Running to example sendSamples

README.md

@@ -89,25 +89,43 @@ Closing the figure will also disconnect from the camera, as will `delete(D)`
 ### Start beam pointer and calibrate
 
 ```
-laserObject = beamPointer;
+P = zapit.pointer;
 
 % find transformation of pixel coords into voltage for scan mirrors
-pointLog = laserObject.logPoints;
-[tform, laserObject] = laserObject.runAffineTransform(pointLog);
+P.logPoints;
+
 ```
+You can now click on the image and the beam should go to that location.
+
 
+### Calibrate to mouse skull
+Now you can tell the system where is Bregma and another reference location
+```
+P.getAreaCoordinates
+```
+
+### Generate the parameters for switching the beam
+Here we are switching at 40 Hz with a laser amplitude of 0.36
+```
+P.makeChanSamples(40, 0.36);
+```
 
+### Set up NI task for the stimulation
+```
+P.createNewTask %% TODO - should run this in sendSamples
+```
+
+
+### Let's run it
+For one brain area
+```
+newTrial.area = 1; % first brain area on the list
+newTrial.LaserOn = 1;
+newTrial.powerOption = 1; % if 1 send 2 mW, if 2 send 4 mW (mean)
+```
 
-### Legacy (?) Example
 ```
-bp = beamPointer;
-OUT = bp.logPoints(7) %scales laser to location in image##
-bp.cam.src.Gain =1
-load('C:\Maja\pulsepal_beta\fsm-behaviour-maja\scanner\areas1.mat')
-bp.getAreaCoordinates(template)
-bp.makeChanSamples(40, 0.36);
-bp.createNewTask
-bp.cam.src.Gain = 1;
+P.cam.src.Gain = 1;
 
 %%
 x = randi(6, 300, 1);
@@ -120,17 +138,17 @@ for ii = 1:300
     {'ii' 'x' 't' }
     [ii x(ii) t(ii) ]
     %
-    bp.sendSamples(x(ii), 1);
+    P.sendSamples(x(ii), 1);
     pause(t(ii));
-    bp.hTask.stop;
-    bp.sendSamples(x(ii), 0);
+    P.hTask.stop;
+    P.sendSamples(x(ii), 0);
     pause(t(ii));
-    bp.hTask.stop;
+    P.hTask.stop;
 end
 
 %%
 % get order of inactivated areas
-save('runningtest4', 'x', 't', 'bp');
+save('runningtest4', 'x', 't', 'P');
 
 ```
 

code/+zapit/@config/config.m

@@ -37,7 +37,7 @@ function loadConfig(obj,fname)
             data = zapit.yaml.ReadYaml(fname);
 
             obj.powerOption = data.powerOption;
-            obj.refPoints = data.refPoints;
+            obj.refPoints = cell2mat(data.refPoints);
 
 
             % template is 2 by n (by n?) array

code/+zapit/@pointer/getAreaCoordinates.m

@@ -5,12 +5,18 @@
     % volts
 
     % change illumination to get a clearer image of beam position
-    obj.cam.src.Gain = 25;
-
+    obj.cam.src.Gain = 2;
+
+    % Clear any old coords
+    delete(obj.hAreaCoords)
+    obj.hAreaCoords = [];
+
+    delete(obj.hRefCoords)
+    obj.hRefCoords = [];
+
     % record points in the screen
-    refPoints = obj.config.refPoints;                        % coordinate references on the mouse skull (bregma and 0,-2 marked with pen)
+    refPoints = obj.config.refPoints; % coordinate references on the mouse skull (bregma and 0,-2 marked with pen)
     template = obj.config.template;
-    hold(obj.hImAx, 'on');
     %             plot(obj.hImAx, refPoints(:,1), refPoints(:,2));
     realPoints = recordPoints(obj.hImAx, obj.hFig); % output columns are x and y coords
 
