PSF measurement, simulation, and deconvolution

.flake8

@@ -37,3 +37,4 @@ exclude =
     ignore,
     legacy,
     examples,
+    scripts

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^(docs|notebooks|ignore|/tests/artifacts|examples)/
+exclude: ^(docs|notebooks|ignore|/tests/artifacts|examples|scripts)/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.1.0

Makefile

@@ -10,12 +10,12 @@ uninstall:
 
 .PHONY: check-format
 check-format:
-	black --check -S -t py39 .
+	black --check -S -t py310 .
 	isort --check .
 
 .PHONY: format
 format:
-	black -S -t py39 .
+	black -S -t py310 .
 	isort .
 
 .PHONY: lint

mantis/acquisition/acq_engine.py

@@ -807,8 +807,8 @@ def refocus_ls_path(self):
         # Define relative travel limits, in steps
         o3_z_stage = self.ls_acq.o3_stage
         target_z_position = o3_z_stage.true_position + o3_z_range
-        max_z_position = 500  # O3 is allowed to travel ~10 um towards O2
-        min_z_position = -1000  # O3 is allowed to travel ~20 um away from O2
+        max_z_position = 750  # O3 is allowed to travel ~15 um towards O2
+        min_z_position = -1500  # O3 is allowed to travel ~30 um away from O2
         if np.any(target_z_position > max_z_position) or np.any(
             target_z_position < min_z_position
         ):