unified names of projects

projects/Makefile

@@ -11,7 +11,7 @@ all:
 clean:
 	for d in `ls -d project_*/`; do \
 		echo "Cleaning up $$d" ; \
-		cd $$d; $(MAKE) clean ; cd .. ; \
+		$(MAKE) -C $$d clean ; \
 	done
 
 	rm -f *.zip

projects/project_isipdffit/solution/isipdffit.m

@@ -0,0 +1,72 @@
+%% check Pig implementation:
+mu = 0.01;
+D = 1.0;
+dx=0.0001;
+x = dx:dx:10.0;
+
+for D = [0.1 1 10 100]
+    for mu = [0.01 0.03 0.1 .03]
+        %pig = exp(-(x-mu).^2/4.0/D./x./mu/mu)./sqrt(4*pi*D*x.^3.0);
+        pig = invgauss(x,mu,D);
+        P = sum(pig)*dx;
+        mig = sum(x.*pig)*dx;
+        qig = sum(x.*x.*pig)*dx;
+        vig = qig - mig*mig;
+        dig = 0.5*vig/mig^3;
+        fprintf('Integral=%.3f\n', P);
+        fprintf('Average=%.3f = %.3f\n', mig, mu);
+        %fprintf('Variance=%.3f\n', vig);
+        fprintf('Diffusion=%.3f = %.3f\n\n', dig, D);
+        
+        plot(x, pig)
+        hold on
+        plot([mu mu], [0 max(pig)], 'k')
+        hold off
+        xmax = 3.0*mu;
+        if xmax < 0.1
+            xmax = 0.1;
+        end
+        xlim([0 xmax])
+        text(0.6, 0.8, sprintf('D=%.3g', D), 'units', 'normalized')
+        pause( 1.0 )
+    end
+end
+
+
+%% fit to data:
+trials = 1;
+tmax = 100.0;
+input = 10.0; % the input I
+Dnoise = 1.0; % noise strength
+outau = 0.1; % correlation time of the noise in seconds
+%for input = [9.5 10.1 11.7 15.9]
+%    spikes = lifouspikes(trials, input, tmax, Dnoise, outau);
+for input = [1.0 2.0 5.0 10.0]
+    spikes = pifouspikes(trials, input, tmax, Dnoise, outau);
+    isis = diff(spikes{1});
+    mu = mean(isis);
+    fprintf('mean firing rate = %.0f Hz\n', 1.0/mu)
+    v = var(isis);
+    D = 0.5*v/mu^3;
+    [h,b] = hist(isis, 0:0.001:1);
+    h = h/sum(h)/(b(2)-b(1));
+    bar(b, h);
+    hold on;
+    dx=0.0001;
+    x = dx:dx:max(isis);
+    pig = exp(-(x-mu).^2/4.0/D./x./mu/mu)./sqrt(4*pi*D*x.^3.0);
+    plot(x, pig, 'r', 'linewidth', 2);
+    % mle fit:
+    phat = mle(isis, 'pdf', @invgauss, 'start', [0.1 0.1] );
+    mu = phat(1);
+    D = phat(2);
+    pig = exp(-(x-mu).^2/4.0/D./x./mu/mu)./sqrt(4*pi*D*x.^3.0);
+    plot(x, pig, 'c', 'linewidth', 2);
+    xlim([0 4.0*mu])
+    hold off;
+    pause( 4.0 )
+end
+
+
+
+

projects/project_populationvector/Makefile

@@ -1,10 +1 @@
-latex:
-	pdflatex *.tex > /dev/null
-	pdflatex *.tex > /dev/null
-
-clean:
-	rm -rf *.log *.aux *.zip *.out auto
-	rm -f `basename *.tex .tex`.pdf
-
-zip: latex
-	zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
+include ../project.mk