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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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irc2 manual #44

Open WeissShahaf opened 4 years ago

WeissShahaf commented 4 years ago

Hey James,

is there a manual curation step for irc2? i'm wondering if i'm not using it right. when running irc2 manual,i get the following error on on PC:

irc2 manual irc2 (5.6.11) opening E:\runfolder\irc2\raw_geom.prm Loading irc2\raw_geom.prm... took 14.9s Loading feature 1... took 63713.3s <<<<<-17 Hours! create_Sui: todo Undefined function or variable 'set_'. Error in irc2_ui>figurewait (line 1287) set_(vhFig, 'Pointer', 'watch'); Error in irc2_ui>plotFigWavCor (line 959) figurewait(1, hFig); Error in irc2_ui (line 35) plotFigWavCor(S0); % need S_clu.mrWavCor Error in irc2 (line 131) case {'manual', 'ui'}, irc2_ui(P); return;

And another error on a different PC:

Index in position 3 exceeds array bounds (must not exceed 1). GPU device reset Error using cellfun All of the input arguments must be of the same size and shape. Previous inputs had size 303 in dimension 1. Input #4 has size 1 Error in irc2ui>cellfun (line 871) varargout{1} = cellfun(varargin{:}, 'UniformOutput', 0); Error in irc2_ui>S0_trWavclu (line 1045) cviSpkclu = cellfun(@(x,y,z)x(y==z), S0.S_auto.cviSpk_clu, cviSite_spk_clu, cviSite_clu); Error in irc2_ui>plot_tnWavclu (line 1061) trWav_clu = S0_trWavclu(S0); Error in irc2_ui>plotFigWav (line 73) S_fig = plot_tnWavclu(Sfig, P, S0); %do this after plotSpk Error in irc2_ui (line 34) plotFigWav(S0); % hFigWav %do this after for ordering Error in irc2 (line 149) case {'manual', 'ui'}, irc2_ui(P); return;

jamesjun commented 4 years ago

Sorry, I am still working on the manual step. irc2 uses compressed waveforms which requires different GUI (and it will be fast for large recordings). some components are working like trace viewer but most are not.

I added exporters to phy, klusters and jrclust for now. I am actively working on the GUI now this week. Thanks for your patience.

-James

On Feb 11, 2020, at 3:19 AM, WeissShahaf notifications@github.com wrote:

 Hey James,

is there a manual curation step for irc2? i'm wondering if i'm not using it right. when running irc2 manual,i get the following error on on PC:

irc2 manual irc2 (5.6.11) opening E:\runfolder\irc2\raw_geom.prm Loading irc2\raw_geom.prm... took 14.9s Loading feature 1... took 63713.3s <<<<<-17 Hours! create_Sui: todo Undefined function or variable 'set_'. Error in irc2_ui>figurewait (line 1287) set_(vhFig, 'Pointer', 'watch'); Error in irc2_ui>plotFigWavCor (line 959) figurewait(1, hFig); Error in irc2_ui (line 35) plotFigWavCor(S0); % need S_clu.mrWavCor Error in irc2 (line 131) case {'manual', 'ui'}, irc2_ui(P); return;

And another error on a different PC:

Index in position 3 exceeds array bounds (must not exceed 1). GPU device reset Error using cellfun All of the input arguments must be of the same size and shape. Previous inputs had size 303 in dimension 1. Input #4 has size 1 Error in irc2ui>cellfun (line 871) varargout{1} = cellfun(varargin{:}, 'UniformOutput', 0); Error in irc2_ui>S0_trWavclu (line 1045) cviSpkclu = cellfun(@(x,y,z)x(y==z), S0.S_auto.cviSpk_clu, cviSite_spk_clu, cviSite_clu); Error in irc2_ui>plot_tnWavclu (line 1061) trWav_clu = S0_trWavclu(S0); Error in irc2_ui>plotFigWav (line 73) S_fig = plot_tnWavclu(Sfig, P, S0); %do this after plotSpk Error in irc2_ui (line 34) plotFigWav(S0); % hFigWav %do this after for ordering Error in irc2 (line 149) case {'manual', 'ui'}, irc2_ui(P); return;

