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EasyXT.m
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EasyXT.m
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classdef EasyXT < handle
%%EASYXT Simplified commands to access Imaris Interface
% We're wrapping up some common funtions of Imaris so as to simplify
% the creation of XTensions. Access to most functions is simplified
% using 'PropertyName', 'PropertyValue' pairs.
%
% It is of course a work in progress and will greatly benefit from
% any feedback from the community of users.
%
% Olivier Burri & Romain Guiet, EPFL BioImaging & Optics Platform
% March 2014
% olivier dot burri at epfl.ch
% romain dot guiet at epfl.ch
% The necessary disclaimer:
% We abide by the GNU General Public License (GPL) version 3:
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.co
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
properties
% The class contains the ImarisApplication instance as a property
% so it can be accessed by all functions.
ImarisApp;
% Path To Imaris
imarisPath = 'C:\Program Files\Bitplane\Imaris x64 7.6.5\';
% We can define here the path where ImarisLib.jar is
imarisLibPath = '';
end
methods
function eXT = EasyXT(varargin)
%% EASYXT builds a new EasyXT object
% * eXT = EASYXT(imarisApplication) builds a new EasyXT object
% and attaches it to the currently running Imaris Instance.
% * eXT = EASYXT('setup') prompts the user to define the foler
% where the imaris exectuable is. This only needs to be done
% once.
%
% Optional Arguments
% o imarisApplicationID - in case you'd like to start EasyXT from
% an XTension
% o 'setup' - string to announce that you wish to define the
% path to Imaris.
% Supress Java Duplicate Class warnings
warning('off','MATLAB:Java:DuplicateClass');
eXT.imarisPath = getSavedImarisPath();
eXT.imarisPath = eXT.imarisPath(1:(end-1));
eXT.imarisLibPath = [eXT.imarisPath, 'XT\matlab\ImarisLib.jar'];
if (nargin == 1 && strcmp(varargin{1}, 'setup')) || strcmp(eXT.imarisPath, '') || (exist(eXT.imarisLibPath,'file') ~= 2)
[~,PathName] = uigetfile('.exe','Location of Imaris executable');
eXT.imarisPath = PathName;
eXT.imarisLibPath = [PathName, 'XT\matlab\ImarisLib.jar'];
setSavedImarisPath(eXT.imarisPath);
end
% Start Imaris Connection
javaaddpath(eXT.imarisLibPath);
% Create an instance of ImarisLib
vImarisLib = ImarisLib;
% Re-enable Java Duplicate Class warnings
warning('on','MATLAB:Java:DuplicateClass');
% Attach to given ImarisApplication or create new one
if nargin == 1 && isa(varargin{1}, 'Imaris.IApplicationPrxHelper')
eXT.ImarisApp = varargin{1};
elseif nargin == 1 && ischar(varargin{1})
ID = round(str2double(varargin{1}));
else
% Grab the Imaris server
server = vImarisLib.GetServer();
try
ID = server.GetObjectID(0);
if ischar(ID)
ID = round(str2double(ID));
end
catch err
disp('Seems Imaris is not open: Could not get Imaris Application');
disp('Original error below:');
rethrow(err);
end
end
try
% Open the Imaris Application
eXT.ImarisApp = vImarisLib.GetApplication(ID);
catch err
disp('Could not get Imaris Application with ID');
disp('Original error below:');
rethrow(err);
end
end
end
%% Public methods.
methods
function ImarisObject = GetObject(eXT, varargin)
%% GETOBJECT recovers an object from the Surpass scene
% Imarisobject = GETOBJECT('Name', name, ...
% 'Parent', parent, ...
% 'Number', number, ...
% 'Type', type, ...
% 'Cast', isCast
% )
%
% Returns the imaris object defined by the Optional Name,
% Parent, Number, Type and Cast Parameters.
