Tobias

ImBat_BatchExtract.m

@@ -31,31 +31,31 @@
         disp('.mov files already extracted...');
     else
         % extract .mov files:
-  %      FS_AV_Parse_batch(pwd,'mat_dir','/extracted')
-        % extract c3d files:
-%         processed_dir = [pwd,'/extracted/'];
-%         
-%         c3dList = dir([pwd filesep '*.c3d']);
-%         
-%         %run through list of c3d files in that directory, convert to mat, and save
-%         %to processed directory
-%         for i = 1:length(c3dList)
-%             fileName = extractBefore(c3dList(i).name,'-Bat_Cluster.c3d'); %Bat
-%             %fileName = extractBefore(c3dList(i).name,'-Bat_Cluster.c3d'); %Bat
-%             dateSesh = datestr(datetime(c3dList(i).date),'yymmdd');
-%             batName = extractBefore(fileName,['_' dateSesh]);
-%             %sessionNum = fileName(end);
-% 
-%             
-%             [Markers,VideoFrameRate,AnalogSignals,AnalogFrameRate,Event,ParameterGroup,CameraInfo,ResidualError]=readC3D_analog([cd filesep c3dList(i).name]); %convert file
-%             %plot ttl impulses to check they are linear and not missing ttl
-%             event_ttls = AnalogSignals(:,2);
-%             [R,LT,UT,LL,UL] = risetime(event_ttls,VideoFrameRate);
-% 
-%             %save new mat file in both original directory and copied directory for processing
-%             save([processed_dir fileName '_track' '.mat'],'AnalogFrameRate','AnalogSignals','Markers','VideoFrameRate');
-%             %save([copy_dir fileName '_track' '.mat'],'AnalogFrameRate','AnalogSignals','Markers','VideoFrameRate');
-%         end 
+       FS_AV_Parse_batch(pwd,'mat_dir','/extracted')
+        %extract c3d files:
+        processed_dir = [pwd,'/extracted/'];
+
+        c3dList = dir([pwd filesep '*.c3d']);
+
+        %run through list of c3d files in that directory, convert to mat, and save
+        %to processed directory
+        for i = 1:length(c3dList)
+            fileName = extractBefore(c3dList(i).name,'-Bat_Cluster.c3d'); %Bat
+            %fileName = extractBefore(c3dList(i).name,'-Bat_Cluster.c3d'); %Bat
+            dateSesh = datestr(datetime(c3dList(i).date),'yymmdd');
+            batName = extractBefore(fileName,['_' dateSesh]);
+            %sessionNum = fileName(end);
+
+
+            [Markers,VideoFrameRate,AnalogSignals,AnalogFrameRate,Event,ParameterGroup,CameraInfo,ResidualError]=readC3D_analog([cd filesep c3dList(i).name]); %convert file
+            %plot ttl impulses to check they are linear and not missing ttl
+            event_ttls = AnalogSignals(:,2);
+            [R,LT,UT,LL,UL] = risetime(event_ttls,VideoFrameRate);
+
+            %save new mat file in both original directory and copied directory for processing
+            save([processed_dir fileName '_track' '.mat'],'AnalogFrameRate','AnalogSignals','Markers','VideoFrameRate');
+            %save([copy_dir fileName '_track' '.mat'],'AnalogFrameRate','AnalogSignals','Markers','VideoFrameRate');
+        end 
 
         % Run extraction
         close all;

ImBat_MultiDayAnalysis.m

@@ -12,11 +12,27 @@
     ST3_2 = 1; % Place Cell Overlay
     ST3_3 = 1; %
     ST3_5 = 1;
+saveFlag = 1;
 
 % local Directory:
-LD =  'D:\Bat_Data2\Zack\Processed\'
+LD = 'Z:\users\tobias\flight\data_processed\topQualityData\analysis_done\za\';
+%LD =  'D:\Bat_Data2\Zack\Processed\'
 %LD = '/Users/ARGO/Documents/DATA/Bat_Data_ZuZu';
+if saveFlag == 1
+    %saveDir1 = '/Volumes/Tobias_flig/topQualityData/analysis_done/plots/';
+    saveDir1 = '\\169.229.54.11\server_home\users\tobias\flight\data_processed\topQualityData\ForTobias\plots\';
+    %saveDir1 = '/Users/periscope/Desktop/analysis/flight/plots/';
+    %saveDir1 = 'C:\Users\tobias\Desktop\analysis\plots\';
+    if ~exist([saveDir1 datestr(now,'yymmdd') ])
+        mkdir([saveDir1 datestr(now,'yymmdd')]);
+    else
+        disp('You have been working today...');
+    end
+    saveDir = [saveDir1 datestr(now,'yymmdd') filesep];
+end
+if ~exist(LD)
 mkdir(LD);
+end
 
 % Cell array containing strings of the days you want to look at ( MANUAL)
 % days = {'190528','190529','190530'};
@@ -54,17 +70,17 @@
     % create index into correct subfolder ( get biggest flight and rest
    % Flight Flder
 
-   cd(days{i});
+   cd([days{i} filesep 'extracted']);
    out = ImBat_GetBiggestFolder('fly');
-
-
-    folder = [out,'/processed'];
+    cd(out);
+   processedDir = dir('processed_*');
+    folder = [processedDir(end).name];
     ROI_Data{i}.folder = folder; % save this for indexing later...
 
     disp(['entering into folder for day:  ', days{i}]);
     cd(folder) % index into folder 
     Alignment = load('Alignment.mat'); % get alignment data
-    ROIs = load('Motion_corrected_Data_DS_results.mat'); % Get ROI data
+    ROIs = load('results.mat'); % Get ROI data
 
     % Consolidate ROI and Flight data
     ROI_Data{i}.Alignment = Alignment;
@@ -84,11 +100,16 @@
 
 
 try
- cd(days{i});
-   out = ImBat_GetBiggestFolder('rest1');  
-   folder_rest = [out,'/processed'];
-
-    cd(DIR); cd(folder_rest);
+ %cd(days{i});
+ cd ..;
+ cd ..;
+ out = ImBat_GetBiggestFolder('rest1');  
+cd(out);
+   processedDir = dir('processed_*');
+    folder_rest = [processedDir(end).name];
+
+    %cd(DIR);
+    cd(folder_rest);
     load('Motion_corrected_Data_DS', 'Y','Ysiz');
     disp( 'Getting Max Projection for rest...');
     [MaxProj_rest, ~] = ImBat_Dff(Y);
@@ -103,17 +124,18 @@
 end
 
 % Save data locally somewhere...
-cd(LD);
+cd(saveDir);
 for i = 1:size(ROI_Data,2);
     if i ==1;
         filename = ['ROI_Data_',days{1}]
     else
         filename = [filename,'_',days{i}];
     end
 end
-
-save([filename,'.mat'],'ROI_Data')
 
+save([filename, '.mat'],'ROI_Data')
+%save([filename,'.mat'],'ROI_Data')
+cd(LD)
 end
 
 %% Cell Sort to get 'similar ROIs'