Apply absorption correction after SNIP in polar

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>

Author: psavery

hexrdgui/calibration/polarview.py

@@ -394,6 +394,10 @@ def raw_mask(self):
     def apply_image_processing(self):
         img = self.raw_img.data
         img = self.apply_snip(img)
+
+        # Always apply absorption correction after snip
+        img = self.apply_absorption_correction(img)
+
         # cache this step so we can just re-apply masks if needed
         self.snipped_img = img
 
@@ -440,6 +444,22 @@ def apply_snip(self, img):
 
         return img
 
+    def apply_absorption_correction(self, img):
+        if not HexrdConfig().apply_absorption_correction:
+            return img
+
+        # Warp the absorption correction images to the polar view,
+        # sum them, and apply.
+        absorption_corrections = HexrdConfig().absorption_corrections_dict
+
+        output = {}
+        for det_key, panel in self.detectors.items():
+            corrections = absorption_corrections[det_key]
+            output[det_key] = self.warp_image(corrections, panel)
+
+        correction_field = np.ma.sum(np.ma.stack(output.values()), axis=0)
+        return img * correction_field.data
+
     def apply_visible_masks(self, img):
         # Apply user-specified masks if they are present
         from hexrdgui.masking.mask_manager import MaskManager

hexrdgui/hexrd_config.py

@@ -326,6 +326,7 @@ def __init__(self):
         self._physics_package = None
         self._detector_coatings = {}
         self._instrument_rigid_body_params = {}
+        self.absorption_corrections_dict = {}
 
         # Make sure that the matplotlib font size matches the application
         self.font_size = self.font_size
@@ -986,7 +987,10 @@ def intensity_corrected_images_dict(self):
                 factor = panel.lorentz_factor()
                 images_dict[name] = img / factor
 
+        HexrdConfig().absorption_corrections_dict.clear()
         if HexrdConfig().apply_absorption_correction:
+            absorption_corrections = HexrdConfig().absorption_corrections_dict
+
             transmissions = instr.calc_transmission()
             max_transmission = max(
                 [np.nanmax(v) for v in transmissions.values()])
@@ -995,7 +999,16 @@ def intensity_corrected_images_dict(self):
                 transmission = transmissions[name]
                 # normalize by maximum of the entire instrument
                 transmission /= max_transmission
-                images_dict[name] = img * (1 / transmission)
+                absorption_corrections[name] = 1 / transmission
+
+            if (
+                HexrdConfig().image_mode not in
+                (constants.ViewType.polar, constants.ViewType.stereo)
+            ):
+                # If it's not polar or stereo, go ahead and apply the
+                # corrections
+                for name, img in images_dict.items():
+                    images_dict[name] = img * absorption_corrections[name]
 
         if HexrdConfig().intensity_subtract_minimum:
             minimum = min([np.nanmin(x) for x in images_dict.values()])