%
% The list of options and default values is:
% o Name - Name of the object as it appears on the Surpass
% Scene, like 'Volume', 'Surface 1', 'Spots 10', etc.
% Defaults to [ [] ]
%
% o Parent - The parent object where we should look for the
% object. Useful mostly when creating Groups.
% Defaults to Surpass Scene
%
% o Number - The nth object in the scene (Starting at 1). Can
% be combined with name and type to search for the nth object
% withe the same name or the nth surface, for example.
% Defaults to [ 1 ]
%
% o Type - Defines the type of object Choices are:
% 'All', 'Spots', 'Surfaces', 'Points' and 'Groups'
% Defaults to [ 'All' ]
%
% o Cast - Determines what kind of object you want in return.
% Any Surpass component is of class IDataItem. Surfaces for
% example are of a subclass of IDataItem, called ISurfaces.
% this property, if set to 'true', returns the object of
% the subclass if possible. Otherwise, it returns an IDataItem
% Object. Not too useful but good to have in case it's
% needed.
% Defaults to [ true ]
%
% Examples:
% %Return the active object in the imaris scene
% ImarisObj = GetObject();
% %Returns the first surface object
% spotsObj = GetObject('Type', 'Spots');
% %Returns fourth object in the scene.
% ImarisObj = GetObject('Number', 4);
% %Returns the first surface object with name 'My Surfaces'.
% surfObj = GetObject('Type', 'Surfaces', 'Name', 'My Surfaces');
% %Get the Second Surfaces object inside the folder 'Group 1'
% parentFolder = GetObject('Name', 'Group 1');
% surfObj = GetObject('Type', 'Surfaces', 'Number', 2, 'Parent', parentFolder);
% See also CreateGroup
% Define Defaults:
parent = eXT.ImarisApp.GetSurpassScene;
name = [];
number = 1;
type = 'All';
cast = true;
for i=1:2:length(varargin)
switch varargin{i}
case 'Parent'
parent = varargin{i+1};
case 'Name'
name = varargin{i+1};
case 'Number'
number = varargin{i+1};
case 'Type'
type = varargin{i+1};
case 'Cast'
cast = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
% here are the Existing Types
types = {'All', 'Spots', 'Surfaces', 'Points' , 'Groups'};
if ~any( contains(types, type) )
e = strcat ('Unrecognized Object Type (should be either: All, Spots, Surfaces, Points , Groups)' );
error( e );
end
object = []; %#ok<*NASGU>
ImarisObject = [];
if nargin==1
% Return the active selection
ImarisObject = GetImarisObject(eXT, eXT.ImarisApp.GetSurpassSelection, cast);
else
% Search for the object
specificTypeNum = 0;
nChildren = parent.GetNumberOfChildren;
for i = 1 : nChildren
object = parent.GetChild(i-1);
objName = eXT.GetName(object);
objType = GetImarisType(eXT, object);
if ~isempty(name) % If we're using the name
if strcmp(objName, name) % If the name matches
if strcmp(objType,type) || strcmp(type, 'All') % If the type matches
specificTypeNum = specificTypeNum+1;
if specificTypeNum == number
% GIVE THE OBJECT BACK
ImarisObject = GetImarisObject(eXT, object, cast);
break;
end
end
end
else % Use only the number and type
if strcmp(objType,type) || strcmp(type, 'All') % If the type matches
specificTypeNum = specificTypeNum+1;
if specificTypeNum == number
% GIVE THE OBJECT BACK
ImarisObject = GetImarisObject(eXT, object, cast);
break;
end
end
end
end
end
end
function SelectObject(eXT, varargin)
%% SELECTOBJECT Makes the selected object active on the Surpass Scene
% SELECTOBJECT('Name', name, ...)
