Old or missing code for the Tracker module

[ewiger]

The matlab functionality that was missing or wrong is placed in:

/share/nas/ethz-share5/Data/Users/Nico/110921_PriscaMovie01HardLink/LIB/MATLAB

iBRAIN does not pick it up though. This code has to be moved to iBRAINShared inside folder called Tracker.

Suggested location in iBRAIN/modules is +iBRAIN.+Tracker folder.

Deploy and test the code on iBRAIN_BRUTUS.

[ewiger]

The resubmission always kills results from before, including logs. Next missing function is

>> iBrainTrackerV1: Tracking Stage 1: initilizing tracking parameters.
initTrackingSettings: Parsing setting file /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Nico/110921_PriscaMovie01HardLink/SetTracker_tgoodset2.txt.
initTrackingSettings: Setting structTrackingSettings.TrackingMethod = 'distance';
initTrackingSettings: Setting structTrackingSettings.ObjectName = 'Nuclei';
initTrackingSettings: Setting structTrackingSettings.PixelRadius = 20;
initTrackingSettings: Setting structTrackingSettings.OverlapFactorC = 0.25;
initTrackingSettings: Setting structTrackingSettings.OverlapFactorP = 0.25;
initTrackingSettings: Setting structTrackingSettings.WavelengthID = '_w1';
initTrackingSettings: Setting structTrackingSettings.CreateFrames = 'yes';
initTrackingSettings: Setting structTrackingSettings.TailTime = 1;
initTrackingSettings: Setting structTrackingSettings.MaxGhostAge = 5;
initTrackingSettings: Setting structTrackingSettings.PhyTrees = 'yes';
initTrackingSettings: Setting structTrackingSettings.GlobalLabel = 'yes';
initTrackingSettings: Setting structTrackingSettings.GlobalLabelMergeT = 40;
initTrackingSettings: Setting structTrackingSettings.GlobalLabelImsize = [];
initTrackingSettings: Setting structTrackingSettings.UsePreviousRun = '';
initTrackingSettings: extracted settings from /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Nico/110921_PriscaMovie01HardLink/SetTracker_tgoodset2.txt
Undefined function 'perWellTracking' for input arguments of type 'struct'.

Error in iBrainTrackerV1 (line 107)
[handles] = perWellTracking(handles) ;

[ewiger]

I have found most of the missing functions in CoreMovieDev in the lab repository. Continue testing of the latest commit. After discussion with Mathieu and Nicolas it is clear that iBRAINShared/iBRAIN/CellTracker now contains the latest version of the code.

[Mat-ABM]

Sounds ok to me, but it might be important to have a look at the output of trackovermltiplesitesV1 just to be sure that the fields are referenced in a proper way, as soon as you are there we can have a last check, it follows the convention of the basictracker already, but there is more info stored.

-----Yauhen Yakimovich notifications@github.com schrieb: ----- An: pelkmanslab/iBRAIN_BRUTUS iBRAIN_BRUTUS@noreply.github.com Von: Yauhen Yakimovich notifications@github.com Datum: 21.05.2015 11:02 Betreff: Re: [iBRAIN_BRUTUS] Old or missing code for the Tracker module (#17)

I have found most of the missing functions in CoreMovieDev in the lab repository. Continue testing of the latest commit. After discussion with Mathieu and Nicolas it is clear that iBRAINShared/iBRAIN/CellTracker now contains the latest version of the code.

— Reply to this email directly or view it on GitHub.

[ewiger]

When calling:

I am getting an error that TrackObjects_tNuclei11Features are missing. Indeed BATCH folder does not contain any TrackOutputHandle_tNuclei11Features.mat

This error may come from the version difference between files in

ethz-share5/Data/Users/Nico/110921_PriscaMovie01HardLink/LIB/MATLAB_OldWorkingCellTracker

and

https://github.com/pelkmanslab/LabRepository/tree/master/Mat/Movies/CoreMovieDev

What should output *Features.mat??

[ewiger]

Now testing on iBRAIN the latest fixes. Please check the outputs. Thnx

[ewiger]

Notes:

• The current version of tracker contains the latest merged code of Mathieu and Nicolas
• In current tests the output of frames /share/nas/camelot-share2/Data/Users/Nico/110921_PriscaMovie01HardLink/TRACKING is missing, which is convenient to create movies on the fly. It might be a logical setting in the input .txt files.

It has been decided to use the current module state of iBRAIN/CellTracker and test it further on the real world example in the upcoming days.