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EasyXT.m
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EasyXT.m
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classdef EasyXT
%%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.
%
% 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;
% We can define here the path where ImarisLib.jar is
imarisLibPath = 'C:\Program Files\Bitplane\Imaris x64 7.6.5\XT\matlab\ImarisLib.jar';
end
methods
function eXT = EasyXT(varargin)
%% EASYXT builds a new EasyXT object
% eXT = EASYXT(imarisApplication)
% builds a new EasyXT object and connects to an open Imaris
% Instance.
% Optional input argument: imarisApplicationID
% That way you can start easyXT from an Xtension, like you
% normally would.
% Supress Java Duplicate Class warnings
warning('off','MATLAB:Java:DuplicateClass');
lib = getSavedImarisLib();
if nargin == 1 && (strcmp(varargin{1}, 'setup') || strcmp(lib, ''))
[FileName,PathName] = uigetfile('.jar','Location of ImarisLib.jar');
eXT.imarisLibPath = [PathName, FileName];
setSavedImarisLib(eXT.imarisLibPath);
end
% Start Imaris Connection
javaaddpath(eXT.imarisLibPath);
% Create an instance of ImarisLib
vImarisLib = ImarisLib;
warning('on','MATLAB:Java:DuplicateClass');
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
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, ...
% 'Active Selection', isSelection)
%
% 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.
% Defaults to [ true ]
%
% Examples:
% >> ImarisObj = GetObject(); % Returns the active object
% in the imaris scene
% >> ImarisObj = GetObject('Type', 'Surfaces'); % Returns
% the first surface object
% >> ImarisObj = GetObject('Number', 4); % Returns
% fourth object in the scene.
% >> ImarisObj = GetObject('Type', 'Surfaces', 'Name', 'My Surfaces');
% Returns the first surface object with name 'My Surfaces'.
%
% 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
object = [];
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 = char(object.GetName);
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
% All arguments from GETSELECTEDOBJECT can be applied here
% See also GETSELECTEDOBJECT
obj = GetObject(eXT, varargin{:});
eXT.ImarisApp.SetSurpassSelection(obj);
end
function number = GetNumberOf(eXT, type, varargin)
%% GETNUMBEROF recovers the number of objects with a certain name or type
% number = GETNUMBEROF('Name', name, ...
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 = char(object.GetName);
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(eXT, object)
if any(strcmp(methods(object), 'GetName'))
name = char(object.GetName);
end
end
function name = SetName(eXT, object, name)
if any(strcmp(methods(object), 'SetName'))
object.SetName(name);
end
end
function SetColor(eXT, 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 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. posXYZ is an nx3 array where each row contains the X,
% Y and Z position of the spots, int the unit of the imaris
% dataset (Usually microns).
% spotSizes is 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. Must be the same size
% as posXYZ.
% 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),1);
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);
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 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 to remove this object from.
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] = 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);
% '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 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';
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 '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, aType] = 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 ind=1:size(surfaceMask,1)
switch dataType
case '8-bit'
maskVol = surfaceMask(ind).GetDataVolumeBytes(0,0);
case '16-bit'
maskVol = surfaceMask(ind).GetDataVolumeShorts(0,0);
case '32-bit'
maskVol = surfaceMask(ind).GetDataVolumeFloats(0,0);
end
if strcmp(maskChannel, 'None')
chanVol = aData + 255;
else
switch dataType
case '8-bit'
chanVol = vDataSet.GetDataVolumeBytes(maskChannel-1,time(ind)-1);
case '16-bit'
chanVol = vDataSet.GetDataVolumeShorts(maskChannel-1,time(ind)-1);
case '32-bit'
chanVol = vDataSet.GetDataVolumeFloats(maskChannel-1,time(ind)-1);
end
end
% class(chanVol)
% class(maskVol)
% Write to the dataset.
switch dataType
case '8-bit'
vDataSet.SetDataVolumeBytes(chanVol .* maskVol, newChannel, time(ind)-1);
case '16-bit'
vDataSet.SetDataVolumeShorts(chanVol .* maskVol, newChannel, time(ind)-1);
case '32-bit'
vDataSet.SetDataVolumeFloats(chanVol .* maskVol, newChannel, time(ind)-1);
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');
eXT.ImarisApp.SetDataSet(vDataSet);
end
else
name = char(surface.GetName());
disp([name ' is not a surface.']);
end
newChannel = newChannel + 1;
end
function [newChannel, vDataSet] = MakeChannelFromSpots(eXT, mySpots, varargin)
%% MAKECHANNELFROMSPOTS builds a new channel from a spots mask.