% All arguments from GetObject can be applied here
% See also GetObject
obj = GetObject(eXT, varargin{:});
eXT.ImarisApp.SetSurpassSelection(obj);
end
function number = GetNumberOf(eXT, type, varargin)
%% GETNUMBEROF recovers the number of objects with a certain type
% number = GETNUMBEROF(type, 'Name', name, ... )
% Arguments
% o type - Type of Object: Spots, Surfaces, Group, Points,
% Cells, Filaments, DataSet, Light Source, Camera, Volume,
% Clipping Plane, Application
% Optional Key, Value Pairs:
% o All optional arguments from GetObject can be applied here
%
% This function is nice for iterating among objects of the same
% kind.
%
% Example:
% nSpots = GetNumberOf('Spots');
% for i=1:nSpots
% aSpot = GetObject('Type', 'Spots', 'Number', i);
% % Do something with spot number i here
% end
%
% See also GetObject
parent = eXT.ImarisApp.GetSurpassScene;
name = [];
for i=1:2:length(varargin)
switch varargin{i}
case 'Parent'
parent = varargin{i+1};
case 'Name'
name = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
% Search for the object
number = 0;
nChildren = parent.GetNumberOfChildren;
for i = 1 : nChildren
object = parent.GetChild(i-1);
objName = eXT.GetName(object);
objType = GetImarisType(eXT, object);
if ~isempty(name) % If we're using the name
if strcmp(objName, name) % If the name matches
if strcmp(objType,type) || strcmp(type, 'All') % If the type matches
number = number+1;
end
end
else % Use only the number and type
if strcmp(objType,type) || strcmp(type, 'All') % If the type matches
number = number+1;
end
end
end
end
function name = GetName(~, object)
%% GETNAME returns the name of the object if possible
% name = GETNAME(object)
% This is mainly for convenience so we never forget to cast the
% result of object.GetName to a char()
%
% Arguments
% o object - The Imaris object whose name you want
% See also SetName
if any(strcmp(methods(object), 'GetName'))
name = char(object.GetName);
else
name = [];
%disp(['Object of class ' class(object) ' has no "GetName" method.']);
end
end
function name = SetName(~, object, name)
%% SETNAME sets the name of the object if possible
% name = SETNAME(object, name)
%
% Arguments
% o object - The Imaris object whose name you want to set
% o name - The name you want to give to the object
% See also GetName
if any(strcmp(methods(object), 'SetName'))
object.SetName(name);
else
disp('This object has no "SetName" method.')
end
end
function SetColor(~, object, colors)
%% SETCOLOR sets the color of the object passed as argument
% SETCOLOR(object, colors) Takes an array that can be of the following forms
% - a 1x3 array with each element being an integer between
% [0-255].
% colors(1) is Red
% colors(2) is Green
% colors(3) is Blue
% - a 1x4 array where colors(1:3) are as above
% colors(4) is transparency (values [0-128])
if length(colors) < 4 % check if there is only 3 ,
colors(4) = 0; % means no transparecncy setted, so color(4) = 0
end
if length(colors) == 1 && colors < 255 % if only 1 value
colors(1:3) = colors(1); % set it for each column
end
if length(colors) == 2 || length(colors) > 4
disp('That is not a color, dear... I need a matrix with 1, 3 or 4 elements. Did you forget your medication?');
colors = [128, 128, 128, 0]; % set it to grey
end
if length(colors) == 1 && colors > 255
object.SetColorRGBA(double(colors));
else
col = colors(1) + colors(2)*256 + colors(3)*256^2 + colors(4)*256^3;
% Note that the A value (Transparency, or color(4))can only go to 128, this is a bug in
% Imaris...
object.SetColorRGBA(double(col));
end
end
function color = GetColor(~, object)
%% GETCOLOR returns the color of the current object as a 4 element vector
% color = GETCOLOR(object) checks if there is a getcolor method
% available and retuns a 4-element vector as follows:
% color(1) : RED
% color(2) : GREEN
% color(3) : BLUE
% color(4) : ALPHA
if any(strcmp(methods(object), 'GetColorRGBA'))
col = object.GetColorRGBA();
color = [];
e = 3;
for i = fliplr(0:e)
color(i+1) = floor(col ./ (256.^i)); %#ok<*AGROW>
col = col - color(i+1).*256.^i;
end
else
disp('This object has no "SetName" method.')
