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flatironinstitute / ironclust

Spike sorting software being developed at Flatiron Institute, based on JRCLUST (Janelia Rocket Cluster)
Apache License 2.0
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trWav_clu variable not created #35

Closed WeissShahaf closed 4 years ago

WeissShahaf commented 4 years ago

Every time i try to use ironclust, even at default settings, after completing irc spikesort, and trying to run irc manual i get the following error:

irc manual 20191004_GL485_dual_septum_exvivo_g0_t0.imec1.ap_imec3b_staggered.prm

Reference to non-existent field 'trWav_clu'. Error in irc>plot_tnWavclu (line 6203) trWavclu = ifeq(P.fWav_raw_show, S_clu.trWav_raw_clu, S_clu.trWav_clu);%S_clu.trWav_clu%S_clu.tmrWav_clu Error in irc>plotFigWav (line 5909) S_fig = plot_tnWavclu(Sfig, P); %do this after plotSpk Error in irc>manual_ (line 5545) S0 = plotFigWav(S0); % hFigWav %do this after for ordering Error in irc (line 294) manual_(P);

WeissShahaf commented 4 years ago

fSpatialMask_clu is missing when using the vanilla irc commit pull.

Sorting took 255.3s for GL383_20190815_sleep_plusmaze3_g0_t0.imec0.ap_imec3b_staggered.prm Saving 0.UserData to GL383_20190815_sleep_plusmaze3_g0_t0.imec0.ap_imec3b_staggered_jrc.mat... Saving a struct to GL383_20190815_sleep_plusmaze3_g0_t0.imec0.ap_imec3b_staggered_jrc.mat... took 3.9s. Full parameter settings are exported to GL383_20190815_sleep_plusmaze3_g0_t0.imec0.ap_imec3b_staggered_full.prm Reference to non-existent field 'fSpatialMaskclu'. Error in irc>describe (line 5332) csDesc{end+1} = sprintf(' fSpatialMask_clu %d', P.fSpatialMask_clu); Error in irc>runirc (line 28111) detect(P); sort(P, 0); describe_(P.vcFile_prm); Error in irc (line 230) runirc(P);

then when trying to use the manual GUI, variable trWav_clu is missing

Reference to non-existent field 'trWav_clu'. Error in irc>plot_tnWavclu (line 6203) trWavclu = ifeq(P.fWav_raw_show, S_clu.trWav_raw_clu, S_clu.trWav_clu);%S_clu.trWav_clu%S_clu.tmrWav_clu Error in irc>plotFigWav (line 5909) S_fig = plot_tnWavclu(Sfig, P); %do this after plotSpk Error in irc>manual_ (line 5545) S0 = plotFigWav(S0); % hFigWav %do this after for ordering Error in irc (line 294) manual_(P);

jamesjun commented 4 years ago

Dear Weiss, thanks for reporting the error and thanks for your patience. The bug is now fixed. I am working on the new version (irc2) and the GUI will be developed for the new version shortly.

WeissShahaf commented 4 years ago

thanks James, i pulled the commit but still get:

Reference to non-existent field 'fSpatialMaskclu'. Error in irc>describe (line 5332) csDesc{end+1} = sprintf(' fSpatialMask_clu %d', P.fSpatialMask_clu); Error in irc>runirc (line 28111) detect(P); sort(P, 0); describe_(P.vcFile_prm); Error in irc (line 230) runirc(P);

this time it doesn't help to assign a value to fSpatialMask_clu.

and still manualk gui has the same issue:

Reference to non-existent field 'trWav_clu'. Error in irc>plot_tnWavclu (line 6203) trWavclu = ifeq(P.fWav_raw_show, S_clu.trWav_raw_clu, S_clu.trWav_clu);%S_clu.trWav_clu%S_clu.tmrWav_clu Error in irc>plotFigWav (line 5909) S_fig = plot_tnWavclu(Sfig, P); %do this after plotSpk Error in irc>manual_ (line 5545) S0 = plotFigWav(S0); % hFigWav %do this after for ordering Error in irc (line 294) manual_(P);

can i use irc2 for non .mda files (spikeglx recordings)?

jamesjun commented 4 years ago

I see fSpatialMask_clu being commented out. Could please you run “git stash” and “git pull” to make sure you have the latest commit?

-James

On Dec 16, 2019, at 3:19 AM, WeissShahaf notifications@github.com wrote:

thanks James, i pulled the commit but still get:

Reference to non-existent field 'fSpatialMaskclu'. Error in irc>describe (line 5332) csDesc{end+1} = sprintf(' fSpatialMask_clu %d', P.fSpatialMask_clu); Error in irc>runirc (line 28111) detect(P); sort(P, 0); describe_(P.vcFile_prm); Error in irc (line 230) runirc(P);

this time it doesn't help to assign a value to fSpatialMask_clu.

and still manualk gui has the same issue:

Reference to non-existent field 'trWav_clu'. Error in irc>plot_tnWavclu (line 6203) trWavclu = ifeq(P.fWav_raw_show, S_clu.trWav_raw_clu, S_clu.trWav_clu);%S_clu.trWav_clu%S_clu.tmrWav_clu Error in irc>plotFigWav (line 5909) S_fig = plot_tnWavclu(Sfig, P); %do this after plotSpk Error in irc>manual_ (line 5545) S0 = plotFigWav(S0); % hFigWav %do this after for ordering Error in irc (line 294) manual_(P);

can i use irc2 for non .mda files (spikeglx recordings)?

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WeissShahaf commented 4 years ago

C:\Users\superuser\Dropbox\ironclust>git stash No local changes to save

C:\Users\superuser\Dropbox\ironclust>git pull Already up to date.

C:\Users\superuser\Dropbox\ironclust>

jamesjun commented 4 years ago

I moved my repository to flatironinstitute account from my personal account about a month ago. This might be why it's not updating. Please delete the folder and run "git clone https://github.com/flatironinstitute/ironclust.git"

WeissShahaf commented 4 years ago

i'm using version irc version v5.0.5 (10/14/2019) installed, MD5: 59611c7f8161d352085c5fe9ad1c9739

i deleted and recloned just in case. now sorting runs. but manual gui still does not. irc manual GL603_20191208_OF_g0_t0.imec0.ap_imec3b_staggered.prm Reference to non-existent field 'trWav_clu'. Error in irc>plot_tnWavclu (line 6203) trWavclu = ifeq(P.fWav_raw_show, S_clu.trWav_raw_clu, S_clu.trWav_clu);%S_clu.trWav_clu%S_clu.tmrWav_clu Error in irc>plotFigWav (line 5909) S_fig = plot_tnWavclu(Sfig, P); %do this after plotSpk Error in irc>manual_ (line 5545) S0 = plotFigWav(S0); % hFigWav %do this after for ordering Error in irc (line 294) manual_(P);

WeissShahaf commented 4 years ago

sorry, problem solved. i was using github desktop to clone and update. once i did it in gitbash there were no issues anymore thanks for the patience

jamesjun commented 4 years ago

I am glad the issue is resolved. You could use "irc update" command which calls "git pull".

-James

On Tue, Dec 17, 2019 at 4:10 AM WeissShahaf notifications@github.com wrote:

sorry, problem solved. i was using github desktop to clone and update. once i did it in gitbash there were no issues anymore thanks for the patience

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