all figures compile

marderlab · Jun 29, 2020 · 2f2d6c7 · 2f2d6c7
1 parent 5c0632a
commit 2f2d6c7
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Showing 358 changed files with 45 additions and 25 deletions.
diff --git a/fig5/make_fig_4.m → +fig5/make.m b/fig5/make_fig_4.m → +fig5/make.m
@@ -4,6 +4,14 @@
 addpath('../')
 close all
 
+
+try
+	data_loc = getpref('size_comp','data');
+catch
+	error('Tell this script where the data is using setpref>size_comp>data/')
+end
+
+
 figure('outerposition',[300 300 800 801],'PaperUnits','points','PaperSize',[800 801]); hold on
 for i = 4:-1:1
 	ax(i) = subplot(2,2,i); hold on
@@ -24,7 +32,7 @@
 g0 = [379 165 2.35 .72 297 1713 .46 1370];
 
 % control -- integral controller
-x = singleCompartment.makeNeuron('controller_type','IntegralController');
+x = singleCompartment.makeNeuron('controller_type','oleary/IntegralController');
 x.set('*gbar',g0)
 x.reset
 x.integrate;
@@ -65,9 +73,9 @@
 all_gbar(:,7) = g0(7);
 all_gbar = all_gbar';
 
-if exist('generalized_perturbations.mat','file') == 2
+if exist(fullfile(data_loc,'generalized_perturbations.mat'),'file') == 2
 
-	load('generalized_perturbations.mat','data','params')
+	load(fullfile(data_loc,'generalized_perturbations.mat'),'data','params')
 else
 
 	p = xgrid;
@@ -89,7 +97,7 @@
 	[data, params] = p.gather;
 
 
-	save('generalized_perturbations.mat','data','params')
+	save(fullfile(data_loc,'generalized_perturbations.mat'),'data','params')
 end
 
 metrics = data{1};
@@ -143,7 +151,7 @@
 % now we show calcium nullclines for a whole bunch of very similar neurons
 % but with different properties in the standard projection
 
-allfiles = dir('./perturb-similar-bursters/*calcium.voronoi');
+allfiles = dir(fullfile(data_loc,'perturb-similar-bursters','*calcium.voronoi'));
 alldata = singleCompartment.perturb.consolidateCalciumNullclines(allfiles);
 
 
@@ -182,7 +190,7 @@
 x.set('*gbar',[379 165 2.35 .72 297 1713 .46 1370])
 gbar = x.get('*gbar');
 save_name = hashlib.md5hash([gbar(:); gbar_x(:); gbar_y(:)]);
-load([save_name '_calcium.voronoi'],'-mat','v')
+load(fullfile(data_loc,[save_name '_calcium.voronoi']),'-mat','v')
 
 X = v.boundaries(1).regions.x;
 Y = v.boundaries(1).regions.y;
@@ -198,7 +206,7 @@
 x.set('*gbar',[379 165 2.35 .72 297 1713 .46 1370])
 gbar = x.get('*gbar');
 save_name = hashlib.md5hash([x.hash hashlib.md5hash([gbar_x(:); gbar_y(:)])]);
-load([save_name '_1.voronoi'],'-mat','v')
+load(fullfile(data_loc,[save_name '_1.voronoi']),'-mat','v')
 v.plotBoundaries(ax(1))
 axlib.resolveOverlappingPolyShapes(ax(1))
 
@@ -249,6 +257,8 @@
 	plot_data.X = [];
 	plot_data.Y = [];
 
+	x.integrate;
+
 	parfor j = 1:N
 
 		g = singleCompartment.perturb.scaleG(v.data.g0,all_x(i),all_y(j),gbar_x,gbar_y);
@@ -269,7 +279,7 @@
 	end
 
 	for j = 1:N
-		plotlib.trajectory(ax(1),plot_data(j).X,plot_data(j).Y,'Color',this_color,'ArrowLength',.015,'LineWidth',1,'norm_x',false,'norm_y',false,'n_arrows',1);
+		plotlib.trajectory(ax(1),plot_data(j).X,plot_data(j).Y,'Color',this_color,'ArrowLength',.015,'LineWidth',1,'NormX',false,'NormY',false,'NArrows',1);
 
 	end
 	drawnow
@@ -303,7 +313,7 @@
 x.set('*gbar',[379 165 2.35 .72 297 1713 .46 1370])
 gbar = x.get('*gbar');
 save_name = hashlib.md5hash([gbar(:); gbar_x(:); gbar_y(:)]);
-load([save_name '_calcium.voronoi'],'-mat','v')
+load(fullfile(data_loc,[save_name '_calcium.voronoi']),'-mat','v')
 
