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initialize_tube.m
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initialize_tube.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% filename: name (or path) of xml file to be written
%% ypos,zpos: the spindle is oriented so as to be radially symmetric
%% around the x-axis. Therefore, the y and z positions of
%% the microtubules should remain constant.
%% [l,r]kMTpos: this should be the actual parameter taken by the MS,
%% calculated from the simulation timesteps
%% xplanes: these are calculated from SPINDLE_LENGTH from the Lip csv
%% file, and are used to place the two disks
%% radius: this refers to the radius of the spindle, around which the
%% kMTs are placed
%
function [] = initialize_tube(filename,ypos,zpos, lkMTpos, rkMTpos,xplanes,radius)
leftTubelengths = lkMTpos - xplanes(1);
rightTubelengths = -rkMTpos + xplanes(2);
docNode = com.mathworks.xml.XMLUtils.createDocument('SimulatedExperiments');
SimulatedExperiments = docNode.getDocumentElement;
fn = ['C:/users/chris/Desktop/NSRG/Spindle/script/SpindleSimScript' filename];
SimulatedExperiments.setAttribute('file',fn);
SimulatedExperiments.setAttribute('modified',datestr(now));
SimulatedExperiments.setAttribute('created',datestr(now));
product = docNode.createElement('Version');
product.setAttribute('major','2');
product.setAttribute('minor','0');
product.setAttribute('revision','0');
SimulatedExperiments.appendChild(product);
AFMSimulation = docNode.createElement('AFMSimulation');
AFMSimulation.setAttribute('pixelSize','10.00000');
AFMSimulation.setAttribute('imageWidth','300');
AFMSimulation.setAttribute('imageHeight','300');
AFMSimulation.setAttribute('clipGroundPlane','false');
AFMSimulation.setAttribute('displayAsWireframe','false');
AFMSimulation.setAttribute('surfaceOpacity','1.000000');
SimulatedExperiments.appendChild(AFMSimulation);
FSim = docNode.createElement('FluorescenceSimulation');
FSim.setAttribute('focalPlaneIndex','0');
FSim.setAttribute('focalPlaneSpacing','200.000000');
FSim.setAttribute('numberOfFocalPlanes','1'); %%%%%%% changed for most focused plane
FSim.setAttribute('useCustomFocalPlanePositions','false');
FSim.setAttribute('gain','1');
FSim.setAttribute('offset','0.000000');
FSim.setAttribute('pixelSize','65.000000');
%FSim.setAttribute('psfName','C:/users/chris/Desktop/NSRG/Spindle/script/rescaled_bloom_psf.tif'); %%%%% FIX THIS TO TAKE THE RIGHT PSF %%%%
FSim.setAttribute('psfName','None');
FSim.setAttribute('imageWidth','200');
FSim.setAttribute('imageHeight','200');
FSim.setAttribute('shearInX','0.000000');
FSim.setAttribute('shearInY','0.000000');
FSim.setAttribute('addGaussianNoise','false');
FSim.setAttribute('noiseStdDev','0.000000');
FSim.setAttribute('showImageVolumeOutline','false');
FSim.setAttribute('showRefGrid','false');
FSim.setAttribute('refGridSpacing','50.000000');
FSim.setAttribute('superimposeSimulatedImage','false');
FSim.setAttribute('superimposeComparisonImage','false');
FSim.setAttribute('minimumIntensityLevel','0.000000');
FSim.setAttribute('maximumIntensityLevel','4095.000000');
SimulatedExperiments.appendChild(FSim);
FocalPlanes = docNode.createElement('FocalPlanes');
FSim.appendChild(FocalPlanes);
for i = 0:29
Plane = docNode.createElement('Plane');
