Release 7.0

[teddychao]

Release 7.0

Status: Completed checking PRs listed below and updating the documents.

Checked PRs

• PR Stylise the titles of functions uniformly #205
• PR A global variable refering to the GUI plotting window #407
• PR Update python handling and tests #658 fixes create tests for pspm_check_python and pspm_check_python_modules  #649
• PR fix pspm_pp options call #681 fixes Bug in pspm_pp #680
• PR Update help text in export GUI #683
• PR Refactor pspm_interpolate #684 fixes Refactor pspm_interpolate #673
• PR Unify function output #689 fixes pspm_write_channel variable assignment #421, Streamline function output #519, Improve pspm_write_channel #624
• PR Minor improvements to pspm_extract_segments #690
• PR Small fix in pspm_select_channel #691
• PR Fix markerinfo handling #695 fixes bug in pspm_get_markerinfo #670 and problem running GLM with conditions created from markerinfo #672.
• PR Improve pspm_trim to handle missing epoch files #696 fixes pspm_trim should allow trimming a related missing epochs file #569
• PR Test missing handling in GLM #699 fixes PsPM GLM for PS: exclude_missing settings #346
• PR Improve pmod handling in pspm_glm #700 fixes Parameter modulation only for several conditions, not all #191 and Initialise pmod structure in pspm_glm #195
• PR Improve eyelink #702 fixes specify prefered "markers" to be imported from eyelink .asc data #602
• PR update references in help texts #703 fixes Update references in help text #622
• PR Add new option to DCM #704
• PR Helper function to process multiple channels at a time #705 fixes multiple bugs in pupil and gaze preprocessing #678
• PR Cleanup GUI #706 fixes GUI issues in version 6.1.1 #591, Artefact removal does not have change_data in the GUI #599, Update GUI for segment extracting #671, Check main GUI and make sure deprecated modules are removed #687, Upgrade segment_mean or remove #688, Test missing handling in GLM #699, Issue of the item "data convert" under "tools" #715
• PR Fix load channel #707
• PR Wrong y label corrected #709 fixes pspm_data_editor displays wrong y label #570
• PR fix options handling in pspm_extract_segments #710
• PR Fix issue 668 -- added path handling in pspm_init and pspm_quit #713 fixes Path handling in pspm_init and pspm_quit #668
• PR Fix issue 698 -- new GUI #714 fixes New GUI for PsPM 7.0 #698
• PR Fix issue 698 - new UI #716 fixes New GUI for PsPM 7.0 #698
• PR Fix issue 718 -- display #723 fixes Warning when running Display with full file path #718
• PR Fix issue 717 -- data_editor #724 fixes Data editor does not show output file #717
• PR Fix issue 676 -- adjust UI #725 fixes Minor UI adjustment #676, Older-version MATLAB poorly supports AppDesigner #523
• PR Unifying GUI #728
• PR add new HPR-reward model #729 fixes Implement new HPR model #579
• PR Fix issue 733 #734 fixes Spliting acqread and acqread_python from pspm_get_acq #733
• PR fix edge case of empty epochs file in pspm_trim #736
• PR Fix issue 738 #739 fixes PsPM display issue #738
• PR Fix issue 740 #741 fixes pspm_help_init issue #740
• PR Fix issue 730 #743 fixes Improving pspm_help #730
• PR Multiple bug fixes #745
• PR Fix error of cfg_util #746
• PR Bugfixes #750
• PR Update pspm_display.m #751 fixes pspm_display fails in develop branch #744
• PR Update pspm_data_editor.m #752 fixes Bug in pspm_data_editor  #748
• PR Fix issue 674 -- update documentation #753 fixes Update documentation for Heartpy ppg2hb method #674
• PR Fix issue 692 -- remove varargout #754 fixes Remove varargout in remaining functions #692
• PR Fix main GUI colour issue #760
• PR Improvement to pspm_text #756
• PR Bugfixes #759 fixes Move privately used functions from backroom to a new private folder #103
• PR Update pspm_help #766
• PR Creat help text conversion tool #767
• PR fix edge case in marker value import #768
• PR Error correction in pspm_display #769
• PR created pspm_logical2epochs.m and pspm_logical2epochs_test.m and chan… #770
• PR Fix pspm_extract_segments #771
• PR Fix rev issue #772
• PR Final GUI updates #774
• PR Pspm struct2vec test pspm overwrite new default #776
• PR Update README.md #777
• PR Sort Format #778

General

• PsPM now has an online reference. (update references in help texts #703, Fix issue 730 #743, Update pspm_help #766, Creat help text conversion tool #767, Sort Format #778, New function generating help text documents #780)
• The default path will be automatically added when running pspm_init (Fix issue 668 -- added path handling in pspm_init and pspm_quit #713)
• The help text in PsPM has been reviewed and updated (Improvement to pspm_text #756)
• The consistency of PsPM logic has been reviewed and improved (Bugfixes #759)
• Data importing features were reviewed and improved (fix edge case in marker value import #768)

