Finalise for release 6.1

[teddychao]

General

• Minimum version of MATLAB
  • The minimum version of MATLAB required for running PsPM is MATLAB 7.1 or R14 Service Pack 3 (https://uk.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/SystemRequirements-Release14-ServicePack3_SupportedCompilers.pdf) (Find out minimum MATLAB version #20).
• Entering PsPM
  • Entering PsPM is now hybrid based on the version of MATLAB, namely through AppDesigner or Guide. PsPM will be entered through AppDesigner when supported and through Guide for older versions of MATLAB. To call PsPM, users should still use the command pspm in the Command Window of MATLAB, where the appropriate way of entering PsPM will be recognised automatically.
  • Users can still use their preferred way to enter PsPM. To enter PsPM through AppDesigner, please type pspm_appdesigner. To enter PsPM through Guide, which is the classic entrance, please type pspm_guide.
  • The AppDesigner version of PsPM UI is newly introduced by MATLAB and the encouraged way for launching PsPM, and it has no functionality difference than the Guide version of PsPM UI.
  • Both AppDesigner and Guide are designed and tested for Windows, macOS (either Intel or Apple Silicon) and Linux. Issues of opening PsPM through either of the two UI systems are encouraged to be reported to PsPM developing group at GitHub.
• Introducing pspm_options (Streamline options input between functions #385, Option values for pspm_dcm, pspm_dcm_inv and pspm_get_rf #426, The initial values of channel for some functions #430)
  • A new function pspm_options is introduced to PsPM for controlling the default and acceptable values of the struct options used by most PsPM functions. The default values of the fields in the struct options for various functions can be directly checked by searching in pspm_options.
  • The default values in pspm_options have been checked and tested for PsPM. If preferred values are different from defaults, users can specify them when calling the corresponding PsPM functions, and the corresponding functions and pspm_options will always respect the users' specification with the highest priority. However, the user's specification needs to satisfy the condition set in pspm_options, and invalid values may be reported as errors.
• UI Improvements (Fix pspm_display and heart beat detection #488)
  • The UI for the following features has been improved and tested
    • Launchpad (AppDesigner)
    • Launchpad (Guide)
    • Batch editor
    • Display data
    • Contrast manager
• Help text
  • The help text has been updated for all PsPM functions. Help text can be checked by right clicking the functions. An example of checking the help text of a PsPM function is shown below (Sort out help text #372, Some function headers do not contain the right names #419).

Bug Fixes

• UI
  • A bug that used to make PsPM crash when Pupil size convert and Gaze convert in Data Preprocessing were selected has been fixed (Some items do not work in the main GUI #475).
  • A bug that leads to error when PsPM is started offline has been fixed (PsPM does not start offline #514).
  • A bug that leads to incorrect x labels in pspm_rev_dcm has been fixed (Wrong x-tick labels in pspm_rev_dcm #495).
• pspm_convert_...
  • A bug that leads PsPM to crash, which is caused by outdated UI calling for pspm_convert_... functions, has been fixed (Unable to convert ECG data to Heart Rate Period #508).
• pspm_get_eyelink
  • A bug that causes issues when importing eye link data that is scanned at both left and right sides has been fixed (Different use of the keyword lr for eyes observed or signals #479, Eyes observed incorrectly inherit eye marker #509).
• pspm_glm
  • A bug that incorrectly identifies the NaNs in the input data has been fixed (Generalising missing epoch sorting into pspm_get_timing #499, fix issue 499 #513).
• pspm_sf
  • A bug that has lead to incorrect input datafile assigning has been fixed (Review and fix bugs in pspm_sf #370).
  • A bug that leads PsPM crash when pspm_sf is analysing data with missing epochs has been fixed (Missing epoch issue of pspm_sf #484).
  • A bug that leads to error when pspm_sf analyses data where time unit is defined as marker has been fixed (pspm_sf has issues when processing data whose unit is defined by marker #503).
• pspm_split_sessions
  • pspm_split_sessions now considers marker_chan_num when calling pspm_trim (Fix pspm_split_sessions #506).