@@ -29,23 +35,18 @@
     coordsLibrary = [xVolt' yVolt'];
     coordsLibrary(:,:,2) = [xVolt2' yVolt2'];
 
-    coordsLibrary
     obj.coordsLibrary = coordsLibrary;
     obj.newpoint = newpoint;
 
 
     hold(obj.hImAx, 'on');
-    plot(obj.hImAx, newpoint(1, :, 1), newpoint(2, :, 1), 'o'); % left hemisphere coords
-    plot(obj.hImAx, newpoint(1, :, 2), newpoint(2, :, 2), 'o'); % right hemisphere coords
-
-    % move laser into each position as a check
-    for xx = 1:length(newpoint)
-        for yy = 1:2
-            obj.hTask.writeAnalogData([obj.coordsLibrary(xx, 1, yy), obj.coordsLibrary(xx, 2, yy)]);
-            pause(1)
-        end
-    end
-
+    obj.hAreaCoords(1) = plot(obj.hImAx, newpoint(1,:,1), newpoint(2,:,1), 'o'); % left hemisphere coords
+    obj.hAreaCoords(2) = plot(obj.hImAx, newpoint(1,:,2), newpoint(2,:,2), 'o'); % right hemisphere coords
+    hold(obj.hImAx, 'off');
+
+
+    % Move points through all locations to check visually that all is good
+    obj.testCoordsLibray;
 
 
     %% functions
@@ -65,7 +66,8 @@
             figure(hImFig)
             waitforbuttonpress;
         end
-        figureText = join(['bregma recorded, click ', string(refPoints(:,2)')]);
+
+        figureText = sprintf('bregma recorded, click %d %d ', refPoints(:,2));
         title(hImAx,figureText);
         figure(hImFig)
         waitforbuttonpress;
@@ -76,7 +78,11 @@
         end
 
         title(hImAx, 'both points recorded');
-        plot(hImAx, points(:,1), points(:,2));
+
+        hold(obj.hImAx, 'on');
+        obj.hRefCoords = plot(hImAx, points(:,1), points(:,2));
+        hold(obj.hImAx, 'off');
+
     end
 
     function [newpoint,rotMat] = coordsRotation(template, refPoints, points)
@@ -106,7 +112,7 @@
 
     function [newpoint, opaqueArea] = checkOpaqueArea(obj, newpoint)
         % TODO -- refactor to model/view
-        opaqueArea = input('using an additional opaque area as control? 1 or 0');
+        opaqueArea = input('using an additional opaque area as control?\n[1 or 0] ');
         if opaqueArea
             figure(obj.hFig)
             title(obj.hImAx, 'find opaque area 1')

code/+zapit/@pointer/logPoints.m

@@ -1,4 +1,4 @@
-function OUT = logPoints(obj, nPoints, doPointGrid)
+function varargout = logPoints(obj, nPoints, doPointGrid)
     % Log precision of beam pointing: conduct an affine transform to calibrate camera and beam
     %
     % Purpose
@@ -14,7 +14,9 @@
     % output: target and actual pixel coordinates
 
     % lower camera illumination for precision
-    obj.cam.src.Gain = 1;
+
+    obj.cam.src.Gain = 1; % TODO - hard-coded
+    obj.cam.exposure = 3000; % TODO - hard-coded
 
     if nargin<2
         nPoints = [];
@@ -51,14 +53,17 @@
         % change pixel coords into voltage %TODO -- R and C correct?
         [rVolts(:,1), rVolts(:,2)] = obj.pixelToVolt(R,C);
 
+        fprintf('Running calibration')
         for ii=1:length(R)
             % feed volts into scan mirrors, wait for precise image
             % without smudges and take position in pixels
             obj.hTask.writeAnalogData([rVolts(ii,:), 3.3]);
             pause(0.125)
             v(ii)=obj.getLaserPosAccuracy([R(ii), C(ii)]);
             drawnow
+            fprintf('.')
         end
+        fprintf('\n')
 
     else
         % TODO -- DOES NOT WORK RIGHT NOW FOR SOME REASON
@@ -101,4 +106,8 @@
     obj.hTask.writeAnalogData([0 0 0]); % Zero beam and turn off laser
 