end
end
function chans = ColorCode(eXT, channel, varargin)
theLut = 'parula';
for i=1:2:length(varargin)
switch varargin{i}
case 'LUT'
theLut = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
% Lookup table, and linear space fitting
lut = eval(['colormap(' theLut ')']);
ds = eXT.ImarisApp.GetDataSet.Clone();
% Do this between the min and max Display range of the selected channel
mina = ds.GetChannelRangeMin(channel-1);
maxa = ds.GetChannelRangeMax(channel-1);
chans = (eXT.GetSize('C')+1):(eXT.GetSize('C')+3);
ds.SetSizeC(ds.GetSizeC()+3);
%eXT.SetSize('C', eXT.GetSize('C')+3);
% Prepare 3 new channels... RGB
ds.SetChannelColorRGBA(chans(1)-1, 255);
ds.SetChannelColorRGBA(chans(2)-1, 255*256);
ds.SetChannelColorRGBA(chans(3)-1, 255*255*256);
dimSize = eXT.GetSize('Z');
interpAxis = linspace(0,1,dimSize);
vq1 = interp1(linspace(0,1,size(lut,1)),lut,interpAxis);
theX = eXT.GetSize('X');
theY = eXT.GetSize('Y');
theZ = eXT.GetSize('Z');
for t=1:eXT.GetSize('T')
for z=1:eXT.GetSize('Z')
%Get The Data
vox = double(eXT.GetVoxels(channel, 'Time',t, 'Slice', z, '1D', true));
%Normalize the values
vox = ((vox-mina) ./ (maxa - mina)).*255;
vox(vox<0) = 0;
tmpChan = zeros(size(vox));
fprintf('Slice %d of %d, T%d', z, eXT.GetSize('Z'));
for c=1:3
tmpChan(:,:) = vox.*vq1(z,c);
ds.SetDataSubVolumeAs1DArrayBytes(uint8(round(tmpChan)),0,0,z-1, chans(c)-1, t-1, theX, theY, 1);
end
end
end
eXT.ImarisApp.SetDataSet(ds);
end
function spots = CreateSpots(eXT, PosXYZ, spotSizes, varargin)
%% CREATESPOTS creates and returns a new spot object
% spots = CREATESPOTS(posXYZ, spotSizes, ...,
% 'Name', name, ...
% 'Single Timepoint', isSingle, ...
% 'Time Indexes', t, ... )
% Creates a new spots object with the given xyz positions and
% sizes.
% Input Arguments:
% o posXYZ - an nx3 array where each row contains the X,
% Y and Z position of the spots, in the unit of the imaris
% dataset (Usually microns).
% o spotSizes - either an nx1 or nx3 array containing the radius
% of each spot, making the spot either spherical or defined by
% its X Y and Z semi-major axes lenghts.
% Optional Parameters:
% o Name - The name of the spots object, otherwise it uses
% Imaris's default naming scheme (Spots 1, Spots 2, ...)
% o Single Timepoint - Should the time indexes not be defined
% explicitely using the 'Time Indexes' option, are the spots
% to be created only for the currently selected timepoint or
% for each timepoint in the dataset? Defaults to [ true ]
% o Time Indexes - nx1 array with the time index
% corresponding to each spot. Must be the same length as
% posXYZ.
