diff --git a/projects/Makefile b/projects/Makefile index d582c40..2ed3ed5 100644 --- a/projects/Makefile +++ b/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 diff --git a/projects/project_fano_test/fano.tex b/projects/project_fano_test/fano_test.tex similarity index 100% rename from projects/project_fano_test/fano.tex rename to projects/project_fano_test/fano_test.tex diff --git a/projects/project_isipdffit/solution/isipdffit.m b/projects/project_isipdffit/solution/isipdffit.m new file mode 100644 index 0000000..e518161 --- /dev/null +++ b/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 + + + + diff --git a/projects/project_pca_natural_img/Makefile b/projects/project_pca_natural_images/Makefile similarity index 100% rename from projects/project_pca_natural_img/Makefile rename to projects/project_pca_natural_images/Makefile diff --git a/projects/project_pca_natural_img/natimg.jpg b/projects/project_pca_natural_images/natimg.jpg similarity index 100% rename from projects/project_pca_natural_img/natimg.jpg rename to projects/project_pca_natural_images/natimg.jpg diff --git a/projects/project_pca_natural_img/pca_natural_images.tex b/projects/project_pca_natural_images/pca_natural_images.tex similarity index 100% rename from projects/project_pca_natural_img/pca_natural_images.tex rename to projects/project_pca_natural_images/pca_natural_images.tex diff --git a/projects/project_populationvector/Makefile b/projects/project_populationvector/Makefile index 6422eb4..972e839 100644 --- a/projects/project_populationvector/Makefile +++ b/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 diff --git a/projects/project_q-values/Makefile b/projects/project_qvalues/Makefile similarity index 100% rename from projects/project_q-values/Makefile rename to projects/project_qvalues/Makefile diff --git a/projects/project_q-values/p_values.dat b/projects/project_qvalues/p_values.dat similarity index 100% rename from projects/project_q-values/p_values.dat rename to projects/project_qvalues/p_values.dat diff --git a/projects/project_q-values/qvalues.tex b/projects/project_qvalues/qvalues.tex similarity index 100% rename from projects/project_q-values/qvalues.tex rename to projects/project_qvalues/qvalues.tex diff --git a/projects/project_steady_fi/Makefile b/projects/project_steady_state_fi/Makefile similarity index 100% rename from projects/project_steady_fi/Makefile rename to projects/project_steady_state_fi/Makefile diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-14.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-14.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-14.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-14.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-18.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-18.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-18.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-18.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-2.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-2.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-2.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-2.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-6.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-6.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-6.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-6.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-9.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-9.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_-9.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_-9.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_12.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_12.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_12.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_12.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_15.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_15.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_15.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_15.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_2.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_2.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_2.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_2.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_5.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_5.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_5.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_5.mat diff --git a/projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_9.mat b/projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_9.mat similarity index 100% rename from projects/project_steady_fi/data/p_unit_2012-03-30-aa_fi_curve_9.mat rename to projects/project_steady_state_fi/data/p_unit_2012-03-30-aa_fi_curve_9.mat diff --git a/projects/project_steady_fi/steady_state_fi.tex b/projects/project_steady_state_fi/steady_state_fi.tex similarity index 100% rename from projects/project_steady_fi/steady_state_fi.tex rename to projects/project_steady_state_fi/steady_state_fi.tex