 
 X = v.boundaries(1).regions.x;
@@ -320,7 +330,7 @@
 x.set('*gbar',[379 165 2.35 .72 297 1713 .46 1370])
 gbar = x.get('*gbar');
 save_name = hashlib.md5hash([x.hash hashlib.md5hash([gbar_x(:); gbar_y(:)])]);
-load([save_name '_1.voronoi'],'-mat','v')
+load(fullfile(data_loc,[save_name '_1.voronoi']),'-mat','v')
 v.plotBoundaries(ax(2))
 axlib.resolveOverlappingPolyShapes(ax(2))
 
@@ -390,7 +400,7 @@
 	end
 
 	for j = 1:N
-		plotlib.trajectory(ax(2),plot_data(j).X,plot_data(j).Y,'Color',this_color,'ArrowLength',.015,'LineWidth',1,'norm_x',false,'norm_y',false,'n_arrows',1);
+		plotlib.trajectory(ax(2),plot_data(j).X,plot_data(j).Y,'Color',this_color,'ArrowLength',.015,'LineWidth',1,'NormX',false,'NormY',false,'NArrows',1);
 
 	end
 	drawnow
@@ -425,10 +435,10 @@
 
 
 
-axlib.label(ax(1),'a','x_offset',-.05,'y_offset',0,'font_size',24);
-axlib.label(ax(2),'b','x_offset',-.05,'y_offset',0,'font_size',24);
-axlib.label(ax(3),'c','x_offset',-.05,'y_offset',0,'font_size',24);
-axlib.label(ax(4),'d','x_offset',-.05,'y_offset',0,'font_size',24);
+axlib.label(ax(1),'a','XOffset',-.05,'YOffset',0,'FontSize',24);
+axlib.label(ax(2),'b','XOffset',-.05,'YOffset',0,'FontSize',24);
+axlib.label(ax(3),'c','XOffset',-.05,'YOffset',0,'FontSize',24);
+axlib.label(ax(4),'d','XOffset',-.05,'YOffset',0,'FontSize',24);
 
 ax(3).YLim = [600 1500];
 

diff --git a/+singleCompartment/+perturb/analyzeWithControl.m b/+singleCompartment/+perturb/analyzeWithControl.m
@@ -5,13 +5,19 @@
 
 status = 1;
 
+try
+	data_loc = getpref('size_comp','data');
+catch
+	error('Tell this script where the data is using setpref>size_comp>data/')
+end
+
 
 gbar = x.get('*gbar');
 %save_name = hashlib.md5hash([gbar(:); gbar_x(:); gbar_y(:)]);
 
 save_name = hashlib.md5hash([x.hash hashlib.md5hash([gbar_x(:); gbar_y(:)])]);
 
-if exist([save_name '_1.voronoi'],'file')
+if exist(fullfile(data_loc,[save_name '_1.voronoi']),'file')
 	disp('Already done, skipping...')
 	status = 0;
 	return
@@ -56,7 +62,7 @@
 
 x0 = logspace(-.9,0,10)*x0;
 y0 = logspace(-.9,0,10)*y0;
-singleCompartment.perturb.segmentAndSave(v, x0, y0, [save_name '_1.voronoi']);
+singleCompartment.perturb.segmentAndSave(v, x0, y0, fullfile(data_loc,[save_name '_1.voronoi']));
 
 
 % clean up the start file

diff --git a/+singleCompartment/+perturb/findCalciumNullcline.m b/+singleCompartment/+perturb/findCalciumNullcline.m
@@ -4,6 +4,13 @@
 
 function status = findCalciumNullcline(x, gbar_x, gbar_y)
 
+try
+	data_loc = getpref('size_comp','data');
+catch
+	error('Tell this script where the data is using setpref>size_comp>data/')
+end
+
+
 status = 1;
 
 if nargin == 1
@@ -22,16 +29,14 @@
 
 disp(['Saving using: ' save_name])
 
