v1.81.4 -- Fix issue found by Meryem, where prune channels doesn't work correctly in hmrMotionArtifact.m. (#187)

* v1.81.3

-- Fix failure to load full head probe fullhead_56x144_v3.SD or ninjaNIRS2022_2023-09-19-18-26-16.snirf files because SnirfClass.GetAuxDataMatrix gets an error when resampling with Matlab's resample function which does not handle a huge difference between aux sample rate and the data sample rate. To fix added local resample function resamplee.m to avoid this issue.

DataTree, v1.17.3
-- Fix failure to load full head probe fullhead_56x144_v3.SD or ninjaNIRS2022_2023-09-19-18-26-16.snirf files because SnirfClass.GetAuxDataMatrix gets an error when resampling with Matlab's resample function which does not handle a huge difference between aux sample rate and the data sample rate. To fix added local resample function resamplee.m to avoid this issue.

Utils, v1.8.1
-- Fix in ImageRecon error when setting timerange, such that it is more than or less that tHRF. Fix is to get tHRF when ImageRecon GUI launches and use ceiln and floorn for min and max tHRF to make sure it is not out of range. Added floorn.m and ceiln.m to fix this.
-- Fix failure to load full head probe fullhead_56x144_v3.SD or ninjaNIRS2022_2023-09-19-18-26-16.snirf files because SnirfClass.GetAuxDataMatrix gets an error when resampling with Matlab's resample function which does not handle a huge difference between aux sample rate and the data sample rate. To fix added local resample function resamplee.m to avoid this issue.

* v1.81.4

-- Fix issue found by Meryem, where prune channels doesn't work correctly in hmrMotionArtifact.m because combining mlActAuto and mlActMan isn't done correctly such that manual prunning is erased by auto pruning. Add function mlAct_CombineIndexLists to solve issue. Same issue in hmrR_MotionArtifactByChannel.m and hmrR_MotionCorrectWavelet.m.
-- Make hmrR_PruneChannels.m user parameters drange and SNRthresh greater precision

FuncRegistry, v1.4.2
-- Fix issue found by Meryem, where prune channels doesn't work correctly in hmrMotionArtifact.m because combining mlActAuto and mlActMan isn't done correctly such manual prunning is erased by auto pruning. Same issue in hmrR_MotionArtifactByChannel.m and hmrR_MotionCorrectWavelet.m.
-- Make hmrR_PruneChannels.m user parameters drange and SNRthresh greater precision

DataTree, v1.17.4
-- Fix probe not displaying in Homer3 because probe.sourcePos2D and probe.detectorPos2D are all zeros (which signifies empty but is not detected as empty) instead of actually empty. Also try to make units for generated 2D probe same as 3D by calling new method ProbeClass.ScaleProjection2D()
-- Fix AuxClass eq function to check for different dataTimeSeries sizes when checking if 2 AuxClass objects are equal

Author: jayd1860

DataTree/AcquiredData/Snirf/AuxClass.m

@@ -196,6 +196,12 @@ function Copy(obj, obj2)
             if ~strcmp(obj.name, obj2.name)
                 return;
             end
+            if ~all(size(obj.dataTimeSeries)==size(obj2.dataTimeSeries))
+                return;
+            end
+            if ~all(size(obj.time)==size(obj2.time))
+                return;
+            end
             if ~all(obj.dataTimeSeries(:)==obj2.dataTimeSeries(:))
                 return;
             end

DataTree/AcquiredData/Snirf/ProbeClass.m

@@ -150,8 +150,40 @@ function BackwardCompatibility(obj)
 
 
 
+        % -------------------------------------------------------
+        function ScaleProjection2D(obj)
+            if size(obj.sourcePos2D,1)
+                dm_src2d = distmatrix([obj.sourcePos2D, zeros(size(obj.sourcePos2D,1),1)]);
+            else
+                dm_src2d = distmatrix(obj.sourcePos2D, zeros);
+            end
+            dm_src3d = distmatrix(obj.sourcePos3D);
+            exp = round(log10(mean(dm_src3d(dm_src3d(:)>0)))) - round(log10(mean(dm_src2d(dm_src2d(:)>0))));
+            scaleFactor = 10^exp;
+            obj.sourcePos2D = obj.sourcePos2D*scaleFactor;
+
+            if size(obj.detectorPos2D,1)
+                dm_det2d = distmatrix([obj.detectorPos2D, zeros(size(obj.detectorPos2D,1),1)]);
+            else
+                dm_det2d = distmatrix(obj.detectorPos2D, zeros);
+            end
+            dm_det3d = distmatrix(obj.detectorPos3D);
+            exp = round(log10(mean(dm_det3d(dm_det3d(:)>0)))) - round(log10(mean(dm_det2d(dm_det2d(:)>0))));
+            scaleFactor = 10^exp;
+            obj.detectorPos2D = obj.detectorPos2D*scaleFactor;
+        end
+            
+        
+        
+        
         % -------------------------------------------------------
         function Project_3D_to_2D(obj)             
+            if all(obj.sourcePos2D(:)==0)
+                obj.sourcePos2D = [];
+            end
+            if all(obj.detectorPos2D(:)==0)
+                obj.detectorPos2D = [];
+            end
             if isempty(obj.sourcePos2D) && isempty(obj.detectorPos2D)
                 if isempty(obj.landmarkPos3D) || ~obj.isValidLandmarkLabels()
                     nSource = size(obj.sourcePos3D,1);
@@ -220,6 +252,7 @@ function Project_3D_to_2D(obj)
                         %
                         obj.sourcePos2D = convert_optodepos_to_circlular_2D_pos(obj.sourcePos3D, T, norm_factor);
                         obj.detectorPos2D = convert_optodepos_to_circlular_2D_pos(obj.detectorPos3D, T, norm_factor);
+                        obj.ScaleProjection2D();
                     end
                 end
             end

