diff --git a/tvb/adapters/visualizers/__init__.py b/tvb/adapters/visualizers/__init__.py index dd23bbdc4..74dcaaa72 100644 --- a/tvb/adapters/visualizers/__init__.py +++ b/tvb/adapters/visualizers/__init__.py @@ -35,6 +35,6 @@ __all__ = ["annotations_viewer", "brain", "complex_imaginary_coherence", "connectivity", "connectivity_edge_bundle", "covariance", "cross_coherence", "cross_correlation", "eeg_monitor", "fourier_spectrum", - "histogram", "ica", "local_connectivity_view", "matrix_viewer", "pca", "pearson_cross_correlation", + "histogram", "ica", "local_connectivity_view", "matrix_viewer","new_dual_viewer","pca", "pearson_cross_correlation", "pearson_edge_bundle", "pse_discrete", "pse_isocline", "region_volume_mapping", "sensors", "surface_view", "time_series", "time_series_volume", "tract", "topographic", "wavelet_spectrogram"] diff --git a/tvb/adapters/visualizers/new_dual_viewer.py b/tvb/adapters/visualizers/new_dual_viewer.py new file mode 100644 index 000000000..9de0ac1c3 --- /dev/null +++ b/tvb/adapters/visualizers/new_dual_viewer.py @@ -0,0 +1,127 @@ +# -*- coding: utf-8 -*- +# +# +# TheVirtualBrain-Framework Package. This package holds all Data Management, and +# Web-UI helpful to run brain-simulations. To use it, you also need do download +# TheVirtualBrain-Scientific Package (for simulators). See content of the +# documentation-folder for more details. See also http://www.thevirtualbrain.org +# +# (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others +# +# This program is free software: you can redistribute it and/or modify it under the +# terms of the GNU General Public License as published by the Free Software Foundation, +# either version 3 of the License, or (at your option) any later version. +# This program is distributed in the hope that it will be useful, but WITHOUT ANY +# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. See the GNU General Public License for more details. +# You should have received a copy of the GNU General Public License along with this +# program. If not, see . +# +# +# CITATION: +# When using The Virtual Brain for scientific publications, please cite it as follows: +# +# Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide, +# Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013) +# The Virtual Brain: a simulator of primate brain network dynamics. +# Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010) +# +# + + +from tvb.adapters.visualizers.brain import BrainViewer +from tvb.adapters.visualizers.eeg_monitor import EegMonitor +from tvb.adapters.visualizers.sensors import prepare_sensors_as_measure_points_params +from tvb.adapters.visualizers.sensors import prepare_mapped_sensors_as_measure_points_params +from tvb.basic.filters.chain import FilterChain +from tvb.core.entities.storage import dao +from tvb.datatypes.surfaces import EEGCap, CorticalSurface +from tvb.datatypes.surfaces import Surface +from tvb.datatypes.time_series import TimeSeries, TimeSeriesSEEG, TimeSeriesEEG, TimeSeriesRegion + + +class NewDualViewer(BrainViewer): + """ + New visualizer merging Brain 3D display and EEG lines display. + Same input as the DualBrainViewer + """ + _ui_name = "(Work in progress)New Viewer for Time Series in 3D and 2D" + _ui_subsection = "new_brain_dual" + + def get_input_tree(self): + + return [{'name': 'time_series', 'label': 'Time Series', 'type': TimeSeries, 'required': True, + 'conditions': FilterChain(fields=[FilterChain.datatype + '.type', + FilterChain.datatype + '._has_surface_mapping'], + operations=["in", "=="], + values=[['TimeSeriesEEG', 'TimeSeriesSEEG', + 'TimeSeriesMEG', 'TimeSeriesRegion'], True])}, + + {'name': 'projection_surface', 'label': 'Projection Surface', 'type': Surface, 'required': False, + 'description': 'A surface on which to project the results. When missing, the first EEGCap is taken' + 'This parameter is ignored when InternalSensors measures.'}, + + {'name': 'shell_surface', 'label': 'Shell Surface', 'type': Surface, 'required': False, + 'description': "Wrapping surface over the internal sensors, to be displayed " + "semi-transparently, for visual purposes only."}] + + def populate_surface_fields(self, time_series): + """ + Prepares the urls from which the client may read the data needed for drawing the surface. + """ + + if isinstance(time_series, TimeSeriesRegion): + BrainViewer.populate_surface_fields(self, time_series) + return + + self.one_to_one_map = False + self.region_map = None + self.connectivity = None + + if self.surface is None: + eeg_cap = dao.get_generic_entity(EEGCap, "EEGCap", "type") + if len(eeg_cap) < 1: + raise Exception("No EEG Cap Surface found for display!") + self.surface = eeg_cap[0] + + def retrieve_measure_points_prams(self, time_series): + + if isinstance(time_series, TimeSeriesRegion): + return BrainViewer.retrieve_measure_points_prams(self, time_series) + + self.measure_points_no = time_series.sensors.number_of_sensors + + if isinstance(time_series, TimeSeriesEEG): + return prepare_mapped_sensors_as_measure_points_params(self.current_project_id, + time_series.sensors, self.surface) + + return prepare_sensors_as_measure_points_params(time_series.sensors) + + def launch(self, time_series, projection_surface=None, shell_surface=None): + + self.surface = projection_surface + + if isinstance(time_series, TimeSeriesSEEG) and shell_surface is None: + shell_surface = dao.try_load_last_entity_of_type(self.current_project_id, CorticalSurface) + + params = BrainViewer.compute_parameters(self, time_series, shell_surface) + params.update(EegMonitor().compute_parameters(time_series, is_extended_view=True)) + + params['isOneToOneMapping'] = False + params['brainViewerTemplate'] = 'dual_brain_3d_view.html' + + if isinstance(time_series, TimeSeriesSEEG): + params['brainViewerTemplate'] = "dual_brain_3d_internal_view.html" + # Mark as None since we only display shelf face and no point to load these as well + params['urlVertices'] = None + params['isSEEG'] = True + + if isinstance(time_series, TimeSeriesRegion): + params['withTransparency'] = True + else: + params['withTransparency'] = False + + + return self.build_display_result("new_dual_brain/view", params, + pages=dict(controlPage="new_dual_brain/controls", + channelsPage="commons/channel_selector.html")) diff --git a/tvb/interfaces/web/static/js/d3.v4.min.js b/tvb/interfaces/web/static/js/d3.v4.min.js deleted file mode 100644 index 6a2705865..000000000 --- a/tvb/interfaces/web/static/js/d3.v4.min.js +++ /dev/null @@ -1,2 +0,0 @@ -// https://d3js.org Version 4.10.0. 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3:this._point=4;default:Ga(this,t,n)}this._x0=this._x1,this._x1=t,this._y0=this._y1,this._y1=n}};tc.prototype={lineStart:function(){this._x=[],this._y=[],this._basis.lineStart()},lineEnd:function(){var t=this._x,n=this._y,e=t.length-1;if(e>0)for(var r,i=t[0],o=n[0],u=t[e]-i,a=n[e]-o,c=-1;++c<=e;)r=c/e,this._basis.point(this._beta*t[c]+(1-this._beta)*(i+r*u),this._beta*n[c]+(1-this._beta)*(o+r*a));this._x=this._y=null,this._basis.lineEnd()},point:function(t,n){this._x.push(+t),this._y.push(+n)}};var Xg=function t(n){function e(t){return 1===n?new Ja(t):new tc(t,n)}return e.beta=function(n){return t(+n)},e}(.85);ec.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._x2=this._y0=this._y1=this._y2=NaN,this._point=0},lineEnd:function(){switch(this._point){case 2:this._context.lineTo(this._x2,this._y2);break;case 3:nc(this,this._x1,this._y1)}(this._line||0!==this._line&&1===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2,this._x1=t,this._y1=n;break;case 2:this._point=3;default:nc(this,t,n)}this._x0=this._x1,this._x1=this._x2,this._x2=t,this._y0=this._y1,this._y1=this._y2,this._y2=n}};var $g=function t(n){function e(t){return new ec(t,n)}return e.tension=function(n){return t(+n)},e}(0);rc.prototype={areaStart:Hg,areaEnd:Hg,lineStart:function(){this._x0=this._x1=this._x2=this._x3=this._x4=this._x5=this._y0=this._y1=this._y2=this._y3=this._y4=this._y5=NaN,this._point=0},lineEnd:function(){switch(this._point){case 1:this._context.moveTo(this._x3,this._y3),this._context.closePath();break;case 2:this._context.lineTo(this._x3,this._y3),this._context.closePath();break;case 3:this.point(this._x3,this._y3),this.point(this._x4,this._y4),this.point(this._x5,this._y5)}},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1,this._x3=t,this._y3=n;break;case 1:this._point=2,this._context.moveTo(this._x4=t,this._y4=n);break;case 2:this._point=3,this._x5=t,this._y5=n;break;default:nc(this,t,n)}this._x0=this._x1,this._x1=this._x2,this._x2=t,this._y0=this._y1,this._y1=this._y2,this._y2=n}};var Vg=function t(n){function e(t){return new rc(t,n)}return e.tension=function(n){return t(+n)},e}(0);ic.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._x2=this._y0=this._y1=this._y2=NaN,this._point=0},lineEnd:function(){(this._line||0!==this._line&&3===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1;break;case 1:this._point=2;break;case 2:this._point=3,this._line?this._context.lineTo(this._x2,this._y2):this._context.moveTo(this._x2,this._y2);break;case 3:this._point=4;default:nc(this,t,n)}this._x0=this._x1,this._x1=this._x2,this._x2=t,this._y0=this._y1,this._y1=this._y2,this._y2=n}};var Wg=function t(n){function e(t){return new ic(t,n)}return e.tension=function(n){return t(+n)},e}(0);uc.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._x2=this._y0=this._y1=this._y2=NaN,this._l01_a=this._l12_a=this._l23_a=this._l01_2a=this._l12_2a=this._l23_2a=this._point=0},lineEnd:function(){switch(this._point){case 2:this._context.lineTo(this._x2,this._y2);break;case 3:this.point(this._x2,this._y2)}(this._line||0!==this._line&&1===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){if(t=+t,n=+n,this._point){var e=this._x2-t,r=this._y2-n;this._l23_a=Math.sqrt(this._l23_2a=Math.pow(e*e+r*r,this._alpha))}switch(this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2;break;case 2:this._point=3;default:oc(this,t,n)}this._l01_a=this._l12_a,this._l12_a=this._l23_a,this._l01_2a=this._l12_2a,this._l12_2a=this._l23_2a,this._x0=this._x1,this._x1=this._x2,this._x2=t,this._y0=this._y1,this._y1=this._y2,this._y2=n}};var Zg=function t(n){function e(t){return n?new uc(t,n):new ec(t,0)}return e.alpha=function(n){return t(+n)},e}(.5);ac.prototype={areaStart:Hg,areaEnd:Hg,lineStart:function(){this._x0=this._x1=this._x2=this._x3=this._x4=this._x5=this._y0=this._y1=this._y2=this._y3=this._y4=this._y5=NaN,this._l01_a=this._l12_a=this._l23_a=this._l01_2a=this._l12_2a=this._l23_2a=this._point=0},lineEnd:function(){switch(this._point){case 1:this._context.moveTo(this._x3,this._y3),this._context.closePath();break;case 2:this._context.lineTo(this._x3,this._y3),this._context.closePath();break;case 3:this.point(this._x3,this._y3),this.point(this._x4,this._y4),this.point(this._x5,this._y5)}},point:function(t,n){if(t=+t,n=+n,this._point){var e=this._x2-t,r=this._y2-n;this._l23_a=Math.sqrt(this._l23_2a=Math.pow(e*e+r*r,this._alpha))}switch(this._point){case 0:this._point=1,this._x3=t,this._y3=n;break;case 1:this._point=2,this._context.moveTo(this._x4=t,this._y4=n);break;case 2:this._point=3,this._x5=t,this._y5=n;break;default:oc(this,t,n)}this._l01_a=this._l12_a,this._l12_a=this._l23_a,this._l01_2a=this._l12_2a,this._l12_2a=this._l23_2a,this._x0=this._x1,this._x1=this._x2,this._x2=t,this._y0=this._y1,this._y1=this._y2,this._y2=n}};var Gg=function t(n){function e(t){return n?new ac(t,n):new rc(t,0)}return e.alpha=function(n){return t(+n)},e}(.5);cc.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._x2=this._y0=this._y1=this._y2=NaN,this._l01_a=this._l12_a=this._l23_a=this._l01_2a=this._l12_2a=this._l23_2a=this._point=0},lineEnd:function(){(this._line||0!