Merged in bugfix/RAM-4056_direct_density_600 (pull request #454)

RAM-4056 fix more direct density scans for the catphan 600

Approved-by: Randy Taylor

pylinac/ct.py

@@ -749,8 +749,18 @@ def _setup_geometry_rois(self) -> None:
         xbounds = (int(self.phan_center.x - boxsize), int(self.phan_center.x + boxsize))
         ybounds = (int(self.phan_center.y - boxsize), int(self.phan_center.y + boxsize))
         geo_img = self.image[ybounds[0] : ybounds[1], xbounds[0] : xbounds[1]]
+        # clip to the nearest of the two extremes
+        # this can arise from direct density scans. In that case the
+        # 1 teflon node will not get detected as the edge intensity is much less than the other nodes (unlike normal)
+        # So, we clip the sub-image to the nearest extreme to the median.
+        # This does very little to normal scans. RAM-4056
+        median = np.median(geo_img)
+        nearest_extreme = min(abs(median - geo_img.max()), abs(median - geo_img.min()))
+        geo_clipped = np.clip(
+            geo_img, a_min=median - nearest_extreme, a_max=median + nearest_extreme
+        )
         larr, regionprops, num_roi = get_regions(
-            geo_img, fill_holes=True, clear_borders=False
+            geo_clipped, fill_holes=True, clear_borders=False
         )
         # check that there is at least 1 ROI
         if num_roi < 4:
@@ -2876,8 +2886,15 @@ def find_phantom_roll(self, func: Callable | None = None) -> float:
         It may also find the top air ROI if the water vial isn't there.
         We use the below lambda to select the bottom air and teflon ROIs consistently.
         These two ROIs are at 75 degrees from cardinal. We thus offset the default outcome by 75.
+
+        HOWEVER, for direct density scans, the Teflon ROI might not register because of the reduced
+        HU. 🤦‍♂️. We make a best guess depending on the detected roll. If it's ~75 degrees,
+        we have caught the bottom Air and Teflon. If it's near zero, we have
+        caught the top and bottom Air ROIs.
         """
         angle = super().find_phantom_roll(lambda x: -x.centroid[0])
+        if abs(angle) < 10:
+            return angle
         return angle + 75
 
 

tests_basic/test_cbct.py

@@ -620,6 +620,33 @@ def test_vial_roi(self):
         self.assertIn("Vial", self.cbct.ctp404.rois)
 
 
+class CatPhan600DirectDensity(CatPhanMixin, TestCase):
+    """Direct density scan."""
+
+    catphan = CatPhan600
+    dir_path = ["CBCT", "CatPhan_600"]
+    file_name = "Catphan600 direct density.zip"
+    hu_origin_variance = 200
+    expected_roll = -0.25
+    origin_slice = 105
+    hu_values = {
+        "Poly": -35,
+        "Acrylic": 123,
+        "Delrin": 150,
+        "Air": -994,
+        "Teflon": 431,
+        "PMP": -182,
+        "LDPE": -92,
+        "Vial": 63,
+    }
+    hu_passed = False
+    unif_values = {"Center": 11, "Left": 11, "Right": 11, "Top": 11, "Bottom": 11}
+    mtf_values = {50: 0.31}
+    avg_line_length = 50
+    slice_thickness = 2.1
+    lowcon_visible = 6
+
+
 @mark.catphan604
 class CatPhan604Test(CatPhanMixin, TestCase):
     catphan = CatPhan604