Plane.setAttribute('index',int2str(i));
Plane.setAttribute('position','0.000000');
FocalPlanes.appendChild(Plane);
end
gdfo = docNode.createElement('GradientDescentFluorescenceOptimizer');
FSim.appendChild(gdfo);
gdfoIterations = docNode.createElement('Iterations');
gdfoIterations.setAttribute('value','100');
gdfo.appendChild(gdfoIterations);
dess = docNode.createElement('DerivativeEstimateStepSize');
dess.setAttribute('value','1e-008');
gdfo.appendChild(dess);
ssf = docNode.createElement('StepScaleFactor');
ssf.setAttribute('value','1');
gdfo.appendChild(ssf);
nmfo = docNode.createElement('NelderMeadFluorescenceOptimizer');
FSim.appendChild(nmfo);
maxiter = docNode.createElement('MaximumIterations');
maxiter.setAttribute('value','100');
nmfo.appendChild(maxiter);
pct = docNode.createElement('ParameterConvergenceTolerance');
pct.setAttribute('value','1e-008');
nmfo.appendChild(pct);
pgfo = docNode.createElement('PointsGradientFluorescenceOptimizer');
FSim.appendChild(pgfo);
pgfoStepSize = docNode.createElement('StepSize');
pgfoStepSize.setAttribute('value','1');
pgfo.appendChild(pgfoStepSize);
pgfoIterations = docNode.createElement('Iterations');
pgfoIterations.setAttribute('value','100');
pgfo.appendChild(pgfoIterations);
fcio = docNode.createElement('FluorescenceComparisonImageModelObject');
fcio.setAttribute('name','None');
FSim.appendChild(fcio);
ModelObjectList = docNode.createElement('ModelObjectList');
SimulatedExperiments.appendChild(ModelObjectList);
LPlane = docNode.createElement('DiskModel');
ModelObjectList.appendChild(LPlane);
LName = docNode.createElement('Name');
LPlane.appendChild(LName);
LName.setAttribute('value','LDisk');
lvis = docNode.createElement('Visible');
LPlane.appendChild(lvis);
lvis.setAttribute('value','true');
lposx = docNode.createElement('PositionX');
LPlane.appendChild(lposx);
lposx.setAttribute('value',num2str(xplanes(1)));
lposx.setAttribute('optimize','false');
lposy = docNode.createElement('PositionY');
LPlane.appendChild(lposy);
lposy.setAttribute('value','6500.000000');
lposy.setAttribute('optimize','false');
lposz = docNode.createElement('PositionZ');
LPlane.appendChild(lposz);
lposz.setAttribute('value','0.000000');
lposz.setAttribute('optimize','false');
lRotAngle = docNode.createElement('RotationAngle');
LPlane.appendChild(lRotAngle);
lRotAngle.setAttribute('value','90.000000');
lRotAngle.setAttribute('optimize','false');
lRotVecX = docNode.createElement('RotationVectorX');
LPlane.appendChild(lRotVecX);
lRotVecX.setAttribute('value','0.000000');
lRotVecX.setAttribute('optimize','false');
lRotVecY = docNode.createElement('RotationVectorY');
LPlane.appendChild(lRotVecY);
lRotVecY.setAttribute('value','1.000000');
lRotVecY.setAttribute('optimize','false');
lRotVecZ = docNode.createElement('RotationVectorZ');
LPlane.appendChild(lRotVecZ);
lRotVecZ.setAttribute('value','0.000000');
lRotVecZ.setAttribute('optimize','false');
lRadius = docNode.createElement('Radius');
LPlane.appendChild(lRadius);
lRadius.setAttribute('value',num2str(radius));
lRadius.setAttribute('optimize','false');
lsfm = docNode.createElement('SurfaceFluorophoreModel');
LPlane.appendChild(lsfm);
lsfm.setAttribute('enabled','true');
lsfm.setAttribute('channel','all');
lsfm.setAttribute('density','100.000000');
