Toolbox check

+ndi/+docs/build.m

@@ -14,9 +14,17 @@ function build()
 
 ndi.docs.all_documents2markdown();
 
+ % make sure we don't traverse the the 'site' directory
+ndi_path = ndi_globals.path.path;
+
+if ~isfolder([ndi_path filesep 'site']),
+	mkdir([ndi_path filesep 'site']);
+end;
+
+vlt.file.touch([ndi_path filesep 'site' filesep '.matlab2markdown-ignore']);
+
 disp(['Now writing function reference...']);
 
-ndi_path = ndi_globals.path.path;
 ndi_docs = [ndi_path filesep 'docs' filesep 'reference']; % code reference path
 ymlpath = 'reference';
 

+ndi/+example/+tutorial/tutorial_02_01.m

@@ -1,43 +1,86 @@
-% This script contains all of the code for
+function tutorial_02_01(prefix, testing)
+% ndi.example.tutorials.tutorial_02_01 - runs the code in Tutorial 2.1
+%
+% out = ndi.example.tutorials.tutorial_02_01(PREFIX, [TESTING])
+%
+% Runs (and tests) the code for 
 %
 % NDI Tutorial 2: Analzying your first electrophysiology experiment with NDI
 %    Tutorial 2.1: Reading an example dataset
 % The tutorial is available at 
 %     https://vh-lab.github.io/NDI-matlab/tutorials/analyzing_first_physiology_experiment/1_example_dataset.md
 %
+% PREFIX should be the directory that contains the directory 'ts_exper1'. If it is not
+% provided or is empty, the default is [userpath filesep 'Documents' filesep 'NDI'].
 %
+% If TESTING is 1, then PREFIX is taken to be [userpath filesep 'Documents' filesep' NDI filesep 'Test'], 
+% and the files are copied to the temporary directory before proceeding so that the files 
+% in the directory called PREFIX are not touched. 
+%
+
+if nargin<1 | isempty(prefix),
+	prefix = [userpath filesep 'Documents' filesep 'NDI']; % or '/Users/yourusername/Desktop/' if you put it on the desktop perhaps
+end;
+
+if nargin<2,
+	testing = 0;
+end;
+
+tutorial_dir = 'ts_exper1';
+
+if testing, % copy the files to the temp directory
+	prefix = [userpath filesep 'Documents' filesep 'NDI' filesep 'Test']; 
+	disp(['Assuming clean data files ts_exper1 are in ' prefix '.']);
+	ndi.globals() 
+	disp(['Clearing any ''' tutorial_dir  ''' in the temporary directory']);
+	try,
+		rmdir([ndi_globals.path.temppath filesep tutorial_dir],'s');
+	end;
+	disp(['Copying ''' tutorial_dir ''' to the temporary directory']);
+	copyfile([prefix filesep tutorial_dir], [ndi_globals.path.temppath filesep tutorial_dir]);
+
+	prefix = ndi_globals.path.temppath;
+end
 
  % Code block 2.1.2.1
 
-prefix = [userpath filesep 'Documents' filesep 'NDI']; % or '/Users/yourusername/Desktop/' if you put it on the desktop perhaps
+disp(['Code block 2.1.2.1:']);
+ % prefix line is set above
 ls([prefix filesep 'ts_exper1' filesep 't*']); % list all the files in the t0000N folders
 
  % Code block 2.1.2.2
 
+disp(['Code block 2.1.2.2:']);
 my_smr_file = fullfile(prefix,'ts_exper1','t00001','spike2data.smr')
 ndi.example.tutorial.plottreeshrewdata(my_smr_file);
 
  % Code block 2.1.3.1
 
+disp(['Code block 2.1.3.1:']);
 type (fullfile(prefix,'ts_exper1','t00001','probemap.txt'))
 
  % Code block 2.1.3.2
 
+disp(['Code block 2.1.3.2:']);
 type (fullfile(prefix,'ts_exper1','t00001','stims.tsv'))
 
  % Code block 2.1.4.1
 
+disp(['Code block 2.1.4.1:']);
 S = ndi.session.dir('ts_exper1',[prefix filesep 'ts_exper1'])
 
  % inserted code for the full script:
 
 S.daqsystem_clear() % make sure we don't have old daq systems from the demo
 
  % Code block 2.1.4.2
+disp(['Code block 2.1.4.2:']);
+disp(['(should return empty)']);
 S.getprobes()
 
  % Code block 2.1.4.3
 
+disp(['Code block 2.1.4.3:']);
 ced_filenav = ndi.file.navigator(S, {'.*\.smr\>', 'probemap.txt'}, ...
     'ndi.epoch.epochprobemap_daqsystem','probemap.txt');
 ced_rdr = ndi.daq.reader.mfdaq.cedspike2();
@@ -47,12 +90,14 @@
 
  % Code block 2.1.4.4
 
+disp(['Code block 2.1.4.4:']);
  % let's look at the epochs the daq.system can find
 et = ced_system.epochtable() % should see a 4 element answer
 f = ced_system.filenavigator.getepochfiles(1) % you should see the files from epoch 1, t00001
 
  % Code block 2.1.4.5
 
+disp(['Code block 2.1.4.5:']);
 vis_filenav = ndi.file.navigator(S, {'.*\.smr\>', 'probemap.txt', 'stims.tsv'},...
      'ndi.epoch.epochprobemap_daqsystem','probemap.txt');
 vis_rdr = ndi.daq.reader.mfdaq.cedspike2();
@@ -63,11 +108,13 @@
 