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WeissShahaf commented 4 years ago

i reran irc2 spikesort with today's commit, irc2 runs :) , but in irc2 manual (i'm guessing that is working now as it's in the readme.md) everything loads, but i cannot do anything. again this happens on multiple OSs.

split error: Index in position 3 exceeds array bounds (must not exceed 1). Error in irc2_manual>tnWav_spksites (line 2087) tnWav1 = pc2wav_(S0.mrPv_global, S0.trPc_spk(:,:,viSpk1)); Error in irc2_manual>autosplit (line 266) trSpkWav1 = tnWav2uV_(tnWav_spksites(S_manual.cviSpk_clu{iClu1}, viSites1, S0), P, 0); Error in irc2_manual>keyPressFcnFigWav (line 368) case 's', autosplit(1, S0);
Error while evaluating Figure KeyPressFcn.

merge error:

In E:\ironclustGit\matlab\irc.m>disperr (line 18070) In E:\ironclustGit\matlab\irc.m>test (line 18826) In E:\ironclustGit\matlab\irc.m>call_ (line 18844) In E:\ironclustGit\matlab\irc.m>irc (line 143) In E:\ironclustGit\matlab\irc2_manual.m>callirc (line 1116) In E:\ironclustGit\matlab\irc2_manual.m>uimerge (line 2903) In E:\ironclustGit\matlab\irc2_manual.m>keyPressFcnFigWav (line 359) Error log updated: E:\ironclustGit\matlab\error_log.mat Reference to non-existent field 'vnSpk_clu'. GPU device reset

trying to change projection view:

In E:\ironclustGit\matlab\irc.m>disperr (line 18070) In E:\ironclustGit\matlab\irc.m>test (line 18826) In E:\ironclustGit\matlab\irc.m>call_ (line 18844) In E:\ironclustGit\matlab\irc.m>irc (line 142) In E:\ironclustGit\matlab\irc2_manual.m>callirc (line 1115) In E:\ironclustGit\matlab\irc2_manual.m>projview (line 2884) In E:\ironclustGit\matlab\irc2_manual.m>@(h,e)projview(h) (line 495) Error log updated: E:\ironclustGit\matlab\error_log.mat Reference to non-existent field 'nClu'. GPU device reset

trying to annotate:

In E:\ironclustGit\matlab\irc.m>disperr (line 18070) In E:\ironclustGit\matlab\irc.m>test (line 18826) In E:\ironclustGit\matlab\irc.m>call_ (line 18844) In E:\ironclustGit\matlab\irc.m>irc (line 142) In E:\ironclustGit\matlab\irc2_manual.m>callirc (line 1115) In E:\ironclustGit\matlab\irc2_manual.m>unitannotate (line 2890) In E:\ironclustGit\matlab\irc2_manual.m>@(h,e)unitannotate(h,e,'single') (line 508) Error log updated: E:\ironclustGit\matlab\error_log.mat Reference to non-existent field 'nClu'. GPU device reset

trying to set local drift view > In E:\ironclustGit\matlab\irc.m>disperr_ (line 18070) In E:\ironclustGit\matlab\irc.m>ui_show_driftview (line 30701) In E:\ironclustGit\matlab\irc.m>test (line 18804) In E:\ironclustGit\matlab\irc.m>call (line 18844) In E:\ironclustGit\matlab\irc.m>irc (line 142) In E:\ironclustGit\matlab\irc2_manual.m>callirc (line 1115) In E:\ironclustGit\matlab\irc2_manual.m>ui_show_driftview (line 2889) In E:\ironclustGit\matlab\irc2_manual.m>@(h,e)ui_show_driftview(1,h) (line 489) Error log updated: E:\ironclustGit\matlab\error_log.mat Reference to non-existent field 'cviSpk_clu'. GPU device reset