%
% NOTE: The spot is not added to the scene, use ADDTOSCENE for
% this.
t = zeros(size(PosXYZ,1),1);
isOnlyCurrent = true;
name = [];
% in order to complete for time
for i=1:2:length(varargin)
switch varargin{i}
case 'Single Timepoint'
isOnlyCurrent = varargin{i+1};
case 'Name'
name = varargin{i+1};
case 'Time Indexes'
t = varargin{i+1};
isOnlyCurrent = true;
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
if (all(size(spotSizes) == [1 1]))
spotSizes = repmat(spotSizes, size(PosXYZ,1),3);
end
if size(spotSizes,2) == 1
spotSizes = repmat(spotSizes, 1,3);
end
if ~( size(spotSizes,2) == 3 || size(spotSizes,2) == 1 )&& ( size(spotSizes,1) == size(PosXYZ,1) )
error('Radii must be either an nx1 array or an nx3 array');
end
if size(PosXYZ,2) ~= 3
error('XYZ must be nx3 in size.');
end
% Create the spots
spots = eXT.ImarisApp.GetFactory().CreateSpots();
if isOnlyCurrent
spots.Set(PosXYZ, t, spotSizes(:,1));
spots.SetRadiiXYZ(spotSizes);
else
nT = eXT.GetSize('T');
spots.Set(repmat(PosXYZ,nT,1), repmat(t,nT,1), repmat(spotSizes, nT,1));
end
if ~isempty(name)
spots.SetName(name);
end
end
function OpenImage(eXT, filepath)
%% OPENIMAGE Opens the file in a new imaris scene
% OpenImage(filepath) is useful when batch processing data
CreateNewScene(eXT);
eXT.ImarisApp.FileOpen(filepath,'');
eXT.ImarisApp.GetSurpassCamera.Fit();
end
function analyzeImage(eXT, isAppend, analysis_function)
fileDir =[];
data = [];
[dir filename ext] = eXT.GetCurrentFileName();
nChan = eXT.GetSize('C');
%append name of analysis function to the filename
funcData = functions( analysis_function );
funcName = funcData.function;
fileDir = dir;
if isAppend
file = ['/' funcName '-analysis.csv'];
else
file = ['/' filename '-' funcName '.csv'];
end
filePath = [fileDir file];
if exist(filePath, 'file') == 2 && isAppend
% Read In the data
data = readtable(filePath, 'Delimiter' ,',');
else
data = table;
end
result = analysis_function( eXT );
result.Image = repmat({filename}, size(result,1),1);
% Append file Name here
data = [data; result];
writetable(data,filePath, 'Delimiter' ,',');
end
function RunBatch( eXT, batchPath, analysis_function, isAppend )
%Get the starting path for the directory
lastImgPath = eXT.GetCurrentFileName();
% Ask for the directory
files = dir( fullfile(batchPath) ); % List the files
files = {files.name}'; % Keep only the name as a Cell Array
saveDir = [batchPath,'/Results/'];
mkdir(saveDir);
% Check for files that already exist
processedFiles = dir(saveDir);
processedFileNames = {processedFiles.name}';
% Go through the files
for i = 1:numel(files)
file = files{i};
if eXT.isImage(file) && ~strcmp('.',file) && ~strcmp('..',file)
if ~ismember([file,'.ims'], processedFileNames)
eXT.OpenImage(fullfile(batchPath, file));
% Run the processing
analyzeImage(eXT, isAppend, analysis_function);
eXT.ImarisApp.FileSave([fullfile(saveDir, file) '.ims'],'');
pause(2);
else
fprintf('%s: already processed\n', file)
end
end
end
end
function CreateNewScene(eXT)
%% CREATENEWSCENE Creates a new Surpass scene
% CreateNewScene() is useful for clearning the current scene in
% the case that we are batch opening images, for examples.
