Merge pull request #769 from int-brain-lab/iblrigv8dev

8.27.3

CHANGELOG.md

@@ -1,6 +1,13 @@
 Changelog
 =========
 
+8.27.3
+------
+* changed: reset camera(s) prior to starting task when inconsistencies have been detected
+* changed: include stock subjects if user is stock manager
+* changed: skip validation of Ambient Module if device_bpod.USE_AMBIENT_MODULE is false
+* added: `remove_bonsai_layouts` command for troubleshooting BONSAI GUIs not appearing 
+
 8.27.2
 ------
 * fixed: error when using task arguments of type bool

docs/source/faq.rst

@@ -93,6 +93,15 @@ Camera Issues
    *  If you use a USB 3.1 Host Controller Card check if it requires additional powering through a SATA or Molex cable.
       FLIR offers `a few models <https://www.flir.com/products/usb-3.1-host-controller-card>`_ that should work fine.
 
+*  If the BONSAI panels for the video live view do not show up there might be an issue with the
+   `BONSAI layout settings <https://bonsai-rx.org/docs/articles/editor.html#visualizer-layout-settings>`_.
+   To reset these layout settings, run the following in PowerShell:
+
+   .. code::
+
+      C:\iblrigv8\venv\scripts\Activate.ps1
+      remove_bonsai_layouts
+
 
 Frame2TTL
 =========

docs/source/usage_video.rst

@@ -62,7 +62,7 @@ Below shows how to start the cameras for the subject 'example' with configuratio
 
    cd C:\iblrigv8\
    venv\scripts\Activate.ps1
-   start_video_session example default
+   start_video_session --subject_name example --profile default
 
 Copy command
 ------------

iblrig/__init__.py

@@ -6,4 +6,4 @@
 # 5) git tag the release in accordance to the version number below (after merge!)
 # >>> git tag 8.15.6
 # >>> git push origin --tags
-__version__ = '8.27.2'
+__version__ = '8.27.3'

iblrig/base_tasks.py

@@ -806,11 +806,14 @@ def start_mixin_bonsai_cameras(self):
         if (workflow_file := self._camera_mixin_bonsai_get_workflow_file(configuration, 'setup')) is None:
             return
 
+        # test acquisition and reset cameras if needed
         # enable trigger of cameras (so Bonsai can disable it again ... sigh)
         if PYSPIN_AVAILABLE:
-            from iblrig.video_pyspin import enable_camera_trigger
+            from iblrig import video_pyspin
 
-            enable_camera_trigger(True)
+            if not video_pyspin.acquisition_ok():
+                video_pyspin.reset_all_cameras()
+            video_pyspin.enable_camera_trigger(True)
 
         call_bonsai(workflow_file, wait=True)  # TODO Parameterize using configuration cameras
         log.info('Bonsai cameras setup module loaded: OK')

iblrig/commands.py

@@ -365,3 +365,22 @@ def flush():
     bpod = Bpod(hardware_settings['device_bpod']['COM_BPOD'])
     bpod.flush()
     bpod.close()
+
+
+def remove_bonsai_layouts():
+    """Delete all BONSAI .layout files - if they are backed up with a .layout_template file."""
+    from iblrig.constants import BASE_PATH
+
+    layout_files = [x for x in BASE_PATH.glob('**/*.bonsai.layout') if x.with_suffix('.layout_template').exists()]
+    if len(layout_files) == 0:
+        print('No layout files found.')
+        return
+    print('The following files will be deleted:')
+    for f in layout_files:
+        print(f'- {f.name}')
+    if input('\nContinue? [Y/n] ').lower() in ('y', ''):
+        for f in layout_files:
+            f.unlink()
+        print(f'{len(layout_files)} file{"s" if len(layout_files) > 1 else ""} deleted.')
+    else:
+        print('No files deleted.')

iblrig/gui/wizard.py

@@ -254,10 +254,13 @@ def login(
                 )
             QtWidgets.QMessageBox().critical(None, 'Error', f'{message}\n\n{solution}')
 
