Release 7.0 by teddphil · Pull Request #721 · bachlab/PsPM

teddphil · 2024-06-10T15:13:17Z

Release 7.0

Status: Completed checking PRs listed below and updating the documents.
Last updated on 7th Jan 2025

Checked PRs

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, Update pspm document generation functions for new website #823)
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,functions with incomplete helptext #820)
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)
'PsPM_developers_Guide.pdf' , 'PsPM_Manual.pdf' and 'PsPM_options_documentation.pdf' have been updated. (Manual updates #805, Update documents #824)

GUI

General
- 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)
- Now PsPM can be started up at MATLAB 2019--2024 smoothly without issues. (Fix issue 676 -- adjust UI #725)
- GUI functions have been updated to keep consistency. (Unifying GUI #728)
Text
- Descriptive text of functions for improving readability.
- Help text in the PsPM GUI has been reviewed and updated (Unify help #735)
- 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)
- Plots are now consistently using the label style "measurement [unit]". (Fix issue 738 #739)
Style
- Now PsPM's main GUI is displaying properly. Previously the GUI colour was not displaying. (Fix issue 676 -- adjust UI #725)
Functionality
- Deprecated modules have been removed (Check main GUI and make sure deprecated modules are removed #687, Upgrade segment_mean or remove #688)
- Now the ACQ importing feature is organised consistently to other importing features. (Fix issue 733 #734)
- 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_check_model
- Now also checks the options structure of the models and returns both the model and options validation. This was adjusted in pspm_dcm, pspm_extract_segments, pspm_glm, pspm_sf, and pspm_tam (fix SF issue with timeunits == 'whole' #817)
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_downsample
- Now pspm_downsample will get resampled features from pspm_prepdata. Interaction between the two functions has been updated. (787 pspm_downsample #796)
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)
- Fixed multiple bugs in SMRX import, including channel search, warning handling, and file overwrite behavior. (fix smrx and associated bugs #814)
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_pupil_pp_options
- Updated pspm_pupil_pp_options to compute filter coefficients based on user-provided settings (794 pupil custom setting #815)
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_review
- The first level review GUI now has a new button "Extracted responses" under "Figure selection" that allows plotting the returned data. (598 pspm review glm button #784, Shows extracted responses in first level review (DCM) #802)
pspm_scr_pp
- Now only one data file is allowed to be processed by this function. (Small fix in pspm_select_channel #691)
- pspm_scr_pp now uses pspm_expand_epochs and pspm_epochs2logical instead of internal functions for improved efficiency and consistency. (Changes to pspm_scr_pp #808)
pspm_select_channel
- pupil and pupil_missing are no longer confused. (Small fix in pspm_select_channel #691)
pspm_sf
- Updated to handle a single data file instead of a cell array of files. (fix SF issue with timeunits == 'whole' #817)
pspm_sf_auc
- The unused model.sr has been removed. (fix SF issue with timeunits == 'whole' #817)
pspm_sf_scl
- The unused mean(model.sr) has been removed. (fix SF issue with timeunits == 'whole' #817)
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)
- The `ppm_process_illuminance" GUI no longer has the response function options "duration" and "offset" from the illuminance GLM since they cannot be changed. (fix illuminance GUI #799)
- 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_check_model
- Resolved issues in handling timeunits == 'whole'. (fix SF issue with timeunits == 'whole' #817)
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)
import_eye
- A bug that leads to incorrect channel assignment for longer the data channels has been fixed. (Update import_eyelink.m #793, Changes to "Update import_eyelink.m #793" #806, Changes to "Update import_eyelink.m #793" #807)
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_pupil_pp_options
- A mismatch between pspm_pupil_pp_options and the Custom settings in the Batch Editor has been fixed. (794 pupil custom setting #815)
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)
Test function for pspm_trim has been updated by adding missing epoch checking. (697 write tests for missing epoch file trimming in pspm trim #773)
pspm_check_data_test.m (some test for pspm #795)
pspm_eye_test(some test for pspm #795)
pspm_load_channel_test(some test for pspm #795)
pspm_logical2epochs_test (created pspm_logical2epochs.m and pspm_logical2epochs_test.m and chan… #770)
pspm_select_channels_test(some test for pspm #795)
pspm_struct2vec_test (Pspm struct2vec test pspm overwrite new default #776)
pspm_time2index_test(some test for pspm #795)

Utilities

pspm_expand_epochs
- This new function, internally used by PsPM's functions, allows expanding epochs in time and merges overlapping epochs. (758 pspm_expand_epochs #786).