==this._line&&3===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){if(t=+t,n=+n,this._point){var e=this._x2-t,r=this._y2-n;this._l23_a=Math.sqrt(this._l23_2a=Math.pow(e*e+r*r,this._alpha))}switch(this._point){case 0:this._point=1;break;case 1:this._point=2;break;case 2:this._point=3,this._line?this._context.lineTo(this._x2,this._y2):this._context.moveTo(this._x2,this._y2);break;case 3:this._point=4;default:oc(this,t,n)}this._l01_a=this._l12_a,this._l12_a=this._l23_a,this._l01_2a=this._l12_2a,this._l12_2a=this._l23_2a,this._x0=this._x1,this._x1=this._x2,this._x2=t,this._y0=this._y1,this._y1=this._y2,this._y2=n}};var Jg=function t(n){function e(t){return n?new cc(t,n):new ic(t,0)}return e.alpha=function(n){return t(+n)},e}(.5);sc.prototype={areaStart:Hg,areaEnd:Hg,lineStart:function(){this._point=0},lineEnd:function(){this._point&&this._context.closePath()},point:function(t,n){t=+t,n=+n,this._point?this._context.lineTo(t,n):(this._point=1,this._context.moveTo(t,n))}};dc.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._y0=this._y1=this._t0=NaN,this._point=0},lineEnd:function(){switch(this._point){case 2:this._context.lineTo(this._x1,this._y1);break;case 3:pc(this,this._t0,hc(this,this._t0))}(this._line||0!==this._line&&1===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){var e=NaN;if(t=+t,n=+n,t!==this._x1||n!==this._y1){switch(this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2;break;case 2:this._point=3,pc(this,hc(this,e=lc(this,t,n)),e);break;default:pc(this,this._t0,e=lc(this,t,n))}this._x0=this._x1,this._x1=t,this._y0=this._y1,this._y1=n,this._t0=e}}},(vc.prototype=Object.create(dc.prototype)).point=function(t,n){dc.prototype.point.call(this,n,t)},_c.prototype={moveTo:function(t,n){this._context.moveTo(n,t)},closePath:function(){this._context.closePath()},lineTo:function(t,n){this._context.lineTo(n,t)},bezierCurveTo:function(t,n,e,r,i,o){this._context.bezierCurveTo(n,t,r,e,o,i)}},yc.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x=[],this._y=[]},lineEnd:function(){var t=this._x,n=this._y,e=t.length;if(e)if(this._line?this._context.lineTo(t[0],n[0]):this._context.moveTo(t[0],n[0]),2===e)this._context.lineTo(t[1],n[1]);else for(var r=gc(t),i=gc(n),o=0,u=1;u=0&&(this._t=1-this._t,this._line=1-this._line)},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2;default:if(this._t<=0)this._context.lineTo(this._x,n),this._context.lineTo(t,n);else{var e=this._x*(1-this._t)+t*this._t;this._context.lineTo(e,this._y),this._context.lineTo(e,n)}}this._x=t,this._y=n}};var Qg=function(t,n){if((i=t.length)>1)for(var e,r,i,o=1,u=t[n[0]],a=u.length;o=0;)e[n]=n;return e},tm=function(t){var n=t.map(bc);return Kg(t).sort(function(t,e){return n[t]-n[e]})},nm=function(t){return function(){return t}};Tc.prototype={constructor:Tc,insert:function(t,n){var e,r,i;if(t){if(n.P=t,n.N=t.N,t.N&&(t.N.P=n),t.N=n,t.R){for(t=t.R;t.L;)t=t.L;t.L=n}else t.R=n;e=t}else 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if((n=i.L).C&&(n.C=!1,i.C=!0,Sc(this,i),n=i.L),n.L&&n.L.C||n.R&&n.R.C){n.L&&n.L.C||(n.R.C=!1,n.C=!0,Nc(this,n),n=i.L),n.C=i.C,i.C=n.L.C=!1,Sc(this,i),t=this._;break}n.C=!0,t=i,i=i.U}while(!t.C);t&&(t.C=!1)}}};var em,rm,im,om,um,am=[],cm=[],sm=1e-6,fm=1e-12;Kc.prototype={constructor:Kc,polygons:function(){var t=this.edges;return this.cells.map(function(n){var e=n.halfedges.map(function(e){return Dc(n,t[e])});return e.data=n.site.data,e})},triangles:function(){var t=[],n=this.edges;return this.cells.forEach(function(e,r){if(o=(i=e.halfedges).length)for(var i,o,u,a=e.site,c=-1,s=n[i[o-1]],f=s.left===a?s.right:s.left;++c=a)return null;var c=t-i.site[0],s=n-i.site[1],f=c*c+s*s;do{i=o.cells[r=u],u=null,i.halfedges.forEach(function(e){var r=o.edges[e],a=r.left;if(a!==i.site&&a||(a=r.right)){var c=t-a[0],s=n-a[1],l=c*c+s*s;lt?1:n>=t?0:NaN},t.deviation=_s,t.extent=ys,t.histogram=function(){function t(t){var o,u,a=t.length,c=new Array(a);for(o=0;ol;)h.pop(),--p;var d,v=new 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e=Math.sqrt(n/P_),r=e*C_;t.moveTo(0,-e),t.lineTo(r,0),t.lineTo(0,e),t.lineTo(-r,0),t.closePath()}},R_=Math.sin(M_/10)/Math.sin(7*M_/10),L_=Math.sin(T_/10)*R_,D_=-Math.cos(T_/10)*R_,U_={draw:function(t,n){var e=Math.sqrt(.8908130915292852*n),r=L_*e,i=D_*e;t.moveTo(0,-e),t.lineTo(r,i);for(var o=1;o<5;++o){var a=T_*o/5,u=Math.cos(a),f=Math.sin(a);t.lineTo(f*e,-u*e),t.lineTo(u*r-f*i,f*r+u*i)}t.closePath()}},q_={draw:function(t,n){var e=Math.sqrt(n),r=-e/2;t.rect(r,r,e,e)}},O_=Math.sqrt(3),Y_={draw:function(t,n){var e=-Math.sqrt(n/(3*O_));t.moveTo(0,2*e),t.lineTo(-O_*e,-e),t.lineTo(O_*e,-e),t.closePath()}},B_=Math.sqrt(3)/2,F_=1/Math.sqrt(12),I_=3*(F_/2+1),j_={draw:function(t,n){var e=Math.sqrt(n/I_),r=e/2,i=e*F_,o=r,a=e*F_+e,u=-o,f=a;t.moveTo(r,i),t.lineTo(o,a),t.lineTo(u,f),t.lineTo(-.5*r-B_*i,B_*r+-.5*i),t.lineTo(-.5*o-B_*a,B_*o+-.5*a),t.lineTo(-.5*u-B_*f,B_*u+-.5*f),t.lineTo(-.5*r+B_*i,-.5*i-B_*r),t.lineTo(-.5*o+B_*a,-.5*a-B_*o),t.lineTo(-.5*u+B_*f,-.5*f-B_*u),t.closePath()}},H_=[E_,k_,z_,q_,U_,Y_,j_];Bf.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._y0=this._y1=NaN,this._point=0},lineEnd:function(){switch(this._point){case 3:Yf(this,this._x1,this._y1);case 2:this._context.lineTo(this._x1,this._y1)}(this._line||0!==this._line&&1===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2;break;case 2:this._point=3,this._context.lineTo((5*this._x0+this._x1)/6,(5*this._y0+this._y1)/6);default:Yf(this,t,n)}this._x0=this._x1,this._x1=t,this._y0=this._y1,this._y1=n}},Ff.prototype={areaStart:Of,areaEnd:Of,lineStart:function(){this._x0=this._x1=this._x2=this._x3=this._x4=this._y0=this._y1=this._y2=this._y3=this._y4=NaN,this._point=0},lineEnd:function(){switch(this._point){case 1:this._context.moveTo(this._x2,this._y2),this._context.closePath();break;case 2:this._context.moveTo((this._x2+2*this._x3)/3,(this._y2+2*this._y3)/3),this._context.lineTo((this._x3+2*this._x2)/3,(this._y3+2*this._y2)/3),this._context.closePath();break;case 3:this.point(this._x2,this._y2),this.point(this._x3,this._y3),this.point(this._x4,this._y4)}},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1,this._x2=t,this._y2=n;break;case 1:this._point=2,this._x3=t,this._y3=n;break;case 2:this._point=3,this._x4=t,this._y4=n,this._context.moveTo((this._x0+4*this._x1+t)/6,(this._y0+4*this._y1+n)/6);break;default:Yf(this,t,n)}this._x0=this._x1,this._x1=t,this._y0=this._y1,this._y1=n}},If.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._y0=this._y1=NaN,this._point=0},lineEnd:function(){(this._line||0!==this._line&&3===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){switch(t=+t,n=+n,this._point){case 0:this._point=1;break;case 1:this._point=2;break;case 2:this._point=3;var e=(this._x0+4*this._x1+t)/6,r=(this._y0+4*this._y1+n)/6;this._line?this._context.lineTo(e,r):this._context.moveTo(e,r);break;case 3:this._point=4;default:Yf(this,t,n)}this._x0=this._x1,this._x1=t,this._y0=this._y1,this._y1=n}},jf.prototype={lineStart:function(){this._x=[],this._y=[],this._basis.lineStart()},lineEnd:function(){var t=this._x,n=this._y,e=t.length-1;if(e>0)for(var 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+ } + //upper bound + else if (f.dom_y[1] > f.channels().length) { + var delta = Math.abs(f.channels().length - f.dom_y[1]); + f.dom_y[0] -= delta; + f.dom_y[1] -= delta; + } + + //redraw the lines + var dom = f.dom_y; + var yscl = f.sz_fcs.y / (dom[1] - dom[0]) / 5; + f.sc_fcs_y.domain(dom).range([f.sz_ctx_y.y, 0]); + f.gp_ax_fcs_y.call(f.ax_fcs_y); + f.gp_lines.selectAll("g").attr("transform", function (d, i) { + return "translate(0, " + f.sc_fcs_y(i) + ")" + "scale (1, " + yscl + ")" + }).selectAll("path").attr("stroke-width", "" + (3 / yscl)); + f.scale_focus_stroke(); + + } + + } + }; f.signal_tick_labeler = function (tick_value) { @@ -701,45 +776,59 @@ tv.plot = { // setup groups, scales and axes for context and focus areas f.do_scaffolding = function (rgp) { - // main groups for vertical and horizontal context areas and focus area - f.gp_ctx_y = rgp.append("g").attr("transform", "translate(" + f.ul_ctx_y.x + ", " + f.ul_ctx_y.y + ")"); f.gp_ctx_x = rgp.append("g").attr("transform", "translate(" + f.ul_ctx_x.x + ", " + f.ul_ctx_x.y + ")"); + f.gp_ctx_x.append("rect").attr("width", f.sz_ctx_x.x).attr("height", f.sz_ctx_x.y).classed("tv-data-bg", true); + f.gp_fcs = rgp.append("g").attr("transform", "translate(" + f.ul_fcs.x + ", " + f.ul_fcs.y + ")"); f.gp_fcs.on("mousewheel", f.mouse_scroll); f.gp_fcs.append("rect").attr("width", f.sz_fcs.x).attr("height", f.sz_fcs.y).classed("tv-data-bg", true); - f.gp_ctx_x.append("rect").attr("width", f.sz_ctx_x.x).attr("height", f.sz_ctx_x.y).classed("tv-data-bg", true); - f.gp_ctx_y.append("rect").attr("width", f.sz_ctx_y.x).attr("height", f.sz_ctx_y.y).classed("tv-data-bg", true); + // the plotted time series in the focus and x ctx area are subject to a clipping region new_clip_path(rgp, "fig-lines-clip").append("rect").attr("width", f.sz_fcs.x).attr("height", f.sz_fcs.y); - new_clip_path(rgp, "fig-ctx-x-clip").append("rect").attr("width", f.sz_ctx_x.x).attr("height", f.sz_ctx_x.y); // group with clip path applied for the focus lines f.gp_lines = f.gp_fcs.append("g").attr("style", "clip-path: url(#fig-lines-clip)") .append("g").classed("line-plot", true); // scales for vertical and horizontal context, and the x and y axis of the focus area - f.sc_ctx_y = d3.scale.linear().domain([-1, f.shape()[2]]).range([f.sz_ctx_y.y, 0]); - f.sc_ctx_x = d3.scale.linear().domain([f.t0(), f.t0() + f.dt() * f.shape()[0]]).range([0, f.sz_ctx_x.x]); - f.sc_fcs_x = d3.scale.linear().domain([f.t0(), f.t0() + f.dt() * f.shape()[0]]).range([0, f.sz_fcs.x]); - f.sc_fcs_y = d3.scale.linear().domain([-1, f.shape()[2] + 1]).range([f.sz_fcs.y, 0]); + f.sc_ctx_y = d3.scaleLinear().domain([-1, f.shape()[2]]).range([f.sz_ctx_y.y, 0]); + f.sc_ctx_x = d3.scaleLinear().domain([f.t0(), f.t0() + f.dt() * (f.shape()[0]-1)]).range([0, f.sz_ctx_x.x]); + f.sc_fcs_x = d3.scaleLinear().domain([f.t0(), f.t0() + f.dt() * (f.shape()[0]-1)]).range([0, f.sz_fcs.x]); + f.sc_fcs_y = d3.scaleLinear().domain([-1, f.shape()[2] + 1]).range([f.sz_fcs.y, 0]); + + + f.dom_x = f.sc_ctx_x.domain(); + f.dom_y = f.sc_ctx_y.domain(); // axes for each of the above scales - f.ax_ctx_y = d3.svg.axis().orient("left").scale(f.sc_ctx_y); - f.ax_ctx_x = d3.svg.axis().orient("bottom").scale(f.sc_ctx_x); - f.ax_fcs_x = d3.svg.axis().orient("top").scale(f.sc_fcs_x); - f.ax_fcs_y = d3.svg.axis().orient("left").scale(f.sc_fcs_y); + f.ax_ctx_x = d3.axisBottom(f.sc_ctx_x); + f.ax_fcs_x = d3.axisTop(f.sc_fcs_x); + f.ax_fcs_y = d3.axisLeft(f.sc_fcs_y); f.ax_fcs_y.tickFormat(f.signal_tick_labeler); - f.ax_ctx_y.tickFormat(f.signal_tick_labeler); // groups for each of the above axes - f.gp_ax_ctx_y = f.gp_ctx_y.append("g").classed("axis", true).call(f.ax_ctx_y); f.gp_ax_ctx_x = f.gp_ctx_x.append("g").classed("axis", true).call(f.ax_ctx_x) .attr("transform", "translate(0, " + f.sz_ctx_x.y + ")"); f.gp_ax_fcs_x = f.gp_fcs.append("g").classed("axis", true).call(f.ax_fcs_x); f.gp_ax_fcs_y = f.gp_fcs.append("g").classed("axis", true).call(f.ax_fcs_y); + + if(f.viewer_type()==='svg'){ + // main groups for vertical and horizontal context areas and focus area + f.gp_ctx_y = rgp.append("g").attr("transform", "translate(" + f.ul_ctx_y.x + ", " + f.ul_ctx_y.y + ")"); + f.gp_ctx_y.append("rect").attr("width", f.sz_ctx_y.x).attr("height", f.sz_ctx_y.y).classed("tv-data-bg", true); + + new_clip_path(rgp, "fig-ctx-x-clip").append("rect").attr("width", f.sz_ctx_x.x).attr("height", f.sz_ctx_x.y); + + // vertical context groups + f.ax_ctx_y = d3.axisLeft(f.sc_ctx_y); + f.ax_ctx_y.tickFormat(f.signal_tick_labeler); + f.gp_ax_ctx_y = f.gp_ctx_y.append("g").classed("axis", true).call(f.ax_ctx_y); + } + + }; f.prepare_data = function () { @@ -768,6 +857,7 @@ tv.plot = { da_lines[sig_idx][tt_idx] *= -1; } + da_lines[sig_idx] = {sig: da_lines[sig_idx], id: sig_idx}; } @@ -799,7 +889,7 @@ tv.plot = { } } - // scale average siganl by ptp + // scale average signal by ptp var _dar = new tv.ndar(da_x); var da_max = _dar.max() , da_min = _dar.min() @@ -838,12 +928,12 @@ tv.plot = { }; f.render_focus = function () { - var ts = f.ts() , g = f.gp_lines.selectAll("g").data(f.da_lines, function (d) { return d.id; }); + if (!f.we_are_setup) { f.line_paths = g.enter() .append("g") @@ -854,22 +944,25 @@ tv.plot = { .attr("vector-effect", "non-scaling-stroke"); } - g.select("path").attr("d", function (d) { - return d3.svg.line() - .x(function (dd, i) { + + f.line_paths.attr("d", function (d) { + return d3.line() + .x(function (d, i) { return f.sc_ctx_x(ts.data[i]); }) - .y(function (dd) { - return dd; + .y(function (d) { + //use the scale variable directly + return d*f.magic_fcs_amp_scl; }) (d.sig); }); - }; - f.render_contexts = function () { - var ts = f.ts(); + }; + f.render_contexts = function () { + // draw context lines and average + if(f.viewer_type()==='svg'){ // horizontal context line var f1 = f.gp_ctx_x.append("g").attr("style", "clip-path: url(#fig-ctx-x-clip)"); var f2 = f1.selectAll("g").data([f.da_x]).enter(); @@ -879,7 +972,7 @@ tv.plot = { }) .classed("tv-ctx-line", true); var f4 = f3.append("path") - .attr("d", d3.svg.line() + .attr("d", d3.line() .x(function (d, i) { var time_start = f.sc_ctx_x.domain()[0]; return f.sc_ctx_x((time_start + i + 0.5) * f.da_x_dt); @@ -899,7 +992,7 @@ tv.plot = { .append("g").attr("transform", "translate(0, " + f.sz_ctx_x.y / 2 + ") scale(1, 0.5)") .classed("tv-ctx-error", true) .append("path") - .attr("d", d3.svg.line() + .attr("d", d3.line() .x(function (d, i) { var idx = (i < da_x_len) ? i : (2 * da_x_len - i); var time_start = f.sc_ctx_x.domain()[0]; @@ -910,6 +1003,7 @@ tv.plot = { return f.sz_ctx_x.y * (d + std); })); + // vertical context lines f.gp_ctx_y.append("g").selectAll("g").data(f.da_y) .enter() @@ -918,12 +1012,14 @@ tv.plot = { }) .classed("tv-ctx-line", true) .append("path") - .attr("d", d3.svg.line().x(function (d, i) { + .attr("d", d3.line().x(function (d, i) { return 2 + (f.sz_ctx_y.x - 2) * i / f.sz_ctx_y.x; }) .y(function (d) { return d; })); + + } }; f.scale_focus_stroke = function () { @@ -943,98 +1039,372 @@ tv.plot = { } }; + f.add_brushes = function () { // horizontal context brush var br_ctx_x_fn = function () { - var dom = f.br_ctx_x.empty() ? f.sc_ctx_x.domain() : f.br_ctx_x.extent() - , sc = f.sc_fcs_x - , x_scaling = f.sc_ctx_x.domain()[1] / (dom[1] - dom[0]); + var event_selection_x = []; + // Different extent when it is: + //1.from the brush of 2D Focus Brush + if (d3.event.selection != null && d3.event.selection[0][0] != null) { + event_selection_x[0] = d3.event.selection[0][0]; + event_selection_x[1] = d3.event.selection[1][0]; + } + //2.from the end of focus brush + else if (d3.event.selection == null) { + event_selection_x = [f.sc_ctx_x.range()[0], f.sc_ctx_x.range()[1]]; + f.dom_x = [f.t0(), f.t0() + f.dt() * (f.shape()[0]-1)]; + } + //3.from itself + else { + event_selection_x = d3.event.selection; + } + + + var scale_brushed = d3.scaleLinear().domain(f.dom_x).range(f.sc_ctx_x.range()); + + + //selection is now in coordinates and we have to map it using scales + event_selection_x = event_selection_x.map(scale_brushed.invert, scale_brushed); + + + dom = f.br_ctx_x === null ? f.sc_ctx_x.domain() : event_selection_x; + + f.dom_x = dom; + + sc = f.sc_fcs_x; + x_scaling = scale_brushed.domain()[1] / (dom[1] - dom[0]); sc.domain(dom); f.gp_ax_fcs_x.call(f.ax_fcs_x); + + //keep the x context in the same range for the svg viewer + if(f.viewer_type()!='svg'){ + f.sc_ctx_x.domain(dom); + f.gp_ax_ctx_x.call(f.ax_ctx_x); + } + + // TODO: This seems to cause problems with negative values and commenting it out does not seem to // cause any additional problems. This could do with some double checking. f.gp_lines.attr("transform", "translate(" + sc(0) + ", 0) scale(" + x_scaling + ", 1)"); } - // vertical context brush + // vertical changes , br_ctx_y_fn = function () { - var dom = f.br_ctx_y.empty() ? f.sc_ctx_y.domain() : f.br_ctx_y.extent(); + + var event_selection_y = []; + + if (d3.event == null || d3.event.selection == null) { + event_selection_y = f.sc_ctx_y.range(); + f.dom_y = [-1, f.shape()[2]]; + } + else if (d3.event.selection != null && d3.event.selection[0][0] != null) { + event_selection_y[1] = d3.event.selection[0][1]; + event_selection_y[0] = d3.event.selection[1][1]; + } + else { + event_selection_y[0] = d3.event.selection[1]; + event_selection_y[1] = d3.event.selection[0]; + } + + var scale_brushed = d3.scaleLinear().domain(f.dom_y).range(f.sc_ctx_y.range()); + + + event_selection_y = event_selection_y.map(scale_brushed.invert, scale_brushed); + var dom = f.br_ctx_y === null ? f.sc_ctx_y.domain() : event_selection_y; + f.dom_y = dom; var yscl = f.sz_fcs.y / (dom[1] - dom[0]) / 5; - f.sc_fcs_y.domain(dom); + f.sc_fcs_y.domain(dom).range([f.sz_ctx_y.y, 0]); f.gp_ax_fcs_y.call(f.ax_fcs_y); f.gp_lines.selectAll("g").attr("transform", function (d, i) { return "translate(0, " + f.sc_fcs_y(i) + ")" + "scale (1, " + yscl + ")" }).selectAll("path").attr("stroke-width", "" + (3 / yscl)); - } - , br_ctx_end = function () { - f.scale_focus_stroke(); - // TODO: This f.render() only makes another call to the server bringing back data that is already here. - // Also when rerendering that data it is rendered from the 0 timeline, so if for example you - // zoom on a block from 250-270, 20 points or data ar brought from the server and the plot is - // redrawn with data from 0-20, but you being in the area 250-270 don't see any of it. This needs - // to be tested further to see if it was really needed, and if so look into the problem of zooming - // described above. - - // f.render(); }; f.br_ctx_y_fn = br_ctx_y_fn; + //move the focus with the x context brush in the svg viewer, different from the fn that evokes from the focus brush + br_ctx_x_move=function(){ + if(f.viewer_type()==='svg'){ + var event_selection = []; + // Different extent when it is: + //1.from the brush of 2D Focus Brush + if (d3.event.selection != null && d3.event.selection[0][0] != null) { + event_selection[0] = d3.event.selection[0][0]; + event_selection[1] = d3.event.selection[1][0]; + } + //2.from the end of focus brush + else if (d3.event.selection == null) { + event_selection = [f.sc_ctx_x.range()[0], f.sc_ctx_x.range()[1]]; + + } + + //3.from itself + else { + event_selection = d3.event.selection; + } + //selection is now in coordinates and we have to map it using scales + event_selection = event_selection.map(f.sc_ctx_x.invert, f.sc_ctx_x); + var dom = f.br_ctx_x === null ? f.sc_ctx_x.domain() : event_selection + , sc = f.sc_fcs_x + , x_scaling = f.sc_ctx_x.domain()[1] / (dom[1] - dom[0]); + + sc.domain(dom); + + + f.gp_ax_fcs_x.call(f.ax_fcs_x); + + // TODO: This seems to cause problems with negative values and commenting it out does not seem to + // cause any additional problems. This could do with some double checking. + f.gp_lines.attr("transform", "translate(" + sc(0) + ", 0) scale(" + x_scaling + ", 1)"); + } + } + + br_ctx_y_move=function(){ + var event_selection = []; + if (d3.event.selection != null && d3.event.selection[0][0] != null) { + event_selection[0] = d3.event.selection[0][1]; + event_selection[1] = d3.event.selection[1][1]; + } + else if (d3.event.selection == null) { + event_selection = f.sc_ctx_y.range(); + } + else { + event_selection[0] = d3.event.selection[1]; + event_selection[1] = d3.event.selection[0]; + + } + event_selection = event_selection.map(f.sc_ctx_y.invert, f.sc_ctx_y); + var dom = f.br_ctx_y === null ? f.sc_ctx_y.domain() : event_selection; + var yscl = f.sz_fcs.y / (dom[1] - dom[0]) / 5; + f.sc_fcs_y.domain(dom).range([f.sz_ctx_y.y, 0]); + + f.gp_ax_fcs_y.call(f.ax_fcs_y); + f.gp_lines.selectAll("g").attr("transform", function (d, i) { + return "translate(0, " + f.sc_fcs_y(i) + ")" + "scale (1, " + yscl + ")" + }).selectAll("path").attr("stroke-width", "" + (3 / yscl)); + f.scale_focus_stroke(); + } + + br_ctx_end = function () { + if(f.viewer_type()==='svg'){} + else{ + //get the selected time range + var event_selection_x = []; + if (d3.event.selection != null) { + event_selection_x[0] = d3.event.selection[0]; + event_selection_x[1] = d3.event.selection[1]; + } + event_selection_x = event_selection_x.map(f.sc_ctx_x.invert); + timeselection = event_selection_x; + + // remove the last time's selection + f.gp_ctx_x.selectAll(".selected-time").remove(); + + //change the actual time point in the slider + if (f.viewer_type() === 'dualbrain' && d3.event.selection != null) { + f.timeselection_update_fn() + } + } + + }; // on end of focus brush // this is on f so that f can call it when everything else is done.. + //this function can reset the status of the plot to the initial state f.br_fcs_endfn = function (no_render) { - + if (!d3.event || !d3.event.sourceEvent) { + br_ctx_y_fn(); + f.scale_focus_stroke(); + return; + } br_ctx_x_fn(); br_ctx_y_fn(); + f.gp_br_fcs.node().__brush.selection = null; + f.gp_br_fcs.call(f.br_fcs); f.scale_focus_stroke(); - f.gp_br_fcs.call(f.br_fcs.clear()); + }; + - if (!no_render) { - // TODO: This f.render() only makes another call to the server bringing back data that is already here. - // Also when rerendering that data it is rendered from the 0 timeline, so if for example you - // zoom on a block from 250-270, 20 points or data ar brought from the server and the plot is - // redrawn with data from 0-20, but you being in the area 250-270 don't see any of it. This needs - // to be tested further to see if it was really needed, and if so look into the problem of zooming - // described above. + f.br_fcs_startfn = function () { + //select a channel + var event_selection_y = []; + event_selection_y[1] = d3.event.selection[0][1]; + event_selection_y = event_selection_y.map(f.sc_ctx_y.invert); - //f.render(); + //choose the time point + var event_selection_x = []; + event_selection_x[1] = d3.event.selection[0][0]; + event_selection_x = event_selection_x.map(f.sc_ctx_x.invert); + if (event_selection_x[1] < 0) { + event_selection_x[1] = 0 + f.da_x; } - }; - // focus brush + + timerange = f.sc_fcs_x.domain()[1]; + channelID = parseInt(event_selection_y[1]); + timepoint_length = f.da_lines[channelID].sig.length; + + timepoint = event_selection_x[1] / f.sc_fcs_x.domain()[1]; + timepoint = timepoint * timepoint_length; + timepoint = parseInt(timepoint); + + valuearray = f.ys().data; + channel_number = f.channels().length; + channel_index = f.channels().indexOf(channelID); + + //print out the channel name(label) and value + $("#info-channel").html(' ' + f.labels()[parseInt(event_selection_y[1])]); + $("#info-time").html(" " + timepoint); + $("#info-value").html(" " + valuearray[channel_number * timepoint + channel_index]); + + } + f.br_fcs_brush = function () { - var ex = f.br_fcs.extent(); - f.br_ctx_x.extent([ex[0][0], ex[1][0]]); - f.br_ctx_y.extent([ex[0][1], ex[1][1]]); - f.gp_br_ctx_y.call(f.br_ctx_y); + if(f.viewer_type()==='svg'){ + var ex = d3.event.selection; f.gp_br_ctx_x.call(f.br_ctx_x); + //assign directly because can't use brushSelection to set null brushes' extent + f.gp_br_ctx_x.node().__brush.selection = [[ex[0][0], 0], [ex[1][0], f.sz_ctx_x.y]]; + + f.gp_br_ctx_y.call(f.br_ctx_y); + f.gp_br_ctx_y.node().