PSF measurement, simulation, and deconvolution (#130)

* Create measure_psf.py

* partial psf analysis report

* update psf analysis report

* refactor psf analysis

* refactor psf analysis report

* add report on deskewed data

* initial psf simulations

* GPU peak detection with torch (#129)

* GPU peak detection with torch

* update bead detector

* update psf measurement script

* style

---------

Co-authored-by: Ivan Ivanov <[email protected]>

* ignore psf analysis warnings

* update script with acquisition settings

* better paths formatting

* better paths formatting

* update measurement script

* add html report title

* update psf analysis scripts

* typo

* update dependencies

* larger PSF area

* main fitting script

* simple_psf iteration

* deconvolution prototype

* settings

* cutsom patch size

* deconvolve CLI

* psf-from-beads CLI

* cli boilerplate

* update psf measurement scripts

* first-pass characterize

* fix css issue

* napari-psf-analysis is breaking fresh installations

* auto-open webbrowser

* handle negative with ints and clips

* pass in axis labels

* average beads over multiple FOVs

* adding WIP changes, used for most recent deconvolutions

* style

* add napari-psf-analysis dependency

* refactor characterize cli

* more characterize refactor

* use characterize_peaks in measure_psf

* clean up measure_psf analysis portion

* bugfix

* delete unused scripts

* remove unused _deskew_matrix

* test for incorrectlyt shifted deskew

* correct typo in test

* fix deskew regression

* style

* extend O3 scan range

* Update measure_psf.py

* fix overflow bug

* Update measure_psf.py

* style

* cleanup

* rename psf functions

* Update mantis/cli/characterize_psf.py

Co-authored-by: Talon Chandler <[email protected]>

* Update mantis/cli/estimate_psf.py

Co-authored-by: Talon Chandler <[email protected]>

---------

Co-authored-by: Ivan Ivanov <[email protected]>
Co-authored-by: Ziwen Liu <[email protected]>

.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
         ):