NDI-matlab functionality: reading from ndi.element.timeseries objects, writing ndi.neuron objects

+jrclust/+detect/@DetectController/detectOneRecording.m

@@ -43,7 +43,7 @@
             end
 
             % load raw samples
-            iSamplesRaw = hRec.readRawROI(obj.hCfg.siteMap, 1+loadOffset:loadOffset+nSamples);
+            iSamplesRaw = hRec.readRawROI(obj.hCfg.siteMap, 1+loadOffset:loadOffset+nSamples,obj.hCfg);
 
             % convert samples to int16
             iSamplesRaw = samplesToInt16(iSamplesRaw, obj.hCfg);
@@ -52,7 +52,7 @@
             if iLoad < nLoads && obj.hCfg.nSamplesPad > 0
                 leftBound = loadOffset + nSamples + 1;
                 rightBound = leftBound + obj.hCfg.nSamplesPad - 1;
-                samplesPost = hRec.readRawROI(obj.hCfg.siteMap, leftBound:rightBound);
+                samplesPost = hRec.readRawROI(obj.hCfg.siteMap, leftBound:rightBound,obj.hCfg);
                 samplesPost = samplesToInt16(samplesPost, obj.hCfg);
             else
                 samplesPost = [];
@@ -135,7 +135,7 @@
         % if in import mode, only process loads where there are imported spikes.    
         if isempty(impTimes) || any(inInterval) 
             % load raw samples
-            iSamplesRaw = hRec.readRawROI(obj.hCfg.siteMap, 1+loadOffset:loadOffset+nSamples);
+            iSamplesRaw = hRec.readRawROI(obj.hCfg.siteMap, 1+loadOffset:loadOffset+nSamples,obj.hCfg);
 
             % convert samples to int16
             iSamplesRaw = samplesToInt16(iSamplesRaw, obj.hCfg);
@@ -144,7 +144,7 @@
             if iLoad < nLoads && obj.hCfg.nSamplesPad > 0
                 leftBound = loadOffset + nSamples + 1;
                 rightBound = leftBound + obj.hCfg.nSamplesPad - 1;
-                samplesPost = hRec.readRawROI(obj.hCfg.siteMap, leftBound:rightBound);
+                samplesPost = hRec.readRawROI(obj.hCfg.siteMap, leftBound:rightBound,obj.hCfg);
                 samplesPost = samplesToInt16(samplesPost, obj.hCfg);
             else
                 samplesPost = [];

+jrclust/+detect/@DetectController/findSecondaryPeaks.m

@@ -1,7 +1,7 @@
 function [spikeSites2, spikeSites3] = findSecondaryPeaks(obj, spikeWindows, spikeSites)
     %FINDSECONDARYPEAKS Find secondary peaks
     %   spikeWindows: nSamples x nSites x nSpikes
-    evtNeighbors = 2:obj.hCfg.nSitesEvt; % sites within merge radius, excluding ref sites
+    evtNeighbors = 2:obj.hCfg.nSitesEvt; % sites within merge radius, excluding ref sites 
     siteNeighbors2 = obj.hCfg.siteNeighbors(evtNeighbors, spikeSites);
 
     spikeWindows2 = spikeWindows(:, evtNeighbors, :);
@@ -22,4 +22,4 @@
     else
         spikeSites3 = [];
     end
-end
+end