lsfm.setAttribute('numberOfFluorophores','0');
lsfm.setAttribute('samplingMode','fixedDensity');
lsfm.setAttribute('samplePattern','singlePoint');
lsfm.setAttribute('numberOfRingFluorophores','2');
lsfm.setAttribute('ringRadius','10.000000');
lsfm.setAttribute('randomizePatternOrientations','false');
%%%%%%%%%%%%%%%% LPLANE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%% RPLANE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
RPlane = docNode.createElement('DiskModel');
ModelObjectList.appendChild(RPlane);
RName = docNode.createElement('Name');
RPlane.appendChild(RName);
RName.setAttribute('value','RDisk');
rvis = docNode.createElement('Visible');
RPlane.appendChild(rvis);
rvis.setAttribute('value','true');
rposx = docNode.createElement('PositionX');
RPlane.appendChild(rposx);
rposx.setAttribute('value',num2str(xplanes(2)));
rposx.setAttribute('optimize','false');
rposy = docNode.createElement('PositionY');
RPlane.appendChild(rposy);
rposy.setAttribute('value','6500.000000');
rposy.setAttribute('optimize','false');
rposz = docNode.createElement('PositionZ');
RPlane.appendChild(rposz);
rposz.setAttribute('value','0.000000');
rposz.setAttribute('optimize','false');
rRotAngle = docNode.createElement('RotationAngle');
RPlane.appendChild(rRotAngle);
rRotAngle.setAttribute('value','90.000000');
rRotAngle.setAttribute('optimize','false');
rRotVecX = docNode.createElement('RotationVectorX');
RPlane.appendChild(rRotVecX);
rRotVecX.setAttribute('value','0.000000');
rRotVecX.setAttribute('optimize','false');
rRotVecY = docNode.createElement('RotationVectorY');
RPlane.appendChild(rRotVecY);
rRotVecY.setAttribute('value','1.000000');
rRotVecY.setAttribute('optimize','false');
rRotVecZ = docNode.createElement('RotationVectorZ');
RPlane.appendChild(rRotVecZ);
rRotVecZ.setAttribute('value','0.000000');
rRotVecZ.setAttribute('optimize','false');
rRadius = docNode.createElement('Radius');
RPlane.appendChild(rRadius);
rRadius.setAttribute('value',num2str(radius));
rRadius.setAttribute('optimize','false');
rsfm = docNode.createElement('SurfaceFluorophoreModel');
RPlane.appendChild(rsfm);
rsfm.setAttribute('enabled','true');
rsfm.setAttribute('channel','all');
rsfm.setAttribute('density','100.000000');
rsfm.setAttribute('numberOfFluorophores','0');
rsfm.setAttribute('samplingMode','fixedDensity');
rsfm.setAttribute('samplePattern','singlePoint');
rsfm.setAttribute('numberOfRingFluorophores','2');
rsfm.setAttribute('ringRadius','10.000000');
rsfm.setAttribute('randomizePatternOrientations','false');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% RPlane
%%%%%%%%%%%%%%%%%%%%% make spheres %%%%%%%%%%%%%%%
for i = 1:(numel(lkMTpos))
lkMT = docNode.createElement('SphereModel');
ModelObjectList.appendChild(lkMT);
lname = docNode.createElement('Name');
lkMT.appendChild(lname);
lname.setAttribute('value',['lkMT - ' int2str(i)]);
lvis = docNode.createElement('Visible');
lkMT.appendChild(lvis);
lvis.setAttribute('value','true');
lscan = docNode.createElement('Scannable');
lkMT.appendChild(lscan);
lscan.setAttribute('value','true');
lposx = docNode.createElement('PositionX');
lkMT.appendChild(lposx);
lposx.setAttribute('value',num2str(lkMTpos(i)));
lposx.setAttribute('optimize','false');
lposy = docNode.createElement('PositionY');
