feat: add support to handle RGB brightfield images

bmlab/export/fluorescence_export.py

@@ -52,8 +52,10 @@ def export(self, configuration):
             for image_key in image_keys:
                 channel = repetition.payload.get_channel(image_key)
                 img_data = repetition.payload.get_image(image_key)
-                # Average all images acquired
-                img_data = np.nanmean(img_data, axis=0).astype(np.ubyte)
+
+                # Average all images acquired if grayscale
+                if repetition.payload.get_class(image_key).casefold() == 'image_grayscale':
+                    img_data = np.nanmean(img_data, axis=0).astype(np.ubyte)
 
                 # Construct export path and create it if necessary
                 if self.file.path.parent.name == 'RawData':
@@ -162,8 +164,8 @@ def export(self, configuration):
                     image_warped =\
                         Image.merge("RGB", (blank, blank, image_warped))
                 image_alpha = Image.fromarray(
-                    (255 * np.logical_not(
-                        np.isnan(image_data_warped))).astype(np.ubyte))
+                    np.nanmean(255 * np.logical_not(
+                        np.isnan(image_data_warped)), axis=tuple(range(2,image_data_warped.ndim))).astype(np.ubyte))
                 image_warped.putalpha(image_alpha)
 
                 filename = path / f"{self.file.path.stem}" \

bmlab/file.py

@@ -364,6 +364,28 @@ def get_channel(self, image_key):
         except Exception:
             return None
 
+    def get_class(self, image_key):
+        """"
+        Returns the image class of a payload image
+        with the given key
+        """
+        try:
+            return self.data.get(image_key).attrs\
+                .get('IMAGE_SUBCLASS')[0].decode('utf-8')
+        except Exception:
+            return None
+
+    def get_mode(self, image_key):
+        """"
+        Returns the interlace mode of a payload image
+        with the given key
+        """
+        try:
+            return self.data.get(image_key).attrs\
+                .get('INTERLACE_MODE')[0].decode('utf-8')
+        except Exception:
+            return None
+
     def get_ROI(self, image_key):
         """
         Returns the region of interest of a payload image

tests/test_export_controller.py

@@ -67,6 +67,30 @@ def test_export_fluorescence(tmp_dir):
         assert os.path.exists(plots_dir / image)
 
 
+def test_export_color_images(tmp_dir):
+    shutil.copy(
+        data_file_path('ColorImage.h5'), Path.cwd() / 'ColorImage.h5')
+
+    session = Session.get_instance()
+    session.set_file(Path('ColorImage.h5'))
+
+    ec = ExportController()
+    config = ec.get_configuration()
+    config['fluorescenceCombined']['export'] = False
+    config['brillouin']['export'] = False
+    ec.export(config)
+
+    session.clear()
+
+    plots_dir = tmp_dir.parent / 'Plots'
+    images = [
+        'ColorImage_FLrep0_channelbrightfield.png',
+        'ColorImage_FLrep0_channelbrightfield_aligned.png',
+    ]
+    for image in images:
+        assert os.path.exists(plots_dir / image)
+
+
 def test_export_fluorescence_combined(tmp_dir):
     shutil.copy(
         data_file_path('Fluorescence.h5'), Path.cwd() / 'Fluorescence.h5')