-        # get subjects from Alyx: this is the set of subjects that are alive and not stock in the lab defined in settings
-        rest_subjects = self.alyx.rest(
-            'subjects', 'list', alive=True, stock=False, lab=self.iblrig_settings['ALYX_LAB'], no_cache=True
-        )
+        # get subjects from Alyx: this is the set of subjects that are alive and in the lab defined in settings
+        # stock subjects are excluded, unless the user is stock manager
+        kwargs = {'alive': True, 'lab': self.iblrig_settings['ALYX_LAB'], 'no_cache': True}
+        is_stock_manager = any(self.alyx.rest('subjects', 'list', responsible_user=self.user, stock=True, limit=1, **kwargs))
+        if not is_stock_manager:
+            kwargs['stock'] = False
+        rest_subjects = self.alyx.rest('subjects', 'list', **kwargs)
         self.all_subjects.remove(self.test_subject_name)
         self.all_subjects = [self.test_subject_name] + sorted(set(self.all_subjects + [s['nickname'] for s in rest_subjects]))
 

iblrig/hardware_validation.py

@@ -301,6 +301,11 @@ class ValidatorAmbientModule(Validator):
     _name = 'Bpod Ambient Module'
 
     def _run(self):
+        # skip if ambient module is not being used
+        if not self.hardware_settings.device_bpod.USE_AMBIENT_MODULE:
+            yield Result(Status.SKIP, 'Ambient module is not being used - skipping validation')
+            return False
+
         # yield Bpod's connection status
         bpod = yield from self._get_bpod()
         if bpod is None:

iblrig/pydantic_definitions.py

@@ -96,6 +96,7 @@ class HardwareSettingsBpod(BunchModel):
     SOUND_BOARD_BPOD_PORT: Literal['Serial1', 'Serial2', 'Serial3', 'Serial4', 'Serial5', None] = None
     ROTARY_ENCODER_BPOD_PORT: Literal['Serial1', 'Serial2', 'Serial3', 'Serial4', 'Serial5', None] = None
     DISABLE_BEHAVIOR_INPUT_PORTS: list[BehaviourInputPort] = [2, 3, 4]
+    USE_AMBIENT_MODULE: bool = True
 
 
 class HardwareSettingsFrame2TTL(BunchModel):

iblrig/test/test_meta.py

@@ -0,0 +1,10 @@
+import unittest
+from collections.abc import Callable
+from importlib.metadata import entry_points
+
+
+class TestEntryPoints(unittest.TestCase):
+    def test_entry_points(self) -> None:
+        for ep in [ep for ep in entry_points(group='console_scripts') if ep.value.startswith('iblrig.')]:
+            loaded_ep = ep.load()  # this throws a ModuleNotFound error if the entry-point is invalid
+            assert isinstance(loaded_ep, Callable)

iblrig/video_pyspin.py

@@ -1,34 +1,159 @@
 import logging
+import time
 
 import PySpin
 
 log = logging.getLogger(__name__)
 
 
 class Cameras:
+    """A class to manage camera instances using the PySpin library.
+
+    This class provides a context manager for initializing and deinitializing
+    cameras. It ensures that cameras are properly initialized when entering
+    the context and deinitialized when exiting.
+    """
+
     _instance = None
 
     def __init__(self, init_cameras: bool = True):
+        """Initializes the Cameras instance.
+
+        Parameters
+        ----------
+        init_cameras : bool, optional
+            If True, initializes the cameras upon creation of the instance (default is True).
+        """
         self._instance = PySpin.System.GetInstance()
         self._cameras = self._instance.GetCameras()
-        if not init_cameras:
-            return
-        for camera in self._cameras:
-            camera.Init()
+        self._init_cameras = init_cameras
+        if init_cameras:
+            for camera in self._cameras:
+                camera.Init()
 
     def __enter__(self) -> PySpin.CameraList:
+        """Enters the runtime context related to this object.
+
+        Returns
+        -------
+        PySpin.CameraList
+            The list of initialized cameras.
+        """
         return self._cameras
 
     def __exit__(self, *_):
+        """Exits the runtime context related to this object.
+
+        Deinitializes the cameras if they were initialized and releases the system instance.
+        """
+        if self._init_cameras:
+            for camera in self._cameras:
+                camera.DeInit()
+            del camera  # Clean up the camera reference
         self._cameras.Clear()
         self._instance.ReleaseInstance()
 
