Merge pull request #24 from gardner-lab/Liberti

Liberti

ActiveComm/Software/ActiveCommMk1/ActiveCommMk1.ino

@@ -3,34 +3,34 @@
 // 01.13.15
 // WALIII
 
-// Hall sensor controlled actove commutator, driven by a servo motor
+// Hall sensor controlled active commutator, driven by a servo motor
 // Inspired by :
-// 
 //
-#include <Servo.h> 
-
-Servo myservo;  
-
-int pos = 90;    
-const int analogInPin = 8;  
+//
+#include <Servo.h>
+
+Servo myservo;
+
+int pos = 90;
+const int analogInPin = 8;
 int sensorValue = 0;        // value read from the pot
 int setpoint = 510;
 
 void setup() {
   // initialize serial communications at 9600 bps:
-  Serial.begin(9600); 
-  myservo.attach(9);  // attaches the servo on pin 9 to the servo object 
+  Serial.begin(9600);
+  myservo.attach(9);  // attaches the servo on pin 9 to the servo object
 }
 
 void loop() {
-  
-  
-  sensorValue = analogRead(analogInPin);            
- 
-  Serial.print("sensor = " );                       
-  Serial.println(sensorValue);      
-
-  
+
+
+  sensorValue = analogRead(analogInPin);
+
+  Serial.print("sensor = " );
+  Serial.println(sensorValue);
+
+
   if(sensorValue> setpoint+10){
       pos = pos+5;
   myservo.write(pos);
@@ -48,5 +48,5 @@ pos = 90;
    myservo.write(pos);
 }
 
-  delay(20);                     
+  delay(20);
 }

ActiveComm/Software/ActiveCommMk2/ActiveCommMk2.ino

@@ -3,7 +3,7 @@
 // 01.13.15
 // WALIII
 
-// Hall sensor controlled actove commutator, driven by a servo motor
+// Hall sensor controlled active commutator, driven by a servo motor
 // Inspired
 //
 //

Analysis Pipeline/FS_tiff.m

@@ -1,61 +1,66 @@
 
 function FS_tiff(videodata,varargin)
-  % FS_tiff
+% FS_tiff
 
-  %   Create multipage Tiff stack from the .mov files form the FreedomScope
+%   Create multipage Tiff stack from the .mov files form the FreedomScope
 
-  %   Created: 2016/02/12
-  %   By: WALIII
-  %   Updated: 2016/02/15
-  %   By: WALIII
+%   Created: 2016/02/12
+%   By: WALIII
+%   Updated: 2016/02/15
+%   By: WALIII
 
-  % FS_BatchDff_TM will do several things:
-  %
-  %   1. Create a grayscale mtif, called 'G.tif'
-  %   2. Creates a RGB mtif, called 'RGB.tif'
-  %
-  %
+% FS_BatchDff_TM will do several things:
+%
+%   1. Create a grayscale mtif, called 'G.tif'
+%   2. Creates a RGB mtif, called 'RGB.tif'
+%
+%
 
-
 
-  filename = 'G';
+
+filename = 'G';
 format_switch = 1;
-  nparams=length(varargin);
+nparams=length(varargin);
 
 % if mod(nparams,2)>0
 % 	error('Parameters must be specified as parameter/value pairs');
 % end
 for i=1:2:nparams
-	switch lower(varargin{i})
-		case 'colors'
-			colors=varargin{i+1};
+    switch lower(varargin{i})
+        case 'colors'
+            colors=varargin{i+1};
 
         case 's_smooth'
             a=varargin{i+1};
-			for i = 1: size(files,3)
+            for i = 1: size(files,3)
                 files(:,:,i) = wiener2(files(:,:,i),[a a]);
             end
 
         case 't_smooth'
-			b=varargin{i+1};
-                files = convn(files, single(reshape([1 1 1] / b, 1, 1, [])), 'same');
+            b=varargin{i+1};
+            files = convn(files, single(reshape([1 1 1] / b, 1, 1, [])), 'same');
         case 'fname'
             filename=varargin{i+1};
         case 'format'
             format_switch=varargin{i+1};
-        end
-
     end
+
+end
 
 
 if format_switch == 1;
-[files, n] = FS_Format(videodata,1);
-else 
+    try
+        [files, n] = FS_Format(videodata,1);
+    catch
+        disp('only one frame in this extraction');
+        files = videodata;
+    end
+else
     files = videodata;
 end
-  
+
 % if rm_artifacts ==1;
-%     
+%
 
 % d = files2;
 % files2 = ((d-min(d(:))) ./ (max(d(:)-min(d(:)))))*255;
@@ -71,7 +76,7 @@ function FS_tiff(videodata,varargin)
 
 imwrite(uint8(files(:,:,1)),[filename,'.tif']);
 if size(size(videodata),2) ==4
-imwrite(uint8(videodata(:,:,:,1)),[filename,'_','RGB.tif']);
+    imwrite(uint8(videodata(:,:,:,1)),[filename,'_','RGB.tif']);
 end
 
 %imwrite(bitshift(uint16(files(:,:,1)), 8),'G_16.tif');
@@ -80,19 +85,17 @@ function FS_tiff(videodata,varargin)
 for i=2:size(files,3) %number of images to be read
 
     K = files(:,:,i);
-%     K = wiener2(K,[5 5]);
-if size(size(videodata),2) ==4
-
-    K2 = videodata(:,:,:,i);
-end
-    %G  = filter2(fspecial('average',3),files2(:,:,i));
-    %GG = medfilt2(G);
-
-imwrite(uint8(K),[filename,'.tif'],'WriteMode','append');
-if size(size(videodata),2) ==4
-
-imwrite(uint8(K2),[filename,'_','RGB.tif'],'WriteMode','append');
-end
+    %     K = wiener2(K,[5 5]);
+    if size(size(videodata),2) ==4
+
+        K2 = videodata(:,:,:,i);
+    end
+
+    imwrite(uint8(K),[filename,'.tif'],'WriteMode','append');
+    if size(size(videodata),2) ==4
+
+        imwrite(uint8(K2),[filename,'_','RGB.tif'],'WriteMode','append');
+    end
 end
 
 end