Improvements

• channel (Legacy use of chan #470, Compatibility of chantype #478, Load_data checking logic #497)
  • We have generalised the channel related variables throughout PsPM, which are given as
    • chan/channel → channel
    • chans/channels → channels
    • channel_units/channels_units/chan_units/chans_units → channel_units
    • chan_combine → channel_combine
    • chan_action → channel_action
    • channels_header → channel_header
    • chantype → channeltype
• import_eyelink
  • Improved import_eyelink for adding some support for importing eyelink data converted by higher version of .EDF files. (Fail to import pupil size data (.asc) #459 and Eyelink (.asc) import issue #465)
• pspm_con2
  • pspm_con2 is now using pspm_overwrite (Missing overwrite behaviour in pspm_con2 #422).
• pspm_dcm and pspm_dcm_inv
  • .flexevents and .fixevents are now fields of model instead of options (Unsorted fields between model and options in pspm_dcm #458).
  • pspm_dcm now uses pspm_get_timing to handle missing epochs (Generalising missing epoch sorting into pspm_get_timing #499).
  • Improved missing epoch support
    • The field .missing is now allocated from options to model (Generalise missing epochs allocation #491).
    • .missing_data is used to load missing epoch data that was loaded from dcm, as an optional field (Generalise missing epochs allocation #491).
  • The index is changed so that the first event will not be excluded when at time 0 in session (pspm_dcm incorrectly assign first value of dcm.stats to be always NaN #504).
• pspm_extract_segments
  • The first channel is always referred by marker_chan as default (marker_chan / marker_chan_num unclearly defined #427).
• pspm_glm
  • The fallback for options.exclude_missing has been set for pspm_glm, which is not to exclude any missing epochs (Two fields of options in pspm_glm #429).
  • A bug that leads to incorrect missing epoch checking has been fixed (pspm_glm produce no results when facing many short missing epochs #338).
  • Help text was updated (Help text misleading in pspm_glm #467).
  • marker_chan_num now refers to the first marker channel as default (marker_chan / marker_chan_num unclearly defined #427).
  • pspm_glm now uses pspm_get_timing to handle missing epochs (Generalising missing epoch sorting into pspm_get_timing #499).
• pspm_interp1
  • pspm_interp1 now considers the data where no valid values are detected and interpolation is not possible, and warnings will be reported in this case (pspm_interp1 needs to consider data without valid values #500).
• pspm_merge
  • The default value is set to be [1,2], meaning the first channel will be merged as the default option (marker_chan / marker_chan_num unclearly defined #427).
• pspm_prepdata
  • pspm_prepdata now uses interpolation to handle data with NaN. (Implement a new NaN handling strategy for pspm_prepdata #35, 434)
    • Data that begins and/or ends with NaN will be filled with the first/last non-NaN values in those positions.
• pspm_sf
  • pspm_sf now supports missing epochs (Enable data with NaN for pspm_sf_dcm #457).
    • Now allow input with NaN that indicates missing epochs.
    • Missing epochs can be specified with options.missing or the automatic NaN detection.
    • Missing epochs will be verified with options.missingthresh.
    • When the missing epochs are longer than 2s, the result out will be converted to [].
    • The UI of SF analysis now allows using missing epochs from files or not to define any missing epochs.
  • pspm_sf now uses pspm_get_timing to handle missing epochs (Generalising missing epoch sorting into pspm_get_timing #499).
  • marker_chan_num now refers to the first marker channel as default (marker_chan / marker_chan_num unclearly defined #427).
• pspm_sf_dcm
  • pspm_sf_dcm now uses pspm_interp1 for interpolating data (Generalise missing epochs allocation #491).
• pspm_text
  • The Matlab file that stores the information of help text pspm_text.mat will be stored inside the source folder of PsPM and will be deleted when PsPM is quit (Path to save pspm_text.mat #450).
• pspm_trim
  • marker_chan_num now refers to the first marker channel as default (marker_chan / marker_chan_num unclearly defined #427).

Minor Adjustments

• pspm_sf, pspm_glm and pspm_dcm (GLM select incorrect default channel #490, Fix issue 490 --- generalising first marker channel and last data channel #493)
  • The option marker_chan_num_event is removed.
  • In default, the first marker channel / event channel is always selected and no users' customisation is allowed.
  • The last data channel / wave channel is always selected.

Reference document

• New document PsPM Reference for checking the default values and restrictions of options fields (Manual updates #432).

User-interface improvement

Launchpad, AppDesigner

Mac

Windows

Launchpad, Guide

Mac

Windows

Batch Editor

Mac

Windows

Display

Mac

Windows

Contrast Manager

Mac

Windows

[dominikbach]

some last fixes in pull request 522

[teddychao]

Hi @uzaygokay I noticed pspm_display was not working very well when you visualise the PPG data. Please check this version if you are interested to see if it gets improved data and metadata display. Thanks