-if exist([save_name '_calcium.voronoi'],'file')
+if exist(fullfile(data_loc,[save_name '_calcium.voronoi']),'file')
 	disp('Already done, skipping...')
 	status = 0;
 	return
 end
 
 x.reset;
 
-% write to disk just so we know where it's writing
-save([save_name '.start'],'status')
 
 
 disp('==========================================')
@@ -46,7 +51,7 @@
 if data.metrics_base.firing_rate == 0
 	disp('Bad model, skipping...')
 	delete([save_name '.start'])
-	save([save_name '.bad_model'],'status')
+	save(fullfile(data_loc,[save_name '.bad_model']),'status')
 	return
 end
 
@@ -80,9 +85,7 @@
 x0 = logspace(-.9,.4,10)*x0;
 y0 = logspace(-.9,.4,10)*y0;
 
-singleCompartment.perturb.segmentAndSave(v, x0, y0, [save_name '_calcium.voronoi']);
+singleCompartment.perturb.segmentAndSave(v, x0, y0, fullfile(data_loc,[save_name '_calcium.voronoi']));
 
-% clean up the start file
-delete([save_name '.start'])
 
 
diff --git a/.gitignore b/.gitignore
@@ -15,4 +15,5 @@ images/
 *.log
 *.aux
 *.out
-*.start
+*.start
+*.voronoi
diff --git a/9395145c8e98069c30447d3ef7d1d4fb_calcium.voronoi b/9395145c8e98069c30447d3ef7d1d4fb_calcium.voronoi
diff --git a/fig5/0375581e3759b8156c50942bd4243c88_calcium.voronoi b/fig5/0375581e3759b8156c50942bd4243c88_calcium.voronoi
diff --git a/fig5/3b08ad1e9f82e53f2ebf4fa54563389e_1.voronoi b/fig5/3b08ad1e9f82e53f2ebf4fa54563389e_1.voronoi
diff --git a/fig5/89bb546e1642d11c3fd3957a0aeddc5c_1.voronoi b/fig5/89bb546e1642d11c3fd3957a0aeddc5c_1.voronoi
diff --git a/fig5/94b371a2765ac3e9e52d5e127c99d5d6_1.voronoi b/fig5/94b371a2765ac3e9e52d5e127c99d5d6_1.voronoi
diff --git a/fig5/a7ed08b90cc5936e9d4a6898d99fe05d_calcium.voronoi b/fig5/a7ed08b90cc5936e9d4a6898d99fe05d_calcium.voronoi
diff --git a/fig5/e01e666b8d3316665b7c11dc03368178_1.voronoi b/fig5/e01e666b8d3316665b7c11dc03368178_1.voronoi
diff --git a/fig5/perturb-similar-bursters/004264956f3dfc1bc18a902e91ed2682_calcium.voronoi b/fig5/perturb-similar-bursters/004264956f3dfc1bc18a902e91ed2682_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/004aa1d35d1f357201d1cb01227cae46_calcium.voronoi b/fig5/perturb-similar-bursters/004aa1d35d1f357201d1cb01227cae46_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/014327c2ff60abe84d27d2d8e27ca13c_calcium.voronoi b/fig5/perturb-similar-bursters/014327c2ff60abe84d27d2d8e27ca13c_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/02c42b4c27e381a790b48bdd4e677cac_calcium.voronoi b/fig5/perturb-similar-bursters/02c42b4c27e381a790b48bdd4e677cac_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0360934531265cf7eb1b37285136e05c_calcium.voronoi b/fig5/perturb-similar-bursters/0360934531265cf7eb1b37285136e05c_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/03663d6bd27ff570bb60ad7b2a96c7ff_calcium.voronoi b/fig5/perturb-similar-bursters/03663d6bd27ff570bb60ad7b2a96c7ff_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/04408c3bc3aa02e393bcf17074470174_calcium.voronoi b/fig5/perturb-similar-bursters/04408c3bc3aa02e393bcf17074470174_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0453d5b05e2840b75d6493dce95b016f_calcium.voronoi b/fig5/perturb-similar-bursters/0453d5b05e2840b75d6493dce95b016f_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/059ffbd16c8f72012f50471b5fc7dccf_calcium.voronoi b/fig5/perturb-similar-bursters/059ffbd16c8f72012f50471b5fc7dccf_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/05da09d93ecc1df75a90536ae024c585_calcium.voronoi b/fig5/perturb-similar-bursters/05da09d93ecc1df75a90536ae024c585_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/05e1aa2414368ffac0160da129093e7b_calcium.voronoi