Bugfix/autofocus (#21)

* autofocus fixes

* refactor set_z_position

* update autofocus docstring

* formatting

.git-blame-ignore-revs

@@ -7,4 +7,4 @@
 # isort
 65de377b45fea923ddce70677b2364edbce16d2a
 # linting
-dd016a50659c285c27d458dd341275bb2147d240
+dd016a50659c285c27d458dd341275bb2147d240

CONTRIBUTING.md

@@ -43,4 +43,4 @@ make format # run black and isort formatting
 make lint # run flark8 linting
 make pre-commit # run pre-commit hooks on all files
 make test # run pytest
-```
+```

README.md

@@ -25,7 +25,7 @@ Data are acquired using the `run-mantis-acquisition` command. A list of the comm
 
 ```
 run-mantis-acquisition --help
-``` 
+```
 
 The mantis acquisition is configures using a YAML settings file. An example of a settings file can be found [here](mantis/acquisition/settings/example_acquisition_settings.yaml).
 
@@ -50,4 +50,4 @@ run-mantis-acquisition \\
 
 ## Contributing
 
-If you would like to contribute to this package, please read the [contributing guide](CONTRIBUTING.md)
+If you would like to contribute to this package, please read the [contributing guide](CONTRIBUTING.md)

mantis/acquisition/acq_engine.py

@@ -570,12 +570,20 @@ def go_to_position(self, position_index: int):
         microscope_operations.wait_for_device(
             self.lf_acq.mmc, self.lf_acq.mmc.get_xy_stage_device()
         )
-        # Note: moving z stage disengages autofocus
-        # microscope_operations.set_z_position(
-        #     self.lf_acq.mmc,
-        #     self.lf_acq.microscope_settings.autofocus_stage,
-        #     self.position_settings.xyz_positions[position_index][2]
-        # )
+
+        # Note: only set the z position if not using autofocus. Calling
+        # set_z_position will disengage continuous autofocus. The autofocus
+        # algorithm sets the z position independently
+        if not self.lf_acq.microscope_settings.use_autofocus:
+            microscope_operations.set_z_position(
+                self.lf_acq.mmc,
+                self.lf_acq.microscope_settings.autofocus_stage,
+                self.position_settings.xyz_positions[position_index][2],
+            )
+            microscope_operations.wait_for_device(
+                self.lf_acq.mmc,
+                self.lf_acq.microscope_settings.autofocus_stage,
+            )
 
     def setup(self):
         """

mantis/acquisition/microscope_operations.py

@@ -159,36 +159,44 @@ def get_total_num_daq_counter_samples(CtrTask: nidaqmx.Task or list):
 
 
 def autofocus(mmc, mmStudio, z_stage_name: str, z_position):
-    """_summary_
-    0000000000000000 - Off and out of range?
-    0000000100000000 - Off
-    0000001100001001 - In Range
-    0000001100001010 - In range and engaged?
-    0000001000011001 - Out of Range
-
-    Args:
-        mmc (_type_): _description_
-        mmStudio (_type_): _description_
-        z_stage_name (str): _description_
-        z_position (_type_): _description_
-
-    Returns:
-        _type_: _description_
+    """
+    Attempt to engage Nikon PFS continuous autofocus. This function will log a
+    message and continue if continuous autofocus is already engaged. Otherwise,
+    it will attempt to engage autofocus, moving the z stage by amounts given in
+    `z_offsets`, if necessary.
+
+    Nikon PFS status codes:
+        0000000000000000 - Off and out of range?
+        0000000100000000 - Off
+        0000001100001001 - In Range
+        0000001100001010 - In range and engaged?
+        0000001000011001 - Out of Range
+        0010001000001001 - ?
+
+    Returns
+    -------
+    bool
+        True if continuous autofocus successfully engaged, False otherwise.
     """
     logger.debug('Engaging autofocus')
     autofocus_success = False
     error_occurred = False
 
     af_method = mmStudio.get_autofocus_manager().get_autofocus_method()
-    z_offsets = [0, -10, 10, -20, 20, -30, 30]
+    z_offsets = [0, -10, 10, -20, 20, -30, 30]  # in um
 
-    # turn on autofocus if it has been turned off
-    if af_method.get_property_value('PFS Status') in ['0000000000000000', '0000000100000000']:
+    # Turn on autofocus if it has been turned off. This call has no effect is
+    # continuous autofocus is already engaged
+    try:
         af_method.full_focus()
+    except Exception:
+        logger.debug('Call to full_focus() method failed')
+    else:
+        logger.debug('Call to full_focus() method succeeded')
 
     if af_method.is_continuous_focus_locked():  # True if autofocus is engaged
         autofocus_success = True
-        logger.debug('Autofocus is already engaged')
+        logger.debug('Continuous autofocus is already engaged')
     else:
         for z_offset in z_offsets:
             mmc.set_position(z_stage_name, z_position + z_offset)
@@ -204,7 +212,7 @@ def autofocus(mmc, mmStudio, z_stage_name: str, z_position):
                 logger.debug(f'Autofocus call failed with z offset of {z_offset} um')
 
     if error_occurred and autofocus_success:
-        logger.debug(f'Autofocus call succeeded with z offset of {z_offset} um')
+        logger.debug(f'Continuous autofocus call succeeded with z offset of {z_offset} um')
 
     if not autofocus_success:
         logger.error(f'Autofocus call failed after {len(z_offsets)} tries')