…velop

* fix test and fix typo in pspm_extract_segments * fix typo * Update cfg_util.m * Update pspm_doc.m * created pspm_logical2epochs.m and pspm_logical2epochs_test.m and changed pspm_overwrite.m * Add tests for missing epoch file trimming in pspm_trim * Update pspm_help.m * Update pspm_help.m * fix how pspm_test_github_actions sets develop mode * fix overwrite behaviour in develop mode, and fix one test with improperly defined overwrite behaviour * fix test with improperly defined overwrite behaviour * new option in overwrite GUI item * final GUI updates after fixes to pspm_help * Add tests for missing epoch file trimming in pspm_trim * changed overwrite default == 2 in pspm_options and wrote a test for pspm_struct2vec * add test function for pspm_doc * update for subfields * update to allow "outputs" section * Update README.md * update a few formats * sort sections * Delete pspm_pupil_pp_options.md * Delete pspm_pupil_pp_options.md Sorry this file shall not be uploaded. * Update pspm_doc_test.m * update final sorting * update format descriptions * old pspm_trim_test.m * overwrite = 1 in convert_gaze_test and gaze_pp_test * added to biosemi_test struct2vec warning and added warning-ID to struct2vec * initial upload of generating help documents * change foldername to "markerdown" * improve doc generation * update index link * added test * added button in fig file and made the button clickable * fix bug of tables * fix bug * Update pspm_doc_test.m * update * Update GUI tags * update inits * Update pspm_doc_test.m * minor fixes * Update pspm_doc_test.m * fix display add empty lines to make sure tables display properly * update home link for docs * Update pspm_doc_gen.m * Update pspm_doc_test.m * changed button font * made pspm_expand_epochs and added to pspm_remove * fixed the boundry cases * fix edge case * plot .segments.means * pspm_expand_epochs varagin structure * added time vector * added pspm_overwrite to pspm_extract_segments and checkout pspm_review.fig develop * added *.fig back * Update import_eyelink.m correct import for both eyes * some test for pspm * pspm_review.fig button normalized * bug in GUI and prettification of figure code * delete orphaned file * pspm_downsample changed, pspm_prepdata changed and pspm_downsample_test writen * added pspm_downsample to pspm_dcm and pspm_downsample can now downsample logical arrays * pspm_downsample ask first for signaltoolbox and converts logical arrays before resampling * changed error handeling * fixed helptext * streamline pspm_expand_epochs * streamline pspm_downsample and pspm_dcm * fix illuminance GUI * change run_ function accordingly * correct PS-FC-GLM defaults in GUI, and make clearer in pspm_init * improve help text for SPS basis functions * improve help text and GUI for find_valid_fixations and pupil_pp * added new pspm_expand_epochs to pspm_remove_epochs * pspm_remove_epochs with pspm_expand_epochs * added comment * update pspm_downsample for integer ratios * final fixes * align hprf_fc defaults with GUI and publication * align rarf_fc help with GUI and publication * make import GUI and help textx consistent, and change start/quit message * Show extracted responses in first level review (DCM) #589 * fix dependencies in GUI * correct text in pspm_overwrite * fix ylabel in pspm_display * fix error handling in pspm_convert_gaze * improve error handling in pspm_convert_gaze * fix cfg for find_valid_fixations (wrong option added) * improve display and fix cfg * disable buttonRemoveModel by start * moved plotting of segments to * fixed call of pspm_rev_dcm * add missing semicolon * fix column warning and added parsing check * fix pupil size GUI and double overwrite question in pspm_glm * improve pspm_extract_segments for DCM with trial names * fix extract_segments * gui updates * gui updates * improve error handling in pspm_export * fix run_find_sounds * updates and small fixes * bugfixes, GUI changes, and improved helps * bufixes and improvements * update model review plots * update HPRF_rew based on exps1-2 in Xia et al. 2024 * remove outdated bf * Manual updates * further updates * complete manual updates * update heartpy reference in function help * added new pspm-functions to pspm_scr_pp and added control for negative epoch diff * commenting * unify missing epochs selector and fix overwrite settings in SF * adapt variable names in test of find_valid_fixations * the revison pspm_expand_epochs * fix smrx and associated bugs * pspm_expand_epochs returns [] by empty epoch/epoch files and can not use negative expansion vectors * added pspm_expand_epochs_test, changed pspm_get_timing error handeling. * added handeling for datafiles without artifacts in pspm_expand_epochs and changed negative expand of data epochs to expand of missing epochs * updated helptext in pspm_pupil_pp_options.m changed the default setting in the batcheditor (pspm_cfg_pupil_preprocess.m ) ResdFiltLPCF.val 100 -> 16(raw) * comment about wrong tag * fix comment * further updates * added test and changed overwrite default to 1 * changed overwrite default back to 2 and updated the helptext * fix SF issue with timeunits == 'whole' * fix problem with pspm_overwrite in pspm_sf * update pspm_check_model for overwrite checking * fix edge case * improve and modify SF input to allow one data file at a time * further fixes * fix * fix edge case * temporary check for 2nd channel is empty * pspm_pupil processes now custom_settings * added helptext, finished pspm_pupil_pp_options * stylistic edits * functions with incomplete helptext * complete help text updates * more files to update * removed edit * updates to pupil model in manual.lyx * fix my name * update pspm_doc * update gen function and fix linebreak bug * Delete pspm_glm.md * Update pspm_doc_test.m * Create #PsPM_Developers_Guide.lyx# * Update PsPM_Developers_Guide.lyx * Delete #PsPM_Developers_Guide.lyx# * update documents * add pspm_expand_epochs to list of functions for reference * change help in pspm_expand_epochs to comply with pspm_help * update documents * added the right release version and date. updated the release_checklist * Update PsPM_Developers_Guide.lyx * Update PsPM_Developers_Guide.lyx * update doc * update description * Release 7.0 (#721) * update authors * update documents * update developer's guide * update documentation * update documentation * update doc * update documents * update * Update release_notes.tex * update release notes * Update developer's guide * Delete #PsPM_Developers_Guide.lyx# --------- Co-authored-by: Bernhard <90285552+4gwe@users.noreply.github.com> Co-authored-by: Dominik Bach <dominik.bach@gmail.com> --------- Co-authored-by: Dominik Bach <dominik.bach@uzh.ch> Co-authored-by: dadi.zhao <dadi.zhao@outlook.com> Co-authored-by: Bernhard <90285552+4gwe@users.noreply.github.com> Co-authored-by: Sihui Zhang <42986258+ZhangSihui999@users.noreply.github.com> Co-authored-by: Dominik Bach <dbach@uni-bonn.de>