% [newChannel, vDataSet] = MAKECHANNELFROMSPOTS(spots, ...
% 'IDs', spotIDs, ...
% 'Time Indexes', tInd;
% 'Add Channel', isAdd
% 'Interpolate', isInterp, ...
% 'DataSet', vDataSet) ;
% Creates a new channel containing
% A mask based on the spots used OR
%
% 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 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 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 ]
% o Interpolate - Whether or not to use interpolation at the
% edge of the spots. if True, you will not have a mask
% channel, as there will be values between 0 and 1.
% o DataSet - Provide the dataset to draw the spots in
% explicitly. This is useful if you want to update a dataset
% with multiple calls to this function, so that you don't
% need to update the Scene every time.
%
% Output Arguments
% newChannel returns the number of the new channel
% aDataSet returns the newly created IDataSet object.
%
% Example usage
% >> newChannel = MakeChannelFromSurfaces(spots, 'Interpolate', true);
% Creates a new channel based on spots with interpolation
isInterpolate = false;
isAddChannel = true;
spotIDs = 'All';
time = [];
vDataSet = []
for i=1:2:length(varargin)
switch varargin{i}
case 'IDs'
spotIDs = varargin{i+1};
case 'Time Indexes'
time = varargin{i+1};
case 'Add Channel'
isAddChannel = varargin{i+1};
case 'Interpolate'
isInterp olate = 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
% Grab the spots Info
vSpotsXYZ = mySpots.GetPositionsXYZ;
vSpotsRadius = mySpots.GetRadiiXYZ;
vSpotsTime = mySpots.GetIndicesT;
if ~strcmp(spotIDs, 'All')
% Append to the processing only the selected spot IDs
vSpotsXYZ = vSpotsXYZ(spotIDs, :);
vSpotsRadius = vSpotsRadius(spotIDs, :);
vSpotsTime = vSpotsTime(spotIDs);
end
if isempty(vDataSet)
vDataSet = eXT.ImarisApp.GetDataSet.Clone;
end
[aData, aSize, aMin, aMax, vType] = GetDataSetData(vDataSet);
% Prepare the new channel.
newChannel = vDataSet.GetSizeC;
vDataSet.SetSizeC(newChannel+1);
% Start Building the spots
for vTime = time
aData(:) = 0; % Initialize vData to 0 for each new timepoint
% Select spots associated with current time
vSpotsIndex = find(vSpotsTime == (vTime-1))';
for vIndex = vSpotsIndex
vPos = vSpotsXYZ(vIndex, :); % Get their positions
vRadius = vSpotsRadius(vIndex,:); % And their Radii
aData = DrawSphere(aData, vPos, vRadius, aMin, aMax, vType, isInterpolate); % Now draw the sphere
end
% If there were spots drawn at this time, set the dataset
% of the appropriate type.
if ~isempty(vSpotsIndex)
if strcmp(vDataSet.GetType, 'eTypeUInt8')
vDataSet.SetDataVolumeBytes(aData, newChannel, (vTime-1));
elseif strcmp(vDataSet.GetType, 'eTypeUInt16')
vDataSet.SetDataVolumeShorts(aData, newChannel, (vTime-1));
else
vDataSet.SetDataVolumeFloats(aData, newChannel, (vTime-1));
end
end
end
% Give the channel the same color as the spot object
vRGBA = mySpots.GetColorRGBA;
vDataSet.SetChannelColorRGBA(newChannel, vRGBA);
vDataSet.SetChannelName(newChannel, mySpots.GetName);
% Finally Add everyting to the dataset
if (isAddChannel)
eXT.ImarisApp.SetDataSet(vDataSet);
end
newChannel = newChannel+1;
end
function [newChannel, vDataSet] = ChannelMath(eXT, expression, varargin)
%% CHANNELMATH Perform channel-based operations
% [newChannel, vDataSet] = CHANNELMATH(expression) recovers
% data from imaris channels (Called using ch1, ch2, ...) and
% evaluates a matlab operation on those channels. All Matlab
% functions are accessible.
