Automated Analysis - GoldbergLab/RodentJoystick GitHub Wiki

#Automated Analysis Organization All automated analysis is run through the auto_anlys_gui application, which handles multiple aspects of the automated analysis, including post processing, writing logs, displaying mouse performance, and recommending contingency updates.

#How to Use auto_anlys_gui

images/auto_anlys_gui.PNG

  • A: First select an experiment directory. Data to be analyzed should be in a subdirectory called 'data' (See Core Analysis for more information about expected file organization).
  • B: Once an experiment directory has been selected, and provided there are folders in the directory containing analyzed data (See Core Analysis for what this constitutes), the recommend button will retrieve information about mice performance and display them on the panels G for all 4 boxes if available. It will also recommend contingency updates based on the parameters specified by C, E, F. The blue computing flag is to indicate when the GUI is busy retrieving this information. Currently, the GUI supports automatic contingency updates. This is what the automate checkbox and "Update" button do. However, since automatic contingency updates are not supported by the LabVIEW software at this time, the GUI simply just writes text files to the experiment directory and stores old contingency writings to a folder called ArchivedContingencies in the experiment directory.
  • C: When recommending the next contingency, the GUI only computes recommendation for one component of the contingency - this panel selects which component to compute.
  • D: When retrieving information, this panel instructs how many days to select. 1 selects the most recent analyzed day, 2 selects the last two most recent analyzed days.
  • E: The reward rate to compute recommended contingencies for the next day.
  • F: This feature (by default) ensures that if a mouse received an unsually low pellet count, the recommended contingency will be the same, even if performance suggests a more difficult task.
  • G: Panel displaying mouse performance, current contingency, and suggested changes.
  • H: Automated Post Processing Control - Enter a time (in 24 hr format, colon separated), and hit start. Automated post processing will be run at that time every 24 hours. Note that once a time is entered, it is not sufficient to simply change the time in the text box. You must stop and restart the analysis timer to change the timing.

#auto_anlys_gui Design and Documentation There are several supporting functions/scripts in the Automation Folder. For more specific information, see the function documentation:

  • auto_anlys_gui.m (main gui).
  • directories_to_do identifies all data directories that need post processing in the data folder.
  • scheduled_analysis performs a suite of functions related to automated post processing. Besides immediate post processing, this function also handles log writes, and supports email notifications.
  • init_automated_analysis returns a matlab timer object that periodically executes scheduled analysis.
  • matlabmailcpy is a copy of the mail notification system. to use, this should be copied to an outside folder, renamed matlabmail, and then passwords can be added.
  • update_all_boxes_anlys_gui is called to update the information on the G panels
  • recommend_contingencies is called to update the recommendations and handles some of the logic. Currently only the inner threshold recommendation is nontrivial (uses js_touch_dist). This file should be changed to add support for computing other features.