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runMechanicsGene.m
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runMechanicsGene.m
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% /* --------------------------------------------------------------------------------------
% * File: runMechanicsGene.m
% * Date: 01/12/2017
% * Author: David Pastor Escuredo, [email protected]
% * Version: 0.2
% * License: BSD
% * --------------------------------------------------------------------------------------
% Copyright (c) 2013-2018, David Pastor Escuredo
% with Biomedical Image Technology, UPM (BIT-UPM)
% with BioEmergences, CNRS
% with LifeD lab
% All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear;
StatsPath='../MechanicsStats/'
v_tag=''
addpath('ReadData3D/')
addpath('libUtils/io')
chg='_ch01'
%%%%%%%%%%%%%%%%%%%%%%%%%% User's Configuration %%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%% List of datasets to process. datasetListBioEmergences
dNs=[14]
tinilags=[61 62 39 8 39 95]%for each dataset
tinilags(18)=69
tinilags(14)=105
%t_max_cluster=177
%t_max_cluster=213
%t_max_cluster=194
hasgene=1
redo=0
genclus=1
genProfiling=1
ac=0
der=0
normalizeG=1
cN=3
if cN==1
chg='_ch00'
end
format='.vtk'
colorg=[255 100 100]
modes_colors={[97 97 97; 174 119 40; 150 150 150;],[97 97 97; 174 119 40; 150 150 150;],{},{},[97 97 97; 174 119 40; 150 150 150;],[0 0 143; 218 179 255; 191 0 191],[20 20 83; 238 209 175; 211 0 121],[0 153 153; 0 204 0; 0 255 100],[97 97 97; 174 119 40; 150 150 150;],[97 97 97; 174 119 40; 150 150 150;],[97 97 97; 174 119 40; 150 150 150;],[97 97 97; 174 119 40; 150 150 150;],[97 97 97; 174 119 40; 150 150 150;],[97 97 97; 174 119 40; 150 150 150;]}
%071226a
%61 and 118 155 -> 178
%081018a
%95 and 154 190-> 213
%091021aF
%105 154 -> 204
%%%%%%%%%%%%%%%% Descriptor Set and Descriptor Index %%%%%%%%%%%%%%%%%%%%%
%1 Topology
%2 Strain rates
%3 Displacements Field descriptors (Unstable)
%4 Left Lagrangian descriptors
%5 Right Lagrangian descriptors
DescriptorsSets=[5]
%For 4-5
DescriptorsIndexes=[5 6 7 8]%check libStats/loadStatsMetadata
%For 1
DescriptorsIndexes=[4]%check libStats/loadStatsMetadata
%For 2
DescriptorsIndexes=[1 2]%check libStats/loadStatsMetadata
%%%%%%%%%%%%%%%% Tissue selection from Movit. Original domain to get modes
%Tissue selection to get the modes
withSelection=1%keep 1
seltagBasis='-all'%all71'%Selection of the material domain basis
clusterSelecBasis=[4]%Selec numbers
xtag='-1-0'
old=0
reclimit=480
%%%%%%%%%%%%%%%% Configuration Modes by Unsupervised Clustering
useDefault=1;%Number of modes in loadStatsMetadata
mxCluster=3;%Number of modes to find
clus_method=0%0: K-means uses distanceK 1: Hierarchical clustering uses distanceT
distanceType=2%0:correlation 1: euclidean 2: cosine 3: mahalanobis
smoothN=5%window for 1D filtering of profiles before clustering (timesteps)
cluster2movit=1%export clustering after monomodal or multimodal segmentation into a new label file for MovIt
exportBasisMap=0%Distances map when generating the modes to Movit
%Kmeans options
startCluster=0%if 1 it uses 10% of samples for preliminary clustering
%Hierarchical options
methodHier='ward'
tagDis=''
if distanceType==1
distanceK='sqEuclidean'
distanceT='Euclidean';
tagDis='euc'
elseif distanceType==0
sameRangeDis=1
distanceK='correlation'
distanceT='correlation'
tagDis='cor'
elseif distanceType==2
distanceK='cosine'
distanceT='cosine'
tagDis='cos'
elseif distanceType==3
distanceK='mahalanobis'
distanceT='mahalanobis'
tagDis='mah'
end
%%%%%%%%%%%%%%%%% Plotting options
extraPlots=0
seePlots=1
savePlots=1
textSimple=1
fsize=36
%%%%%%%%%%%%%%%%% time
tfinal_m=-1
tini_m=-1
hini=6
hfin=12
hpf_limits=1
crop_time_axis=1
phys_time=1
plotZero=0
plotHPF=1%Flag
step_time=20
gridOn=1
widthMode=5
use_defaultRange=1
saveClusterData=0%save
removeProfileWithInvalid=1
%%%%%%%%%%%%%%%%%%%%% User's Configuration End %%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%% RUNNING %%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
selections=[1 2 3 1]
only_selection=withSelection%considers only the selection
derive=0
doCluster=0
doProfile=0
doBasis=1
doProjection=0
drawClusterProfile=0
for idN=1:length(dNs)
'Dataset';
dN=dNs(idN)
tinilag=tinilags(dN)
loadParametersKinematics;
for DescriptorsSet=DescriptorsSets
%for DescriptorIndex=DescriptorsIndexes
%nameSel=[datapath dataset '_t_sim/' dd '_t' seltag '_all_T']
debug_this=0
invalidValue=-1
loadStatsMetadata
nameSel=[datapath dataset '_t/' dd '_t' seltagBasis '_all_T']
if withSelection
selec=dlmread([nameSel '.csv'], ';', 1, 0);
else
seltag='-all'
end
selCtag=selection2tissue(clusterSelecBasis,'');
%runGeneModes (deprecated)
if hasgene
runMechGenProfile
else
runMechProfile
end
end
end