lkMT.appendChild(lposy);
lposy.setAttribute('value',num2str(ypos(i)));
lposy.setAttribute('optimize','false');
lposz = docNode.createElement('PositionZ');
lkMT.appendChild(lposz);
lposz.setAttribute('value',num2str(zpos(i)));
lposz.setAttribute('optimize','false');
lradius = docNode.createElement('Radius');
lkMT.appendChild(lradius);
lradius.setAttribute('value','10.000000');
lradius.setAttribute('optimize','false');
end
for i = 1:(numel(rkMTpos))
rkMT = docNode.createElement('SphereModel');
ModelObjectList.appendChild(rkMT);
rname = docNode.createElement('Name');
rkMT.appendChild(rname);
rname.setAttribute('value',['rkMT - ' int2str(i)]);
rvis = docNode.createElement('Visible');
rkMT.appendChild(rvis);
rvis.setAttribute('value','true');
rscan = docNode.createElement('Scannable');
rkMT.appendChild(rscan);
rscan.setAttribute('value','true');
rposx = docNode.createElement('PositionX');
rkMT.appendChild(rposx);
rposx.setAttribute('value',num2str(rkMTpos(i)));
rposx.setAttribute('optimize','false');
rposy = docNode.createElement('PositionY');
rkMT.appendChild(rposy);
rposy.setAttribute('value',num2str(ypos(i)));
rposy.setAttribute('optimize','false');
rposz = docNode.createElement('PositionZ');
rkMT.appendChild(rposz);
rposz.setAttribute('value',num2str(zpos(i)));
rposz.setAttribute('optimize','false');
rradius = docNode.createElement('Radius');
rkMT.appendChild(rradius);
rradius.setAttribute('value','10.000000');
rradius.setAttribute('optimize','false');
end
%%%%%%%%%%%%%%%%%% make the tubules %%%%%%%%%%%%%%%%%%%%%%%%%5
for i = 1:(numel(rkMTpos))
rtube = docNode.createElement('FlexibleTubeModel');
ModelObjectList.appendChild(rtube);
rtubeName = docNode.createElement('Name');
rtube.appendChild(rtubeName);
rtubeName.setAttribute('value',['RTubule - ' num2str(i)]);
rtubeVis = docNode.createElement('Visible');
rtube.appendChild(rtubeVis);
rtubeVis.setAttribute('value','true');
rtubePosX = docNode.createElement('PositionX');
rtube.appendChild(rtubePosX);
rtubePosX.setAttribute('value',num2str(xplanes(2)));
rtubePosX.setAttribute('optimize','false');
rtubePosY = docNode.createElement('PositionY');
rtube.appendChild(rtubePosY);
rtubePosY.setAttribute('value',num2str(ypos(i)));
rtubePosY.setAttribute('optimize','false');
rtubePosZ = docNode.createElement('PositionZ');
rtube.appendChild(rtubePosZ);
rtubePosZ.setAttribute('value',num2str(zpos(i)));
rtubePosZ.setAttribute('optimize','false');
rtubeRotAngle = docNode.createElement('RotationAngle');
rtube.appendChild(rtubeRotAngle);
rtubeRotAngle.setAttribute('value','0.000000');
rtubeRotAngle.setAttribute('optimize','false');
rtubeRotVecX = docNode.createElement('RotationVectorX');
rtube.appendChild(rtubeRotVecX);
rtubeRotVecX.setAttribute('value','1.000000');
rtubeRotVecX.setAttribute('optimize','false');
rtubeRotVecY = docNode.createElement('RotationVectorY');
rtube.appendChild(rtubeRotVecY);
rtubeRotVecY.setAttribute('value','0.000000');
rtubeRotVecY.setAttribute('optimize','false');
rtubeRotVecZ = docNode.createElement('RotationVectorZ');
rtube.appendChild(rtubeRotVecZ);
rtubeRotVecZ.setAttribute('value','0.000000');
rtubeRotVecZ.setAttribute('optmize','false');
rtubeRadius = docNode.createElement('Radius');
rtube.appendChild(rtubeRadius);
rtubeRadius.setAttribute('value','5.000000');
