. fiddle with autocrop algorithm

ornlneutronimaging · Sep 21, 2018 · f8eae90 · f8eae90
1 parent df4efa2
commit f8eae90
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Showing 2 changed files with 27 additions and 7 deletions.
diff --git a/python/imars3d/autocrop.py b/python/imars3d/autocrop.py
@@ -14,15 +14,17 @@ def save(d, p):
     # make sure all numbers are smaller than 1.
     max = np.max(sm);  sm/=max
     # get background intensities
-    left = np.median(sm[:, :10])
-    top = np.median(sm[:10, :])
-    right = np.median(sm[:, -10:])
-    bottom = np.median(sm[-10:, :])
+    left = sm[:, :10];    left_median = np.median(left)
+    top = sm[:10, :];     top_medain = np.median(top)
+    right = sm[:, -10:];  right_median = np.median(right)
+    bottom = sm[-10:, :]; bottom_median = np.median(bottom)
     #
-    background_int = np.median([left, top, right, bottom])
+    background_int = np.median([left_median, top_medain, right_median, bottom_median])
     # if background is dark
-    if background_int < .05:
-        Y1, X1 = np.where(sm>0.1)
+    if background_int < .08:
+        max_bg = np.max(map(np.max, [left, top, right, bottom]))
+        max_bg = np.max( (max_bg, 0.1) )
+        Y1, X1 = np.where(sm>max_bg)
         xmin = np.min(X1); xmax = np.max(X1)
         ymin = np.min(Y1); ymax = np.max(Y1)
         return xmin, xmax, ymin, ymax

diff --git a/tests/imars3d/test_autocrop.py b/tests/imars3d/test_autocrop.py
@@ -24,17 +24,34 @@ def test2():
     dir = os.path.abspath(dir)
     angles = np.arange(0., 10, 0.85)
     series = io.ImageFileSeries(os.path.join(dir, "20180704_Transmission_CT_%s_0080.*"), ['0010'])
+    # print autocrop.calculateCropWindow(series)
     assert np.allclose(
         autocrop.calculateCropWindow(series),
         (627, 1442, 648, 1468)
     )
     return
 
 
+def test2a():
+    dir = os.path.join(here, "..", "iMars3D_data_set", "autocrop", "darkboundaries")
+    dir = os.path.abspath(dir)
+    series = io.ImageFileSeries(
+        os.path.join(dir, "20180918_A49_4_CT_afterStableCycling_normalized_%7.3f.tiff"),
+        [300.300],
+        decimal_mark_replacement='.',
+    )
+    assert np.allclose(
+        autocrop.calculateCropWindow(series),
+        (767, 1309, 566, 1163),
+    )
+    return
+
+
 def test3():
     dir = os.path.join(here, "..", "iMars3D_data_set", "autocrop", "dark-bottom")
     dir = os.path.abspath(dir)
     series = io.ImageFileSeries(os.path.join(dir, "sm-estimate-ave%s.tiff"), [''])
+    # print autocrop.calculateCropWindow(series)
     assert np.allclose(
         autocrop.calculateCropWindow(series),
         (0, 2047, 1163, 2047)
@@ -45,6 +62,7 @@ def test3():
 def main():
     test()
     test2()
+    test2a()
     test3()
     return