+jrclust/+detect/ndiRecording.m

@@ -0,0 +1,105 @@
+classdef ndiRecording < jrclust.interfaces.RawRecording
+    %NDIRECORDING Model of an element in NDI
+    %% NDI-SPECIFIC PROPERTIES
+
+    properties (GetAccess=public,SetAccess=private)
+        S; % ndi.session.dir that holds the experimental session data
+        E; % the ndi.element object that holds the data
+        epoch_id; % the epoch ids that are included
+        nsamples; % the number of samples per epoch
+        t0_t1; % start and end times, in local device time, of each epoch
+    end;
+
+    %% LIFECYCLE    
+    methods
+        function obj = ndiRecording(epochname, hCfg)
+            %NDIRECORDING Construct an instance of this class
+            % set object data type
+            obj = obj@jrclust.interfaces.RawRecording(epochname, hCfg);
+            % file not found error is not an error for ndi
+            obj.errMsg = '';
+            obj.isError = 0;
+            obj.S = ndi.session.dir(hCfg.ndiPath);
+            E = getelements(obj.S,'element.name',hCfg.ndiElementName,'element.reference',hCfg.ndiElementReference);
+            if iscell(E) & numel(E)==1,
+                obj.E = E{1};
+            else,
+                obj.isError = 1;
+                obj.errMsg = 'No such element found.';
+                return;
+            end;
+
+            try
+                obj.hCfg = hCfg;
+            catch ME
+                obj.errMsg = ME.message;
+                obj.isError = 1;
+                return;
+            end
+
+            et = epochtable(obj.E);
+
+            [parentdir,epoch_id] = fileparts(epochname);
+            match = find(strcmp(epoch_id,{et.epoch_id}));
+            if isempty(match),
+                 obj.isError = 1;
+                 obj.errMsg = ['No such epoch ' epoch_id '.'];
+                 return;
+            end;
+            obj.epoch_id = et(match).epoch_id;
+            % find clock that is dev local time
+            foundMatch = 0;
+            for i=1:numel(et(match).epoch_clock),
+                 if strcmp(et(match).epoch_clock{i}.type,'dev_local_time'),
+                     foundMatch = i;
+                     break;
+                 end;
+            end;
+            if foundMatch,
+                obj.t0_t1 = et(match).t0_t1{foundMatch};
+            else,
+                error(['No clock type ''dev_local_time''.']);
+            end;
+            obj.nsamples = 1+diff(times2samples(obj.E,epoch_id,obj.t0_t1));
+            obj.dshape = [hCfg.nChans, obj.nsamples];
+            mksqlite('close');
+        end % ndiRecording()
+
+        function openRaw(obj)
+            %OPENRAW Open the raw recording file for reading - does nothing for ndiRecording
+            obj.rawIsOpen = 1;
+        end
+        function closeRaw(obj)
+            %CLOSERAW Close the raw recording file for reading - does nothing for ndiRecording
+            obj.rawIsOpen = 0;
+        end
+
+        function roi = readRawROI(obj, rows, cols,hCfg)
+            %READRAWROI Get a region of interest by rows/cols from the raw file
+            t0t1 = samples2times(obj.E, obj.epoch_id, cols([1 end]));
+            roi = hCfg.ndiScale*readtimeseries(obj.E, obj.epoch_id, t0t1(1), t0t1(2));
+            roi = roi'; % switch to column-based samples
+            roi = single(roi(rows,:)); % if only a subset requested, return only the subset
+        end % readRawROI()
+
+
+    end % methods
+
+    %% GETTERS/SETTERS
+    methods
+        function set.S(obj, val)
+            if ~isa(val,'ndi.session.dir'),
+                 error(['S must be of type ndi.session.dir']);
+            end;
+            obj.S = val;
+        end
+        function set.E(obj,val)
+            if ~isa(val,'ndi.element') & ~isa(val,'ndi.time.timeseries'),
+                 error(['E must be an ndi.element and an ndi.time.timeseries']);
+            end;
+            obj.E = val;
+        end;
+
+    end
+end
+

+jrclust/+detect/newRecording.m

@@ -3,10 +3,10 @@
     switch hCfg.recordingFormat
         case 'Intan'
             hRec = jrclust.detect.IntanRecording(rawPath, hCfg);
-
+	case 'ndi',
+            hRec = jrclust.detect.ndiRecording(rawPath, hCfg);
         otherwise % SpikeGLX .bin/.dat
             hRec = jrclust.detect.Recording(rawPath, hCfg);
-
     end
 end