dadi.zhao added 2 commits June 10, 2024 12:25

update authors

6efd5a3

Merge branch 'release-7-0' of https://github.com/bachlab/PsPM into de…

fe7559b

…velop

teddphil self-assigned this Jun 17, 2024

teddphil added the In Progress Currently being worked on label Jun 17, 2024

Dadi Zhao (Cancer and Genomic Sciences) added 12 commits July 1, 2024 02:50

Merge branch 'develop' into R7.0

c326190

update documents

4413ba6

Merge branch '740-pspm_help_init-issue' into R7.0

ea09273

Merge branch '738-pspm-display-issue' into R7.0

c6df3c4

Merge branch '668-Path-Handling' into R7.0

01f7304

Merge branch 'unifying-GUI' into R7.0

b4b7c5e

update developer's guide

474029e

Merge branch 'develop' into R7.0

6ad2e27

Merge branch 'develop' into R7.0

cb93119

Merge branch 'develop' into R7.0

2702410

Merge branch 'develop' into R7.0

27f8be6

Merge branch 'develop' into R7.0

528b4a1

teddphil added this to the v7.0 milestone Aug 25, 2024

Teddy added 13 commits September 9, 2024 02:09

Merge branch 'develop' into R7.0

02f1d81

update documentation

9a612f9

Merge branch 'develop' into R7.0

bf382e2

update documentation

9f37d46

Merge branch 'develop' into R7.0

d36f4e2

Merge branch 'develop' into R7.0

35e0cbc

update doc

75a6db2

update documents

ea41e70

update

7beb9be

Update release_notes.tex

3679cef

update release notes

93bd926

Update developer's guide

39bbd59

Delete #PsPM_Developers_Guide.lyx#

d04a7ee

Teddy and others added 5 commits October 28, 2024 14:43

Merge branch 'develop' into R7.0

4aadb3c

Merge branch 'develop' into R7.0

b87fdc9

Resolved lyx/PDF merge conflicts

4656cce

Merge branch 'develop' into R7.0

b8a394e

Merge branch 'develop' into R7.0

e82fa9e

dominikbach approved these changes Feb 10, 2025

View reviewed changes

dominikbach marked this pull request as ready for review February 10, 2025 16:37

dominikbach merged commit 3cc1751 into develop Feb 10, 2025

dominikbach deleted the R7.0 branch February 10, 2025 16:39

dominikbach restored the R7.0 branch February 10, 2025 16:39

dominikbach added Approved The pull request has been approved and can be checked and then merged. and removed In Progress Currently being worked on labels Feb 12, 2025

dominikbach mentioned this pull request Apr 15, 2024

Release 7.0 #603

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release 7.0#721

Release 7.0#721
dominikbach merged 32 commits intodevelopfrom
R7.0

teddphil commented Jun 10, 2024 •

edited by 4gwe

Loading

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Conversation

teddphil commented Jun 10, 2024 • edited by 4gwe Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Release 7.0

Checked PRs

General

GUI

New Features

Improvements

Bug fixes

New test functions

Utilities

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

teddphil commented Jun 10, 2024 •

edited by 4gwe

Loading