% expression is a string that contains the Matlab-language
% calculation you want to perform on the channels.
% Channel names: ch1, ch2, Use matlab operators, i.e.
% +, -, .*, ./, .^, sqrt
% Optional parameters:
% o Add Channel - Adds the computed channel to the Imaris
% DataSet. Defaults to [ true ]. If false, the result is in
% the vDataSet output.
% o DataSet - Provide the dataset to draw the spots in
% explicitly. This is useful if you want to update a dataset
% with multiple calls to this function, so that you don't
% need to update the Scene every time.
% Output parameters
% o newChannel - The index of the new channel in the DataSet
% o vDataSet - A clone of the original dataset with the new
% channel.
vDataSet = [];
isAddChannel = true;
for i=1:2:length(varargin)
switch varargin{i}
case 'Add Channel'
isAddChannel = varargin{i+1};
case 'DataSet'
vDataSet = varargin{i+1};
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
if isempty(expression)
disp('Write an expression, guy')
end
if isempty(vDataSet)
vDataSet = eXT.ImarisApp.GetDataSet.Clone;
end
vLastC = vDataSet.GetSizeC;
vDataSet.SetSizeC(vLastC + 1);
vMin = vDataSet.GetChannelRangeMin(0);
vMax = vDataSet.GetChannelRangeMax(0);
vDataSet.SetChannelRange(vLastC, vMin, vMax);
%Iterate through all time points
for vTime = 1:vDataSet.GetSizeT
for vSlice = 1:vDataSet.GetSizeZ
for vChannel = 1:vLastC
% works on double to allow division and prevent overflows
eval(sprintf(['ch%i = double(vDataSet.GetDataSliceFloats(', ...
'vSlice-1, vChannel-1, vTime-1));'], vChannel));
end
try
vData = eval(expression{1});
catch er
fprintf(['Error while evaluating the expression.\n\n', ...
'Possible causes: invalid variable names (ch1, ch2, ...), ', ...
'invalid operators (use .* instead of *)...\n\n', er.message])
return
end
try
if strcmp(vDataSet.GetType,'eTypeUInt8')
vDataSet.SetDataSliceBytes(uint8(vData), vSlice-1, vLastC, vTime-1);
elseif strcmp(vDataSet.GetType,'eTypeUInt16')
vDataSet.SetDataSliceShorts(uint16(vData), vSlice-1, vLastC, vTime-1);
elseif strcmp(vDataSet.GetType,'eTypeFloat')
vDataSet.SetDataSliceFloats(single(vData), vSlice-1, vLastC, vTime-1);
end
catch er
fprintf(['The result of the expression is not a valid dataset.\n\n', ...
'Possible causes: invalid result size.\n\n', er.message])
return
end
end
end
%NewChannel is the channel number as displayed by Imaris
%(Starting at 1), and not the channel index from the XTensions
%(Starting at 0)
newChannel = vLastC+1;
vDataSet.SetChannelName(vLastC, expression{1});
if isAddChannel
eXT.ImarisApp.SetDataSet(vDataSet);
end
end
function surface = DetectSurfaces(eXT, channel, varargin)
%%DETECTSURFACES Applies the Imaris Surfaces Detection Functions
% surface = DETECTSURFACES(channel, 'Name', surfaceName, ...
% 'Color', color, ...
% 'Smoothing', smooth, ...
% 'Local Contrast', isLocContrast, ...
% 'Threshold', thr, ...
% 'Filter', filterString, ...
% 'Seed Diameter', seedD, ...
% 'Seed Local Contrast', isSeedLocC, ...
% 'Seed Filter', seedFilterString, ...
% 'DataSet', aDataSet, ...
% Detects a surface from channel channel with optinal
% parameters:
% o Name - The name of the new surface object. Defaults to
% Imaris standard name.
% o Color - a single value or, 1x3 or 1x4 arrays with the
% color in RGBA format.
% colors(1) is Red (or gray if color is 1x1)
% colors(2) is Green
% colors(3) is Blue
% colors(4) is transparency (values [0-128])
% Defaults to white [255, 255, 255].
% o Smoothing - The smoothing kernel of the gaussian blur, in
% microns, usually. Defaults to twice the pixel size in XY.