vSurpassScene = eXT.ImarisApp.GetFactory.CreateDataContainer;
vSurpassScene.SetName('Scene');
%% Add a light source
vLightSource = eXT.ImarisApp.GetFactory.CreateLightSource;
vLightSource.SetName('Light source');
%% Add a frame (otherwise no 3D rendering)
vFrame = eXT.ImarisApp.GetFactory.CreateFrame;
vFrame.SetName(strcat('Frame'));
%% Add a Volume (otherwise no 3D rendering)
vVolume = eXT.ImarisApp.GetFactory.CreateVolume;
vVolume.SetName(strcat('Volume'));
%% Set up the surpass scene
eXT.ImarisApp.SetSurpassScene(vSurpassScene);
AddToScene(eXT, vLightSource);
AddToScene(eXT, vFrame);
AddToScene(eXT, vVolume);
end
function ResetScene(eXT)
%% ResetScene Creates a new Surpass scene
% RESETSCENE() is useful for clearning the current scene.
scene = eXT.ImarisApp.GetSurpassScene;
nChildren = scene.GetNumberOfChildren;
% objectsToRemove = [];
for i = nChildren:-1:1
object = scene.GetChild(i-1);
objectType = GetImarisType(eXT, object);
if (~( strcmp ( objectType , 'Light Source' ) || ...
strcmp ( objectType , 'Frame' ) || ...
strcmp ( objectType , 'Volume') ))
scene.RemoveChild(object) ;
end
end
end
function AddToScene(eXT, object, varargin)
%% ADDTOSCENE adds the object to the Imaris Scene
% ADDTOSCENE(object, 'Parent', parent) adds the object to the
% Imaris Scene or to the optional parent object.
% Optional Parameter/Value pairs
% o Parent - The parent object to add this new object to.
parent = eXT.ImarisApp.GetSurpassScene;
for i=1:2:length(varargin)
switch varargin{i}
case 'Parent'
parent = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
parent.AddChild(object, -1);
end
function RemoveFromScene(eXT, object, varargin)
%% REMOVEFROMSCENE removes the object from Imaris Scene
% Optional Parameter/Value pairs
% o Parent - The parent object inside which the object lives.
parent = eXT.ImarisApp.GetSurpassScene;
for i=1:2:length(varargin)
switch varargin{i}
case 'Parent'
parent = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
parent.RemoveChild(object);
end
function [newChannel, vDataset] = MaskChannelWithSurface( eXT, channel, surface, varargin )
outside = 0;
inside = 'same';
for i=1:2:length(varargin)
switch varargin{i}
case 'Outside'
outside = varargin{i+1};
case 'Inside'
inside = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
vDataSet = eXT.ImarisApp.GetDataSet.Clone;
% Get some info from the scene
[aData, aSize, aMin, aMax, ~] = GetDataSetData(vDataSet);
time = 1:eXT.GetSize('T');
slices = 1:eXT.GetSize('Z');
% Iterate through all selected timepoints and slices
for ind=1:size(time,2)
surfaceMask(ind) = surface.GetMask( aMin(1), aMin(2),aMin(3), ...
aMax(1), aMax(2), aMax(3), ...
aSize(1), aSize(2), aSize(3), ...