GUI

• Description text of functions for improving readability.
• Channel processing is now done by universal functions for improving robustness and consistency.
• GUI has been updated for compatibility with MATLAB version 2019--2024. (Fix issue 698 -- new GUI #714, Update to support Matlab 2019 #747)
• Deprecated modules have been removed (Check main GUI and make sure deprecated modules are removed #687, Upgrade segment_mean or remove #688)
• Now PsPM can be started up at MATLAB 2019--2024 smoothly without issues. (Fix issue 676 -- adjust UI #725)
• Now PsPM's main GUI is displaying properly. Previously the GUI colour was not displaying. (Fix issue 676 -- adjust UI #725)
• Now the ACQ importing feature is organised consistently to other importing features. (Fix issue 733 #734)
• GUI functions have been updated to keep consistency. (Unifying GUI #728)
• Plots are now consistently using the label style "measurement [unit]". (Fix issue 738 #739)
• The text in the input blocks for `pspm_display" is now displaying properly. (Fix issue 738 #739)
• Unexpected blank lines in help text are now removed. (Fix issue 740 #741)
• GUI functions (display, data_editor, ecg_editor, review) are reviewed for improving consistency (A global variable refering to the GUI plotting window #407, Error correction in pspm_display #769)

New Features

• New HPR model based on Xia, Liu et al. (add new HPR-reward model #729)
  • Provided as pspm_bf_hprf_rew.

Improvements

• General

  • New helper function for processing multiple data channel simultaneously. (Dependencies do not work on Batch in 6.0 (works fine in 5.1.1) #507)
  • Functions always work on one data file only unless explicitly designed to work on multiple files. (Unify function output #689)
  • Functions that write data into channels always return [sts, channel_index] and potentially further output arguments, and functions that create new files always return [sts, newfilename] and potentially further output arguments (Unify function output #689)

• pspm_check_data

  • A new function for checking input data, now used by pspm_load_data and pspm_write_channel. (Unify function output #689)

• pspm_check_python, pspm_check_python_modules, pspm_find_python

  • New functions checking python modules for calling corresponding packages. (Update python handling and tests #658)

• pspm_combine_markerchannels

  • Now pspm_combine_markerchannels only process one specific data file or data channel. (Fix markerinfo handling #695)

• pspm_convert_hb2hp

  • Improved interpolation by using nearest neighbour instead of linear extrapolation (including a new regression test). (Multiple bug fixes #745)

• pspm_dcm

  • Now the option depth has been implemented. The option can invert an entire session at the same time. (Add new option to DCM #704)

• pspm_extract_segments

  • Updated missing epoch checking. (Minor improvements to pspm_extract_segments #690)
  • Incomplete options will no longer give warnings, instead, it will use the default values. (fix options handling in pspm_extract_segments #710)
  • GUI has been updated for corresponding the function updates. (Update GUI for segment extracting #671)
  • Compatibility with pspm_glm has been improved. (Fix pspm_extract_segments #771)

• pspm_get_eyelink

  • Now it will import not only ethernet ('msg') but also parallel/serial ('input') input to Eyelink eyetracker. (Improve eyelink #702)

• pspm_get_timing

  • Now catches an edge case in epoch definition (negative epoch onsets). (Multiple bug fixes #745)

• pspm_glm

  • Unnecessary and impossible orthogonalisation in edge case has been removed. (Multiple bug fixes #745)
  • Now allows saving events. (Fix pspm_extract_segments #771)
  • Computation of events in case of edge cases were corrected. (Fix pspm_extract_segments #771)
  • The output now includes time stamps for troubleshooting. (Fix pspm_extract_segments #771)

• pspm_import

  • Now only one data file is allowed to be processed by this function. (Small fix in pspm_select_channel #691)

• pspm_interpolate

  • Only one data file is allowed to be processed, and multiple data files are no longer supported. (Refactor pspm_interpolate #684)
  • One or all data channel(s) are accepted, and multiple selected data channels are no longer supported. Correspondingly, pspm_load_channel and pspm_select_channels are used for handling a single channel or all channels, respectively. To select all the data channels, the channel specification needs to be all. (Refactor pspm_interpolate #684)
  • An input as struct is no longer supported. (Refactor pspm_interpolate #684)
  • Extrapolation has been improved by avoiding adding unsolicited 1 in the beginning. (Refactor pspm_interpolate #684)

• pspm_load_channel

  • Updated to allow detecting whether a channel is a wave or events channel.
  • Function will no longer terminate if wrong channel type is provided, instead, it will give a warning and continue processing. (Fix load channel #707)

• pspm_logical2epochs

  • New function that processes index values. (created pspm_logical2epochs.m and pspm_logical2epochs_test.m and chan… #770)

• pspm_merge

  • Now only one data file is allowed to be processed by this function. (Small fix in pspm_select_channel #691)

• pspm_options

  • Updated for pspm_interpolate to deal with the larger number of methods allowed. (Refactor pspm_interpolate #684)

• pspm_pupil_pp

  • Improved by using a different criterion for the decision on whether to combine pupils. (Multiple bug fixes #745)