__brush.selection = [[0, ex[0][1]], [f.sz_ctx_y.x, ex[1][1]]]; + } }; // create brushes - f.br_ctx_x = d3.svg.brush().x(f.sc_ctx_x).on("brush", br_ctx_x_fn) - .on("brushend", br_ctx_end); - - f.br_ctx_y = d3.svg.brush().y(f.sc_ctx_y).on("brush", br_ctx_y_fn) - .on("brushend", br_ctx_end); + if(f.viewer_type()==='svg'){ + // y context brush + f.br_ctx_y = d3.brushY().extent([[0, 0], [f.sz_ctx_y.x, f.sz_ctx_y.y]]).on("brush", br_ctx_y_move); + f.gp_br_ctx_y = f.gp_ctx_y.append("g"); + f.gp_br_ctx_y.append("g").classed("brush", true).call(f.br_ctx_y).selectAll("rect").attr("width", f.sz_ctx_y.x); + } - f.br_fcs = d3.svg.brush().x(f.sc_fcs_x) - .y(f.sc_fcs_y).on("brushend", f.br_fcs_endfn) + f.br_ctx_x = d3.brushX().extent([[f.sc_ctx_x.range()[0], 0], [f.sc_ctx_x.range()[1], f.sz_ctx_x.y]]).on("end", br_ctx_end) + .on("brush", br_ctx_x_move); + f.br_fcs = d3.brush().extent([[f.sc_fcs_x.range()[0], 0], [f.sc_fcs_x.range()[1], f.sz_fcs.y]]) + .on("end", f.br_fcs_endfn).on("start", f.br_fcs_startfn) .on("brush", f.br_fcs_brush); - // add brush groups and add brushes to them - f.gp_br_ctx_y = f.gp_ctx_y.append("g"); + // add time selection brush group f.gp_br_ctx_x = f.gp_ctx_x.append("g"); - f.gp_br_fcs = f.gp_fcs.append("g").classed("brush", true).call(f.br_fcs); + //add title for the time selection area + f.timeselection_title = f.gp_br_ctx_x.append("text").text("Time Selection").attr("y", -10); + f.gp_br_ctx_x.classed("brush", true).attr("class", "time-selection-brush").call(f.br_ctx_x).selectAll("rect").attr("height", f.sz_ctx_x.y); - f.gp_br_ctx_y.append("g").classed("brush", true).call(f.br_ctx_y).selectAll("rect").attr("width", f.sz_ctx_y.x); - f.gp_br_ctx_x.append("g").classed("brush", true).call(f.br_ctx_x).selectAll("rect").attr("height", f.sz_ctx_x.y); + //add main focus brush group + f.gp_br_fcs = f.gp_fcs.append("g").classed("brush", true).call(f.br_fcs).call(f.br_fcs_endfn); + + //default selection + if(f.viewer_type()==='dualbrain'){ + f.timeselection_default(); + } + }; + + //functions for the time selection window + f.timeselection_default = function () { + if (f.t0() + f.dt() * (f.shape()[0] - 1) > 100) { + d3.select(f.gp_br_ctx_x.node()).call(f.br_ctx_x.move, [f.t0(), 100].map(f.sc_ctx_x)); + } + else { + d3.select(f.gp_br_ctx_x.node()).call(f.br_ctx_x.move, [f.t0(),f.t0() + f.dt() * (f.shape()[0] - 1)].map(f.sc_ctx_x)); + } + } + + f.timeselection_update_fn = function () { + //display the selected time range + d3.select("#SetIntervalStart").property('value', timeselection[0].toFixed(2)); + d3.select("#SetIntervalEnd").property('value', timeselection[1].toFixed(2)); + $("#info-interval").html((timeselection[1] - timeselection[0]).toFixed(2) + "ms"); + + if (triggered_by_timeselection) { + //update the time in the input tag + var time_index = parseInt((timeselection[0] - f.t0()) / f.dt()); + triggered_by_changeinput = true; + $('#TimeNow').val(timeselection[0].toFixed(2)); + $('#slider').slider('value', time_index); + triggered_by_changeinput = false; + //update 3D viewer's time + if (f.viewer_type() === 'dualbrain') { + loadFromTimeStep(time_index); + } + + var timeselection_lasttime = timeselection_interval_length; + timeselection_interval = timeselection[1] - timeselection[0]; + timeselection_interval_length = parseInt(timeselection_interval / f.dt()) - 1; + //retrieve energy for the whole timeline rather than a slice + var all_slice = f.current_slice(); + all_slice[0].di = f.shape()[1]; + all_slice[0].hi = f.shape()[0]; + all_slice[0].lo = 0; + + //call the energy computation method and block until get the enery data if channel or time range is changed + if (timeselection_lasttime != timeselection_interval_length || f.channel_lasttime !== f.channels()) { + showBlockerOverlay(50000); + f.update_energy(); + } + else if (timeselection_lasttime === timeselection_interval_length && timeselection_interval_length != 0) { + if (isInternalSensorView) { + VSI_change_energySphericalMeasurePoints() + } + else { + changeSphereMeasurePoints_energy(); + } + } + f.channel_lasttime = f.channels(); + } + }; + + //move the time selection window with the slider + f.timeselection_move_fn = function () { + //only change by movie playing + if (!triggered_by_changeinput) { + redrawSelection() + } + }; + + function redrawSelection() { + if (parseInt(timeselection[1]) == parseInt(f.sc_ctx_x.domain()[1])) { + f.jump_to_next_time_range() + } + else if (timeselection[0] >= f.sc_ctx_x.domain()[1] - f.dt()) { + dom = [0, f.t0() + f.dt() * (f.shape()[0] - 1)]; + f.sc_ctx_x.domain(dom); + f.gp_ax_ctx_x.call(f.ax_ctx_x); + d3.select(f.gp_br_ctx_x.node()).call(f.br_ctx_x.move, [0, timeselection[1] - timeselection[0]].map(f.sc_ctx_x)); + } + + d3.select(f.gp_br_ctx_x.node()).call(f.br_ctx_x.move, [f.t0()+currentTimeValue*f.dt(),f.t0()+currentTimeValue*f.dt()+timeselection_interval].map(f.sc_ctx_x)); + } + + f.jump_to_next_time_range = function () { + var time_data_length = f.shape()[0]; + var current_slice_length = f.current_slice()[0].hi - f.current_slice()[0].lo; + if (f.current_slice()[0].hi + current_slice_length < time_data_length) { + dom = f.sc_ctx_x.domain(); + var slice_length = dom[1] - dom[0]; + dom[0] = dom[1] - timeselection_interval; + dom[1] = dom[1] + slice_length; + f.sc_ctx_x.domain(dom); + f.gp_ax_ctx_x.call(f.ax_ctx_x); + } + else if (f.current_slice()[0].hi == current_slice_length) { + } + else { + dom = [timeselection[1], f.t0() + f.dt() * (f.shape()[0] - 1)]; + f.sc_ctx_x.domain(dom); + f.gp_ax_ctx_x.call(f.ax_ctx_x); + } + }; + + f.timeselection_interval_set = function (start, end) { + d3.select(f.gp_br_ctx_x.node()).call(f.br_ctx_x.move, [start, end].map(f.sc_ctx_x)); }; f.parameters = ["w", "h", "p", "baseURL", "preview", "labels", "shape", - "t0", "dt", "ts", "ys", "point_limit", "channels", "mode", "state_var"]; + "t0", "dt", "ts", "ys", "point_limit", "channels", "mode", "state_var","viewer_type"]; f.parameters.map(function (name) { f[name] = tv.util.gen_access(f, name); }); @@ -1042,6 +1412,7 @@ tv.plot = { return f; }, + components: function () { var f = function (root) { @@ -1086,7 +1457,7 @@ tv.plot = { for (var i = 0; i < nkeep; i++) { vt_data[i] = []; for (var j = 0; j < n; j++) { - vt_data[i][j] = [j * w / 2.25 / n, ( 2 * h / 3 / nkeep / 2 / vt_scl) * cs.data[i * n + j]]; + vt_data[i][j] = [j * w / 2.25 / n, (2 * h / 3 / nkeep / 2 / vt_scl) * cs.data[i * n + j]]; } } diff --git a/tvb/interfaces/web/static/style/subsection_timeseries.css b/tvb/interfaces/web/static/style/subsection_timeseries.css index 5578e7ae7..82f075cb1 100644 --- a/tvb/interfaces/web/static/style/subsection_timeseries.css +++ b/tvb/interfaces/web/static/style/subsection_timeseries.css @@ -25,6 +25,32 @@ color: #000; } +/* !------------------------------------------------------- */ +/* ! COMPONENT: New dual brain viewer */ +/* !------------------------------------------------------- */ + +/*overlay changed in d3v5 for new dual brain viewer*/ +rect.overlay{ + visibility: hidden; +} + +/*universal html font styling not working while using d3v5 in the new dual brain viewer*/ +text{ + font-size:small; +} + +/*d3v5 extent=>selection*/ +rect.selection { + stroke: red; + +} + +/*remove the styling for the left and right handle*/ +rect.handle { + stroke:none; +} + + /* !------------------------------------------------------- */ /* ! COMPONENT: Volume Time Series Visualizer LEFT COLUMN */ /* !------------------------------------------------------- */ diff --git a/tvb/interfaces/web/structure.py b/tvb/interfaces/web/structure.py index a9002efb1..17da7d548 100644 --- a/tvb/interfaces/web/structure.py +++ b/tvb/interfaces/web/structure.py @@ -122,6 +122,8 @@ class WebStructure(object): SUB_SECTION_VIEW_23 = "view_wavelet" SUB_SECTION_VIEW_24 = "view_annotations" SUB_SECTION_VIEW_25 = "view_matrix" + SUB_SECTION_VIEW_26 = "view_new_brain_dual" + ### Texts to appear in HTML page headers as section-title. @@ -209,7 +211,8 @@ class WebStructure(object): SUB_SECTION_VIEW_22: "Topography Visualizer", SUB_SECTION_VIEW_23: "Wavelet Visualizer", SUB_SECTION_VIEW_24: "Annotations Visualizer", - SUB_SECTION_VIEW_25: "Matrix Visualizer" + SUB_SECTION_VIEW_25: "Matrix Visualizer", + SUB_SECTION_VIEW_26: "(work in progress)New Brain Dual Activity Visualizer (3D and 2D)" } @@ -242,7 +245,8 @@ class WebStructure(object): SUB_SECTION_VIEW_22: "topographic-visualizer", SUB_SECTION_VIEW_23: "wavelet-spectrogram-visualizer", SUB_SECTION_VIEW_24: "annotations-visualizer", - SUB_SECTION_VIEW_25: "matrix-visualizer" + SUB_SECTION_VIEW_25: "matrix-visualizer", + SUB_SECTION_VIEW_26: "new-brain-dual-visualiser" } diff --git a/tvb/interfaces/web/templates/genshi/visualizers/brain/view.html b/tvb/interfaces/web/templates/genshi/visualizers/brain/view.html index a216f2cf7..b23f8beab 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/brain/view.html +++ b/tvb/interfaces/web/templates/genshi/visualizers/brain/view.html @@ -16,6 +16,6 @@ '${urlRegionBoundaries}', '${measurePointsSelectionGID}'); }); - + \ No newline at end of file diff --git a/tvb/interfaces/web/templates/genshi/visualizers/commons/activity_toolbar_paused.html b/tvb/interfaces/web/templates/genshi/visualizers/commons/activity_toolbar_paused.html new file mode 100644 index 000000000..b79e28132 --- /dev/null +++ b/tvb/interfaces/web/templates/genshi/visualizers/commons/activity_toolbar_paused.html @@ -0,0 +1,12 @@ +
    +
    + +
    +
    ms
    +
    +
  • + + ${drawTimeseriesSelectorButton(measurePointsTitle,labelsStateVar, labelsModes, groupedLabels, initialSelection)} +
  • +
diff --git a/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/internalBrain.js b/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/internalBrain.js index 3f88321ec..733c5240b 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/internalBrain.js +++ b/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/internalBrain.js @@ -1,5 +1,5 @@ /** - * TheVirtualBrain-Framework Package. This package holds all Data Management, and + * TheVirtualBrain-Framework Package. This package holds all Data Management, and * Web-UI helpful to run brain-simulations. To use it, you also need do download * TheVirtualBrain-Scientific Package (for simulators). See content of the * documentation-folder for more details. See also http://www.thevirtualbrain.org @@ -26,6 +26,29 @@ function _VSI_bufferAtPoint(p, idx) { return [bufferVertices, bufferNormals, bufferTriangles, vertexRegionBuffer]; } +function VSI_change_energySphericalMeasurePoints() { + let energyIndex = 0; + for (let i = 0; i < NO_OF_MEASURE_POINTS; i++) { + if (tsView.channels().includes(i)) { + const result = HLPR_sphereBufferAtPoint(gl, measurePoints[i], timeselection_energy[energyIndex][currentTimeValue], 12, 12); + energyIndex++; + const bufferVertices = result[0]; + const bufferNormals = result[1]; + const bufferTriangles = result[2]; + const vertexRegionBuffer = VSI_createColorBufferForSphere(i, bufferVertices.numItems * 3); + measurePointsBuffers[i] = [bufferVertices, bufferNormals, bufferTriangles, vertexRegionBuffer]; + } + else { + const result = HLPR_sphereBufferAtPoint(gl, measurePoints[i], 3, 12, 12); + const bufferVertices = result[0]; + const bufferNormals = result[1]; + const bufferTriangles = result[2]; + const vertexRegionBuffer = VSI_createColorBufferForSphere(i, bufferVertices.numItems * 3); + measurePointsBuffers[i] = [bufferVertices, bufferNormals, bufferTriangles, vertexRegionBuffer]; + } + } +} + /** * Method used for creating a color buffer for a cube (measure point). */ @@ -73,4 +96,7 @@ function VSI_StartInternalActivityViewer(baseDatatypeURL, onePageSize, urlTimeLi isFaceToDisplay = true; _VSI_init_sphericalMeasurePoints(); + + //pause by default + AG_isStopped = true; } diff --git a/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/virtualBrain.js b/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/virtualBrain.js index ae4ae99ea..a76040a46 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/virtualBrain.js +++ b/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/virtualBrain.js @@ -127,6 +127,8 @@ var activityMin = 0, activityMax = 0; var isOneToOneMapping = false; var isDoubleView = false; var isEEGView = false; +//apply transparency on the shell surface +var withTransparency = false; var drawingMode; var VS_showLegend = true; var isInternalSensorView = false; @@ -157,10 +159,35 @@ var near = 0.1; // index of the currently selected node. This is equivalent to CONN_pickedIndex var VS_pickedIndex = -1; - var VB_BrainNavigator; +//indicating we are drawing the energy spheres and applying material colors + +//time selection vars that appear in the new dual view +var isDrawingSpheres = false; +var timeselection_interval=0; +var timeselection = []; + +var isnewDoubleView=false; +/** + * Change transparency of cortical surface from user-input. + * + * @param inputField user given input value for transparency of cortical-surface + */ +var _alphaValue = 1; +function changeSurfaceTransparency(inputField) { + var newValue = inputField.value; + + if (!isNaN(parseFloat(newValue)) && isFinite(newValue) && parseFloat(newValue) >= 0 && parseFloat(newValue) <= 1) { + _alphaValue = parseFloat(newValue); + } else { + inputField.value = _alphaValue; + displayMessage("Transparency value should be a number between 0 and 1.", "warningMessage"); + } +} + + function VS_init_hemisphere_mask(hemisphere_chunk_mask) { VS_hemisphere_chunk_mask = hemisphere_chunk_mask; if (hemisphere_chunk_mask !