time(ind)-1);
end
newChannel = eXT.GetSize('C');
vDataSet.SetSizeC(newChannel+1);
dataType = eXT.GetDataType();
for z=slices
progress(z-1,eXT.GetSize('Z'));
for ind=1:size(surfaceMask,1)
switch dataType
case '8-bit'
maskSlice = surfaceMask(ind).GetDataSliceBytes(z-1, 0,0);
case '16-bit'
maskSlice = surfaceMask(ind).GetDataSliceShorts(z-1, 0,0);
case '32-bit'
maskSlice = surfaceMask(ind).GetDataSliceFloats(z-1, 0,0);
end
switch dataType
case '8-bit'
chanSlice = vDataSet.GetDataSliceBytes(z-1, channel-1,time(ind)-1);
case '16-bit'
chanSlice = vDataSet.GetDataSliceShorts(z-1, channel-1,time(ind)-1);
case '32-bit'
chanSlice = vDataSet.GetDataSliceFloats(z-1, channel-1,time(ind)-1);
end
newSlice = chanSlice;
% Here we have the mask, now we take the channel we
if ~strcmp( inside, 'same' )
% Modify the inside to be the given value
newSlice(maskSlice==1) = inside;
end
if ~strcmp( outside, 'same' )
newSlice(maskSlice==0) = outside;
end
switch dataType
case '8-bit'
vDataSet.SetDataSliceBytes(newSlice, z-1, newChannel, time(ind)-1);
case '16-bit'
vDataSet.SetDataSliceShorts(newSlice, z-1, newChannel, time(ind)-1);
case '32-bit'
vDataSet.SetDataSliceFloats(newSlice, z-1, newChannel, time(ind)-1);
end
end
end
% Name the channel
vDataSet.SetChannelName(newChannel, ['Masked Channel: ' char(vDataSet.GetChannelName(channel-1)) ' using "' char(surface.GetName) ' "']);
% Give the channel the same color as the Surface object
vRGBA = vDataSet.GetChannelColorRGBA(channel-1);
vDataSet.SetChannelColorRGBA(newChannel, vRGBA);
eXT.ImarisApp.SetDataSet(vDataSet);
newChannel = newChannel + 1;
end
function [newChannel, vDataSet] = MakeChannelFromSurfaces(eXT, surface, varargin)
%% MAKECHANNELFROMSURFACES builds a new channel from a surface mask.
% [newChannel vDataSet] = MAKECHANNELFROMSURFACES(surface, ...
% 'Mask Channel', maskChannel, ...
% 'IDs', surfIDs, ...
% 'Time Indexes', tInd, ...
% 'Inside', inVal, ... ...
% 'Outside', outVal, ...
% 'Add Channel', isAdd);
% Creates a new channel containing one of either:
% A mask based on the surface used OR
% An exsisting channel, masked by the surface object. All
% values outside the surface object are set to 0. Inside values
% are set to the value of the original channel.
% In all cases, this function creates a new channel and returns
% the index of that channel, as well as the new IDataSet object.
% Optional parameters are:
% o Mask Channel - If set, the number of the channel to mask
% with surface.
% o Time Indexes - The timepoints to consider. If not set,
% all timepoints will be treated. Index starts at 1.
% o IDs - IDs of the surfaces to use as masks. You cannot use
% this option in conjunction with time indexes, as surface
% IDs are unique for each surface, this includes timepoints.
% Masking based on track IDs could be implemented at a later
% date if needed.
% o Inside - The voxel value that you want the voxels inside
% the surface to have. Defaults to 255 or the value of the
% Mask Channel.
% o Outside - The voxel value that you want the voxels
% outside the surface to have. Defaults to 0;
% o Add Channel - Defines whether the function adds the
% channel to the current or not. You can grab the updated
% dataset through the second output argument. [ true ]
%
% Output Arguments
% newChannel returns the number of the new channel
% aDataSet returns the newly created IDataSet object.
%
% Example usage
% >> newChannel = MakeChannelFromSurfaces(surface, 'Mask Channel', 1);
% Creates a new channel based on channel 1 and masked using
% surface.
% >> newChannel = MakeChannelFromSurfaces(surface); Creates a
% mask of surface and puts it in a new channnel.
% >> [newChannel aDataSet] = MakeChannelFromSurfaces(surface, 'Add Channel', false);
% Creates a mask of surface and only returns the dataset without creating it.