trying to set avg waveform view

In E:\ironclustGit\matlab\irc.m>disperr (line 18070) In E:\ironclustGit\matlab\irc.m>test (line 18826) In E:\ironclustGit\matlab\irc.m>call_ (line 18844) In E:\ironclustGit\matlab\irc.m>irc (line 142) In E:\ironclustGit\matlab\irc2_manual.m>callirc (line 1115) In E:\ironclustGit\matlab\irc2_manual.m>ui_show_allchan (line 2888) In E:\ironclustGit\matlab\irc2_manual.m>@(h,e)ui_show_allchan(1,h) (line 487) Error log updated: E:\ironclustGit\matlab\error_log.mat Reference to non-existent field 'cviSpk_clu'. GPU device reset

trying to view traces Opening GL383_2019009_small_square_g0_tcat.imec0.ap.bin

In E:\ironclustGit\matlab\irc.m>disperr (line 18070) In E:\ironclustGit\matlab\irc.m>test (line 18826) In E:\ironclustGit\matlab\irc.m>call_ (line 18844) In E:\ironclustGit\matlab\irc.m>irc (line 142) In E:\ironclustGit\matlab\irc2_manual.m>callirc (line 1115) In E:\ironclustGit\matlab\irc2manual.m>traces (line 2887) In E:\ironclustGit\matlab\irc2manual.m>@(h,e)traces() (line 478) Error log updated: E:\ironclustGit\matlab\error_log.mat Reference to non-existent field 'viT_offset_file'. GPU device reset

RaphaelSteinfeld commented 4 years ago

We are having the same issue. irc2 runs very nicely - but then manual merging or annotating does not work.

Furthermore, when trying to export to another format for manual sorting, neither exporting to jrclust, nor phy format works.

exporting to phy:

Error using irc2>load_irc2_
Too many input arguments.

Error in irc2 (line 173)
    case {'export-phy', 'phy'}, open_phy_(load_irc2_(vcFile_prm, vcArg2));
    return;

exporting to Jrclust:

Error using dlmread (line 147)
Mismatch between file and format character vector.
Trouble reading 'Numeric' field from file (row number 1, field number 1)
==> nSites = 10;\n

Error in csvread (line 48)
    m=dlmread(filename, ',', r, c);

Error in irc2>geom2mat_ (line 261)
geometry = csvread(vcFile_geom);

Error in irc2 (line 181)
        geom2mat_(vcFile_prm);

Is there an estimate of when either of those will be available?

jamesjun commented 4 years ago

Thanks for your helpful feedback,

I wish to complete the GUI and export tool as soon as possible but I am also in the middle of preparing for the Cosyne conference. I am most likely to finish them after I return in two weeks.

-James

On Fri, Feb 21, 2020 at 10:09 AM RSteinfeld notifications@github.com wrote:

We are having the same issue. irc2 runs very nicely - but then manual merging or annotating does not work.

Furthermore, when trying to export to another format for manual sorting, neither exporting to jrclust https://github.com/flatironinstitute/ironclust/issues/46, nor phy format works.

exporting to phy:

Error using irc2>loadirc2 Too many input arguments.

Error in irc2 (line 173) case {'export-phy', 'phy'}, openphy(loadirc2(vcFile_prm, vcArg2)); return;

exporting to Jrclust:

Error using dlmread (line 147) Mismatch between file and format character vector. Trouble reading 'Numeric' field from file (row number 1, field number 1) ==> nSites = 10;\n

Error in csvread (line 48) m=dlmread(filename, ',', r, c);

Error in irc2>geom2mat_ (line 261) geometry = csvread(vcFile_geom);

Error in irc2 (line 181) geom2mat_(vcFile_prm);

Is there an estimate of when either of those will be available?

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