Redo overlay2 (#425)

* pull out time loops

* save list of tensors in one line with torch.stack

* pass ND, pad to 4D, then save

* fix 2d bug

* factor out recorder-to-waveorder model conversion

* minor niceties

* error never catches

* less verbose

* label (nm) wavelength on gui

* wip birefringence working

* phase and fluorescence added

* fix indentation error

* fixed issue with torch thread global variable causing crashdump

* isort and black

* pass um consistently to config files

* adding tests for cli

* option to have or remove multiprocessing.

* fixing test and removing printf in applyaffine

* iohub upgrade integration

* fix comment

* convert to nm in recorder models

* fix minor phase bug

* bump waveorder dependency

* handle birefringence parameters more clearly

* better docs

* trigger on latest "Orientation*" layer

* walk the layer list backwards

* simplify

* document birefringence overlay behavior

---------

Co-authored-by: Eduardo Hirata-Miyasaki <edhiratam@gmail.com>

recOrder/plugin/main_widget.py

@@ -1171,31 +1171,41 @@ def handle_bg_bire_image_update(self, value):
  )
 
  def handle_layers_updated(self, event: Event):
+ """Whenever a layer is inserted or moved, we check if the top layer
+ starts with 'Orientation*'. If it is, we search for a layer that starts
+ with 'Retardance*' and has the same suffix as 'Orientation*', then use the
+ 'Orientation*'-'Retardance*' pair to generate a 'BirefringenceOverlay*'
+ layer.
+
+ We also color the 'Orientation*' layer in an HSV colormap.
+ """
+
  layers: LayerList = event.source
- latest_layer_name = layers[-1].name
- channels = ["Retardance", "Orientation"]
- for ch in channels:
- if latest_layer_name.startswith(ch):
- suffix = latest_layer_name.replace(ch, "")
- other_name = channels[1 - channels.index(ch)] + suffix
- overlay_name = "BirefringenceOverlay" + suffix
- if other_name in layers and overlay_name not in layers:
- logging.info(
- "Detected updated birefringence layers: "
- f"'{latest_layer_name}', '{other_name}'"
- )
- self._draw_bire_overlay(
- [ch + suffix, other_name], overlay_name
- )
- if latest_layer_name.startswith(channels[1]):
+ # if the first channel starts with "Orientation"
+ if layers[-1].name.startswith("Orientation"):
+ orientation_name = layers[-1].name
+ suffix = orientation_name.replace("Orientation", "")
+ retardance_name = "Retardance" + suffix
+ overlay_name = "BirefringenceOverlay" + suffix
+ # if the matching retardance layer is present, generate an overlay
+ if retardance_name in layers:
+ logging.info(
+ "Detected updated birefringence layers: "
+ f"'{retardance_name}', '{orientation_name}'"
+ )
+ self._draw_bire_overlay(
+ retardance_name, orientation_name, overlay_name
+ )
+
+ # always display layers that start with "Orientation" in hsv
  logging.info(
  "Detected orientation layer in updated layer list."
  "Setting its colormap to HSV."
  )
- self.viewer.layers[latest_layer_name].colormap = "hsv"
+ self.viewer.layers[orientation_name].colormap = "hsv"
 
  def _draw_bire_overlay(
- self, source_names: list[str, str], overlay_name: str
+ self, retardance_name: str, orientation_name: str, overlay_name: str
  ):
  def _layer_data(name: str):
  data = self.viewer.layers[name].data
@@ -1210,7 +1220,6 @@ def _layer_data(name: str):
  def _draw(overlay):
  self._add_or_update_image_layer(overlay, overlay_name, cmap="rgb")
 
- orientation_name, retardance_name = sorted(source_names)
  retardance = _layer_data(retardance_name)
  orientation = _layer_data(orientation_name)
  worker = create_worker(