     @property
     def instance(self):
+        """Gets the singleton instance of the PySpin system.
+
+        Returns
+        -------
+        PySpin.System
+            The singleton instance of the PySpin system.
+        """
         return self._instance
 
 
+def acquisition_ok() -> bool:
+    """Test image acquisition for all available cameras.
+
+    This function attempts to acquire an image from each camera and checks if the acquisition
+    was successful. It logs the results of the acquisition test for each camera.
+
+    Returns
+    -------
+    bool
+        True if all cameras successfully acquired an image, False otherwise.
+    """
+    success = True
+    with Cameras() as cameras:
+        for camera in cameras:
+            log.debug(f'Testing image acquisition with camera #{camera.DeviceID()}')
+            camera.BeginAcquisition()
+            try:
+                image = camera.GetNextImage(1000)
+                if image.IsValid() and image.GetImageStatus() == PySpin.SPINNAKER_IMAGE_STATUS_NO_ERROR:
+                    log.info(f'Acquisition test for camera #{camera.DeviceID()} was successful.')
+                else:
+                    log.error(f'Inconsistency detected during acquisition test for camera #{camera.DeviceID()}.')
+                    success = False
+            except PySpin.SpinnakerException as e:
+                log.error(f'Acquisition test for camera #{camera.DeviceID()} failed with an exception: {e.message}')
+                success = False
+            else:
+                if image.IsValid():
+                    image.Release()
+            finally:
+                camera.EndAcquisition()
+        del camera
+    return success
+
+
+def reset_all_cameras():
+    """Reset all available cameras and wait for them to come back online.
+
+    This function initializes each camera, attempts to reset it, and then deinitializes it.
+    After resetting, it waits for all cameras to come back online, logging the status of each camera.
+    """
+    with Cameras(init_cameras=False) as cameras:
+        if len(cameras) == 0:
+            return
+
+        # Iterate through each camera and reset
+        for camera in cameras:
+            camera.Init()
+            try:
+                camera.DeviceReset()
+            except PySpin.SpinnakerException as e:
+                log.error(f'Error resetting camera #{camera.DeviceID()}: {e}')
+            else:
+                log.info(f'Resetting camera #{camera.DeviceID.ToString()} ...')
+            finally:
+                camera.DeInit()
+
+        # Wait for all cameras to come back online
+        log.info(f'Waiting for {"camera" if len(cameras) == 1 else "cameras"} to come back online (~10 s) ...')
+        all_cameras_online = False
+        while not all_cameras_online:
+            all_cameras_online = True
+            for camera in cameras:
+                try:
+                    camera.Init()
+                except PySpin.SpinnakerException:
+                    all_cameras_online = False
+                else:
+                    log.info(f'Camera #{camera.DeviceID()} is back online.')
+                    camera.DeInit()
+            if not all_cameras_online:
+                time.sleep(0.2)
+        del camera
+
+
 def enable_camera_trigger(enable: bool, camera: PySpin.CameraPtr | None = None):
+    """Enable or disable the trigger for a specified camera or all cameras.
+
+    This function allows you to enable or disable the trigger mode for a given camera.
+    If no camera is specified, it will enable or disable the trigger mode for all available cameras.
+
+    Parameters
+    ----------
+    enable : bool
+        A flag indicating whether to enable (True) or disable (False) the camera trigger.
+    camera : PySpin.CameraPtr | None, optional
+        A pointer to a specific camera instance. If None, the function will apply the trigger setting
+        to all cameras managed by the Cameras context manager (default is None).
+    """
     if camera is None:
         with Cameras() as cameras:
             for cam in cameras:
@@ -39,4 +164,4 @@ def enable_camera_trigger(enable: bool, camera: PySpin.CameraPtr | None = None):
         node_trigger_mode = PySpin.CEnumerationPtr(node_map.GetNode('TriggerMode'))
         node_trigger_mode_value = node_trigger_mode.GetEntryByName('On' if enable else 'Off').GetValue()
         node_trigger_mode.SetIntValue(node_trigger_mode_value)
-        log.debug(('Enabled' if enable else 'Disabled') + f' trigger for camera #{camera.DeviceID.ToString()}.')
+        log.debug(('Enabled' if enable else 'Disabled') + f' trigger for camera #{camera.DeviceID()}.')