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added roi object, fixed bugs in absorptionimage and cloudimage
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@bec5
bec5 committed Aug 25, 2013
1 parent 45c9319 commit b7e7201
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Showing 8 changed files with 395 additions and 173 deletions.
216 changes: 152 additions & 64 deletions @AbsorptionImageObject/AbsorptionImageObject.m
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Original file line number Diff line number Diff line change
@@ -1,18 +1,22 @@
classdef AbsorptionImageObject < ImageObject
%ABSORPTIONIMAGEOBJECT
%ABSORPTIONIMAGEOBJECT is an image class that implements ImageObject.
%Contains data selection routines,

properties (SetAccess = immutable)
filename %string containing filename
path %string containing the path
imagingDetuning %detuning from resonance in imaging light (MHz)
SCATTERING_XS %resonant xs corrected for imaging detuning
MAGNIFICATION %magnification in the optical train
end
end
properties(SetAccess = protected)
regionOfInterest %struct containing vectors of x and y pixels ('.x' and '.y')
roiMask %imrect or imellipse object
opticalDensity %array containing optical densities at each pixel
thumbnail %.1 scale image stored in RAM
% thumbnail %.1 scale image stored in RAM
variables = {}; %cell array contaning names of variables imported from Cicero
imagingDetuning %detuning from resonance in imaging light (MHz)
generalizedXS %resonant xs corrected for imaging detuning
magnification %magnification in the optical train
nC %discrete summation of optical density
xProjection %
yProjection %
end
properties (Dependent, SetAccess = protected)
xCoordinates %x coordinates of the region of interest
Expand All @@ -22,15 +26,20 @@
darkField %dark field image; 1392*1040 pixels (greyscale 1-4095)
normalizedImage %(atoms-dark field)/(light-dark field) image;
end
properties(Hidden, Access = protected)
lastroiPos
end
methods

%Constructor
function obj = AbsorptionImageObject(varargin) %constructor for AbsorptionImageObjects

%Define expected inputs
p = inputParser;
p.CaseSensitive = false;
addOptional(p,'file','');
addOptional(p,'magnification',.25,@isnumeric);
addOptional(p,'resetROI',true,@islogical);
addOptional(p,'resetroi',true,@islogical);
addOptional(p,'objAlreadyExists',false,@islogical);
addOptional(p,'keepImageData',false,@islogical);
addOptional(p,'imagingDetuning',0,@isnumeric);
Expand All @@ -39,59 +48,47 @@
parse(p,varargin{:});
magnification=p.Results.magnification;
file = p.Results.file;
resetROI=p.Results.resetROI;
resetroi=p.Results.resetroi;
objAlreadyExists=p.Results.objAlreadyExists;
keepImageData = p.Results.keepImageData;
imagingDetuning = p.Results.imagingDetuning;
delete(p)

%avoid reprocessing data if it exists in memory
%check for flag from subclass constructor
if ~objAlreadyExists
if strcmp(file,'')
[obj.filename, obj.path]=AbsorptionImageObject.selectFile();
[filename,path]=AbsorptionImageObject.checkForFilename(file);
%avoid reprocessing data if it exists in memory
if ~AbsorptionImageObject.objExists(filename)
obj.filename = filename;
obj.path = path;
obj.imagingDetuning=imagingDetuning;
obj.magnification=magnification;
loadFromFile(obj,[obj.path obj.filename],keepImageData,resetroi);
else
[dir, name, ext] = fileparts(file);
if strcmpi(ext,'.aia')
if strcmp(dir,'')
obj.path=pwd;
else
obj.path=[dir '\'];
end
obj.filename=[name ext];
else
error('File is not a .aia');
end
%obj already exists, do nothing
end
obj.imagingDetuning=imagingDetuning;
obj.MAGNIFICATION=magnification;
obj.SCATTERING_XS=obj.RESONANT_XS/(1+(2*imagingDetuning*10^6/obj.LINE_WIDTH)^2);
loadFromFile(obj,[obj.path obj.filename],keepImageData,resetROI);
else
%obj already exists, do nothing
end

end
function h = show(obj, varargin) %displays whole normalized image
h = imagesc(obj.normalizedImage);
end
function adjustRegionOfInterest(obj) %allows the user to pick a new region of interest
obj.regionOfInterest = getRegionOfInterest(obj.normalizedImage);
end
function set.regionOfInterest(obj, val) %dispalys the image and a drawable rectangle to select region of interest
if isempty(val)
val=getRegionOfInterest(obj.normalizedImage);
end
obj.regionOfInterest=val;

%%Set methods. Error checking goes here
function set.roiMask(obj, val) %dispalys the image and a drawable rectangle to select region of interest
obj.roiMask=val;
end
function set.opticalDensity(obj,val) %sets the optical density based on raw image data
obj.opticalDensity=val;
end
function xCoordinates = get.xCoordinates(obj) %
xCoordinates=1:size(obj.opticalDensity,2);
end
function yCoordinates = get.yCoordinates(obj) %
yCoordinates=1:size(obj.opticalDensity,1);
function set.nC(obj,val)
if val>=0
obj.nC = val;
else
error('nC is negative!')
end
end

%%Get methods for dependent properties
function atoms = get.atoms(obj) %
if isprop(obj,'imageData')
atoms=obj.imageData{1}{2};
Expand All @@ -117,45 +114,136 @@ function adjustRegionOfInterest(obj) %allows the user to pick a new region of in
end
end
function normalizedImage = get.normalizedImage(obj) %
atoms=obj.atoms;
darkField=obj.darkField;
light=obj.light;
atoms=atoms-darkField;
light=light-darkField;
scaling=mean(mean(atoms(10:90,450:750)))/mean(mean(light(10:90,450:750)));
%%scaling=1;
light(light==0)=Inf;
normalizedImage = atoms./(scaling*light);
normalizedImage(normalizedImage<=0)=1;
normalizedImage = obj.calculateNormalizedImage();
end
function xCoordinates = get.xCoordinates(obj) %
xCoordinates=1:size(obj.opticalDensity,2);
end
function yCoordinates = get.yCoordinates(obj) %
yCoordinates=1:size(obj.opticalDensity,1);
end