b/fig5/perturb-similar-bursters/05e1aa2414368ffac0160da129093e7b_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/068df0a15d566b2f1feafc2f04bf6c52_calcium.voronoi b/fig5/perturb-similar-bursters/068df0a15d566b2f1feafc2f04bf6c52_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/07fa1ab6fd0e476dc5382b5062469b4e_calcium.voronoi b/fig5/perturb-similar-bursters/07fa1ab6fd0e476dc5382b5062469b4e_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/08ec900d1b465b0bea9827574c13ad8c_calcium.voronoi b/fig5/perturb-similar-bursters/08ec900d1b465b0bea9827574c13ad8c_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/09f9c51d14e31640b2812533a69ff1ff_calcium.voronoi b/fig5/perturb-similar-bursters/09f9c51d14e31640b2812533a69ff1ff_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0ab315e1add9a577bd16090459f9832b_calcium.voronoi b/fig5/perturb-similar-bursters/0ab315e1add9a577bd16090459f9832b_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0b69327f6957622e3ca03b35f0fcb9a1_calcium.voronoi b/fig5/perturb-similar-bursters/0b69327f6957622e3ca03b35f0fcb9a1_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0c0ed25db8ed2cba348907985ef2a430_calcium.voronoi b/fig5/perturb-similar-bursters/0c0ed25db8ed2cba348907985ef2a430_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0c7e6f966b0070a89b01d28923b4901d_calcium.voronoi b/fig5/perturb-similar-bursters/0c7e6f966b0070a89b01d28923b4901d_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0d42dfda52c29d4977e9acf4bd4fe88c_calcium.voronoi b/fig5/perturb-similar-bursters/0d42dfda52c29d4977e9acf4bd4fe88c_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0dea7e804b9255ac7bba7df3c3b015ff_calcium.voronoi b/fig5/perturb-similar-bursters/0dea7e804b9255ac7bba7df3c3b015ff_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0e3666dd62b36b78d75d01cee1242b7e_calcium.voronoi b/fig5/perturb-similar-bursters/0e3666dd62b36b78d75d01cee1242b7e_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0f7bb4e55a3b6387ec18eb9847079e1b_calcium.voronoi b/fig5/perturb-similar-bursters/0f7bb4e55a3b6387ec18eb9847079e1b_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/0ffeffda3ba9bb8120a851c7d39e29cd_calcium.voronoi b/fig5/perturb-similar-bursters/0ffeffda3ba9bb8120a851c7d39e29cd_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/117f4d2ce637ce7ff7c562cb8db4c672_calcium.voronoi b/fig5/perturb-similar-bursters/117f4d2ce637ce7ff7c562cb8db4c672_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1267f2badaab45fd0143d4942848c223_calcium.voronoi b/fig5/perturb-similar-bursters/1267f2badaab45fd0143d4942848c223_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/12fb58788608fd280f7ee653d245f3b5_calcium.voronoi b/fig5/perturb-similar-bursters/12fb58788608fd280f7ee653d245f3b5_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1369bbf8bd08806253d1eaa55dbe18dd_calcium.voronoi b/fig5/perturb-similar-bursters/1369bbf8bd08806253d1eaa55dbe18dd_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/17b10fa3c3a3d7c422b7b48deb7af21d_calcium.voronoi b/fig5/perturb-similar-bursters/17b10fa3c3a3d7c422b7b48deb7af21d_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/17e52a04553c8031f73038c0427c79e1_calcium.voronoi b/fig5/perturb-similar-bursters/17e52a04553c8031f73038c0427c79e1_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1893c7f16ec8dd7e667f4fa1bf2b20e7_calcium.voronoi b/fig5/perturb-similar-bursters/1893c7f16ec8dd7e667f4fa1bf2b20e7_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/18b309a0abfa85a67140d5c8f4d66344_calcium.voronoi b/fig5/perturb-similar-bursters/18b309a0abfa85a67140d5c8f4d66344_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/18e453e1a6ab639a6d2b2b2e27ea66b2_calcium.voronoi