Major upstream merge

.gitignore

@@ -0,0 +1,37 @@
+# Autosave files
+*.asv
+*.m~
+*.autosave
+*.slx.r*
+*.mdl.r*
+
+# Derived content-obscured files
+*.p
+
+# Compiled MEX files
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Deployable archives
+*.ctf
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Code generation folders
+slprj/
+sccprj/
+codegen/
+
+# Cache files
+*.slxc
+
+# Cloud based storage dotfile
+.MATLABDriveTag
+
+# buildtool cache folder
+.buildtool/
+

models/RunCLSfixed.m

@@ -12,35 +12,118 @@
 % See the License for the specific language governing permissions and
 % limitations under the License.
 %%
-clear;
+clear all;
+%bdclose('all');
+path_var=pwd;
+if ~contains('models',path_var)
+    path_var = [path_var, filesep 'models'];
+end
+warning('off','all')
+% Opening Main GUI which determines whether to edit model network
+% structure, parameters, and add pacemaker
+global outputs 
+outputs = main_settings();
+Heart_GUI_preset(outputs);
+%Millisecond: parasNormal, Multi[2,3,_Bradycardia]
+%Second: parasMulti[_second,_AV_block]
+if outputs.units == 2
+    switch outputs.param
+        case 'Normal'        %1
+            updatePara='parasMulti_second.mat';
+        case 'AV Block' %2
+            updatePara='parasMulti_AV_block.mat';
+        otherwise 
+            updatePara='parasMulti_second.mat';
+    end
+else
+    switch outputs.param
+        case 'Normal'        %1
+            updatePara='parasNormal.mat';
+        case 'parasMulti' %2
+            updatePara='parasMulti.mat';
+        case 'parasMulti2' %3
+            updatePara='parasMulti2.mat';
+        case 'parasMulti3' %4
+            updatePara='parasMulti3.mat';
+        case 'Bradycardia' %5
+            updatePara = 'parasMulti_Bradycardia.mat';
+        otherwise 
+            updatePara='parasNormal.mat';
+    end
+end
+assignin('base','sens_units',outputs.units) % Sensing charts Chart (unit) subsystem
 %Prepare the parameters
+if outputs.units == 2 
+    filename='N3Cfg_second.mat'; 
+    datafile='N3Data_second.mat';
+    pathsheet='Path_second';
+    nodesheet='Node_second'; 
+    assignin('base','solvertime',5); % solving time for the GUI cells 
+    assignin('base','stepsize',0.0005); % step size for solving the GUI cells and the CLS sample time
+    assignin('base','timescale','s'); % time scale for GUI plots
+    assignin('base','buffer',0.599); % for Libs_unified/Path_V3/Path Buffer_i and Buffer_j
+    assignin('base','unit_conversion',1); % used with the N node ms/s setting in RR
+    assignin('base','stoptime',2) % CLSfixed initial stop time
+elseif outputs.units == 1
+    filename='N3Cfg.mat'; 
+    datafile='N3Data.mat'; 
+    pathsheet='Path'; 
+    nodesheet='Node'; 
+    assignin('base','solvertime',5000);
+    assignin('base','stepsize',0.1);
+    assignin('base','timescale','ms');
+    assignin('base','buffer',599);
+    assignin('base','unit_conversion',1000);
+    assignin('base','stoptime',2000)
+end
+
+% Extract the node classification data from the xlsx file
+[~,~,nodes_raw]=xlsread('Heart_N3_second.xlsx',nodesheet);
+[~,~,path_raw]=xlsread('Heart_N3_second.xlsx',pathsheet);
+[~,~,probes_raw]=xlsread('Heart_N3_second.xlsx','Probe');
+% Edit the network model
+if outputs.editmodel
+    global node_atts
+    global node_atts_copy
+    global path_atts
+    global path_atts_copy
+    global params
+    global nodes_name %potentially join the nodes_name into the front of node_atts
+    global probes_name 
+    temp = nodes_raw(:,2:end);
+    temp(:,end-2) = [];
+    temp(end,:) = [];
+    assignin('base','node_atts',temp);
+    assignin('base','node_atts_copy',temp);
+    assignin('base','path_atts',path_raw);
+    assignin('base','path_atts_copy',path_raw);
+
+    temp1 = nodes_raw(:,1:2);
+    temp1(end,:) = [];
+    assignin('base','nodes_name',temp1);
+    temp2 = probes_raw(2:end,1:5);
+    assignin('base','probes_name',temp2);
+    Heart_Editing_GUI(filename,nodes_name,probes_name,params,node_atts,node_atts_copy,path_atts,path_atts_copy,timescale,outputs.pacemaker);
+end
+
 % contains all configurations of heart model
-filename='N3Cfg.mat'; 
-% contains all parameters of heart model
-datafile='N3Data.mat'; 
 load(filename);
+% contains all parameters of heart model
 load(datafile);
-path_var=pwd;
-% Contains all the range of new parameters for run-time update
-updatePara='parasMulti.mat';
+% Load in the new parameter range
 load(updatePara);
-%% Parameter settings
-% parasMulti:
-% Bradycardia+AV block+premature ventricular complex (PVC), RBBB (slow velocity):
-% % SA BCL=1400; the automaticity of Node 24 (RBB) enabled (para48=0); path 10 backward enabled (para7=1.0); Path 15 cv=0.04, path 27 cv=0.4; 
-% parasMulti2: PVC introduces PMT
-% Bradycardia+AV block+premature ventricular complex (PVC), RBBB (complete blockage, i.e.,cv=0):
-% % SA BCL=1400; the automaticity of Node 24 (RBB) enabled (para48=0); path 10 backward enabled (para7=1.0); Path 15 cv=0.04, path 27 cv=0;
-% parasMulti3: extra VP introduces AVNRT
-% % SA BCL=814; CS BCL=1194 enabled (para48=0); path 10 backward enabled (para7=0.8); ppR5
-% cfg=[814,1194,2,0,0.100000000000000,0.250000000000000,278,0.0146200000000000,0.00872000000000000,2300,2,1,0.100000000000000,0.250000000000000,1.100000000000000,0.0700000000000000,0.0700000000000000,0.0700000000000000,0.0700000000000000];
-%%parasNormal Normal but slight AV delay compared to device AVI.
-%% Run the GUI
+% Global parameters
+assignin('base','paras_length',length(pp))
+assignin('base','cfg_length',length(cfgdata))
+assignin('base','pNode_length',length(pNode))
+assignin('base','pPath_length',length(pPath))
+models={'CLSfixed', 'CLSfixed_pace', 'CLSfixed_nopace'};
 % Specify the model name
-modelName='CLSfixed';
+modelName = models{outputs.pacemaker};
 % Specify the model path
 mdl=[path_var,filesep, modelName];
 % Specify the data save path
 savepath=[path_var,filesep 'Cells.mat'];
+
 % In the model, there should be a S-function to save data to the same structure of the GUI.
-Heart_GUI(mdl,modelName,filename,savepath); 
+Heart_GUI(mdl,modelName,filename,savepath,nodes_raw,probes_raw);