%%UI routines/methods
function h = show(obj, varargin) %displays whole normalized image
h = imagesc(obj.normalizedImage);
end
function adjustroi(obj) %allows the user to pick a new region of interest
obj.initializeroi();
obj.initializeValues();
end
function [roiPos,roiMask] = roiPrompt(obj)
global roi_global
global roiMask_global

f = figure('name','Select Analysis Range and Press Any Key','NumberTitle','off',...
'WindowStyle','modal');
im = imshow(obj.normalizedImage,'Border','tight','InitialMagnification',55);

if isempty(obj.lastroiPos)
if isempty(roi_global)
roi = imellipse(gca);
else
roi = imellipse(gca,roi_global);
end
else
roi = imellipse(gca,obj.lastroiPos);
end

fcn = makeConstrainToRectFcn('imellipse',get(gca,'XLim'),get(gca,'YLim'));
setPositionConstraintFcn(roi,fcn);
pause
roiMask = roi.createMask();
roiPos = roi.getPosition();
roi_global = roi.getPosition();
roiMask_global = roi.createMask();
close(gcf)
end
end

methods (Access = protected)

%%Object initialization routines
function loadFromFile(obj,filename,keepImageData,resetROI) %routine which initializes the properties of the object
p = addprop(obj,'imageData'); %adds a temporary field that conatins raw image data
obj.imageData = ImageObject.readAIA(filename); %get image data from file
if length(obj.imageData)>3 %add properties based on cicero list variables
for i=4:length(obj.imageData)
propMeta = addprop(obj,obj.imageData{i}{1});
obj.variables {length(obj.variables)+1} = obj.imageData{i}{1};
obj.(obj.imageData{i}{1})=obj.imageData{i}{2};
%propMeta.SetAccess='protected';
obj.(obj.imageData{i}{1})=obj.imageData{i}{2};
end
end
normalizedImage = obj.normalizedImage; %calculate the normalized image
obj.thumbnail=imresize(normalizedImage,.1);
obj.opticalDensity = -log(normalizedImage);%calculate and store optical density
if resetROI
obj.regionOfInterest = getRegionOfInterest(normalizedImage); %set the region of interest
else
global regionOfInterest_global
obj.regionOfInterest = regionOfInterest_global;
end
normalizedImage = obj.normalizedImage; %get and temporarily store the normalized image
% obj.thumbnail=imresize(normalizedImage,.1); %create and store a thumbnail

obj.initializeroi(resetROI)
obj.initializeValues();
if ~keepImageData
delete(p); %get rid of the temporary imageData field
end
end
function initializeroi(obj,varargin)
global roi_global
global roiMask_global

if nargin==1
[obj.lastroiPos,obj.roiMask] = obj.roiPrompt();
elseif varargin{1}
[obj.lastroiPos,obj.roiMask] = obj.roiPrompt();
else
if ~isempty(obj.roiMask)
%doNothing
elseif ~isempty(roiMask_global)
obj.roiMask = roiMask_global;
else
[obj.lastroiPos,obj.roiMask] = obj.roiPrompt();
end
end
end
function initializeValues(obj)
obj.generalizedXS=obj.calculategeneralizedXS();
obj.opticalDensity = obj.calculateopticalDensity();
obj.xProjection = obj.calculatexProjection();
obj.yProjection = obj.calculateyProjection();
obj.nC = obj.calculatenC();
end

%%Calculation methods. Any science goes here.
function nC = calculatenC(obj)
opticalDensity = obj.opticalDensity;
nC = (obj.PIXEL_SIZE/obj.magnification)^2/obj.generalizedXS*...
sum(sum(opticalDensity.*obj.roiMask));
end
function normalizedImage = calculateNormalizedImage(obj)
atoms=obj.atoms;
darkField=obj.darkField;
light=obj.light;
atoms=atoms-darkField;
light=light-darkField;
scaling=mean(mean(atoms(900:1000,600:800)))/mean(mean(light(900:1000,600:800)));
%%scaling=1;
light(light==0)=Inf;
normalizedImage = atoms./(scaling*light);
normalizedImage(normalizedImage<=0)=1;
end
function xProjection = calculatexProjection(obj)
xProjection = sum(obj.opticalDensity.*obj.roiMask,1);
end
function yProjection = calculateyProjection(obj)
yProjection = sum(obj.opticalDensity.*obj.roiMask,2)';
end
function generalizedXS = calculategeneralizedXS(obj)
generalizedXS = obj.RESONANT_XS/(1+(2*obj.imagingDetuning*10^6/obj.LINE_WIDTH)^2);
end
function opticalDensity = calculateopticalDensity(obj)
opticalDensity = -log(obj.normalizedImage);%calculate and store optical density
end
end
methods (Static=true)

%%Class utility methods
objList = findall()
tf = objExists(filename)
[filename, path] = checkForFilename(file)
end
end
17 changes: 17 additions & 0 deletions @AbsorptionImageObject/checkForFilename.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
function [filename, path] = checkForFilename(file)
if strcmp(file,'')
[filename, path]=AbsorptionImageObject.selectFile();
else
[dir, name, ext] = fileparts(file);
if strcmpi(ext,'.aia')
if strcmp(dir,'')
path=pwd;
else
path=[dir '\'];
end
filename=[name ext];
else
error('File is not a .aia');
end
end
end
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