Background scaling, naming, and squeezing (#429)

* correctly scale background images * improve background layer names * squeeze arrays before adding to viewer * fix import * online squeeze first dimension
mehta-lab · Aug 26, 2023 · 2f5ae16 · 2f5ae16
1 parent 7f56ed0
commit 2f5ae16
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Showing 2 changed files with 13 additions and 4 deletions.
diff --git a/recOrder/calib/Calibration.py b/recOrder/calib/Calibration.py
@@ -9,6 +9,7 @@
 import numpy as np
 from importlib_metadata import version
 from iohub import open_ome_zarr
+from iohub.ngff_meta import TransformationMeta
 from mpl_toolkits.axes_grid1.axes_divider import make_axes_locatable
 from napari.utils.notifications import show_warning
 from scipy.interpolate import interp1d
@@ -1081,6 +1082,7 @@ def capture_bg(self, n_avg, directory):
             yx_list.append(self._capture_state(f"State{channel}", n_avg))
             logging.debug(f"Saving Background State{channel}")
         cyx_data = np.array(yx_list)
+        yx_scale = self.mmc.getPixelSizeUm()
 
         # Save to zarr
         with open_ome_zarr(
@@ -1095,6 +1097,11 @@ def capture_bg(self, n_avg, directory):
                 shape=(1, num_states, 1, cyx_data.shape[1], cyx_data.shape[2]),
                 dtype=np.float32,
                 chunks=(1, 1, 1, cyx_data.shape[1], cyx_data.shape[2]),
+                transform=[
+                    TransformationMeta(
+                        type="scale", scale=[1, 1, 1, yx_scale, yx_scale]
+                    )
+                ],
             )
             position["0"][0, :, 0] = cyx_data  # save to 1C1YX array
 

diff --git a/recOrder/plugin/main_widget.py b/recOrder/plugin/main_widget.py
@@ -1154,6 +1154,8 @@ def _add_or_update_image_layer(
         move_to_top : bool, optional
             whether to move the updated layer to the top of layers list, by default True
         """
+        if image.shape[0] == 1:
+            image = image.squeeze(axis=0)
         scale = scale[-image.ndim :]  # match shapes
 
         if name in self.viewer.layers:
@@ -1181,16 +1183,16 @@ def _add_or_update_image_layer(
     @Slot(tuple)
     def handle_bg_image_update(self, value):
         data, scale = value
-        self._add_or_update_image_layer(data, "Background Images", scale=scale)
+        self._add_or_update_image_layer(data, "Raw Background", scale=scale)
 
     @Slot(tuple)
     def handle_bg_bire_image_update(self, value):
         data, scale = value
         self._add_or_update_image_layer(
-            data[0], "Background Retardance", scale=scale
+            data[0], "Retardance Background", scale=scale
         )
         self._add_or_update_image_layer(
-            data[1], "Background Orientation", cmap="hsv", scale=scale
+            data[1], "Orientation Background", cmap="hsv", scale=scale
         )
 
     def handle_layers_updated(self, event: Event):
@@ -1209,7 +1211,7 @@ def handle_layers_updated(self, event: Event):
             orientation_name = layers[-1].name
             suffix = orientation_name.replace("Orientation", "")
             retardance_name = "Retardance" + suffix
-            overlay_name = "BirefringenceOverlay" + suffix
+            overlay_name = "Birefringence Overlay" + suffix
             # if the matching retardance layer is present, generate an overlay
             if retardance_name in layers:
                 logging.info(