== null && hemisphere_chunk_mask !== undefined) { @@ -351,6 +378,17 @@ function _VS_init_cubicalMeasurePoints() { } } +function _VS_init_sphereMeasurePoints() { + for (let i = 0; i < NO_OF_MEASURE_POINTS; i++) { + const result = HLPR_sphereBufferAtPoint(gl, measurePoints[i], 2);//2 for the default radius value now, we will modify it later + const bufferVertices = result[0]; + const bufferNormals = result[1]; + const bufferTriangles = result[2]; + const bufferColor = createColorBufferForCube(false); + measurePointsBuffers[i] = [bufferVertices, bufferNormals, bufferTriangles, bufferColor]; + } +} + function VS_StartSurfaceViewer(urlVerticesList, urlLinesList, urlTrianglesList, urlNormalsList, urlMeasurePoints, noOfMeasurePoints, urlRegionMapList, urlMeasurePointsLabels, boundaryURL, shelveObject, minMeasure, maxMeasure, urlMeasure, hemisphereChunkMask) { @@ -375,19 +413,24 @@ function VS_StartBrainActivityViewer(baseDatatypeURL, onePageSize, urlTimeList, urlTrianglesList, urlNormalsList, urlMeasurePoints, noOfMeasurePoints, urlRegionMapList, minActivity, maxActivity, oneToOneMapping, doubleView, shelfObject, hemisphereChunkMask, - urlMeasurePointsLabels, boundaryURL, measurePointsSelectionGID) { + urlMeasurePointsLabels, boundaryURL, measurePointsSelectionGID, transparencyStatus) { _VS_movie_entrypoint(baseDatatypeURL, onePageSize, urlTimeList, urlVerticesList, urlLinesList, urlTrianglesList, urlNormalsList, urlMeasurePoints, noOfMeasurePoints, urlRegionMapList, minActivity, maxActivity, oneToOneMapping, doubleView, shelfObject, hemisphereChunkMask, urlMeasurePointsLabels, boundaryURL); - _VS_init_cubicalMeasurePoints(); + _VS_init_sphereMeasurePoints(); if (!isDoubleView) { // If this is a brain activity viewer then we have to initialize the selection component _initChannelSelection(measurePointsSelectionGID); // For the double view the selection is the responsibility of the extended view functions } + withTransparency = transparencyStatus; + //pause by default + AG_isStopped = true; + _alphaValue=0.3; + displayMeasureNodes=true; } function _isValidActivityData() { @@ -542,6 +585,17 @@ function _initSliders() { sliderSel = true; currentTimeValue = target.value; $('#TimeNow').val(currentTimeValue); + if(isDoubleView && timeselection_interval!=0){ + tsView.timeselection_move_fn(); + } + }, + change: function () { + if (isDoubleView && timeselection_interval!=0){ + triggered_by_timeselection = false; + tsView.timeselection_move_fn(); + triggered_by_timeselection = true; + } + }, stop: function (event, target) { sliderSel = false; @@ -913,6 +967,8 @@ function drawBuffer(drawMode, buffers) { setMatrixUniforms(); if (isOneToOneMapping) { SHADING_Context.one_to_one_program_draw(GL_shaderProgram, buffers[0], buffers[1], buffers[3], buffers[2], drawMode); + } else if (isDrawingSpheres) { + SHADING_Context.region_program_draw(GL_shaderProgram, buffers[0], buffers[1], buffers[0], buffers[2], drawMode); } else { SHADING_Context.region_program_draw(GL_shaderProgram, buffers[0], buffers[1], buffers[3], buffers[2], drawMode); } @@ -937,6 +993,12 @@ function drawBuffers(drawMode, buffersSets, bufferSetsMask, useBlending, cullFac // Blending function for alpha: transparent pix blended over opaque -> opaque pix if (cullFace) { gl.enable(gl.CULL_FACE); + if (withTransparency) { + gl.uniform1f(GL_shaderProgram.alphaUniform, _alphaValue); + } + else { + gl.uniform1f(GL_shaderProgram.alphaUniform, 1); + } gl.cullFace(cullFace); } } @@ -945,11 +1007,34 @@ function drawBuffers(drawMode, buffersSets, bufferSetsMask, useBlending, cullFac if (bufferSetsMask !== null && bufferSetsMask !== undefined && !bufferSetsMask[i]) { continue; } - drawBuffer(drawMode, buffersSets[i]); + + //display spheres with full alpha value + if (isDrawingSpheres) { + gl.uniform1i(GL_shaderProgram.useVertexColors, false); + gl.uniform1f(GL_shaderProgram.alphaUniform, 1); + + // set sphere color green for the selected channels and yellow for the others + if (VS_selectedRegions.includes(i)) { + gl.uniform4f(GL_shaderProgram.materialColor, 0.99, 0.99, 0.0, 1.0); + drawBuffer(drawMode, buffersSets[i]); + } + else { + gl.uniform4f(GL_shaderProgram.materialColor, 0.34, 0.95, 0.37, 1.0); + drawBuffer(drawMode, buffersSets[i]); + } + gl.uniform1i(GL_shaderProgram.useVertexColors, true); + + if (withTransparency) { + gl.uniform1f(GL_shaderProgram.alphaUniform, _alphaValue); + } + } + else { + drawBuffer(drawMode, buffersSets[i]); + } + } if (useBlending) { - gl.disable(gl.BLEND); gl.disable(gl.CULL_FACE); setLighting(lightSettings); // Draw the same transparent object the second time @@ -1011,7 +1096,7 @@ function tick() { if (currentTimeValue > MAX_TIME) { // Next time value is no longer in activity data. initActivityData(); - if (isDoubleView) { + if (!isnewDoubleView&&isDoubleView) { loadEEGChartFromTimeStep(0); drawGraph(false, 0); } @@ -1025,7 +1110,7 @@ function tick() { if (shouldChangeCurrentActivitiesFile()) { changeCurrentActivitiesFile(); } - if (isDoubleView) { + if (!isnewDoubleView&&isDoubleView) { drawGraph(true, TIME_STEP); } } @@ -1034,6 +1119,15 @@ function tick() { const currentTimeInFrame = Math.floor((currentTimeValue - totalPassedActivitiesData) / TIME_STEP); updateColors(currentTimeInFrame); + //update energy + if(isDoubleView && timeselection_interval!=0 && !AG_isStopped){ + if(isInternalSensorView){ + VSI_change_energySphericalMeasurePoints() + } + else{ + changeSphereMeasurePoints_energy(); + } + } drawScene(); /// Update FPS and Movie timeline @@ -1048,7 +1142,18 @@ function tick() { lastTime = timeNow; if (timeData.length > 0 && !AG_isStopped) { - document.getElementById("TimeNow").value = toSignificantDigits(timeData[currentTimeValue], 2); + if (isDoubleView && timeselection[0] >= 0 && timeStepsPerTick < 1) { + document.getElementById("TimeNow").value = (timeselection[0]).toFixed(2); + } + else if (isDoubleView && timeselection[0] > 0 && timeStepsPerTick >= 1) { + //syncing time with the d3 plot + //add dt because the 2d will add one step after the slider changes + document.getElementById("TimeNow").value = (timeselection[0] + tsView.dt() * timeStepsPerTick).toFixed(2); + } + else { + //3d movie playing only + document.getElementById("TimeNow").value = toSignificantDigits(timeData[currentTimeValue], 2); + } } let meanFrameTime = 0; for (let i = 0; i < framestime.length; i++) { @@ -1099,7 +1204,14 @@ function drawScene() { if (isInternalSensorView) { // for internal sensors we render only the sensors drawBuffers(gl.TRIANGLES, measurePointsBuffers); - } else { + } + else { + //draw the nodes first to make it appear + if (displayMeasureNodes) { + isDrawingSpheres = true; + drawBuffers(gl.TRIANGLES, measurePointsBuffers); + isDrawingSpheres = false; + } // draw surface drawBuffers(drawingMode, brainBuffers, bufferSetsMask); @@ -1108,9 +1220,6 @@ function drawScene() { if (drawTriangleLines) { drawBrainLines(brainLinesBuffers, brainBuffers, bufferSetsMask); } - if (displayMeasureNodes) { - drawBuffers(gl.TRIANGLES, measurePointsBuffers); - } } if (isFaceToDisplay) { @@ -1127,7 +1236,6 @@ function drawScene() { } else { gl.bindFramebuffer(gl.FRAMEBUFFER, GL_colorPickerBuffer); - gl.disable(gl.BLEND); gl.disable(gl.DITHER); gl.clear(gl.COLOR_BUFFER_BIT | gl.DEPTH_BUFFER_BIT); setLighting(pickingLightSettings); @@ -1136,12 +1244,18 @@ function drawScene() { GL_initColorPickingData(NO_OF_MEASURE_POINTS); } + isDrawingSpheres = true; for (let i = 0; i < NO_OF_MEASURE_POINTS; i++) { const mpColor = GL_colorPickerInitColors[i]; gl.uniform4fv(GL_shaderProgram.materialColor, mpColor); drawBuffer(gl.TRIANGLES, measurePointsBuffers[i]); } + isDrawingSpheres = false; VS_pickedIndex = GL_getPickedIndex(); + //display the channel name + if (VS_pickedIndex != -1) { + displayMessage("The highlighted node is " + measurePointsLabels[VS_pickedIndex], "infoMessage") + } doPick = false; gl.bindFramebuffer(gl.FRAMEBUFFER, null); } @@ -1205,7 +1319,7 @@ function loadFromTimeStep(step) { currentActivitiesFileLength = activitiesData.length * TIME_STEP; totalPassedActivitiesData = currentTimeValue; // Also sync eeg monitor if in double view - if (isDoubleView) { + if (!isnewDoubleView&&isDoubleView) { loadEEGChartFromTimeStep(step); } closeBlockerOverlay(); @@ -1311,3 +1425,29 @@ function readFileData(fileUrl, async, callIdentifier) { /////////////////////////////////////// ~~~~~~~~~~ END DATA RELATED METHOD ~~~~~~~~~~~~~ ////////////////////////////////// +/////////////////////////////////////// ~~~~~~~~~~ START ENERGY RELATED METHOD ~~~~~~~~~~~~~ ////////////////////////////////// +//init spheres with energy controlling the radius +function changeSphereMeasurePoints_energy() { + let energyIndex = 0; + for (let i = 0; i < NO_OF_MEASURE_POINTS; i++) { + if (tsView.channels().includes(i)) { + const result = HLPR_sphereBufferAtPoint(gl, measurePoints[i], timeselection_energy[energyIndex][currentTimeValue]); + energyIndex++; + const bufferVertices = result[0]; + const bufferNormals = result[1]; + const bufferTriangles = result[2]; + const bufferColor = createColorBufferForCube(false); + measurePointsBuffers[i] = [bufferVertices, bufferNormals, bufferTriangles, bufferColor]; + } + else { + const result = HLPR_sphereBufferAtPoint(gl, measurePoints[i], 2); + const bufferVertices = result[0]; + const bufferNormals = result[1]; + const bufferTriangles = result[2]; + const bufferColor = createColorBufferForCube(false); + measurePointsBuffers[i] = [bufferVertices, bufferNormals, bufferTriangles, bufferColor]; + } + } +} + +/////////////////////////////////////// ~~~~~~~~~~ END ENERGY RELATED METHOD ~~~~~~~~~~~~~ ////////////////////////////////// \ No newline at end of file diff --git a/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/visualizers_commons.js b/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/visualizers_commons.js index 0e49b1149..679ab5843 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/visualizers_commons.js +++ b/tvb/interfaces/web/templates/genshi/visualizers/commons/scripts/visualizers_commons.js @@ -42,6 +42,12 @@ function