Improved birefringence overlays

recOrder/acq/acquisition_workers.py

@@ -33,6 +33,20 @@
  from recOrder.plugin.main_widget import MainWidget
 
 
+def _check_scale_mismatch(
+ recon_scale: np.array,
+ ngff_scale: tuple[float, float, float, float, float],
+) -> None:
+ if not np.allclose(np.array(ngff_scale[2:]), recon_scale, rtol=1e-2):
+ show_warning(
+ f"Requested reconstruction scale = {recon_scale} "
+ f"and OME-Zarr metadata scale = {ngff_scale[2:]} are not equal. "
+ "recOrder's reconstruction uses the GUI's "
+ "Z-step, pixel size, and magnification, "
+ "while napari's viewer uses the input array's metadata."
+ )
+
+
 def _generate_reconstruction_config_from_gui(
  reconstruction_config_path,
  mode,
@@ -117,8 +131,8 @@ class PolarizationAcquisitionSignals(WorkerBaseSignals):
  Custom Signals class that includes napari native signals
  """
 
- phase_image_emitter = Signal(object)
- bire_image_emitter = Signal(object)
+ phase_image_emitter = Signal(tuple)
+ bire_image_emitter = Signal(tuple)
  phase_reconstructor_emitter = Signal(object)
  aborted = Signal()
 
@@ -128,7 +142,7 @@ class BFAcquisitionSignals(WorkerBaseSignals):
  Custom Signals class that includes napari native signals
  """
 
- phase_image_emitter = Signal(object)
+ phase_image_emitter = Signal(tuple)
  phase_reconstructor_emitter = Signal(object)
  aborted = Signal()
 
@@ -258,7 +272,7 @@ def work(self):
  # Reconstruct snapped images
  self.n_slices = stack.shape[2]
 
- phase = self._reconstruct()
+ phase, scale = self._reconstruct()
  self._check_abort()
 
  # Warn the user about axial
@@ -267,11 +281,18 @@ def work(self):
  "Inverting the phase contrast. This affects the visualization and saved reconstruction."
  )
 
+ # Warn user about mismatched scales
+ recon_scale = np.array(
+ (self.calib_window.z_step,)
+ + 2 * (self.calib_window.ps / self.calib_window.mag,)
+ )
+ _check_scale_mismatch(recon_scale, scale)
+
  logging.info("Finished Acquisition")
  logging.debug("Finished Acquisition")
 
  # Emit the images and let thread know function is finished
- self.phase_image_emitter.emit(phase)
+ self.phase_image_emitter.emit((phase, scale))
 
  def _reconstruct(self):
  """
@@ -301,8 +322,9 @@ def _reconstruct(self):
  # Read reconstruction to pass to emitters
  with open_ome_zarr(reconstruction_path, mode="r") as dataset:
  phase = dataset["0/0/0/0"][0]
+ scale = dataset["0/0/0"].scale
 
- return phase
+ return phase, scale
 
  def _cleanup_acq(self):
  # Get display windows
@@ -479,7 +501,7 @@ def work(self):
  # Reconstruct snapped images
  self._check_abort()
  self.n_slices = stack.shape[2]
- birefringence, phase = self._reconstruct()
+ birefringence, phase, scale = self._reconstruct()
  self._check_abort()
 
  # Warn the user about rotations and flips
@@ -492,12 +514,19 @@ def work(self):
  "Applying a flip to orientation channel. This affects the visualization and saved reconstruction."
  )
 
+ # Warn user about mismatched scales
+ recon_scale = np.array(
+ (self.calib_window.z_step,)
+ + 2 * (self.calib_window.ps / self.calib_window.mag,)
+ )
+ _check_scale_mismatch(recon_scale, scale)
+
  logging.info("Finished Acquisition")
  logging.debug("Finished Acquisition")
 
  # Emit the images and let thread know function is finished
- self.bire_image_emitter.emit(birefringence)
- self.phase_image_emitter.emit(phase)
+ self.bire_image_emitter.emit((birefringence, scale))
+ self.phase_image_emitter.emit((phase, scale))
 
  def _check_exposure(self) -> None:
  """
@@ -579,8 +608,9 @@ def _reconstruct(self):
  phase = czyx_data[4]
  except:
  phase = None
+ scale = dataset["0/0/0"].scale
 
- return birefringence, phase
+ return birefringence, phase, scale
 
  def _cleanup_acq(self):
  # Get display windows

recOrder/calib/calibration_workers.py

@@ -53,8 +53,8 @@ class BackgroundSignals(WorkerBaseSignals):
  Custom Signals class that includes napari native signals
  """
 
- bg_image_emitter = Signal(object)
- bire_image_emitter = Signal(object)
+ bg_image_emitter = Signal(tuple)
+ bire_image_emitter = Signal(tuple)
  bg_path_update_emitter = Signal(Path)
  aborted = Signal()
 
@@ -358,6 +358,7 @@ def work(self):
  with open_ome_zarr(reconstruction_path, mode="r") as dataset:
  self.retardance = dataset["0/0/0/0"][0, 0, 0]
  self.birefringence = dataset["0/0/0/0"][0, :, 0]
+ scale = dataset["0/0/0"].scale
 
  # Save metadata file and emit imgs
  meta_file = bg_path / "polarization_calibration.txt"
@@ -381,8 +382,10 @@ def work(self):
  self._check_abort()
 
  # Emit background images + background birefringence
- self.bg_image_emitter.emit(imgs)
- self.bire_image_emitter.emit((self.retardance, self.birefringence[1]))
+ self.bg_image_emitter.emit((imgs, scale))
+ self.bire_image_emitter.emit(
+ ((self.retardance, self.birefringence[1]), scale)
+ )
 
  # Emit bg path
  self.bg_path_update_emitter.emit(bg_path)

recOrder/io/utils.py

@@ -1,7 +1,7 @@
 import os
 import textwrap
 from pathlib import Path
-from typing import Literal
+from typing import Literal, Union
 
 import numpy as np
 import psutil
@@ -130,7 +130,10 @@ def generic_hsv_overlay(
 
 
 def ret_ori_overlay(
- retardance, orientation, ret_max=10, cmap: Literal["JCh", "HSV"] = "JCh"
+ retardance,
+ orientation,
+ ret_max: Union[float, Literal["auto"]] = 10,
+ cmap: Literal["JCh", "HSV"] = "JCh",
 ):
  """
  This function will create an overlay of retardance and orientation with two different colormap options.
@@ -154,6 +157,9 @@ def ret_ori_overlay(
  f"{retardance.shape} vs. {orientation.shape}"
  )
 
+ if ret_max == "auto":
+ ret_max = np.percentile(np.ravel(retardance), 99.99)
+
  # Prepare input and output arrays
  ret_ = np.clip(retardance, 0, ret_max) # clip and copy
  # Convert 180 degree range into 360 to match periodicity of hue.