function [ChannelsPerGroupSuperficialToDeep,SpatialChannelXY,NumChansPerProbe,GroupsPerChannel] =...

bz_ReadProbeGeometryFiles(probemaplist,extrachannelgroups)

% USAGE

% [ChannelsPerGroupSuperficialToDeep,SpatialChannelXY,NumChansPerProbe,GroupsPerChannel] =...

% bz_ReadProbeGeometryFiles(probemaplist)

%

% INPUTS

% probemaplist - character cell (cell array of strings), each

% string is the name of a probemap .xlsx file that is on the

% matlab path. these are typically at

% /buzcode/generalComputation/gemetries

%

% Probe .xlsx files must have the following format features:

% - A column with row 1 having text "BY VERTICAL POSITION/SHANK (IE FOR DISPLAY)".

% In this row must be cells specifying SHANK 1,

% SHANK 2, etc.

% - Two rows right of that a column with channel

% numbers listed from superficial to deep in the

% shank group specified two to the left.

% See NRX_Buzsaki32_4X8.xlsx or NRX_Buzsaki64_6X10.xlsx

% as templates

%

% extrachannelgroups

% For groups of channels to be added to array but not

% in probes/maps... ie for behavioral or opto stim

% monitoring channels. Format: Vector of numbers of

% channels to added to new groups at the end of the

% probe-based groups. So an input of [3,5] will make one

% additional electrode group of 3 channels and a second

% extra of group composed of the last 5 channels.

%

% OUTPUTS

% ChannelsPerGroupSuperficialToDeep - Cell array of cell arrays,

% one cell compartment per probe. Per-probe cell arrays list

% channels in each spike group, in format of a

% cellarray of vectors, each vector is the channels in a spike

% group, most superficial channel listed first in each vector,

% most deep is last. One

% SpatialChannelXY - Cell array of double arrays, one cell compartment

% per probe. The double arrays per probe, are nchannels x 3

% giving within-probe geometry in probe -centric coordinates. In

% some probes the 0,0 point is the bottom site of shank 1.

% Column 1 = channel number

% Column 2 = X coordinate (horizontal) coord within probe

% Column 3 = Y coordinate (horizontal) coord within probe

% NumChansPerProbe - Cell array of double arrays, one cell compartment

% per probe. Single number per probe denoting number of channels

% in each probe

% GroupsPerChannel - Cell array of double arrays, one cell compartment

% per probe. Single number per probe denoting number of groups

% in each probe

%

% DESCRIPTION

%

% Uses xlsread to open the specified .xlsx file, finds columns with

% specificaions as above, finds channels within shanks/spike groups

% assuming they are listed in the .xlsx file in superficial-to-deep order.

% Also gathers probe geometry by looking for columns with "X" and "Y" at

% tops.

%

% Current format of .xlsx files was totally rushed and seat of the pants,

% my want to modify them.

%

% See NRX_Buzsaki32_4X8.xlsx or NRX_Buzsaki64_6X10.xlsx as templates

%

% SEE ALSO

%

%

% Brendon Watson 2017

if ~exist('extrachannelgroups','var')

extrachannelgroups = 0;

end

extrachannelgroups = extrachannelgroups(:)';%ensuring shape

% grouplist_all = [];

% groupchans_all = [];

channelcountoffset = 0;

groupcountoffset = 0;

for pmidx = 1:length(probemaplist)

tpf = probemaplist{pmidx};

if ~strcmp(probemaplist{pmidx}(end-4:end),'.xlsx')

tpf = strcat(tpf,'.xlsx');

end

tpp = which(tpf);

[tpnum,tptxt,tpraw] = xlsread(tpp,1);

%find shanks/groups

groupcolumn = strmatch('BY VERTI',tptxt(1,:));

groupdenoterows = strmatch('SHANK ',tptxt(:,groupcolumn));

groupperchannel = [];

for ridx = 1:length(groupdenoterows);

groupperchannel = cat(1,groupperchannel,str2num(tptxt{groupdenoterows(ridx),groupcolumn}(7:end)));

end

tgroups = unique(groupperchannel);

tnumgroups = length(tgroups);

grouplist_byprobe{pmidx} = 1:length(tgroups)+groupcountoffset;

% grouplist_all = cat(1,grouplist_all,unique(groupperchannel));

%find channels

%HARD CODED!!! groupcolumn+2!!!

channelcolumn = groupcolumn+2;%may definitely want to change this

% groupcolumn = strmatch('Neuroscope channel',tptxt(1,:));

tc = tpraw(groupdenoterows,channelcolumn);

for cidx = 1:length(tc)

channelnums(cidx,1) = tc{cidx};

end

%for each group, find the channels in it, save in sequence

for gidx = 1:length(tgroups)

tgidx = groupperchannel==tgroups(gidx);%find rows whith this group/shank denotation

ChannelsPerGroupSuperficialToDeep{pmidx,gidx} = channelnums(tgidx)+channelcountoffset;

% groupchans_all = cat(1,groupchans_all,channelnums(tgidx));

end

NumChansPerProbe(pmidx) = length(channelnums);

channelcountoffset = channelcountoffset + NumChansPerProbe(pmidx);

% numchans = length(groupchans_all);

%% Get XY information per channel

Xcolumn = strmatch('X',tptxt(1,:));

Ycolumn = strmatch('Y',tptxt(1,:));

if isempty(Xcolumn) | isempty(Ycolumn)

warning(['No/Insufficient XY information found in probe channel .xlsx file for ' tpf])

SpatialChannelXY{pmidx} = [];

else

tx = tpraw(groupdenoterows,Xcolumn);

ty = tpraw(groupdenoterows,Ycolumn);

for cidx = 1:length(tx)

X(cidx,1) = tx{cidx};

Y(cidx,1) = ty{cidx};

end

SpatialChannelXY{pmidx} = [channelnums X Y];

end

GroupsPerChannel{pmidx} = groupperchannel(channelnums+1)+groupcountoffset;

groupcountoffset = groupcountoffset + tnumgroups;%To have offset for next cycle

clear channelnums X Y

end

%% Adding extra channels after probe channels - if any

if ~isempty(extrachannelgroups)

if extrachannelgroups(1)>0

for eidx = 1:length(extrachannelgroups)

tchannels = (0:extrachannelgroups(eidx)-1)'+channelcountoffset;

ChannelsPerGroupSuperficialToDeep{end+1,1} = (0:extrachannelgroups(eidx)-1)'+channelcountoffset;

channelcountoffset = channelcountoffset + extrachannelgroups(eidx);

SpatialChannelXY{end+1} = cat(2,tchannels,nan(extrachannelgroups(eidx),2));

GroupsPerChannel{end+1} = groupcountoffset+eidx*ones(extrachannelgroups(eidx),1);

end

NumChansPerProbe = cat(2,NumChansPerProbe,extrachannelgroups);

end

end

1;