time = [];
surfIDs = 'All';
maskChannel = 'None';
inVal = 255;
outVal = 0;
isAddChannel = true;
vDataSet = [];
for i=1:2:length(varargin)
switch varargin{i}
case 'IDs'
surfIDs = varargin{i+1};
case 'Time Indexes'
time = varargin{i+1};
case 'Mask Channel'
maskChannel = varargin{i+1};
case 'Inside'
inVal = varargin{i+1};
case 'Outside'
outVal = varargin{i+1};
case 'Add Channel'
isAddChannel = varargin{i+1};
case 'DataSet'
vDataSet = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
% Do all timepoints if nothing is specified
if isempty(time)
time = 1:eXT.GetSize('T');
end
if isempty(vDataSet)
vDataSet = eXT.ImarisApp.GetDataSet.Clone;
end
% Get some info from the scene
[aData, aSize, aMin, aMax, ~] = GetDataSetData(vDataSet);
% Make sure the object is a surface
if strcmp(eXT.GetImarisType(surface), 'Surfaces')
% Get the mask for the surface
if ~strcmp(surfIDs,'All')
for ind=1:size(surfIDs,1)
surfaceMask(ind) = surface.GetSingleMask( surfIDs(ind), ...
aMin(1), aMin(2),aMin(3), ...
aMax(1), aMax(2), aMax(3), ...
aSize(1), aSize(2), aSize(3));
% Get the time index
time(ind) = surface.GetTimeIndex(surfIDs(ind))+1;
end
else
% Iterate through all selected timepoints
for ind=1:size(time,2)
surfaceMask(ind) = surface.GetMask( aMin(1), aMin(2),aMin(3), ...
aMax(1), aMax(2), aMax(3), ...
aSize(1), aSize(2), aSize(3), ...
time(ind)-1);
end
end
% Now make the new channel for each timepoint
newChannel = eXT.GetSize('C');
vDataSet.SetSizeC(newChannel+1);
dataType = eXT.GetDataType();
% And now create the new volumes for each timepoint or for
% each subsurface
for z=1:eXT.GetSize('Z')
progress(z-1,eXT.GetSize('Z'));
for ind=1:size(surfaceMask,1)
switch dataType
case '8-bit'
maskSlice = surfaceMask(ind).GetDataSliceBytes(z-1, 0,0);
case '16-bit'
maskSlice = surfaceMask(ind).GetDataSliceShorts(z-1, 0,0);
case '32-bit'
maskSlice = surfaceMask(ind).GetDataSliceFloats(z-1, 0,0);
end
if strcmp(maskChannel, 'None')
chanSlice = aData(:,:,z) + inVal - 1;
else
switch dataType
case '8-bit'
chanSlice = vDataSet.GetDataSliceBytes(z-1, maskChannel-1,time(ind)-1);
case '16-bit'
chanSlice = vDataSet.GetDataSliceShorts(z-1, maskChannel-1,time(ind)-1);
case '32-bit'
chanSlice = vDataSet.GetDataSliceFloats(z-1, maskChannel-1,time(ind)-1);
end
end
% class(chanVol)
% class(maskVol)
% Write to the dataset.
% Set the outside value
outSlice = maskSlice;
outSlice(maskSlice==0) = outVal;
switch dataType
case '8-bit'
vDataSet.SetDataSliceBytes(chanSlice .* maskSlice + outSlice, z-1, newChannel, time(ind)-1);
case '16-bit'
vDataSet.SetDataSliceShorts(chanSlice .* maskSlice + outSlice, z-1, newChannel, time(ind)-1);
case '32-bit'
vDataSet.SetDataSliceFloats(chanSlice .* maskSlice + outSlice, z-1, newChannel, time(ind)-1);
end
end
end
% Name the channel
if ~strcmp(maskChannel, 'None')
vDataSet.SetChannelName(newChannel, ['Masked Channel: ' char(vDataSet.GetChannelName(maskChannel-1)) ' using "' char(surface.GetName) ' "']);
% Give the channel the same color as the Surface object
vRGBA = vDataSet.GetChannelColorRGBA(maskChannel-1);
vDataSet.SetChannelColorRGBA(newChannel, vRGBA);
else
vDataSet.SetChannelName(newChannel, ['Masked from Surface ' char(surface.GetName)]);
% Give the channel the same color as the Masked Channel
vRGBA = surface.GetColorRGBA;
vDataSet.SetChannelColorRGBA(newChannel, vRGBA);
end
if isAddChannel
disp('Adding');