b/fig5/perturb-similar-bursters/18e453e1a6ab639a6d2b2b2e27ea66b2_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/193de8efbe79a2a754a7d31b84f9fc2c_calcium.voronoi b/fig5/perturb-similar-bursters/193de8efbe79a2a754a7d31b84f9fc2c_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1b638c6ca2d3a0bde40a79cc34f297b0_calcium.voronoi b/fig5/perturb-similar-bursters/1b638c6ca2d3a0bde40a79cc34f297b0_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1c7c1851e9c5ead5d54e4829661fe75a_calcium.voronoi b/fig5/perturb-similar-bursters/1c7c1851e9c5ead5d54e4829661fe75a_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1c9c32f6da1fa05b7d1f59a954c1a6ce_calcium.voronoi b/fig5/perturb-similar-bursters/1c9c32f6da1fa05b7d1f59a954c1a6ce_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1d0feed50a9f0d96f42d78fcfbd8b80a_calcium.voronoi b/fig5/perturb-similar-bursters/1d0feed50a9f0d96f42d78fcfbd8b80a_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1db88d93f38bf62f35526c44bc3a6b4c_calcium.voronoi b/fig5/perturb-similar-bursters/1db88d93f38bf62f35526c44bc3a6b4c_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/1f82b8e8143b2d5ec30987fb798adf72_calcium.voronoi b/fig5/perturb-similar-bursters/1f82b8e8143b2d5ec30987fb798adf72_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/2100d12632d74e820dcbc4f28cd5e4df_calcium.voronoi b/fig5/perturb-similar-bursters/2100d12632d74e820dcbc4f28cd5e4df_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/21a07be56dad7d77bb475a26b255a007_calcium.voronoi b/fig5/perturb-similar-bursters/21a07be56dad7d77bb475a26b255a007_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/22aea840edfcdbd04e56cfb6b0e437f4_calcium.voronoi b/fig5/perturb-similar-bursters/22aea840edfcdbd04e56cfb6b0e437f4_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/234af4a9bd581a2699001c70f68eff63_calcium.voronoi b/fig5/perturb-similar-bursters/234af4a9bd581a2699001c70f68eff63_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/242e530770f6f6dbf7bea4f58b45c6a0_calcium.voronoi b/fig5/perturb-similar-bursters/242e530770f6f6dbf7bea4f58b45c6a0_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/2435fb52b8dbd99e3f411fc4a7a5c132_calcium.voronoi b/fig5/perturb-similar-bursters/2435fb52b8dbd99e3f411fc4a7a5c132_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/24a5f8aa4136ae0aad2ca2c418e50ace_calcium.voronoi b/fig5/perturb-similar-bursters/24a5f8aa4136ae0aad2ca2c418e50ace_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/252f238cf3afcd801c0de6ffffa9d2d8_calcium.voronoi b/fig5/perturb-similar-bursters/252f238cf3afcd801c0de6ffffa9d2d8_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/257de988965a3b4c8fc2f5b12f11212d_calcium.voronoi b/fig5/perturb-similar-bursters/257de988965a3b4c8fc2f5b12f11212d_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/258a96e69ba36700e357d38e865157e0_calcium.voronoi b/fig5/perturb-similar-bursters/258a96e69ba36700e357d38e865157e0_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/259029ba267369a68a34637683887316_calcium.voronoi b/fig5/perturb-similar-bursters/259029ba267369a68a34637683887316_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/26411b52099ec1b93f73d834317cc949_calcium.voronoi b/fig5/perturb-similar-bursters/26411b52099ec1b93f73d834317cc949_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/266097df5ae7c3b0600f264abca8c0cc_calcium.voronoi b/fig5/perturb-similar-bursters/266097df5ae7c3b0600f264abca8c0cc_calcium.voronoi
diff --git a/fig5/perturb-similar-bursters/26be830165bf153ef9f798c092eb890c_calcium.voronoi b/fig5/perturb-similar-bursters/26be830165bf153ef9f798c092eb890c_calcium.voronoi
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