% o Local Contrast - if different than 0, the local contrast
% filter size.
% o Threshold - The threshold value for determining the
% surfaces. If local contrast is 0, it is an absolute
% intensity threshold. Otherwise it is the threshold to apply
% on the Local Contrast-filtered image.
% o Surface Filter - A string containing the filter you want
% to apply to your surfaces. Example: '"Quality" above 7.000'
% Defaults to '"Number of Voxels" above 10.0'
% o Seed Diameter - The diameter of the seed detection for if
% you want to split the surfaces
% o Seed Local Contrast - If you want to use local contrast
% or absolute intensity when looking for seeds
% o Seed Filter - Filter string for the seeds. Defaults to
% [ '' ]
% o DataSet - Provide the dataset to detect the surfaces in
% explicitly. This is useful if you want to update a dataset
% with multiple calls to this function, so that you don't
% need to update the Scene every time.
%
%Defaults
th = 0;
gb = [];
filter = '"Number of Voxels" above 10.0';
name = '';
isAutoThr = true;
bgLocContrast = 0; % No automatic background
color = 255;
vDataSet = [];
isSplit = false;
seedDiam = 1;
isSeedLocContrast = false;
seedFilter = '';
% get the value of each argement you have specified, if you
% have specified one :)
for i=1:2:length(varargin)
switch varargin{i}
case 'Smoothing'
gb = varargin{i+1};
case 'Local Contrast'
bgLocContrast = varargin{i+1};
case 'Threshold'
th = varargin{i+1};
if th ~= 0;
isAutoThr = false;
end
case 'Filter'
filter = varargin{i+1};
case 'Name'
name = varargin{i+1};
case 'Color'
color = varargin{i+1};
case 'DataSet'
vDataSet = varargin{i+1};
case 'Seed Diameter'
seedDiam = varargin{i+1};
isSplit = true;
case 'Seed Local Contrast'
isSeedLocContrast = varargin{i+1};
isSplit = true;
case 'Seed Filter'
seedFilter = varargin{i+1};
isSplit = true;
otherwise
error(['Unrecognized Command:' varargin{i}]);
end
end
if isempty(vDataSet)
vDataSet = eXT.ImarisApp.GetDataSet;
end
if isempty(gb)
[voxelXY, voxelZ] = eXT.getVoxelSize();
gb = voxelXY*2;
end
if ~isSplit
surface = eXT.ImarisApp.GetImageProcessing.DetectSurfaces(vDataSet,[], channel-1,gb,bgLocContrast,isAutoThr,th,filter);
else
surface = eXT.ImarisApp.GetImageProcessing.DetectSurfacesRegionGrowing(vDataSet,[], channel-1,gb,bgLocContrast,isAutoThr,th,seedDiam, isSeedLocContrast, seedFilter, filter);
end
if ~strcmp(name, '') % give name if defined else default by Imaris
surface.SetName(name);
end
SetColor(eXT, surface, color);
end
function spots = DetectSpots(eXT, channel, varargin)
%%DETECTSPOTS Applies the Imaris Spots Detection Functions
% spot = DETECTSPOTS(channel, 'Name', surfaceName, ...
% 'Color', color, ...
% 'Diameter XY', dXY, ...
% 'Diameter Z', dZ, ...
% 'Subtract BG, isSubtractBG, ...
% 'Local Contrast', isLocContrast, ...
% 'Spots Filter', filterString, ...
% 'Seed Diameter', seedD, ...
% 'Seed Local Contrast', isSeedLocC, ...
% 'Seed Filter', seedFilterString, ...
% 'DataSet', aDataSet, ...
% Detects a spots from channel channel with optinal
% parameters:
% o Name - The name of the new spots object. Defaults to
% Imaris standard name.
% o Color - a single value or, 1x3 or 1x4 arrays with the
% color in RGBA format.
% colors(1) is Red (or gray if color is 1x1)
% colors(2) is Green
% colors(3) is Blue
% colors(4) is transparency (values [0-128])
% Defaults to white [255, 255, 255].
% o Diameter XY - the diameter of the spots, usually in
% microns, for the spot renderind and detection if using
% local contrast. If Diameter Z is not defined, these will be
% spherical spots. Defaults to 2x the voxel size in XY