mutualinfo_CSUS_trace5.m

function f = mutualinfo_CSUS_trace5(spike_structure, CSUS_structure, do_you_want_pretrial)
%finds 'mutual info' for CS/US/ non CS/US
%CSUS_structure should come from BULKconverttoframe.m
%do_you_want_pretrial: 0 for only cs us, 1 for cs us pretrial
%how many divisions you wanted-- for ex,
    % do_you_want_pretrial = 1
    % how_many_divisions = 2 will just split between cs and us
                        %= 10 will split CS and US each into 5
%right now because im lazy how_many_divisions must be a factor of 10

fprintf('running mutualinfo_CSUS_trace')

divisions = 5;
fields_spikes = fieldnames(spike_structure);
fields_CSUS = fieldnames(CSUS_structure);
          set(0,'DefaultFigureVisible', 'off');

if numel(fields_spikes) ~= numel(fields_CSUS)
  error('your spike and US structures do not have the same number of values. you may need to pad your US structure for exploration days')
end


for i = 1:numel(fields_spikes)
      fieldName_spikes = fields_spikes{i};
      fieldValue_spikes = spike_structure.(fieldName_spikes);
      peaks_time = fieldValue_spikes;

      index = strfind(fieldName_spikes, '_');
      spikes_date = fieldName_spikes(index(2)+1:end);

      fieldName_CSUS = fields_CSUS{i};
      fieldValue_CSUS = CSUS_structure.(fieldName_CSUS);
      CSUS = fieldValue_CSUS;

      index = strfind(fieldName_spikes, '_');
      CSUS_date = fieldName_spikes(index(2)+1:end)

      mutinfo = NaN(size(peaks_time,1),1);

      if length(peaks_time) <5
        mutualinfo_struct.(sprintf('MI_%s', spikes_date)) = NaN;
        continue
      end


      time = CSUS(2,:);
      CSUS = CSUS(1,:);

      if size(peaks_time,2)>length(CSUS)
        peaks_time = peaks_time(:,1:length(CSUS));
      else
        CSUS = CSUS(1:size(peaks_time,2));
      end

      occ_in_CS_US = zeros(1,10);
      occ_intertrial = zeros(1,1);
      occ_pretrial = zeros(1,1);

        numbering = 10./divisions;
        previousz = 0;
        for z=0:numbering:10
          if z==0
            occ_pretrial = length(find(CSUS ==-1));
            occ_intertrial = length(find(CSUS ==0));
            else
              wanted1 = find(CSUS > previousz);
              wanted2 = find(CSUS <= z);
              wanted = intersect(wanted1,wanted2);
              occ_in_CS_US(z) = length(wanted);
              CSUS(wanted) = z;
              previousz = z;
            end
          end


      if length(peaks_time)<3 || length(unique(CSUS))<3
          mutualinfo_struct.(sprintf('MI_%s', spikes_date)) = NaN;
          warning('you have no spikes')
      else
        for k=1:size(peaks_time,1)
          currspikes = peaks_time(k,:);



              if length(currspikes)>0 && length(unique(CSUS))>=3 %finding how many spikes in each time bin
                occ_in_CS_US = NaN(length(unique(CSUS))-1,1);
                spikes_in_CS_US = NaN(length(unique(CSUS))-1,1);
                spikes_pretrial = zeros(1,1);
                occ_pretrial = zeros(1,1);

                      for q=0:numbering:10

                            if q == 0 %%%%%%%%%%ADD THIS LATER
                              wanted = (find(CSUS == -1));
                              occ_pretrial = length(wanted);
                              spikes_pretrial = nanmean(currspikes(wanted));
                              index=1;

                            else
                              wantedtimes = find(CSUS == q);
                              wantedtimes = wantedtimes(find(wantedtimes<=length(currspikes)));
                              trace_mean = nanmean(currspikes(wantedtimes));
                              occ_in_CS_US(index) = length(wantedtimes);
                              spikes_in_CS_US(index) = trace_mean;
                              index = index+1;
                            end
                      end
                      if do_you_want_pretrial == 1
                            pretrial_occprob = occ_pretrial*(1/7.5);
                            spikes_occprob = occ_in_CS_US.*(1/7.5);
                            occprob = [pretrial_occprob, spikes_occprob'];
                            occprob = occprob./nansum(occprob);
                            spikeprob =  [spikes_pretrial, spikes_in_CS_US'];
                            if (size(spikeprob,1)) < (size(spikeprob,2))
                              spikeprob = spikeprob';
                            end
                            if (size(occprob,1)) < (size(occprob,2))
                              occprob = occprob';
                            end
                            mutinfo(k) = mutualinfo([spikeprob, occprob]); %is this oriented the right way
                      else
                            occprob = occ_in_CS_US.*(1/7.5);
                            occprob = occprob./nansum(occprob);
                            spikeprob =  [spikes_in_CS_US];
                            if (size(spikeprob,1)) < (size(spikeprob,2))
                              spikeprob = spikeprob';
                            end
                            if (size(occprob,1)) < (size(occprob,2))
                              occprob = occprob';
                            end
                            mutinfo(k) = mutualinfo([spikeprob, occprob]); %is this oriented the right way
                      end
                else

                  mutinfo(k) = NaN;
                end

            end
          end
      mutualinfo_struct.(sprintf('MI_%s', spikes_date)) = mutinfo';
      end


      f = mutualinfo_struct;