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Merge pull request #107 from RNA-FRETools/improve-tm
Various improvements and bug fixes in VP, TP and HA
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| { | ||
| "tag" : "1.3.3.1", | ||
| "prev_commit_hash" : "4f414d4c" | ||
| "tag" : "1.3.3.2", | ||
| "prev_commit_hash" : "cbe25179" | ||
| } |
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56 changes: 56 additions & 0 deletions
56
MASH-FRET/source/GUI/mod-histogram-analysis/buildPanelScrollHA.m
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| function h = buildPanelScrollHA(h,p) | ||
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| % default | ||
| hpop0 = 22; | ||
| hedit0 = 20; | ||
| htxt0 = 14; | ||
| wedit0 = 40; | ||
| fact = 5; | ||
| fntsz2 = 10; | ||
| str5 = 'Gaussian fitting'; | ||
| str6 = 'relative pop.:'; | ||
| ttl0 = 'Histogram and plot'; | ||
| ttl1 = 'State configuration'; | ||
| ttl2 = 'State populations'; | ||
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| % parents | ||
| h_pan = h.uipanel_HA_scroll; | ||
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| % dimensions | ||
| pospan = get(h_pan,'position'); | ||
| wcb0 = getUItextWidth(str5,p.fntun,p.fntsz1,'normal',p.tbl)+p.wbox; | ||
| wtxt0 = getUItextWidth(str6,p.fntun,p.fntsz1,'normal',p.tbl); | ||
| htxt1 = (fntsz2/p.fntsz1)*htxt0; | ||
| hpan0 = p.mgpan+htxt0+hedit0+p.mg/2+hedit0+p.mg; | ||
| hpan1 = p.mgpan+hedit0+p.mg+htxt0+(hpop0-hedit0)/2+hedit0+p.mg/fact+hedit0+p.mg+... | ||
| htxt1+p.mg/2+htxt0+hpop0+p.mg; | ||
| hpan2_1 = p.mgpan+p.mg+p.mg/2+4*p.mg/fact+6*hedit0; | ||
| hpan2_2 = 2*p.mgpan+2*p.mg+3*p.mg/2+2*p.mg/fact+5*hedit0+hpop0+htxt0; | ||
| hpan2 = p.mgpan+p.mg+p.mg/2+hpan2_1+hpan2_2; | ||
| wpan0_1 = wcb0+2*p.mg; | ||
| wpan0_2 = 2*p.mg+2*p.mg/fact+2*wedit0+wtxt0; | ||
| wpan0 = 3*p.mg+wpan0_1+wpan0_2; | ||
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| % GUI | ||
| x = 0; | ||
| y = pospan(4)-p.mg-hpan0; | ||
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| h.uipanel_HA_histogramAndPlot = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan0],'title',ttl0); | ||
| h = buildPanelHAhistogramAndPlot(h,p); | ||
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| y = y-p.mg-hpan1; | ||
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| h.uipanel_HA_stateConfiguration = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan1],'title',ttl1); | ||
| h = buildPanelHAstateConfiguration(h,p); | ||
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| y = y-p.mg-hpan2; | ||
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| h.uipanel_HA_statePopulations = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan2],'title',ttl2); | ||
| h = buildPanelHAstatePopulations(h,p); | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| function h = buildPanelScrollSim(h,p) | ||
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| % default | ||
| fact = 5; | ||
| htxt0 = 14; | ||
| hedit0 = 20; | ||
| hpop0 = 22; | ||
| wedit0 = 40; | ||
| str0 = 'nb. of states (J)'; | ||
| ttl0 = 'Video parameters'; | ||
| ttl1 = 'Molecules'; | ||
| ttl2 = 'Experimental setup'; | ||
| ttl3 = 'Export options'; | ||
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| % parents | ||
| h_pan = h.uipanel_S_scroll; | ||
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| % dimensions | ||
| pospan = get(h_pan,'position'); | ||
| wtxt0 = getUItextWidth(str0,p.fntun,p.fntsz1,'normal',p.tbl); | ||
| wspan0 = p.mg+wtxt0+wedit0+p.mg/2+wedit0+p.mg/fact+wedit0+p.mg/fact+wedit0+... | ||
| p.mg; | ||
| wpan0 = 2*p.mg+wspan0; | ||
| hspan0 = p.mgpan+hpop0+p.mg/2+hedit0+p.mg/fact+hedit0+p.mg/fact+hedit0+... | ||
| p.mg/2; | ||
| hpan0 = p.mgpan+htxt0+hedit0+p.mg/2+htxt0+hedit0+p.mg/2+hspan0+p.mg/2; | ||
| hspan1 = p.mgpan+htxt0+hpop0+p.mg/2+htxt0+5*(1+hedit0)+htxt0+p.mg/2; | ||
| hspan2 = p.mgpan+htxt0+hedit0+p.mg/fact+hedit0+p.mg/2+htxt0+hedit0+p.mg/2+... | ||
| hedit0+p.mg/2; | ||
| hpan1 = p.mgpan+hedit0+p.mg/fact+hedit0+p.mg+hedit0+p.mg/2+hspan1+p.mg/2+... | ||
| hspan2+p.mg/2; | ||
| hspan3 = p.mgpan+hpop0+p.mg/2+htxt0+hedit0+p.mg/2+htxt0+hedit0+p.mg/2; | ||
| hpan2 = p.mgpan+htxt0+hedit0+p.mg/2+htxt0+hedit0+p.mg/2+hspan3+p.mg; | ||
| hpan3 = p.mgpan+7*hedit0+p.mg/2+hedit0+hpop0+p.mg/2; | ||
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| % builds GUI | ||
| x = 0; | ||
| y = pospan(4)-p.mg/2-hpan0; | ||
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| h.uipanel_S_videoParameters = uipanel('parent',h_pan,'title',ttl0,'units',... | ||
| p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold',... | ||
| 'position',[x,y,wpan0,hpan0]); | ||
| h = buildPanelSimVideoParametes(h,p); | ||
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| y = y-p.mg-hpan1; | ||
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| h.uipanel_S_molecules = uipanel('parent',h_pan,'title',ttl1,'units',... | ||