• pspm_rename

  • The function, previously known as pspm_ren, has been renamed for enhanced transparency. (Unify function output #689)
  • pspm_rename now uses pspm_load_data to save data and checks whether new file already exist. (Unify function output #689)

• pspm_resp_pp

  • Improved interpolation by using nearest neighbour instead of linear extrapolation (including a new regression test). (Multiple bug fixes #745)

• pspm_scr_pp

  • Now only one data file is allowed to be processed by this function. (Small fix in pspm_select_channel #691)

• pspm_select_channel

  • pupil and pupil_missing are no longer confused. (Small fix in pspm_select_channel #691)

• pspm_split_sessions

  • Now uses pspm_trim (Improve pspm_trim to handle missing epoch files #696)

• pspm_trim

  • Now only one data file is allowed to be processed by this function. (Small fix in pspm_select_channel #691)
  • Now able to trim missing epoch files (Improve pspm_trim to handle missing epoch files #696)
  • Now uses pspm_load_channel for data processing. (Multiple bug fixes #745)
  • Now catch an edge case in epoch definition (negative epoch onsets). (Multiple bug fixes #745)

• pspm_write_channel

  • pspm_write_channel now uses pspm_select_channels for checking channels (Unify function output #689)

Bug fixes

• General

  • Data channel index handling has been updated (Multiple bug fixes #745)

• GUI

  • Buttons, which previously did not respond when being clicked, have been working properly now. (Fix issue 698 - new UI #716)
  • Main GUI colour profile has been reviewed and re-adjusted. (Fix issue 698 - new UI #716)
  • The feature "artefact removal" now displays the option "change data". (Artefact removal does not have change_data in the GUI #599)
  • The "Data convert" item appears under "Tools" in the main GUI, which was previously non-selectable, is now working properly. (Issue of the item "data convert" under "tools" #715)
  • The pspm_display GUI, previously threw a warning when called with full file path, has been working properly now. (Fix issue 718 -- display #723)
  • The pspm_data_editor GUI, previously did not show the output file when specified, has been working properly now. (Fix issue 717 -- data_editor #724)
  • An issue that appears when PsPM starts up, which is related to path, has been fixed. (Fix error of cfg_util #746)
  • An issue that causes GUI colour missing has been fixed (Fix main GUI colour issue #760)

• pspm_check_data

  • Ensure backwards data file compatibility by modifying wrong markerinfo handling. (Bugfixes #750)

• pspm_combine_markerchannels

  • Incorrect processing for markerinfo.name, which previously created a char rather than a cell array, has been fixed. (Fix markerinfo handling #695)

• pspm_data_editor

  • A bug causing incorrect Y axis display has been fixed (Wrong y label corrected #709).
  • A bug causing unsuccessful initialisation of handles.options has been fixed. (Update pspm_data_editor.m #752)

• pspm_dcm / pspm_dcm_inv

  • A bug, which makes inf not recognised properly by pspm_options, has been fixed. (Multiple bug fixes #745)

• pspm_display

  • An issue, which caused failure of running pspm_display, has been fixed. (pspm_display fails in develop branch #744)

• pspm_extract_segments

  • A bug, which improperly normalised with missing value, has been fixed. (Multiple bug fixes #745)

• pspm_get_eyelink

  • A bug causing marker importing has been fixed. (Improve eyelink #702)

• pspm_get_markerinfo

  • Function is updated by improving data checking for avoiding importing bugs (Fix markerinfo handling #695)

• pspm_get_timing

  • The function used to cause problem running GLM with conditions created from marker info, now it is fixed (Fix markerinfo handling #695, problem running GLM with conditions created from markerinfo #672)

• pspm_glm

  • A GUI issue has been fixed. (Fix markerinfo handling #695).
  • An issue, which caused incorrect trial exclusion, has been addressed. (Test missing handling in GLM #699)
  • An issue, which was caused by pmod setting, has been fixed. (Improve pmod handling in pspm_glm #700)
  • The option overwrite is now adjustable through GUI. (GUI issues in version 6.1.1 #591)
  • GLM for SPS now parse the modelling properly if "best eye" is selected (GUI issues in version 6.1.1 #591)
  • A bug related to incorrect sample rate has been fixed. (Multiple bug fixes #745)

• pspm_init

  • Duplicated path removal has been removed. (Multiple bug fixes #745)

• pspm_multi2index

  • A bug related to missing index for a vector has been fixed. (Multiple bug fixes #745)

• pspm_options

  • A bug that caused incorrect function calling has been fixed.
  • Argument updates for some functions, pspm_pp. (fix pspm_pp options call #681)

• pspm_process_illuminance

  • options.missing, when specified as "no missing epochs", can allow processing as expected and no longer give warnings. (GUI issues in version 6.1.1 #591)

• pspm_scr_pp

  • A bug that causes unsuccessful data loading has been fixed. (Bugfixes #750)

• pspm_trim

  • pspm_trim no longer exits if the missing epochs are empty. (fix edge case of empty epochs file in pspm_trim #736)

New test functions

• New test functions for Python package calling have been added. (Update python handling and tests #658)