rtubeRadius.setAttribute('optimize','false');
rtubeNoP = docNode.createElement('NumberofPoints');
rtube.appendChild(rtubeNoP);
rtubeNoP.setAttribute('value','2');
rtubeSFM = docNode.createElement('SurfaceFluorophoreModel');
rtube.appendChild(rtubeSFM);
rtubeSFM.setAttribute('enabled','true');
rtubeSFM.setAttribute('channel','all');
rtubeSFM.setAttribute('density','100.000000');
rtubeSFM.setAttribute('numberOfFluorophores','0');
rtubeSFM.setAttribute('samplingMode','fixedDensity');
rtubeSFM.setAttribute('samplePattern','singlePoint');
rtubeSFM.setAttribute('numberOfRingFluorophores','2');
rtubeSFM.setAttribute('ringRadius','10.000000');
rtubeSFM.setAttribute('randomizePatternOrientations','false');
rtubeVFM = docNode.createElement('VolumeFluorophoreMode');
rtube.appendChild(rtubeVFM);
rtubeVFM.setAttribute('enabled','true');
rtubeVFM.setAttribute('channel','all');
rtubeVFM.setAttribute('density','100.000000');
rtubeVFM.setAttribute('numberOfFluorophores','0');
rtubeVFM.setAttribute('samplingMode','fixedDensity');
rtubeVFM.setAttribute('samplePattern','singlePoint');
rtubeVFM.setAttribute('numberOfRingFluorophores','2');
rtubeVFM.setAttribute('ringRadius','10.000000');
rtubeVFM.setAttribute('randomizePatternOrientations','false');
rtubeX1 = docNode.createElement('X1');
rtube.appendChild(rtubeX1);
rtubeX1.setAttribute('value',num2str(-1*rightTubelengths(i)));
rtubeX1.setAttribute('optimize','false');
rtubeY1 = docNode.createElement('Y1');
rtube.appendChild(rtubeY1);
rtubeY1.setAttribute('value','0.000000');
rtubeY1.setAttribute('optimize','false');
rtubeZ1 = docNode.createElement('Z1');
rtube.appendChild(rtubeZ1);
rtubeZ1.setAttribute('value','0.000000');
rtubeZ1.setAttribute('optimize','false');
rtubeX2 = docNode.createElement('X2');
rtube.appendChild(rtubeX2);
rtubeX2.setAttribute('value','0.000000');
rtubeX2.setAttribute('optimize','false');
rtubeY2 = docNode.createElement('Y2');
rtube.appendChild(rtubeY2);
rtubeY2.setAttribute('value','0.000000');
rtubeY2.setAttribute('optimize','false');
rtubeZ2 = docNode.createElement('Z2');
rtube.appendChild(rtubeZ2);
rtubeZ2.setAttribute('value','0.000000');
rtubeZ2.setAttribute('optimize','false');
end
for i = 1:(numel(lkMTpos))
ltube = docNode.createElement('FlexibleTubeModel');
ModelObjectList.appendChild(ltube);
ltubeName = docNode.createElement('Name');
ltube.appendChild(ltubeName);
ltubeName.setAttribute('value',['LTubule - ' num2str(i)]);
ltubeVis = docNode.createElement('Visible');
ltube.appendChild(ltubeVis);
ltubeVis.setAttribute('value','true');
ltubePosX = docNode.createElement('PositionX');
ltube.appendChild(ltubePosX);
ltubePosX.setAttribute('value',num2str(xplanes(1)));
ltubePosX.setAttribute('optimize','false');
ltubePosY = docNode.createElement('PositionY');
ltube.appendChild(ltubePosY);
ltubePosY.setAttribute('value',num2str(ypos(i)));
ltubePosY.setAttribute('optimize','false');
ltubePosZ = docNode.createElement('PositionZ');
ltube.appendChild(ltubePosZ);
ltubePosZ.setAttribute('value',num2str(zpos(i)));
ltubePosZ.setAttribute('optimize','false');
ltubeRotAngle = docNode.createElement('RotationAngle');
ltube.appendChild(ltubeRotAngle);
ltubeRotAngle.setAttribute('value','0.000000');
ltubeRotAngle.setAttribute('optimize','false');
