Save HCS position label in NDTiff dataset axes (#70)

* refactor reading current mm position

* use position label instead of position index in events dict

* update hook functions

* pin ndtiff dependency

* bump iohub dependency

mantis/acquisition/acq_engine.py

@@ -397,33 +397,24 @@ def update_position_settings(self):
         """
         Fetch positions defined in the Micro-manager Position List Manager
         """
-        mm_pos_list = self.lf_acq.mmStudio.get_position_list_manager().get_position_list()
-        mm_number_of_positions = mm_pos_list.get_number_of_positions()
         autofocus_stage = self.lf_acq.microscope_settings.autofocus_stage
 
         if self.position_settings.num_positions == 0:
-            if mm_number_of_positions > 0:
-                logger.debug('Fetching position list from Micro-manager')
+            logger.debug('Fetching position list from Micro-manager')
 
-                xyz_position_list, position_labels = microscope_operations.get_position_list(
-                    self.lf_acq.mmStudio, autofocus_stage
+            xyz_positions, position_labels = microscope_operations.get_position_list(
+                self.lf_acq.mmStudio, autofocus_stage
+            )
+
+            if not xyz_positions:
+                logger.debug('Micro-manager position list is empty. Fetching current position')
+
+                xyz_positions, position_labels = microscope_operations.get_current_position(
+                    self.lf_acq.mmc, autofocus_stage
                 )
-            else:
-                logger.debug('Fetching current position from Micro-manager')
-
-                xyz_position_list = [
-                    (
-                        self.lf_acq.mmc.get_x_position(),
-                        self.lf_acq.mmc.get_y_position(),
-                        self.lf_acq.mmc.get_position(autofocus_stage)
-                        if autofocus_stage
-                        else None,
-                    )
-                ]
-                position_labels = ['Current']
 
             self.position_settings = PositionSettings(
-                xyz_positions=xyz_position_list,
+                xyz_positions=xyz_positions,
                 position_labels=position_labels,
             )
 
@@ -822,22 +813,17 @@ def acquire(self):
 
         # define LF hook functions
         if self._demo_run:
-            lf_pre_hardware_hook_fn = partial(
-                log_preparing_acquisition, self.position_settings.position_labels
-            )
+            lf_pre_hardware_hook_fn = log_preparing_acquisition
             lf_post_camera_hook_fn = None
         else:
             lf_pre_hardware_hook_fn = partial(
                 log_preparing_acquisition_check_counter,
-                self.position_settings.position_labels,
                 [self._lf_z_ctr_task, self._lf_channel_ctr_task],
             )
             lf_post_camera_hook_fn = partial(
                 start_daq_counters, [self._lf_z_ctr_task, self._lf_channel_ctr_task]
             )
-        lf_post_hardware_hook_fn = partial(
-            log_acquisition_start, self.position_settings.position_labels
-        )
+        lf_post_hardware_hook_fn = log_acquisition_start
         lf_image_saved_fn = check_lf_acq_finished
 
         # define LF acquisition
@@ -932,13 +918,13 @@ def acquire(self):
                 lf_events = deepcopy(lf_cz_events)
                 for _event in lf_events:
                     _event['axes']['time'] = t_idx
-                    _event['axes']['position'] = p_idx
+                    _event['axes']['position'] = p_label
                     _event['min_start_time'] = 0
 
                 ls_events = deepcopy(ls_cz_events)
                 for _event in ls_events:
                     _event['axes']['time'] = t_idx
-                    _event['axes']['position'] = p_idx
+                    _event['axes']['position'] = p_label
                     _event['min_start_time'] = 0
 
                 config.lf_last_img_idx = lf_events[-1]['axes']

mantis/acquisition/hook_functions/post_hardware_hook_functions.py

@@ -3,17 +3,16 @@
 logger = logging.getLogger(__name__)
 
 
-def log_acquisition_start(position_labels: list, events):
+def log_acquisition_start(events):
     if isinstance(events, list):
         _event = events[0]
     else:
         _event = events  # events is a dict
 
     t_idx = _event['axes']['time']
-    p_idx = _event['axes']['position']
-    logger.info(
-        f'Starting acquisition of timepoint {t_idx} at position {position_labels[p_idx]}'
-    )
+    p_label = _event['axes']['position']
+
+    logger.info(f'Starting acquisition of timepoint {t_idx} at position {p_label}')
 
     return events
 
@@ -35,8 +34,8 @@ def update_daq_freq(z_ctr_task, channels: list, acq_rates: list, events):
     return events
 
 
-def update_daq_freq_log_start_acq(z_ctr_task, channels, acq_rates, position_labels, events):
+def update_daq_freq_log_start_acq(z_ctr_task, channels, acq_rates, events):
     events = update_daq_freq(z_ctr_task, channels, acq_rates, events)
-    events = log_acquisition_start(position_labels, events)
+    events = log_acquisition_start(events)
 
     return events

mantis/acquisition/hook_functions/pre_hardware_hook_functions.py

@@ -10,17 +10,16 @@
 logger = logging.getLogger(__name__)
 
 
-def log_preparing_acquisition(position_labels, events):
+def log_preparing_acquisition(events):
     if isinstance(events, list):
         _event = events[0]
     else:
         _event = events  # events is a dict
 
     t_idx = _event['axes']['time']
-    p_idx = _event['axes']['position']
-    logger.debug(
-        f'Preparing to acquire timepoint {t_idx} at position {position_labels[p_idx]}'
-    )
+    p_label = _event['axes']['position']
+
+    logger.debug(f'Preparing to acquire timepoint {t_idx} at position {p_label}')
 
     return events
 
@@ -44,8 +43,8 @@ def check_num_counter_samples(ctr_tasks, events):
     return events
 
 
-def log_preparing_acquisition_check_counter(position_labels, ctr_tasks, events):
-    events = log_preparing_acquisition(position_labels, events)
+def log_preparing_acquisition_check_counter(ctr_tasks, events):
+    events = log_preparing_acquisition(events)
     events = check_num_counter_samples(ctr_tasks, events)
 
     return events

mantis/acquisition/microscope_operations.py

@@ -74,11 +74,11 @@ def get_position_list(mmStudio, z_stage_name):
     mm_pos_list = mmStudio.get_position_list_manager().get_position_list()
     number_of_positions = mm_pos_list.get_number_of_positions()
 
-    xyz_position_list = []
+    xyz_positions = []
     position_labels = []
     for i in range(number_of_positions):
         _pos = mm_pos_list.get_position(i)
-        xyz_position_list.append(
+        xyz_positions.append(
             [
                 _pos.get_x(),
                 _pos.get_y(),
@@ -87,7 +87,20 @@ def get_position_list(mmStudio, z_stage_name):
         )
         position_labels.append(_pos.get_label())
 
-    return xyz_position_list, position_labels
+    return xyz_positions, position_labels
+
+
+def get_current_position(mmc, z_stage_name):
+    xyz_position = [
+        (
+            mmc.get_x_position(),
+            mmc.get_y_position(),
+            mmc.get_position(z_stage_name) if z_stage_name else None,
+        )
+    ]
+    position_label = ['Current']
+
+    return xyz_position, position_label
 
 
 def set_z_position(mmc, z_stage_name: str, z_position: float):

pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
 
 # list package dependencies here
 dependencies = [
-  "iohub==0.1.0.dev4",
+  "iohub==0.1.0.dev5",
   "matplotlib",
   "napari; 'arm64' in platform_machine",                 # without Qt5 and skimage
   "napari[all]; 'arm64' not in platform_machine",        # with Qt5 and skimage