readDataChannelURL(baseDatatypeMethodURL, fromIdx, toIdx, stateVariable return baseURL.replace('read_data_page', 'read_channels_page') + ';channels_list=' + channels; } +function readDataEnergyURL(baseDatatypeMethodURL, fromIdx, toIdx, stateVariable, mode, step, channels,timeselectionlLength) { + const baseURL = readDataPageURL(baseDatatypeMethodURL, fromIdx, toIdx, stateVariable, mode, step); + return baseURL.replace('read_data_page', 'read_time_selection_energy') + ';channels_list=' + channels+ + ';interval_length=' + timeselectionlLength ; +} + // ------ Datatype methods mappings end here diff --git a/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/shading.js b/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/shading.js index 5b48f5eb7..dce9506b6 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/shading.js +++ b/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/shading.js @@ -145,6 +145,8 @@ SHADING_Context.region_progam_init = function(shader, measure_point_nr, legendGr for (let i = 0; i <= measure_point_nr + 1 + legendGranularity; i++) { shader.activityUniform[i] = gl.getUniformLocation(shader, "uActivity[" + i + "]"); } + //for alpha channel in the new dual brain viewer + shader.alphaUniform = gl.getUniformLocation(shader, "uAlpha"); }; /** Init the program that uses both a vertex activity and a vertex color */ diff --git a/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/vertex_region.glsl b/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/vertex_region.glsl index 7d332809c..bf879bfbf 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/vertex_region.glsl +++ b/tvb/interfaces/web/templates/genshi/visualizers/commons/shading/vertex_region.glsl @@ -10,6 +10,8 @@ attribute vec3 aVertexNormal; attribute float aVertexRegion; // 127 is the legend granularity uniform vec2 uActivity[${abs(noOfMeasurePoints) + 2} + 127]; +//for surface transparency +uniform float uAlpha; varying vec4 vColor; varying vec3 posInterp; @@ -19,6 +21,6 @@ void main(void) { transformed_pos(aVertexPosition, aVertexNormal, gl_Position, posInterp, normInterp); vec2 uv = uActivity[int(aVertexRegion)]; - vColor = colorSchemeLookup(uv); + vColor.a = uAlpha; } diff --git a/tvb/interfaces/web/templates/genshi/visualizers/connectivity_edge_bundle/view.html b/tvb/interfaces/web/templates/genshi/visualizers/connectivity_edge_bundle/view.html index c00f890be..0e75f0d54 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/connectivity_edge_bundle/view.html +++ b/tvb/interfaces/web/templates/genshi/visualizers/connectivity_edge_bundle/view.html @@ -1,6 +1,6 @@
- + + + + + + + + + + + + + + +
+ +
    + + +
  • + Channel + 0 +
  • + +
  • + Time + 0 +
  • + +
  • + Value + 0 +
  • + + + + + + +
  • + + ${drawTimeseriesSelectorButton( + name, tsStateVars[name], tsModes[name], + groupedLabels[idx], initialSelection[idx], + containerId="channelSelector" + str(idx), + buttonTitle="Select signals from Input %d" % (idx+1))} +
  • +
+ +
    + +
    + Time Selection + to + ms +
    + Submit +
    +
  • +
  • + Interval: + 0 +
    + + +
+ + +
+ + + + +
+
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\ No newline at end of file diff --git a/tvb/interfaces/web/templates/genshi/visualizers/new_dual_brain/scripts/dualBrainViewer.js b/tvb/interfaces/web/templates/genshi/visualizers/new_dual_brain/scripts/dualBrainViewer.js new file mode 100644 index 000000000..760f86027 --- /dev/null +++ b/tvb/interfaces/web/templates/genshi/visualizers/new_dual_brain/scripts/dualBrainViewer.js @@ -0,0 +1,861 @@ +/** + * TheVirtualBrain-Framework Package. This package holds all Data Management, and + * Web-UI helpful to run brain-simulations. To use it, you also need do download + * TheVirtualBrain-Scientific Package (for simulators). See content of the + * documentation-folder for more details. See also http://www.thevirtualbrain.org + * + * (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others + * + * This program is free software: you can redistribute it and/or modify it under the + * terms of the GNU General Public License as published by the Free Software Foundation, + * either version 3 of the License, or (at your option) any later version. + * This program is distributed in the hope that it will be useful, but WITHOUT ANY + * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A + * PARTICULAR PURPOSE. See the GNU General Public License for more details. + * You should have received a copy of the GNU General Public License along with this + * program. If not, see . + * + **/ + +/* globals doAjaxCall, readDataPageURL, HLPR_readJSONfromFile */ + +// //it contains all the points that have to be/have been displayed (it contains all the points from the read file); +// //it is an array of arrays (each array contains the points for a certain line chart) +var AG_allPoints = []; +// it supplies the labels for x axis (time in milliseconds) +var AG_time = []; +//it is used for clearing timing events (the event that calls the drawGraph method after a specified time-interval) +var t = null; +//how many elements will be visible on the screen +//computed on the server +var AG_numberOfVisiblePoints = 0; +//all the points that are visible on the screen at a certain moment; the points are read from the AG_allPoints array +//and are translated with a value equal to [AG_translationStep * (AG_noOfLines - the index of the current line)] +//THE FORM of this matrix is: [ [[t1, a1], [t2, a2], ...], [[t1, b1], [t2, b2], ...], ..., [[t1, n1], [t2, n2], ...]] +// t1, t2, ... - represents time that is visible on the screen at a certain moment; +// a1, a2,... - represents the translated values +var AG_displayedPoints = []; +//All the times values that are displayed at a certain moment. To be used by the vertical time line. +var AG_displayedTimes = []; +//the last element that was displayed on the screen is located at this index; the index refers to AG_allPoints array +var AG_currentIndex = 0; +//this var should be set to the length of the AG_allPoints array +var AG_noOfLines = 0; +// the step used for translating the drawn line charts; we translate the drawn line charts because we don't want them to overlap +// the lines will be translated with AG_translationStep * AG_computedStep +var AG_translationStep = 1; +// a scaling factor for the displayed signal +var AG_scaling = 1; +// this var is computed on the server. It is used for line translation (AG_translationStep * AG_computedStep). +var AG_computedStep = 50; +//The normalization steps for each of the channels, in order to bring them centered near the channel bar +var AG_normalizationSteps = []; +//If the animation is paused using pause/start button +var AG_isStopped = true; +//If animation speed is set at a 0 value +var AG_isSpeedZero = false; +//the number of points that are shifted/unshift at a moment +var noOfShiftedPoints = 1; +// List of channels that will be submited on a change of the displayed channels +var AG_submitableSelectedChannels = []; +// contains the indexes of the channels that are displayed +var displayedChannels = []; +// a list of urls pointing to the files from where we should read the time +var timeSetUrls = []; +//a list containing the number of channel in each file specified in 'dataSetUrls' fields +var noOfChannelsPerSet = []; +// the number of points from the longest channel +var maxChannelLength = 0; +// the maximum number of data files from all the submited datatypes +var maxDataFileIndex = 0; +// represents the file index from the dataset that is displayed in the chart +var currentDataFileIndex = 0; +// contains the parsed data for the next file from the dataset +var nextData = []; +// contains the time for the next file from the dataset +var nextTimeData = []; +// true only if the next file from dataset was loaded into memory +var isNextDataLoaded = false; +// true only if the next time data was loaded into memory +var isNextTimeDataLoaded = false; +// true only if the the process of loading a file is started +var AG_isLoadStarted = false; +// this is the number of steps left before updating the next file +var threshold = 10; +// the amount of data that has passed +var totalPassedData = 0; +// the number of channels +var totalNumberOfChannels = 0; +// true only if any of the displayed channels contains NaN values +var nanValueFound = false; +//Channel prefix for each array of data +var channelPrefix = "Channel: "; +// +var totalTimeLength = 0; +//Default values for the x and y axis of the plot +//NOTE: do not remove from the axis AG_options 'labelWidth' and 'labelHeight' because +//this will slow down the animation +var lbl_x_width = 100; +var lbl_x_height = 30; +var zoom_range = [0.1, 20]; + + +// the index of the cached file (the file that was loaded asynchronous) +var cachedFileIndex = 0; +//The displayed labels for the graph +var chanDisplayLabels = []; +// setup plot +var AG_options = { + grid: { + backgroundColor: 'white', + hoverable: true, + clickable: true + }, + points: { + show: false, + radius: 0.001 + }, + zoom: { + interactive: false + }, + selection: { + mode: "xy" + }, + legend: { + show: false + } +}; + +var DEFAULT_MAX_CHANNELS = 10; +var plot = null; + +var followingLine = []; +//The required position from which the following vertical time line will start moving with the array +//Expressed as a number from [0, 1], 0 - start from begining, 1 start only at end +var procentualLinePosition = 0.5; +//The actual position in the graph of the following vertical line. Start from -speed to account for the initial translation. +var currentLinePosition = 0; +//The number of points used to display the vertical line. +var numberOfPointsForVerticalLine = 1000; +var isDoubleView = false; + +var AG_homeViewYValues = []; +var AG_homeViewXValues = {zoomRange: zoom_range, labelWidth: lbl_x_width, labelHeight: lbl_x_height}; +//This will be set to true in the launch_viewer method called by burst small previews +var isSmallPreview = false; + +var targetVerticalLinePosition; + +// The base url for calling any methods on a given datatype +var baseDataURLS = []; +var nrOfPagesSet = []; +var dataPageSize = []; +var tsModes = [0, 0, 0]; +var tsStates = [0, 0, 0]; +var longestChannelIndex = 0; + +// region selection component +var AG_regionSelector = null; +// State mode selector. Used as a global only in dual view +var AG_modeSelector = null; + + +// GID for the D3 viewer +var filterGid = null; + +//timeseries viewer +var ts = null; + +window.onresize = function () { + resizeToFillParent(); +}; + +/** + * Animated graph entry point + */ +function AG_startAnimatedChart(ag_settings) { + isSmallPreview = false; + _AG_initGlobals(ag_settings); + _AG_initPaginationState(ag_settings.number_of_visible_points); + _AG_preStart(); + drawSliderForAnimationSpeed(); + _AG_init_selection(ag_settings.measurePointsSelectionGIDs); + + +} + +function AG_startAnimatedChartPreview(ag_settings) { + isSmallPreview = true; + AG_isStopped = true; + _AG_initGlobals(ag_settings); + _AG_initPaginationState(ag_settings.number_of_visible_points); + _AG_preStart(); + + // Initialize AG_submitableSelectedChannels + // warning: Assumes channel values are a range + if (AG_submitableSelectedChannels.length === 0) { + // Viewer breaks if this is empty. Fill the first few channels + const defaultSelectionLength = Math.min(totalNumberOfChannels, DEFAULT_MAX_CHANNELS); + for (let i = 0; i < defaultSelectionLength; i++) { + AG_submitableSelectedChannels.push(i); + } + } + + refreshChannels(); +} + +function AG_rePaginate(number_of_visible_points) { + _AG_initPaginationState(number_of_visible_points); + $('#display-page-size').html('' + number_of_visible_points); + refreshChannels(); + if (isDoubleView) { + initActivityData(); + } +} + +/** + * Initialize