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updated xGaussianFit to xFit and yGaussianFit to yFit for modularity
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@bec5
bec5 committed Aug 20, 2013
1 parent ec9fa24 commit 72f5dfd
Showing 1 changed file with 47 additions and 38 deletions.
85 changes: 47 additions & 38 deletions @CloudImageObject/CloudImageObject.m
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
nX%Integrated area of Gaussian fit in x projection
nY%Integrated area of Gaussian fit in y projection
photonsPerAtom %Number of photon counts registered by the CCD per atom per pixel
xGaussianFit %Fit objected containing Gaussian fit in x projection
yGaussianFit %Fit object containing Gaussian fit in y projection
xFit %Fit objected containing Gaussian fit in x projection
yFit %Fit object containing Gaussian fit in y projection
end
properties(Dependent)
xProjection %
Expand All @@ -24,6 +24,7 @@
phaseSpaceDensity %
averageDensity %
peakDensity %
aspectRatio %
end
methods
function obj = CloudImageObject(varargin)
Expand All @@ -36,6 +37,7 @@
addOptional(p,'resetROI',true,@islogical);
addOptional(p,'imagingDetuning',0,@isnumeric);
addOptional(p,'last',false,@islogical);

parse(p,varargin{:});
magnification = p.Results.magnification;
file = p.Results.file;
Expand Down Expand Up @@ -83,9 +85,9 @@
if objAlreadyExists
obj=currentObjects{objIndex};
else
obj.xGaussianFit=CloudImageObject.fitOffsetGaussian(...
obj.xFit=CloudImageObject.fitOffsetGaussian(...
obj.regionOfInterest.x,obj.xProjection,'offset',fitOffset);
obj.yGaussianFit=CloudImageObject.fitOffsetGaussian(...
obj.yFit=CloudImageObject.fitOffsetGaussian(...
obj.regionOfInterest.y,obj.yProjection,'offset',fitOffset);
setNumberOfAtoms(obj);
setPhotonsPerAtom(obj);
Expand All @@ -99,18 +101,18 @@
end
function avOD = get.avOD(obj)

avODRangeX=max(round(obj.xGaussianFit.b-obj.xGaussianFit.c),1):...
min(round(obj.xGaussianFit.b+obj.xGaussianFit.c),obj.xCoordinates(end));
avODRangeY=max(round(obj.yGaussianFit.b-obj.yGaussianFit.c),1):...
min(round(obj.yGaussianFit.b+obj.yGaussianFit.c),obj.yCoordinates(end));
avODRangeX=max(round(obj.xFit.b-obj.xFit.c),1):...
min(round(obj.xFit.b+obj.xFit.c),obj.xCoordinates(end));
avODRangeY=max(round(obj.yFit.b-obj.yFit.c),1):...
min(round(obj.yFit.b+obj.yFit.c),obj.yCoordinates(end));
avOD=sum(sum(obj.opticalDensity(avODRangeY,avODRangeX)))...
/(length(avODRangeX)*length(avODRangeY));
end
function peakOD = get.peakOD(obj)
avODRangeX=max(round(obj.xGaussianFit.b-obj.xGaussianFit.c),1):...
min(round(obj.xGaussianFit.b+obj.xGaussianFit.c),obj.xCoordinates(end));
avODRangeY=max(round(obj.yGaussianFit.b-obj.yGaussianFit.c),1):...
min(round(obj.yGaussianFit.b+obj.yGaussianFit.c),obj.yCoordinates(end));
avODRangeX=max(round(obj.xFit.b-obj.xFit.c),1):...
min(round(obj.xFit.b+obj.xFit.c),obj.xCoordinates(end));
avODRangeY=max(round(obj.yFit.b-obj.yFit.c),1):...
min(round(obj.yFit.b+obj.yFit.c),obj.yCoordinates(end));
peakOD=max(max(obj.opticalDensity(avODRangeY,avODRangeX)));
end
function phaseSpaceDensity = get.phaseSpaceDensity(obj)
Expand All @@ -120,10 +122,10 @@
averageDensity = obj.nC / (obj.xMetricWidth^2 * obj.yMetricWidth) * 10^-6 / 4 / pi * 3*0.397496;
end
function peakDensity = get.peakDensity(obj)
avODRangeX=max(round(obj.xGaussianFit.b-obj.xGaussianFit.c),1):...
min(round(obj.xGaussianFit.b+obj.xGaussianFit.c),obj.xCoordinates(end));
avODRangeY=max(round(obj.yGaussianFit.b-obj.yGaussianFit.c),1):...
min(round(obj.yGaussianFit.b+obj.yGaussianFit.c),obj.yCoordinates(end));
avODRangeX=max(round(obj.xFit.b-obj.xFit.c),1):...
min(round(obj.xFit.b+obj.xFit.c),obj.xCoordinates(end));
avODRangeY=max(round(obj.yFit.b-obj.yFit.c),1):...
min(round(obj.yFit.b+obj.yFit.c),obj.yCoordinates(end));
nToAverage = max([round(length(avODRangeX)*length(avODRangeY)*.001) 5]);
orderedDensities = sort(reshape(obj.opticalDensity(avODRangeY,avODRangeX),[],1),'descend');
peakDensity = 1/obj.SCATTERING_XS*...
Expand All @@ -136,10 +138,10 @@
yProjection = sum(obj.opticalDensity(obj.regionOfInterest.y,obj.regionOfInterest.x),2)';
end
function xWidth = get.xWidth(obj)
xWidth = obj.xGaussianFit.c;
xWidth = min(obj.xFit.c,280);
end
function yWidth = get.yWidth(obj)
yWidth = obj.yGaussianFit.c;
yWidth = min(obj.yFit.c,280);
end
function xMetricWidth = get.xMetricWidth(obj)
xMetricWidth=obj.xWidth*obj.PIXEL_SIZE/obj.MAGNIFICATION;
Expand All @@ -148,27 +150,34 @@
yMetricWidth=obj.yWidth*obj.PIXEL_SIZE/obj.MAGNIFICATION;
end
function xPeakHeight= get.xPeakHeight(obj)
xPeakHeight = obj.xGaussianFit.a;
xPeakHeight = obj.xFit.a;
end
function yPeakHeight= get.yPeakHeight(obj)
yPeakHeight = obj.yGaussianFit.a;
yPeakHeight = obj.yFit.a;
end
function xPeakLocation= get.xPeakLocation(obj)
xPeakLocation = obj.xGaussianFit.b;
xPeakLocation = obj.xFit.b;
end
function yPeakLocation= get.yPeakLocation(obj)
yPeakLocation = obj.yGaussianFit.b;
yPeakLocation = obj.yFit.b;
end
function aspectRatio = get.aspectRatio(obj)
aspectRatio = obj.xWidth/obj.yWidth;
end
function set.xGaussianFit(obj,val)
obj.xGaussianFit=val;
function set.xFit(obj,val)
obj.xFit=val;
end
function set.yGaussianFit(obj,val)
obj.yGaussianFit=val;
function set.yFit(obj,val)
obj.yFit=val;
end
function h = show(obj)
function h = show(obj,varargin)
opticalDensity=obj.opticalDensity(obj.regionOfInterest.y,obj.regionOfInterest.x);
opticalDensity(opticalDensity<0)=0;
hh=figure;
if nargin>1
hh=figure(varargin{1});
else
hh=figure;
end
subplot(3,3,[4 5 7 8]);
imagesc(opticalDensity);
blu=transpose([1:-1/255:0;1:-1/255:0;ones(1,256)]);
Expand All @@ -179,12 +188,12 @@
set(gca,'YTickLabel',{'-s','0','s/2'})

