Merge pull request #1 from RomeshA/removed_chisq_outliers

Removed chisq outlier removal from analysis

Author: RomeshA

+mcmc/@feather/blobs.m

@@ -2,14 +2,12 @@ function blobs(f)
 	figure
 
 	xyz = f.xyz;
-	chisq = f.chisq;
 	state_color = f.state_colors;
 	cdata = braintrack_utils.state_cdata;
-	contaminated = braintrack_utils.chisq_outliers(chisq);
 
 
 	for j = 1:size(cdata,1)
-		pts = state_color == j & ~contaminated(:);
+		pts = state_color == j;
 		if any(pts)
 			h = utils.alphavol_wrapper(xyz(pts,:),Inf);
 

+mcmc/@feather/clouds.m

@@ -2,10 +2,6 @@ function clouds(f)
 	figure
 
 	xyz = f.xyz;
-
-	chisq = f.chisq;
-	contaminated = braintrack_utils.chisq_outliers(chisq);
-
 	state_color = f.state_colors;
 	cdata = braintrack_utils.state_cdata;
 
@@ -17,7 +13,7 @@ function clouds(f)
     gridres = 0.025;
 
     for j = 1:size(cdata,1)
-		pts = state_color == j & ~contaminated(:);
+		pts = state_color == j;
 		if any(pts)
 			[Vcount] = utils.simple_bin3d(xyz(pts,:),xyzlim,gridres);
 			vol = mcmc.viewer.vol3d_alpha_fast(gca,xyzlim,j*+(Vcount>0),Vcount);

+mcmc/@feather/cones.m

@@ -2,9 +2,7 @@ function cones(f)
 	    %if ~isnumeric(varargin{1})
 	    	%f = varargin{1};
     	xyz = f.xyz;
-    	chisq = f.chisq;
-    	contaminated = braintrack_utils.chisq_outliers(chisq);
-    	fitted = isfinite(chisq) & ~contaminated;
+    	fitted = isfinite(chisq);
     	valid = [fitted(2:end)==1 & fitted(1:end-1)==1]; % This says 
 	    % else
 	    %     xyz = varargin{1};
@@ -97,9 +95,7 @@ function cones(f)
         f = mcmc.feather.import(sprintf('postmaster/control_apnea_art_%d_postmaster',j));
 
         xyz = f.xyz;
-        chisq = f.chisq;
-        contaminated = braintrack_utils.chisq_outliers(chisq);
-        fitted = isfinite(chisq) & ~contaminated;
+        fitted = isfinite(chisq);
         valid = [fitted(2:end)==1 & fitted(1:end-1)==1]; % This says 
 
         xyzdiff = [xyzdiff; diff(xyz)]; 

+mcmc/@feather/plot_track.m

@@ -18,6 +18,4 @@
 		xyz = f.xyz;
 	end
 
-	contaminated = braintrack_utils.chisq_outliers(f.chisq);
-	xyz(contaminated,:) = NaN;
 	h_out = f.plot_statecolored(xyz(:,1),xyz(:,2),xyz(:,3));

+mcmc/@feather/timecourse.m

@@ -48,8 +48,6 @@ function plot_timecourse(f,nocolor,smoothed)
 
 	xv = 1:f.latest;
 
-	contaminated = braintrack_utils.chisq_outliers(f.chisq);
-	yv(contaminated,:) = NaN;
 
 	for j = 1:length(param_names)
 		ax(end+1) = subplot(n_rows,n_cols,1+a_idx(ceil(j/2),mod(j-1,2)));

+mcmc/@viewer/viewer.m

@@ -364,8 +364,6 @@ function set_spec_electrode(self,idx)
 
 		function prep_animation(self)
 			chisq = self.feather.chisq;
-			contaminated = braintrack_utils.chisq_outliers(chisq);
-			chisq(contaminated) = NaN;
 
 			fixed_idx = arrayfun(@(x) x.skip_fit(1),self.feather.fit_data) == 3;
 			time_idx = self.feather.time;