| p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold',... | ||
| 'position',[x,y,wpan0,hpan1]); | ||
| h = buildPanelSimMolecules(h,p); | ||
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| y = y-p.mg-hpan2; | ||
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| h.uipanel_S_experimentalSetup = uipanel('parent',h_pan,'title',ttl2,... | ||
| 'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight',... | ||
| 'bold','position',[x,y,wpan0,hpan2]); | ||
| h = buildPanelSimExperimentalSetup(h,p); | ||
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| y = y-p.mg-hpan3; | ||
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| h.uipanel_S_exportOptions = uipanel('parent',h_pan,'title',ttl3,'units',... | ||
| p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold',... | ||
| 'position',[x,y,wpan0,hpan3]); | ||
| h = buildPanelSimExportOptions(h,p); |
91 changes: 91 additions & 0 deletions
91
MASH-FRET/source/GUI/mod-trace-processing/buildPanelScrollTP.m
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,91 @@ | ||
| function h = buildPanelScrollTP(h,p) | ||
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| % defaults | ||
| hedit0 = 20; | ||
| htxt0 = 13; | ||
| hpop0 = 22; | ||
| fact = 5; | ||
| ttl1 = 'Plot'; | ||
| ttl2 = 'Sub-images'; | ||
| ttl3 = 'Background correction'; | ||
| ttl4 = 'Cross-talks'; | ||
| ttl5 = 'Factor corrections'; | ||
| ttl6 = 'Denoising'; | ||
| ttl7 = 'Photobleaching'; | ||
| ttl8 = 'Find states'; | ||
|
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| % parents | ||
| h_pan = h.uipanel_TP_scroll; | ||
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| % dimensions | ||
| pospan = get(h_pan,'position'); | ||
| wpan0 = pospan(3); | ||
| hpan1 = p.mgpan+htxt0+hpop0+p.mg/fact+htxt0+hpop0+p.mg/fact+htxt0+hedit0+... | ||
| p.mg+hedit0+p.mg; | ||
| hpan2 = p.mgpan+3*htxt0+p.mg/fact+htxt0+p.mg/fact+htxt0+hpop0+p.mg; | ||
| hpan3 = p.mgpan+htxt0+hpop0+p.mg/fact+htxt0+hedit0+p.mg/fact+hedit0+... | ||
| p.mg/fact+hedit0+p.mg; | ||
| hpan4 = p.mgpan+hpop0+p.mg/2+2*(htxt0+hpop0+p.mg/2)+p.mg/2; | ||
| hpan5 = p.mgpan+p.mg+p.mg/fact+hpop0+hedit0; | ||
| hpan6 = p.mgpan+p.mg+p.mg/fact+2*hpop0+2*htxt0; | ||
| hpan7 = p.mgpan+htxt0+hpop0+p.mg/fact+htxt0+hedit0+p.mg+p.mg/2; | ||
| hpan8 = p.mgpan+3*(htxt0+hpop0+p.mg)+htxt0+hedit0+p.mg/fact+hedit0+p.mg+... | ||
| htxt0+hpop0+p.mg; | ||
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| % GUI | ||
| x = 0; | ||
| y = pospan(4)-hpan1; | ||
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| h.uipanel_TP_plot = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan1],'title',ttl1); | ||
| h = buildPanelTPplot(h,p); | ||
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| y = y-p.mg-hpan2; | ||
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| h.uipanel_TP_subImages = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan2],'title',ttl2); | ||
| h = buildPanelTPsubImages(h,p); | ||
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| y = y-p.mg-hpan3; | ||
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| h.uipanel_TP_backgroundCorrection = uipanel('parent',h_pan,'units',... | ||
| p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold',... | ||
| 'position',[x,y,wpan0,hpan3],'title',ttl3); | ||
| h = buildPanelTPbackgroundCorrection(h,p); | ||
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| y = y-p.mg-hpan4; | ||
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| h.uipanel_TP_crossTalks = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan4],'title',ttl4); | ||
| h = buildPanelTPcrossTalks(h,p); | ||
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| y = y-p.mg-hpan5; | ||
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| h.uipanel_TP_denoising = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan5],'title',ttl6); | ||
| h = buildPanelTPdenoising(h,p); | ||
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| y = y-p.mg-hpan6; | ||
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| h.uipanel_TP_photobleaching = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan6],'title',ttl7); | ||
| h = buildPanelTPphotobleaching(h,p); | ||
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| y = y-p.mg-hpan7; | ||
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| h.uipanel_TP_factorCorrections = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan7],'title',ttl5); | ||
| h = buildPanelTPfactorCorrections(h,p); | ||
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| y = y-p.mg-hpan8; | ||
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| h.uipanel_TP_findStates = uipanel('parent',h_pan,'units',p.posun,... | ||
| 'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',... | ||
| [x,y,wpan0,hpan8],'title',ttl8); | ||
| h = buildPanelTPfindStates(h,p); |
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