subplot(3,3,[1 2])
plot(obj.xGaussianFit,'--r',obj.regionOfInterest.x,obj.xProjection,'b');
plot(obj.xFit,'--r',obj.regionOfInterest.x,obj.xProjection,'b');
axis tight
xlabel(''),ylabel(''),legend('off')

subplot(3,3,[6 9]);
plot(obj.yGaussianFit,'--r',obj.regionOfInterest.y,obj.yProjection,'b');
plot(obj.yFit,'--r',obj.regionOfInterest.y,obj.yProjection,'b');
xlabel(''),ylabel(''),legend('off')
view(90,90);
axis tight
Expand Down Expand Up @@ -212,8 +221,8 @@
hold on
plot(obj.regionOfInterest.x,obj.xProjection,'b');
plot(obj.regionOfInterest.y,obj.yProjection,'g');
plot(obj.xGaussianFit,'--r');
plot(obj.yGaussianFit,'--r');
plot(obj.xFit,'--r');
plot(obj.yFit,'--r');
legend('X projection', 'Y projection');
xlabel('pixel')
ylabel('projected OD')
Expand All @@ -225,9 +234,9 @@
end
methods (Access = protected, Hidden = true)
function setNumberOfAtoms(obj)
nX=abs(sqrt(2*pi)*obj.xGaussianFit.a*obj.xGaussianFit.c*...
nX=abs(sqrt(2*pi)*obj.xFit.a*obj.xFit.c*...
(obj.PIXEL_SIZE/obj.MAGNIFICATION)^2/obj.SCATTERING_XS);
nY=abs(sqrt(2*pi)*obj.yGaussianFit.a*obj.yGaussianFit.c*...
nY=abs(sqrt(2*pi)*obj.yFit.a*obj.yFit.c*...
(obj.PIXEL_SIZE/obj.MAGNIFICATION)^2/obj.SCATTERING_XS);
nC=(obj.PIXEL_SIZE/obj.MAGNIFICATION)^2/obj.SCATTERING_XS*...
sum(sum(obj.opticalDensity(obj.regionOfInterest.y,obj.regionOfInterest.x)));
Expand All @@ -236,10 +245,10 @@ function setNumberOfAtoms(obj)
obj.nY=nY;
end
function setPhotonsPerAtom(obj)
ppaRangeX=max(round(obj.xGaussianFit.b-obj.xGaussianFit.c),1):...
min(round(obj.xGaussianFit.b+obj.xGaussianFit.c),obj.xCoordinates(end));
ppaRangeY=max(round(obj.yGaussianFit.b-obj.yGaussianFit.c),1):...
min(round(obj.yGaussianFit.b+obj.yGaussianFit.c),obj.yCoordinates(end));
ppaRangeX=max(round(obj.xFit.b-obj.xFit.c),1):...
min(round(obj.xFit.b+obj.xFit.c),obj.xCoordinates(end));
ppaRangeY=max(round(obj.yFit.b-obj.yFit.c),1):...
min(round(obj.yFit.b+obj.yFit.c),obj.yCoordinates(end));
adjustedOpticalDensity=obj.opticalDensity;
adjustedOpticalDensity(adjustedOpticalDensity==0)=1;
obj.photonsPerAtom=abs(obj.light(ppaRangeY,ppaRangeX)./...
Expand Down

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