     % TODO: now demonstrate that it worked
+
+    if nargout>0
+        varargout{1} = OUT;
+    end
 end

code/+zapit/@pointer/pointer.m

@@ -31,7 +31,7 @@
         newpoint
         topUpCall
         rampDown % Not used
-        chanSamples
+        chanSamples %Structure describing waveforms to send the scanners for each brain area
         topCall = 1;
         freqLaser
         numSamplesPerChannel
@@ -46,6 +46,9 @@
         hImLive
         hLastPoint % plot handle with location of the last clicked point
 
+        hAreaCoords % locations where the beam will be sent. see getAreaCoords
+        hRefCoords  % The two reference coords
+
         axRange
         imSize % Size of the displayed image
 
@@ -61,8 +64,13 @@
 
 
     methods
-        function obj = pointer
+        function obj = pointer(fname)
             % Constructor
+
+            if nargin < 1
+                fname = [];
+            end
+
             disp('STARTING BEAMPOINTER')
             obj.cam = zapit.camera(2); % TODO -  Hard-coded selection of camera ID
 
@@ -87,10 +95,13 @@
 
             obj.zeroScanners
 
-
             % load configuration files
-            [fname,fpath] = uigetfile('*.yaml','Pick a config file');
-            pathToConfig = fullfile(fpath,fname);
+            if isempty(fname)
+                [fname,fpath] = uigetfile('*.yaml','Pick a config file');
+                pathToConfig = fullfile(fpath,fname);
+            else
+                pathToConfig = fname;
+            end
             obj.config = zapit.config(pathToConfig);
         end
 
@@ -145,6 +156,7 @@ function sendSamples(obj, new_trial)
             %         powerOption - if 1 send 2 mW, if 2 send 4 mW (mean)
             % output: nothing. The function just sends correct samples to
             % the pointer
+
             CoordNum = new_trial.area;
             LaserOn = new_trial.LaserOn;
             trialPower = new_trial.powerOption;
@@ -155,7 +167,7 @@ function sendSamples(obj, new_trial)
                 % right properties. hTask is an object that 'rests' on the NI
                 % board and gives it information to play back once command start
                 % arrives. It contains a clock and sampled voltages.
-                createNewTask(obj, taskName);
+                obj.createNewTask(taskName);
             end
 
             % update coordinate parameters/channel samples
@@ -167,15 +179,19 @@ function sendSamples(obj, new_trial)
 
             % write voltage samples onto the task
             obj.hTask.writeAnalogData(voltChannel);
+
             % start the execution of the new task
             obj.hTask.start;
+
+            % TODO the task is continuing to run, which is wrong. It should play out the finite
+            % samples then it stops.
         end
 
 
         function createNewTask(obj, taskName)
 
             devName = 'Dev2';
-            
+
             % channel 0 = x Axis
             % channel 1 = y Axis
             % channel 2 = analog laser
@@ -262,7 +278,20 @@ function topUpBuffer(obj)
                 obj.hTask.writeAnalogData(obj.voltChannel);
             end
         end
-
+
+        function testCoordsLibray(obj)
+            % move laser into each position as a check
+            for xx = 1:length(obj.newpoint)
+                for yy = 1:2
+                    fprintf('Testing coordinate %0.2f %0.2f\n', ...
+                     obj.coordsLibrary(xx, 1, yy), ...
+                     obj.coordsLibrary(xx, 2, yy))
+                    obj.hTask.writeAnalogData([obj.coordsLibrary(xx, 1, yy), obj.coordsLibrary(xx, 2, yy),2]);
+                    pause(0.25)
+                end
+            end
+        end
+
 
         function pointBeamToLocationInImage(obj,~,~)
             % This callback function obtains the mouse position in the