DataTree/AcquiredData/Snirf/SnirfClass.m

@@ -1178,7 +1178,11 @@ function SetMetaDataTags(obj, val)
                     p = length(obj2.GetTime());
                     q = length(obj.aux(ii).GetTime());
                 end
-                datamat(:,ii) = resample(obj.aux(ii).GetDataTimeSeries(), p, q);
+                m = resamplee(obj.aux(ii).GetDataTimeSeries(), p, q);
+                if isrow(m)
+                    m = m';
+                end
+                datamat = [datamat, m]; %#ok<AGROW>
             end
         end
 

DataTree/Version.txt

@@ -1 +1 @@
-1.17.2
+1.17.4

FuncRegistry/UserFunctions/hmrR_MotionArtifact.m

@@ -99,9 +99,7 @@
     % Get list of active channels 
     mlActMan{iBlk} = mlAct_Initialize(mlActMan{iBlk}, MeasList);
     mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, MeasList);
-    lstAct1 = mlAct_Matrix2IndexList(mlActAuto{iBlk}, MeasList);
-    lstAct2 = mlAct_Matrix2IndexList(mlActMan{iBlk}, MeasList);
-    lstAct = unique([lstAct1(:)', lstAct2(:)']);
+    lstAct = mlAct_CombineIndexLists( mlActMan{iBlk}, mlActAuto{iBlk}, MeasList );
 
     if length(fs)~=1
         fs = 1/(fs(2)-fs(1));

FuncRegistry/UserFunctions/hmrR_MotionArtifactByChannel.m

@@ -108,9 +108,7 @@
     % get list of active channels
     mlActMan{iBlk} = mlAct_Initialize(mlActMan{iBlk}, MeasList);
     mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, MeasList);
-    lstAct1 = mlAct_Matrix2IndexList(mlActAuto{iBlk}, MeasList);
-    lstAct2 = mlAct_Matrix2IndexList(mlActMan{iBlk}, MeasList);
-    lstAct = unique([lstAct1(:)', lstAct2(:)']);
+    lstAct = mlAct_CombineIndexLists( mlActMan{iBlk}, mlActAuto{iBlk}, MeasList );
 
     % set artifact buffer for tMask seconds on each side of spike
     art_buffer = round(tMask*fs); % time in seconds times sample rate    

FuncRegistry/UserFunctions/hmrR_MotionCorrectWavelet.m

@@ -70,9 +70,7 @@
 
     mlActMan{iBlk} = mlAct_Initialize(mlActMan{iBlk}, MeasList);
     mlActAuto{iBlk} = mlAct_Initialize(mlActAuto{iBlk}, MeasList);
-    lstAct1 = mlAct_Matrix2IndexList(mlActAuto{iBlk}, MeasList);
-    lstAct2 = mlAct_Matrix2IndexList(mlActMan{iBlk}, MeasList);
-    lstAct = unique([lstAct1(:)', lstAct2(:)']);
+    lstAct = mlAct_CombineIndexLists( mlActMan{iBlk}, mlActAuto{iBlk}, MeasList );
 
     SignalLength = size(dod,1); % #time points of original signal
     N = ceil(log2(SignalLength)); % #of levels for the wavelet decomposition

FuncRegistry/UserFunctions/hmrR_PruneChannels.m

@@ -30,8 +30,8 @@
 % Prune_Channels: mlActAuto = hmrR_PruneChannels(data, probe, mlActMan, tIncMan, dRange, SNRthresh, SDrange)
 %
 % PARAMETERS:
-% dRange: [1e4, 1e7]
-% SNRthresh: 2
+% dRange: [1.0e4, 1.0e7]
+% SNRthresh: 2.0
 % SDrange: [0.0, 45.0]
 %
 % TO DO:

