Merge pull request #678 from int-brain-lab/iblrigv8dev

8.20.0

CHANGELOG.md

@@ -1,7 +1,13 @@
 Changelog
----------
+=========
 
 
+8.20.0
+------
+* tab for displaying local sessions and their respective status
+* additional task parameters for passiveChoiceWorld
+* work on making the GUI code more modular
+
 8.19.6
 ------
 * hotfix: fix race-condition that caused scrambled online-plots
@@ -43,16 +49,22 @@ Changelog
 * add ambient sensor reading back to trial log
 * allow negative stimulus gain (reverse wheel contingency)
 
+-------------------------------
+
 8.18.0
 ------
 * valve calibration routine
 
+-------------------------------
+
 8.17.0
 ------
 * consolidated data transfer routine across all rig computers
 * new video workflow with support for multiple named camera setups
 * various small fixes, work on documentation, unit-tests
 
+-------------------------------
+
 8.16.1
 ------
 * Hoferlab: when bpod returns inconsistent error, time-out or correct, throw the exception after logging
@@ -64,6 +76,8 @@ Changelog
 * Support for Zapit Optostim (NM)
 * more robust handling of Bpod's serial messages: iblrig.hardware._define_message
 
+-------------------------------
+
 8.15.6
 ------
 * Task specifications: The time from the stimulus offset to the quiescence period is targeted to 1 second instead of 1.5 seconds
@@ -100,6 +114,8 @@ Changelog
 * feature: calibration routine for frame2ttl v1-3 in Tools menu
 * feature: debug-flag for IBLRIG Wizard
 
+-------------------------------
+
 8.14.2
 ------
 * hotfix: wrong return-type in _iterate_protocols - pt 2
@@ -112,6 +128,8 @@ Changelog
 ------
 * show dialog boxes and plots for appended sessions
 
+-------------------------------
+
 8.13.5
 ------
 * make sure unused arguments passed up to BaseChoiceWorld do not crash the task (example delay_secs in passiveChoiceWorld)
@@ -147,6 +165,8 @@ Changelog
 * cleaned-up logging
 * various improvements under the hood, clean-up and unit-tests
 
+-------------------------------
+
 8.12.13
 -------
 * fix problem with corrupt acquisition descriptions in history

docs/source/changelog.rst

@@ -0,0 +1,2 @@
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.sphinx_

docs/source/faq.rst

@@ -75,6 +75,23 @@ session? To redefine the default position and size of the Bonsai visualizer:
 #. Save the workflow.
 
 
+Camera Issues
+=============
+
+*  If a camera is not detected by the computer or causes intermittent issues it might be an issue with the USB connection.
+
+   *  Ensure that the camera is connected to the computer on a USB3 port (usually indicated by a blue plastic tab in the port).
+      USB2 (black tabs) neither provides the necessary transfer rates nor sufficient current to power the camera.
+   *  Use the `original USB3.1 cable <https://www.flir.com/products/usb-3.1-locking-cable>`_ provided by FLIR.
+      It comes in 3 m or 5 m - stick with the shorter version if possible.
+   *  Try to avoid USB extensions.
+      The original cable (see above) should be sufficiently long in most situations.
+   *  Ideally, use one of the onboard USB3 ports of your computer facing to the back of the machine.
+      Front-facing ports may not be able to provide enough power.
+   *  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.
+
+
 Frame2TTL
 =========
 

docs/source/index.rst

@@ -1,13 +1,8 @@
-.. iblrig documentation master file, created by
-   sphinx-quickstart on Tue Jun 20 15:51:34 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 IBLRIG documentation
 ====================
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: Contents:
 
    installation
@@ -16,3 +11,8 @@ IBLRIG documentation
    hardware
    reference_developer_guide
    faq
+
+.. toctree::
+   :maxdepth: 1
+
+   changelog

iblrig/__init__.py

@@ -6,7 +6,7 @@
 # 5) git tag the release in accordance to the version number below (after merge!)
 # >>> git tag 8.15.6
 # >>> git push origin --tags
-__version__ = '8.19.6'
+__version__ = '8.20.0'
 
 
 from iblrig.version_management import get_detailed_version_string

iblrig/base_choice_world.py

@@ -625,7 +625,7 @@ class ActiveChoiceWorldSession(ChoiceWorldSession):
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
-        self.trials_table['stim_probability_left'] = np.zeros(NTRIALS_INIT, dtype=np.float32)
+        self.trials_table['stim_probability_left'] = np.zeros(NTRIALS_INIT, dtype=np.float64)
 
     def _run(self):
         # starts online plotting

iblrig/base_tasks.py

@@ -22,6 +22,7 @@
 from pathlib import Path
 
 import numpy as np
+import pandas as pd
 import scipy.interpolate
 import serial
 import yaml
@@ -732,7 +733,9 @@ def run_passive_visual_stim(self, map_time='00:05:00', rate=0.1, sa_time='00:05:
             'Stim.ReceptiveFieldMappingStim.MappingTime': map_time,
             'Stim.ReceptiveFieldMappingStim.Rate': rate,
         }
-        log.info('Starting spontaneous activity and RF mapping stims')
+        map_seconds = pd.to_timedelta(map_time).seconds
+        sa_seconds = pd.to_timedelta(sa_time).seconds
+        log.info(f'Starting spontaneous activity ({sa_seconds} s) and RF mapping stims ({map_seconds} s)')
         s = call_bonsai(workflow_file, parameters, editor=False)
         log.info('Spontaneous activity and RF mapping stims finished')
         return s

iblrig/constants.py

@@ -23,3 +23,7 @@
     HAS_PYSPIN = False
 PYSPIN_AVAILABLE = HAS_SPINNAKER and HAS_PYSPIN
 COPYRIGHT_YEAR = 2024
+URL_DOC = 'https://int-brain-lab.github.io/iblrig'
+URL_REPO = 'https://github.com/int-brain-lab/iblrig/tree/iblrigv8'
+URL_ISSUES = 'https://github.com/int-brain-lab/iblrig/issues'
+URL_DISCUSSION = 'https://github.com/int-brain-lab/iblrig/discussions'

iblrig/gui/resources.qrc

@@ -1,5 +1,7 @@
 <RCC>
   <qresource prefix="images">
+    <file alias="sessions">resources/icon_sessions.svg</file>
+    <file alias="clipboard">resources/icon_clipboard.svg</file>
     <file alias="validation_pending">resources/icon_validation_pending.svg</file>
     <file alias="logo_ibl">resources/logo_ibl.svg</file>
     <file alias="validation_warn">resources/icon_validation_warn.svg</file>