  % Code block 2.1.4.6
 
+disp(['Code block 2.1.4.6:']);
 nsf = ndi.time.syncrule.filematch(struct('number_fullpath_matches',2));
 S.syncgraph_addrule(nsf);
 
  % Code block 2.1.5.1
 
+disp(['Code block 2.1.5.1:']);
 p = S.getprobes() % get all of the probes that are in the ndi.session S
 for i=1:numel(p), p{i}, end; % display the probe information for each probe
 
@@ -79,6 +126,7 @@
 epoch_to_read = 1;
 
  % Code block 2.1.5.2
+disp(['Code block 2.1.5.2:']);
 
 [data,t,timeref_p_ctx1]=p_ctx1.readtimeseries(epoch_to_read,-Inf,Inf); % read all data from epoch 1
 figure(100);
@@ -89,17 +137,20 @@
 box off;
 
  % Code block 2.1.5.3
+disp(['Code block 2.1.5.3:']);
 
 p_visstim_list = S.getprobes('name','vis_stim','reference',1) % returns a cell array of matches
 p_visstim = p_visstim_list{1}; % take the first one, should be the only one
 et = p_visstim.epochtable()
 for i=1:numel(et), et(i), end; % display the epoch table entries
 
  % Code block 2.1.5.4
+disp(['Code block 2.1.5.4:']);
 
 timeref_p_ctx1
 
  % Code block 2.1.5.5
+disp(['Code block 2.1.5.5:']);
 
 [data,t,timeref_stim]=p_visstim.readtimeseries(timeref_p_ctx1,-Inf,Inf); % read all data from epoch 1 of p_ctx1 !
 figure(100);
@@ -108,6 +159,7 @@
 
  % Code block 2.1.5.6
 
+disp(['Code block 2.1.5.6:']);
 t, % show timestamps
 t.stimon,
 data, % show data

+ndi/+example/+tutorial/tutorial_02_02.m

@@ -0,0 +1,70 @@
+function tutorial_02_02(prefix, testing)
+% ndi.example.tutorials.tutorial_02_02 - runs the code in Tutorial 2.2
+%
+% out = ndi.example.tutorials.tutorial_02_02(PREFIX, [TESTING])
+%
+% Runs (and tests) the code for 
+%
+% NDI Tutorial 2: Analzying your first electrophysiology experiment with NDI
+%    Tutorial 2.2: The automated way
+% The tutorial is available at 
+%     https://vh-lab.github.io/NDI-matlab/tutorials/analyzing_first_physiology_experiment/2_theautomatedway
+%
+% PREFIX should be the directory that contains the directory 'ts_exper2'. If it is not
+% provided or is empty, the default is [userpath filesep 'Documents' filesep 'NDI'].
+%
+% If TESTING is 1, then the files are copied to the temporary directory before proceeding so that the files 
+% in the directory called PREFIX are not touched.
+%
+
+if nargin<1 | isempty(prefix),
+	prefix = [userpath filesep 'Documents' filesep 'NDI']; % or '/Users/yourusername/Desktop/' if you put it on the desktop perhaps
+end;
+
+
+if nargin<2,
+	testing = 0;
+end;
+
+tutorial_dir = 'ts_exper2';
+
+if testing, % copy the files to the temp directory
+	ndi.globals() 
+        prefix = [userpath filesep 'Documents' filesep 'NDI' filesep 'Test'];
+        disp(['Assuming clean data files ts_exper2 are in ' prefix '.']);
+
+	disp(['Clearing any ''' tutorial_dir  ''' in the temporary directory']);
+	try,
+		rmdir([ndi_globals.path.temppath filesep tutorial_dir],'s');
+	end;
+	disp(['Copying ''' tutorial_dir ''' to the temporary directory']);
+	copyfile([prefix filesep tutorial_dir], [ndi_globals.path.temppath filesep tutorial_dir]);
+
+	prefix = ndi_globals.path.temppath;
+end
+
+ % Code block 2.2.7.1
+
+disp(['Code block 2.2.7.1:']);
+ % prefix line is set above
+S = ndi.setup.vhlab('ts_exper2',[prefix filesep 'ts_exper2']);
+
+p_ctx1_list = S.getprobes('name','ctx','reference',1) % returns a cell array of matches
+p_ctx1 = p_ctx1_list{1}; % take the first one, should be the only one
+
+epoch_to_read = 1;
+[data,t,timeref_p_ctx1]=p_ctx1.readtimeseries(epoch_to_read,-Inf,Inf); % read all data from epoch 1
+figure(100);
+plot(t,data);
+xlabel('Time(s)');
+ylabel('Voltage (V)');
+set(gca,'xlim',[t(1) t(end)]);
+box off;
+
+p_visstim_list = S.getprobes('type','stimulator') % returns a cell array of matches
+p_visstim = p_visstim_list{1}; % take the first one, should be the only one
+[data,t,timeref_stim]=p_visstim.readtimeseries(timeref_p_ctx1,-Inf,Inf); % read all data from epoch 1 of p_ctx1 !
+figure(100);
+hold on;
+vlt.neuro.stimulus.plot_stimulus_timeseries(7,t.stimon,t.stimoff,'stimid',data.stimid);
+