makeProbeMap_phoenix.m

function [] = makeProbeMap_phoenix(varargin)
%% this function takes an xml file with spike groups already assigned and 
%% generates *.prb files for each shank for spike detection/masking/clustering

%% IMPORTANT: this function ASSUMES that the order of the channels for each shank
%% in the spike groups map onto a specific geometrical arrangement of channels on the shank
%% starting from the top left recording site, and moving right then downward to make the 
%% nearest neighbor graph

if nargin == 3
    folder=varargin{1};
    xmlfile=varargin{2};
    shank=varargin{3}
else
    folder = pwd;
    s = strsplit(folder,'/')
    shank = str2num(s{end});
    s{end}='';
    folder = strjoin(s,'/')
    cd ..
    xmlfile = dir('*xml');
    xmlfile = xmlfile.name;

end

parameters = LoadParameters([folder ]);
warning off

for shank = shank
    % make a folder for each directory
    % if ~exist([folder '/' num2str(shank)])
        disp(['working on shank #' num2str(shank)])
    mkdir([folder '/' num2str(shank)]);
    
    channels = parameters.spikeGroups.groups{shank};
    c=1;
    for i=1:length(channels)-1
        for j=1
        l(c,:) = [channels(i),channels(i+j)];
        c=1+c;
        end
    end
    if length(channels) < 32
        for i=1:length(channels)-2
            for j=2 
            l(c,:) = [channels(i),channels(i+j)];
            c=1+c;
            end
        end
        for i=1:length(channels)-3
            for j=3
            l(c,:) = [channels(i),channels(i+j)];
            c=1+c;
            end
        end
    end
    list = l;

    
    s=['channel_groups = {\n' num2str(shank) ': {\n'];
    
    s=[s, '\t"channels": [\n' ];
    for i =1:length(channels)-1
    s=[s, '' num2str(channels(i)) ', ' ];
    end
    s=[s, '' num2str(channels(i+1))];
    s=[s, '],\n' ];

    s=[s, '\t"graph": [\n' ];
    for i =1:length(list)-1
    s=[s, '\t(' num2str(list(i,1)) ', ' num2str(list(i,2)) '),\n'];
    end
%     s=[s, '\t(' num2str(list(i+1,1)) ', ' num2str(list(i+1,2)) ')\n'];
    s=[s, '\t],\n' ];
 
    s=[s, '\t"geometry": {\n' ];
    for i =1:length(channels)
        if mod(i,2)
           pn = -1;
        else
           pn = 1;
        end
%     s=[s, '\t' num2str(channels(i)) ': [' num2str(pn*(-(20+1-i)*2)) ', ' num2str(-i*10) '], \n'];
    s=[s, '\t' num2str(channels(i)) ': [' num2str(pn*20) ', ' num2str(-i*10) '], \n'];
    end
    s=[s, '\t},\n},\n}' ];
    
    % write .prb files to each shank folder
    fid = fopen([folder '/' num2str(shank) '/' num2str(shank) '.prb'],'wt');
    fprintf(fid,s);
    fclose(fid); 
    
    % write .prm file as well
    fid = fopen('generic_spikedetekt.prm');
    i = 1;
    tline = fgetl(fid);
    generic{i} = tline;
    while ischar(tline)
        i = i+1;
        tline = fgetl(fid);
        generic{i} = tline;
    end
    fclose(fid);
    % change the location of the *.dat file in the *.prm file
%     generic{4} = ;
    fid = fopen([folder '/' num2str(shank) '/' xmlfile(1:end-4) '_sh' num2str(shank) '.prm'],'wt');
    ss = ['EXPERIMENT_NAME = ''' folder '/' num2str(shank) '/' xmlfile(1:end-4) '_sh' num2str(shank) '''\n',...
        'RAW_DATA_FILES=[''' folder  '/' xmlfile(1:end-4) '.dat'  ''']\n',...
        'PRB_FILE = ''' num2str(shank) '.prb''\n',...
        'NCHANNELS = ' num2str(parameters.nChannels) '\n',...
        'sample_rate = ' num2str(parameters.rates.wideband) '.\n',...
        'NBITS = ' num2str(parameters.nBits) '\n'];
        
    fprintf(fid,ss);
    for i = 1:numel(generic)
    if generic{i+1} == -1
        fprintf(fid,'%s', generic{i});
        break
    else
        fprintf(fid,'%s\n', generic{i});
    end
    % end
    clear s l list c ss
end
end
if nargin ~= 3
cd(num2str(shank))
end
end