Fix issue 559

[teddychao]

Summary

This pull request aims at

1. Solving the issue pspm_convert_ppg2hb supports both options.replace and options.channel_action #559.
2. Review all the cfg_run functions for preparing the next release.
3. Make sure all the cfg_run functions initialise options before using it and check fields are available in job before transferring data to options.

New functions

There is now a new function pspm_update_struct. The function can assess the struct fields and transfer the information to the new struct when the field is available.

New test function

There is now a new text function pspm_update_struct_test. The function tests whether pspm_update_struct can transfer field values correctly.

Function-specific updates

Function	Updates
pspm_cfg_run_artefact_rm	Use pspm_update_struct (lines 4, 19--24)
pspm_cfg_run_contrast1	Use pspm_update_struct (lines 18)
pspm_cfg_run_contrast2	Use pspm_update_struct (lines 37)
pspm_cfg_run_data_convert	Use pspm_update_struct (lines 18--19)
pspm_cfg_run_dcm	Initialise options (line 12). Use pspm_update_struct (lines 82, 90--102)
pspm_cfg_run_downsample	Initialise options (line 3). Use pspm_update_struct (line 9)
pspm_cfg_run_ecg_editor	Use pspm_update_struct (line 20--22)
pspm_cfg_run_export	Use pspm_update_struct (line 15)
pspm_cfg_run_extract_segments	Use pspm_update_struct (line 45)
pspm_cfg_run_find_sounds	Initialise options (line 5). Use pspm_update_struct (line 18, 24)
pspm_cfg_run_find_valid_fixations	Use pspm_update_struct (line 23, 33, 46)
pspm_cfg_run_gaze_convert	Initialise options (line 4). Use pspm_update_struct (line 5, 8)
pspm_cfg_run_get_markerinfo	Use pspm_update_struct (line 9)
pspm_cfg_run_glm	Initialise options (line 5). Use pspm_update_struct (line 72, 107)
pspm_cfg_run_glm_sps	The [] at line 22 and 25 (were 35 and 38) for soa was removed because it does not seem to be necessary.
pspm_cfg_run_import	Initialise options (line 86). Use pspm_update_struct (line 51--53, 78--83, 87)
pspm_cfg_run_interpolate	Use pspm_update_struct (line 6, 18)
pspm_cfg_run_merge	Initialise options (line 8). Use pspm_update_struct (line 10--13)
pspm_cfg_run_pp_emg_data	Use pspm_update_struct (line 4)
pspm_cfg_run_pp_heart_data	Use pspm_update_struct (line 37, 40, 46, 53, 59--66, 72, 80)
pspm_cfg_run_proc_illuminance	Use pspm_update_struct (line 11--12)
pspm_cfg_run_pupil_correct	Use pspm_update_struct (line 10--19, 21--25)
pspm_cfg_run_pupil_preprocess	Use pspm_update_struct (line 14, 20)
pspm_cfg_run_pupil_size_convert	Use pspm_update_struct (line 6)
pspm_cfg_run_segment_mean	Use pspm_update_struct (line 6)
pspm_cfg_run_sf	Use pspm_update_struct (line 65--68)
pspm_cfg_run_trim	Use pspm_update_struct (line 4)

[teddychao]

Hi @dominikbach
I am using this pull request to review and polish the cfg_run functions. I think some of them are outdated and should be fixed in line with the new pspm_options. I will mark it to be "ready for review" when I finish.
Best wishes
Teddy

[dominikbach]

The first step (import) of the GLM tutorial yields the following error:

------------------------------------------------------------------------
24-Jan-2024 16:35:59 - Running job #1
------------------------------------------------------------------------
24-Jan-2024 16:36:00 - Running 'Import'
24-Jan-2024 16:36:00 - Failed  'Import'
Brace indexing is not supported for variables of this type.
In file "/Users/dominik/Documents/PublicData/PsPM/src/pspm_cfg/pspm_update_struct.m" (???), function "pspm_update_struct" at line 13.
In file "/Users/dominik/Documents/PublicData/PsPM/src/pspm_cfg/pspm_cfg_run_import.m" (???), function "pspm_cfg_run_import" at line 87.

The following modules did not run:
Failed: Import
If the problem can be fixed without modifying the job, the computation can be resumed by running
   cfg_util('cont',1)
from the MATLAB command line.

[teddychao]

The first step (import) of the GLM tutorial yields the following error:

------------------------------------------------------------------------
24-Jan-2024 16:35:59 - Running job #1
------------------------------------------------------------------------
24-Jan-2024 16:36:00 - Running 'Import'
24-Jan-2024 16:36:00 - Failed  'Import'
Brace indexing is not supported for variables of this type.
In file "/Users/dominik/Documents/PublicData/PsPM/src/pspm_cfg/pspm_update_struct.m" (???), function "pspm_update_struct" at line 13.
In file "/Users/dominik/Documents/PublicData/PsPM/src/pspm_cfg/pspm_cfg_run_import.m" (???), function "pspm_cfg_run_import" at line 87.

The following modules did not run:
Failed: Import
If the problem can be fixed without modifying the job, the computation can be resumed by running
   cfg_util('cont',1)
from the MATLAB command line.

I apologise for this stupid error. I have fixed this bug systemically now. Please allow me to do some more tests...

[teddychao]

Tested the new version and found it working now

Test GUI: Import

Not to overwrite

Overwrite

Test GUI: Trim

Not to overwrite

Overwrite

Test GUI: SCR for GLM

Not to overwrite

Overwrite