christiankeine/heka_patchmaster_importer

Matlab class to import HEKA Patchmaster files

heka_patchmaster_importer's Issues

current amplitudes scaled incorrectly from Patchmaster NEXT files

Currents in ans.RecTable.stimWave are labeled as A (amps), but numerical values are scaled incorrectly.

Mismatch (offset?) of data where zero=1 in PGF

This is a very great tool. However, I have found that for some of the protocols I inherited, the data read from .dat files were offset. For example, here's the file as loaded within PatchMaster

And here was the same data read in using the importer and plotted with MATLAB

At first I thought it was somehow multiplied by a factor of 2, but looking closely I realized it was shifted around -70mV (for example, the AP amplitude). I tried exporting these traces to an ITX file and it was fine.

I noticed that I had this particular issue with protocols that has this:

whereas protocols with Zero=0 are fine (as in no offset).

Do you know what's happening?

System info:
PatchMaster v2x90.1 on Windows 7
MATLAB R2018b on Windows 10

EDIT:
Apparently the data have already been zeroed when saved (I think). I have turned this line assignment to 0.

HEKA_Patchmaster_Importer/@HEKA_Importer/HI_readPulseFileHEKA.m

Line 250 in a0ef82a

tr.TrZeroData = fread(fh, 1, 'double=>double');% = 88; (* LONGREAL *)

tr.TrZeroData = 0; % instead of fread(fh, 1, 'double=>double');%

And it worked for some reason. Is this right? Is there a place that we can check for that?

add support for non-standard stimuli

Currently, only a limited number of stimuli can be reconstructed and the stimulus channel names are somewhat arbitrary.
Add support for ramps, alternating segments, sine waves etc.

New error when attempting to run HEKA Importer

I've successfully incorporated your HEKA_Importer code into another of my codes for about a year, but recently, I've been encountering an unexpected issue. It only appears to happen on select files, but when I attempt to import a .dat file into MATLAB, I receive the following error:

"Output argument "ser_row" (and maybe others) not assigned during call to
"HEKA_Importer.HI_ImportHEKAtoMat>getSeriesHeaders".

Error in HEKA_Importer/HI_ImportHEKAtoMat>LocalImportGroup

Error in HEKA_Importer/HI_ImportHEKAtoMat (line 144)
matData2{iGr}=LocalImportGroup(fh, obj.trees.dataTree, iGr, grp_row);

Error in HEKA_Importer/HI_loadHEKAFile (line 23)
obj.HI_ImportHEKAtoMat;

Error in HEKA_Importer (line 107)
obj.HI_loadHEKAFile;

Error in Heka_importer (line 9)
HEKA_Importer(file)

This is by far the best code for importing HEKA files for my own analysis and I'd prefer not to export out all the individual traces if possible. Any ideas on what may be going wrong? It seems I can't upload the .dat file, but I can email it.