FuncRegistry/UserFunctions/mlAct_CombineIndexLists.m

@@ -0,0 +1,9 @@
+function lstAct = mlAct_CombineIndexLists( mlAct1, mlAct2, ml )
+
+lstAct1 = mlAct_Matrix2IndexList(mlAct1, ml);
+lstAct2 = mlAct_Matrix2IndexList(mlAct2, ml);
+lstAct = [lstAct1(:)', lstAct2(:)'];
+
+k = find(ismember(lstAct,lstAct1) & ismember(lstAct,lstAct2)); 
+lstAct = unique(lstAct(k));
+

FuncRegistry/Version.txt

@@ -1 +1 @@
-1.4.1
+1.4.2

UnitTests/FindUnitTestsFolders.m

@@ -1,6 +1,6 @@
 function groupFolders = FindUnitTestsFolders()
 global logger
-global SCRAMBLE
+global SCRAMBLE_CHANNELS
 
 logger = InitLogger(logger);
 
@@ -22,7 +22,7 @@
     groupFolders{kk} = dirs(ii).name;
     logger.Write('Found unit test folder %s\n', pathfull);
 
-    if SCRAMBLE
+    if SCRAMBLE_CHANNELS
         ScrambleChannelsForGroup(pathfull);
     end
     kk = kk+1;

UnitTests/UnitTests_Init.m

@@ -6,7 +6,7 @@ function UnitTests_Init(standalone, start, appname)
 global logger
 global cfg
 global maingui
-global SCRAMBLE
+global SCRAMBLE_CHANNELS
 global ERROR_ODDS_CONST
 
 if ~exist('standalone','var') || isempty(standalone)
@@ -44,7 +44,7 @@ function UnitTests_Init(standalone, start, appname)
     reg = RegistriesClass();
     reg.DeleteSaved();
 
-    SCRAMBLE         = true;
+    SCRAMBLE_CHANNELS  = true;
     ERROR_ODDS_CONST = generateErrorOddsConstant(0);    
 end
 

Utils/Shared/Version.txt

@@ -1 +1 @@
-1.8.0
+1.8.1

Utils/Shared/ceiln.m

@@ -0,0 +1,8 @@
+function val = ceiln(val0, n)
+if ~exist('n','var')
+    n = 0;
+end
+pw = ceil(log10(abs(val0))); % Find order of magnitude of val.
+res = 10^(pw-n-2); % Resolution to round to.
+valtemp = val0*res;
+val = ceil(valtemp)/res; % < change floor() to ceil(), for ceiling equivalent.

Utils/Shared/floorn.m

@@ -0,0 +1,9 @@
+function val = floorn(val0, n)
+if ~exist('n','var')
+    n = 0;
+end
+pw = ceil(log10(abs(val0))); % Find order of magnitude of val.
+res = 10^(pw-n-2); % Resolution to round to.
+valtemp = val0*res;
+val = floor(valtemp)/res; % < change floor() to ceil(), for ceiling equivalent.
+

Utils/Shared/getAppDir.m

@@ -75,7 +75,9 @@
 else
     dirname = fileparts(which('Homer3.m'));
 end
-
+if ~ispathvalid(dirname)
+    dirname = filesepStandard(pwd);
+end
 dirname(dirname=='\') = '/';
 if dirname(end) ~= '/'
     dirname(end+1) = '/';

Utils/Shared/pretty_print_struct.m

@@ -1,4 +1,4 @@
-function pretty_print_struct(st, indent, option, logger)
+function pretty_print_struct(st, indent, option)
 spaces = '';
 
 if ~exist('st','var') || isempty(st)
@@ -10,18 +10,14 @@ function pretty_print_struct(st, indent, option, logger)
 if ~exist('option','var') || isempty(option)
     option = 1;
 end
-if ~exist('logger','var')
-    logger = [];
-end
-logger = InitLogger(logger);
-
 if iswholenum(indent)
     spaces = blanks(indent);
 elseif ischar(indent)
     spaces = blanks(length(indent));
 end
 
 if isstruct(st) || isobject(st)
+    fields = properties(st);    
     s = evalc('disp(st)');
     c = str2cell_fast(s, char(10));
     for ii=1:length(c)

Utils/Shared/resamplee.m

@@ -0,0 +1,10 @@
+function resig = resamplee(sig,upsample,downsample)
+if upsample*downsample<2^31
+    resig = resample(sig,upsample,downsample);
+else
+    sig1half = sig(1:floor(length(sig)/2));
+    sig2half = sig(floor(length(sig)/2):end);
+    resig1half = resamplee(sig1half, floor(upsample/2), length(sig1half));
+    resig2half = resamplee(sig2half, upsample-floor(upsample/2), length(sig2half));
+    resig = [resig1half(:); resig2half(:)];
+end

Version.txt

@@ -1 +1 @@
-1.81.2
+1.81.4