global state. Part of the AG startup. + * @private + */ +function _AG_initGlobals(ag_settings) { + isDoubleView = ag_settings.extended_view; + // dataSetUrls = $.parseJSON(dataSetPaths); + baseDataURLS = ag_settings.baseURLS; + nrOfPagesSet = ag_settings.nrOfPages; + dataPageSize = ag_settings.pageSize; + chanDisplayLabels = ag_settings.channelLabels; + noOfChannelsPerSet = ag_settings.channelsPerSet; + timeSetUrls = ag_settings.timeSetPaths; + maxChannelLength = parseInt(ag_settings.pageSize); + AG_normalizationSteps = ag_settings.normalizedSteps; + setMaxDataFileIndex(nrOfPagesSet); + totalNumberOfChannels = ag_settings.noOfChannels; + totalTimeLength = ag_settings.totalLength; + nanValueFound = ag_settings.nan_value_found; + AG_computedStep = ag_settings.translationStep; + +} + +/** + * Initialize pagination. Part of AG startup. + * @private + */ +function _AG_initPaginationState(number_of_visible_points) { + AG_numberOfVisiblePoints = parseInt(number_of_visible_points); + if (AG_numberOfVisiblePoints > maxChannelLength) { + AG_numberOfVisiblePoints = maxChannelLength; + } + targetVerticalLinePosition = AG_numberOfVisiblePoints * procentualLinePosition; +} + +/** + * Misc common startup logic. Part of AG startup + * @private + */ +function _AG_preStart() { + // resizeToFillParent(); +} + +/** + * Creates a selection component for each time series displayed by this eeg view + * Part of AG startup + * The order of the filterGids determines the order of the selectors + * It must have the same ordering as all other timeseries arrays + * @private + */ +function _AG_init_selection(filterGids) { + let i; + let selectors = []; + + filterGid = filterGids; + + /** + * Returns the selected channel indices as interpreted by AG_submitableSelectedChannels + * ( starting at 0 and ending at len(timeseries_0_channels) + ... + len(timeseries_final_channels) ) + */ + function getSelectedChannelsAsGlobalIndices() { + let all_selected = []; + let offset = 0; + + for (let i = 0; i < selectors.length; i++) { + const selector = selectors[i]; + const selected_in_current = selector.val(); + + for (let j = 0; j < selected_in_current.length; j++) { + all_selected.push(offset + parseInt(selected_in_current[j], 10)); + } + offset += selector._allValues.length; + } + return all_selected; + } + + // init selectors + let selectorId, selector; + + for (i = 0; i < filterGids.length; i++) { + selectorId = "#channelSelector" + i; + selector = TVBUI.regionSelector(selectorId, {filterGid: filterGids[i]}); + selector.change(function (current_selection) { + AG_submitableSelectedChannels = getSelectedChannelsAsGlobalIndices(); + refreshChannels(); + }); + selectors.push(selector); + } + // the first selector is special. we select by default some channels in it and in case of a dual view + // his selection is synchronized with the brain + AG_regionSelector = selectors[0]; + + // Initialize AG_submitableSelectedChannels + AG_submitableSelectedChannels = getSelectedChannelsAsGlobalIndices(); + + if (AG_submitableSelectedChannels.length === 0) { + // Viewer breaks if this is empty. Fill the first few channels + const defaultSelectionLength = Math.min(totalNumberOfChannels, DEFAULT_MAX_CHANNELS); + // we take the values form the dom, a range(defaultSelectionLength) is not a valid selection if there are multiple time series + AG_submitableSelectedChannels = AG_regionSelector._allValues.slice(0, defaultSelectionLength); + AG_regionSelector.val(AG_submitableSelectedChannels); + } + + // Init the mode selection components. Assumes that there are part of the selector dom + let modeSelectors = []; + for (i = 0; i < filterGids.length; i++) { + selectorId = "#channelSelector" + i; + selector = TVBUI.modeAndStateSelector(selectorId, i); + selector.modeChanged(_AG_changeMode); + selector.stateVariableChanged(_AG_changeStateVariable); + modeSelectors.push(selector); + } + // The dual view needs to subscribe to this selector; so we save it like AG_regionSelector + AG_modeSelector = modeSelectors[0]; + + refreshChannels(); +} + +/** + * Read speed from the dom + * @param defaultSpeed default speed when there is no speed slider + * @private + */ +function _AG_get_speed(defaultSpeed) { + let speed = defaultSpeed; + if (!isSmallPreview && !isDoubleView) { + speed = $("#ctrl-input-speed").slider("value"); + } + return speed; +} + +function refreshChannels() { + submitSelectedChannels(false); +} + +function _AG_changeMode(tsIndex, val) { + tsModes[tsIndex] = parseInt(val); + refreshChannels(); +} + +function _AG_changeStateVariable(tsIndex, val) { + tsStates[tsIndex] = parseInt(val); + refreshChannels(); +} + +function _AG_getSelectedDataAndLongestChannelIndex(data) { + let offset = 0; + let selectedData = []; + let channelLengths = []; + + for (let i = 0; i < data.length; i++) { + const selectedChannels = getDisplayedChannels(data[i], offset); + offset += data[i].length; + if (selectedChannels.length > 0) { + channelLengths.push(selectedChannels[0].length); + } else { + channelLengths.push(-1); + } + selectedData = selectedData.concat(selectedChannels); + } + const longestChannelIndex = channelLengths.indexOf(Math.max.apply(Math, channelLengths)); + return {selectedData: selectedData, longestChannelIndex: longestChannelIndex} +} + +/* + * Get required data for the channels in AG_submitableSelectedChannels. If none + * exist then just use the previous 'displayedChannels' (or default in case of first run). + */ +function submitSelectedChannels(isEndOfData) { + AG_currentIndex = AG_numberOfVisiblePoints; + if (AG_submitableSelectedChannels.length === 0) { + AG_submitableSelectedChannels = displayedChannels.slice(); + } + + if (!(isEndOfData && maxDataFileIndex === 0)) { + AG_allPoints = []; + displayedChannels = AG_submitableSelectedChannels.slice(0); + generateChannelColors(displayedChannels.length); + + let results = []; + for (let i = 0; i < nrOfPagesSet.length; i++) { + const dataURL = readDataPageURL(baseDataURLS[i], 0, dataPageSize, tsStates[i], tsModes[i]); + const data = HLPR_readJSONfromFile(dataURL); + results.push(parseData(data, i)); + } + const r = _AG_getSelectedDataAndLongestChannelIndex(results); + AG_allPoints = AG_allPoints.concat(r.selectedData); + longestChannelIndex = r.longestChannelIndex; + + // keep data only for the selected channels + AG_noOfLines = AG_allPoints.length; + } + + AG_displayedPoints = []; + AG_displayedTimes = []; + for (let ii = 0; ii < AG_noOfLines; ii++) { + AG_displayedPoints.push([]); + } + + if (!(isEndOfData && maxDataFileIndex === 0)) { + //read time + readTimeData(0, false); + AG_time = nextTimeData.slice(0); + } + // reset data + nextData = []; + nextTimeData = []; + AG_isLoadStarted = false; + isNextDataLoaded = false; + isNextTimeDataLoaded = false; + currentDataFileIndex = 0; + totalPassedData = 0; + currentLinePosition = 0; + if (nanValueFound) { + displayMessage('The given data contains some NaN values. All the NaN values were replaced by zero.', 'warningMessage'); + } + + + //create 2D plot + //The shape we use for time series now only uses 1D + var dataShape = [totalTimeLength, 1, AG_submitableSelectedChannels.length, 1]; + var selectedLabels = [] + for (let i = 0; i < AG_submitableSelectedChannels.length; i++) { + selectedLabels.push([chanDisplayLabels[displayedChannels[i]]]); + } + //use d3 to create 2D plot + ts = tv.plot.time_series(); + ts.baseURL(baseDataURLS[0]).preview(false).mode(0).state_var(0); + ts.shape(dataShape).t0(AG_time[1] / 2).dt(AG_time[1]); + ts.labels(selectedLabels); + ts.channels(AG_submitableSelectedChannels); + ts.viewer_type('dualbrain'); + + + resizeToFillParent(ts); + $('#time-series-viewer').empty(); + ts(d3.select("#time-series-viewer")); + tsView = ts; + + isnewDoubleView=true; + + + // This is arbitrarily set to a value. To be consistent with tsview we rescale relative to this value + _initial_magic_fcs_amp_scl = tsView.magic_fcs_amp_scl; + + $("#ctrl-input-scale").slider({ + value: 50, min: 0, max: 100, + slide: function (event, target) { + _updateScalingFromSlider(target.value); + } + }); + +} + +function resizeToFillParent(ts) { + var container, width, height; + + container = $('#eegSectionId').parent(); + width = container.width(); + + //minus toolbar's height + height = container.height() - 60; + + ts.w(width).h(height); + +} + +function _updateScalingFromSlider(value) { + if (value == null) { + value = $("#ctrl-input-scale").slider("value"); + } + var expo_scale = (value - 50) / 50; // [1 .. -1] + var scale = Math.pow(10, expo_scale * 4); // [1000..-1000] + tsView.magic_fcs_amp_scl = _initial_magic_fcs_amp_scl * scale; + tsView.render_focus(); + + if (scale >= 1) { + $("#display-scale").html("1 * " + scale.toFixed(2)); + } else { + $("#display-scale").html("1 / " + (1 / scale).toFixed(2)); + } + +} + + +var isEndOfData = false; +var AG_channelColorsDict = {}; +var AG_reversedChannelColorsDict = {}; + +/* + * Generate different colors for each channel. + */ +function generateChannelColors(nr_of_channels) { + AG_channelColorsDict = {}; + AG_reversedChannelColorsDict = {}; + let step = parseInt(255 / nr_of_channels); + for (let i = 0; i < nr_of_channels; i++) { + const color = "rgb(" + 250 * (i % 2) + "," + (200 - i * step) + "," + 220 * ((i + 1) % 2) + ")"; + AG_channelColorsDict[color] = i; + AG_reversedChannelColorsDict[i] = color; + } +} + +/** + * Translate the given value. + * We use this method to translate the values for the drawn line charts because we don't want them to overlap. + * + * @param value the value that should be translated. + * @param index the number of AG_translationSteps that should be used for translating the given value. + * @return {number} + */ +function AG_addTranslationStep(value, index) { + return value * AG_scaling - AG_normalizationSteps[displayedChannels[index]] + AG_translationStep * AG_computedStep * index; +} + +/* + * Add all required data to AG_displayedPoints and AG_displayedTimes in order to center + * around indexInPage, if some of the required data is on the previous page. + */ +function addFromPreviousPage(indexInPage, currentPage) { + + const previousPageUrl = readDataPageURL(baseDataURLS[0], (currentPage - 1) * dataPageSize, currentPage * dataPageSize, tsStates[0], tsModes[0]); + let previousData = parseData(HLPR_readJSONfromFile(previousPageUrl), 0); + previousData = getDisplayedChannels(previousData, 0).slice(0); + const previousTimeData = HLPR_readJSONfromFile(timeSetUrls[0][currentPage - 1]); + // Compute which slices we would need from the 'full' two-pages data. + // We only need the difference so to center indexInPage at AG_numberOfVisiblePoints / 2 + let fromIdx, toIdx; + fromIdx = previousData[0].length - (AG_numberOfVisiblePoints / 2 - indexInPage); // This is from where we need to read from previous data + AG_currentIndex = toIdx = AG_numberOfVisiblePoints - (AG_numberOfVisiblePoints / 2 - indexInPage); // This is where we need to add from the current page + // Just generate displayed point and displayed times now + for (let idx = 0; idx < previousData.length; idx++) { + let idy; + let oneLine = []; + // Push data that is from previos slice + for (idy = fromIdx; idy < previousData[0].length; idy++) { + oneLine.push([previousTimeData[idy], AG_addTranslationStep(previousData[idx][idy], idx)]); + } + // Now that that is from our current slice + for (idy = 0; idy < toIdx; idy++) { + oneLine.push([AG_time[idy], AG_addTranslationStep(AG_allPoints[idx][idy], idx)]); + } + AG_displayedPoints.push(oneLine); + } + AG_displayedTimes = previousTimeData.slice(fromIdx).concat(AG_time.slice(0, toIdx)); + previousData = null; +} + +/* + * Add all required data to AG_displayedPoints and AG_displayedTimes in