ltubeRotVecX = docNode.createElement('RotationVectorX');
ltube.appendChild(ltubeRotVecX);
ltubeRotVecX.setAttribute('value','1.000000');
ltubeRotVecX.setAttribute('optimize','false');
ltubeRotVecY = docNode.createElement('RotationVectorY');
ltube.appendChild(ltubeRotVecY);
ltubeRotVecY.setAttribute('value','0.000000');
ltubeRotVecY.setAttribute('optimize','false');
ltubeRotVecZ = docNode.createElement('RotationVectorZ');
ltube.appendChild(ltubeRotVecZ);
ltubeRotVecZ.setAttribute('value','0.000000');
ltubeRotVecZ.setAttribute('optmize','false');
ltubeRadius = docNode.createElement('Radius');
ltube.appendChild(ltubeRadius);
ltubeRadius.setAttribute('value','5.000000');
ltubeRadius.setAttribute('optimize','false');
ltubeNoP = docNode.createElement('NumberofPoints');
ltube.appendChild(ltubeNoP);
ltubeNoP.setAttribute('value','2');
ltubeSFM = docNode.createElement('SurfaceFluorophoreModel');
ltube.appendChild(ltubeSFM);
ltubeSFM.setAttribute('enabled','true');
ltubeSFM.setAttribute('channel','all');
ltubeSFM.setAttribute('density','100.000000');
ltubeSFM.setAttribute('numberOfFluorophores','0');
ltubeSFM.setAttribute('samplingMode','fixedDensity');
ltubeSFM.setAttribute('samplePattern','singlePoint');
ltubeSFM.setAttribute('numberOfRingFluorophores','2');
ltubeSFM.setAttribute('ringRadius','10.000000');
ltubeSFM.setAttribute('randomizePatternOrientations','false');
ltubeVFM = docNode.createElement('VolumeFluorophoreMode');
ltube.appendChild(ltubeVFM);
ltubeVFM.setAttribute('enabled','true');
ltubeVFM.setAttribute('channel','all');
ltubeVFM.setAttribute('density','100.000000');
ltubeVFM.setAttribute('numberOfFluorophores','0');
ltubeVFM.setAttribute('samplingMode','fixedDensity');
ltubeVFM.setAttribute('samplePattern','singlePoint');
ltubeVFM.setAttribute('numberOfRingFluorophores','2');
ltubeVFM.setAttribute('ringRadius','10.000000');
ltubeVFM.setAttribute('randomizePatternOrientations','false');
ltubeX1 = docNode.createElement('X1');
ltube.appendChild(ltubeX1);
ltubeX1.setAttribute('value','0.000000');
ltubeX1.setAttribute('optimize','false');
ltubeY1 = docNode.createElement('Y1');
ltube.appendChild(ltubeY1);
ltubeY1.setAttribute('value','0.000000');
ltubeY1.setAttribute('optimize','false');
ltubeZ1 = docNode.createElement('Z1');
ltube.appendChild(ltubeZ1);
ltubeZ1.setAttribute('value','0.000000');
ltubeZ1.setAttribute('optimize','false');
ltubeX2 = docNode.createElement('X2');
ltube.appendChild(ltubeX2);
ltubeX2.setAttribute('value',num2str(leftTubelengths(i)));
ltubeX2.setAttribute('optimize','false');
ltubeY2 = docNode.createElement('Y2');
ltube.appendChild(ltubeY2);
ltubeY2.setAttribute('value','0.000000');
ltubeY2.setAttribute('optimize','false');
ltubeZ2 = docNode.createElement('Z2');
ltube.appendChild(ltubeZ2);
ltubeZ2.setAttribute('value','0.000000');
ltubeZ2.setAttribute('optimize','false');
end
xmlwrite(filename,docNode);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Take this out once the regexp is not necessary (Cory's fix should take care of it) %%%%%%%%
apos = '''';
removeNewline = unix(['sed -i ' apos ':a;N;$!ba;s/\n//g' apos ' ' filename]);
%sed -i 's/>[ \t]*</></g' sedtest.xml
removeSpaces = unix(['sed -i ' apos 's/>[ \t]*</></g' apos ' ' filename]);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end