order to center + * around indexInPage, if some of the required data is on the next page. + */ +function addFromNextPage(indexInPage, currentPage) { + + const followingPageUrl = readDataPageURL(baseDataURLS[0], (currentPage + 1) * dataPageSize, (currentPage + 2) * dataPageSize, tsStates[0], tsModes[0]); + let followingData = parseData(HLPR_readJSONfromFile(followingPageUrl), 0); + followingData = getDisplayedChannels(followingData, 0).slice(0); + const followingTimeData = HLPR_readJSONfromFile(timeSetUrls[0][currentPage + 1]); + let fromIdx, toIdx; + fromIdx = indexInPage - (AG_numberOfVisiblePoints / 2); // We need to read starting from here from the current page + AG_currentIndex = toIdx = fromIdx + AG_numberOfVisiblePoints - AG_allPoints[0].length; // We need to read up to here from next page + for (let idx = 0; idx < AG_allPoints.length; idx++) { + let idy; + const oneLine = []; + // Push data that is from this slice + for (idy = fromIdx; idy < AG_allPoints[0].length; idy++) { + oneLine.push([AG_time[idy], AG_addTranslationStep(AG_allPoints[idx][idy], idx)]); + } + // Now that that is from next slice + for (idy = 0; idy < toIdx; idy++) { + oneLine.push([followingTimeData[idy], AG_addTranslationStep(followingData[idx][idy], idx)]); + } + AG_displayedPoints.push(oneLine); + } + AG_displayedTimes = AG_time.slice(fromIdx).concat(followingTimeData.slice(0, toIdx)); + // Since next page is already loaded, that becomes the current page + AG_allPoints = followingData; + AG_time = followingTimeData; + totalPassedData = (currentPage + 1) * dataPageSize; + currentDataFileIndex = currentPage + 1; + isNextDataLoaded = true; + isNextTimeDataLoaded = true; +} + +/* + * Just re-populate whole displayedPoints and displayedTimes given a start and end index. + */ +function prepareDisplayData(fromIdx, toIdx, pointsArray, timeArray) { + + for (let idx = 0; idx < pointsArray.length; idx++) { + let oneLine = []; + for (let idy = fromIdx; idy < toIdx; idy++) { + oneLine.push([timeArray[idy], AG_addTranslationStep(pointsArray[idx][idy], idx)]); + } + AG_displayedPoints.push(oneLine); + } + AG_displayedTimes = timeArray.slice(fromIdx, toIdx) +} + +/* + * Read the next data file asyncronously. Also get the corresponding time data file. + */ +function loadNextDataFile() { + AG_isLoadStarted = true; + const nx_idx = getNextDataFileIndex(); + cachedFileIndex = nx_idx; + AG_readFileDataAsynchronous(nrOfPagesSet, noOfChannelsPerSet, nx_idx, maxChannelLength, 0); + readTimeData(nx_idx, true); +} + +function changeCurrentDataFile() { + if (!isNextDataLoaded || !isNextTimeDataLoaded) { + return; + } + + if (cachedFileIndex !== getNextDataFileIndex()) { + AG_isLoadStarted = false; + isNextDataLoaded = false; + isNextTimeDataLoaded = false; + nextData = []; + nextTimeData = []; + return; + } + + const speed = _AG_get_speed(100); + const longestChannelLength = AG_allPoints[longestChannelIndex].length; + + if (speed > 0) { + totalPassedData = totalPassedData + longestChannelLength; + if (longestChannelLength < AG_currentIndex) { + AG_currentIndex = -(longestChannelLength - AG_currentIndex); + } else { + AG_currentIndex = 0; + } + } else if (speed < 0) { + totalPassedData = totalPassedData - longestChannelLength; + if (totalPassedData < 0) { + totalPassedData = 0; + } + } else { + return; + } + + AG_allPoints = nextData.slice(0); + nextData = []; + AG_time = nextTimeData.slice(0); + nextTimeData = []; + currentDataFileIndex = getNextDataFileIndex(); + AG_isLoadStarted = false; + isNextDataLoaded = false; + isNextTimeDataLoaded = false; + + if (speed < 0) { + AG_currentIndex = longestChannelLength + AG_currentIndex; + } +} + +function shouldLoadNextDataFile() { + if (!AG_isLoadStarted && maxDataFileIndex > 0) { + const nextFileIndex = getNextDataFileIndex(); + const speed = _AG_get_speed(1); // Assume left to right pass of data + if (currentDataFileIndex !== nextFileIndex) { + if ((speed > 0) && (maxChannelLength - AG_currentIndex < threshold * AG_numberOfVisiblePoints)) { + return true; + } + if ((speed < 0) && (AG_currentIndex - AG_numberOfVisiblePoints < threshold * AG_numberOfVisiblePoints)) { + return true; + } + } + } + return false; +} + +/* + * In case of multiple arrays find out which has the most data files that need + * to be loaded. + */ +function setMaxDataFileIndex(nrOfPagesPerArray) { + let max_ln = 0; + for (let i = 0; i < nrOfPagesPerArray.length; i++) { + if (nrOfPagesPerArray[i] > max_ln) { + max_ln = nrOfPagesPerArray[i]; + } + } + maxDataFileIndex = max_ln - 1; +} + +/* + * Return the index of the next data file that should be loaded. + */ +function getNextDataFileIndex() { + let nextIndex; + const speed = _AG_get_speed(100); + if (speed > 0) { + nextIndex = currentDataFileIndex + 1; + if (nextIndex >= maxDataFileIndex) { + return maxDataFileIndex; + } + } else { + nextIndex = currentDataFileIndex - 1; + if (nextIndex <= 0) { + return 0; + } + } + return nextIndex; +} + +function AG_readFileDataAsynchronous(nrOfPages, noOfChannelsPerSet, currentFileIndex, maxChannelLength, dataSetIndex) { + if (dataSetIndex >= nrOfPages.length) { + isNextDataLoaded = true; + // keep data only for the selected channels + const r = _AG_getSelectedDataAndLongestChannelIndex(nextData); + longestChannelIndex = r.longestChannelIndex; + nextData = r.selectedData; //todo: occasional shape mismatch 3d <- 2d + return; + } + if (nrOfPages[dataSetIndex] - 1 < currentFileIndex && AG_isLoadStarted) { + // todo: assumed that this is computing a padding for smaller signals. check if this is really the purpose of this + let j; + let padding = []; + let oneChannel = []; + for (j = 0; j < maxChannelLength; j++) { + oneChannel.push(0); + } + for (j = 0; j < noOfChannelsPerSet[dataSetIndex]; j++) { + padding.push(oneChannel); + } + nextData.push(padding); + + AG_readFileDataAsynchronous(nrOfPages, noOfChannelsPerSet, currentFileIndex, maxChannelLength, dataSetIndex + 1); + } else { + doAjaxCall({ + url: readDataPageURL(baseDataURLS[dataSetIndex], currentFileIndex * dataPageSize, (currentFileIndex + 1) * dataPageSize, tsStates[dataSetIndex], tsModes[dataSetIndex]), + success: function (data) { + if (AG_isLoadStarted) { + data = $.parseJSON(data); + const result = parseData(data, dataSetIndex); + nextData.push(result); + + AG_readFileDataAsynchronous(nrOfPages, noOfChannelsPerSet, currentFileIndex, maxChannelLength, dataSetIndex + 1); + } + } + }); + } +} + +/* + * Data is received from the HLPR_parseJSON as a 500/74 array. We need to transform it + * into an 74/500 one and in the transformation also replace all NaN values. + */ +function parseData(dataArray, dataSetIndex) { + + let result = []; + for (let i = 0; i < noOfChannelsPerSet[dataSetIndex]; i++) { + result.push([]); + } + for (let j = 0; j < dataArray.length; j++) { + for (let k = 0; k < noOfChannelsPerSet[dataSetIndex]; k++) { + let arrElem = dataArray[j][k]; + if (arrElem === 'NaN') { + nanValueFound = true; + arrElem = 0; + } + result[k].push(arrElem); + } + } + return result; +} + +/** + * + * @param fileIndex + * @param asyncRead true only if the file should be read asynchronous + */ +function readTimeData(fileIndex, asyncRead) { + if (timeSetUrls[longestChannelIndex].length <= fileIndex) { + nextTimeData = []; + for (let i = 0; i < maxChannelLength; i++) { + nextTimeData.push(totalPassedData + i); + } + isNextTimeDataLoaded = true; + } else { + if (asyncRead) { + doAjaxCall({ + url: timeSetUrls[longestChannelIndex][fileIndex], + success: function (data) { + nextTimeData = $.parseJSON(data); + isNextTimeDataLoaded = true; + } + }); + } else { + nextTimeData = HLPR_readJSONfromFile(timeSetUrls[longestChannelIndex][fileIndex]); + isNextTimeDataLoaded = true; + } + } +} + +function getArrayFromDataFile(dataFile) { + let fileData = dataFile.replace(/\n/g, " ").replace(/\t/g, " "); + let arrayData = $.trim(fileData).split(" "); + for (let i = 0; i < arrayData.length; i++) { + arrayData[i] = parseFloat(arrayData[i]); + } + return arrayData; +} + +function getDisplayedChannels(listOfAllChannels, offset) { + let selectedData = []; + for (let i = 0; i < displayedChannels.length; i++) { + if (listOfAllChannels[displayedChannels[i] - offset] !== undefined) { + selectedData.push(listOfAllChannels[displayedChannels[i] - offset].slice(0)); + } + } + return selectedData; +} + +//------------------------------------------------START SPEED RELATED CODE-------------------------------------------------------- + +function drawSliderForAnimationSpeed() { + $("#ctrl-input-speed").slider({ + orientation: 'horizontal', + value: 3, + min: -50, + max: 50, + change: function (event, ui) { + updateSpeedFactor(); + } + }); +} + +function updateSpeedFactor() { + var speed = $("#ctrl-input-speed").slider("option", "value"); + $('#display-speed').html('' + speed); + AG_isSpeedZero = (speed == 0); +} + +//------------------------------------------------END SPEED RELATED CODE-------------------------------------------------------- +//------------------------------------------------START TIME SERIES TIME SELECTION RELATED CODE-------------------------------------------------------- + +function intervalSet() { + var start = $('#SetIntervalStart').val(); + var end = $('#SetIntervalEnd').val(); + if (start>=0 && start < end) { + tsView.timeselection_interval_set(start, end); + } +} \ No newline at end of file diff --git a/tvb/interfaces/web/templates/genshi/visualizers/new_dual_brain/view.html b/tvb/interfaces/web/templates/genshi/visualizers/new_dual_brain/view.html new file mode 100644 index 000000000..d960453b0 --- /dev/null +++ b/tvb/interfaces/web/templates/genshi/visualizers/new_dual_brain/view.html @@ -0,0 +1,33 @@ +
+ + +
+ +
+ +
+ +
+ + + + + +
\ No newline at end of file diff --git a/tvb/interfaces/web/templates/genshi/visualizers/pearson_edge_bundle/view.html b/tvb/interfaces/web/templates/genshi/visualizers/pearson_edge_bundle/view.html index cc3b3cc18..2702a6d27 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/pearson_edge_bundle/view.html +++ b/tvb/interfaces/web/templates/genshi/visualizers/pearson_edge_bundle/view.html @@ -1,7 +1,7 @@
- + diff --git a/tvb/interfaces/web/templates/genshi/visualizers/time_series/scripts/timeseriesSVG.js b/tvb/interfaces/web/templates/genshi/visualizers/time_series/scripts/timeseriesSVG.js index 3eb552d33..08ad4f27f 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/time_series/scripts/timeseriesSVG.js +++ b/tvb/interfaces/web/templates/genshi/visualizers/time_series/scripts/timeseriesSVG.js @@ -129,6 +129,8 @@ function initTimeseriesViewer(baseURL, isPreview, dataShape, t0, dt, channelLabe ts.shape(dataShape).t0(t0).dt(dt); ts.labels(_compute_labels_for_current_selection()); ts.channels(TS_SVG_selectedChannels); + //used in tvbviz to render context lines + ts.viewer_type('svg'); // run resizeToFillParent(ts); ts(d3.select("#time-series-viewer")); @@ -187,6 +189,7 @@ function refreshChannels() { new_ts.baseURL(tsView.baseURL()).preview(tsView.preview()).mode(tsView.mode()).state_var(tsView.state_var()); new_ts.shape(shape).t0(tsView.t0()).dt(tsView.dt()); new_ts.labels(selectedLabels); + new_ts.viewer_type('svg'); // Usually the svg component shows the channels stored in TS_SVG_selectedChannels // and that variable is in sync with the selection component. // But if the selection is empty and we show a timeSeriesSurface diff --git a/tvb/interfaces/web/templates/genshi/visualizers/time_series/view.html b/tvb/interfaces/web/templates/genshi/visualizers/time_series/view.html index 26b87fae5..7d7e36805 100644 --- a/tvb/interfaces/web/templates/genshi/visualizers/time_series/view.html +++ b/tvb/interfaces/web/templates/genshi/visualizers/time_series/view.html @@ -1,5 +1,5 @@
- +