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ChangeLog.m
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%% VolumeCut: Cut images along custom surfaces
% Copyright (C) 2017-2019 Luca Della Santina
%
% This file is part of VolumeCut
%
% 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/>.
% This software is released under the terms of the GPL v3 software license
%
%
% *Change log*
%
% _*Version 6.2* created on 2021-04-17 by Luca Della Santina_
%
% + Sped up startup time with faster screen centering code
% + App window back in focus after manual annotations are done
% + Refactored code fixing main app losing focus after dialog
%
% _*Version 6.1* created on 2020-11-16 by Luca Della Santina_
%
% + New batch density by depth within limits
% + Custom bin size in batch density by depth
% + Timestamp suffix to batch measurements filename
%
% _*Version 6.0* created on 2020-09-19 by Luca Della Santina_
%
% + MATLAB R2020b required
% + New fitting algorithm near 15X faster, requires curve fitting toolbox
% + New reference point drawing near 2X faster
% + loadImageStack uses memory-efficient tiffreadVolume()
% + New slicing algorithm, near 4X faster
% + Single instance of the app allowed
% + Change name of objects in visual editor
%
% _*Version 5.2* created on 2020-09-19 by Luca Della Santina_
%
% + Removed Refine tool
% + Fixed misalignment of sensitive point on crossbar
% + Improved redrawing speed by passing only current frame to redraw
% + Selecting a reference point on-screen selects corresponding on table
%
% _*Version 5.1* created on 2020-09-15 by Luca Della Santina_
%
% + Optional saving of different cut parts
% + Delete objects from graphical editor
% + Renamed loadImage.m to loadImageStack.m to disambiguate among apps
%
% _*Version 5.0* created on 2020-09-14 by Luca Della Santina_
%
% + Visual editor for fiducial cut points
% + Removed Log and Lamp component at the bottom of UI
% + Added progress dialogs for all operations
%
% _*Version 4.9* created on 2020-08-07 by Luca Della Santina_
%
% + Batch recursion into all subfolder levels
%
% _*Version 4.8* created on 2020-04-13 by Luca Della Santina_
%
% + Version in app title
% + New Batch operation: Keep only largest object
%
% _*Version 4.7* created on 2020-01-31 by Luca Della Santina_
%
% + Support for 2D binary masks
%
% _*Version 4.5* created on 2019-12-18 by Luca Della Santina_
%
% + New Automation option to intensity histograms within masked volume
% + App now starts centered within the screen
% + During batch processing a cancellable progressbar informs of status
%
% _*Version 4.5* created on 2019-11-20 by Luca Della Santina_
%
% + New Automation option to calculate voxel "Density by depth" percentage
%
% _*Version 4.4* created on 2019-01-26 by Luca Della Santina_
%
% + New Automation tab allows batch processing of masks
%
% _*Version 4.3* created on 2019-01-23 by Luca Della Santina_
%
% + Fixed bug causing missing interactivity with 3D plots
%
%_*Version 4.2* created on 2019-01-16 by Luca Della Santina_
%
% + Fixed error of Spots not recognized when only one set is loaded
% + Fixed error of 3D plot not visualized due to mispositioned hold(on)
%
% _*Version 4.1* created on 2019-01-09 by Luca Della Santina_
%
% + Inverted x y coordinates when importing skeletons from SNT .traces
%
% _*Version 4.0* created on 2019-01-06 by Luca Della Santina_
%
% + Skeleton tab allows visualization of digital skeletons
% + Support for skeletons created with ImageJ's Simple Neurite Tracer
% + Create binary mask from skeleton according to skeleton's radius
% + Reflect skeletons along the cardinal axis of the containing volume
% + Recalibrate and Rescale skeleton
% + Display skeleton statistics
%
% _*Version 3.3* created on 2019-01-02 by Luca Della Santina_
%
% Changed imclose and imfill to operate in 3D by iterating each plane in 2D
%
% _*Version 3.0* created on 2018-10-16 by Luca Della Santina_
%
% + New Mask visualization and math functions
% + Scroll wheel in mask tab moves current Z plane visualized
% + Logical operations between masks: unite, exclude, subtract, intersect
% + Operations on mask: Revert to original, trace edges, invert
%
% _*Version 2.3* created on 2018-10-12 by Luca Della Santina_
%
% + Keep track on screen of file names of image and cut reference points
% + Automatically change matlab current working directory to Image file's
% + Allows reuse of calculated surfaces to cut additional image stacks
% + Units of measurements can be switched from pixels to microns
% + Render volume generated a new plot every time is pressed
% + Render window's title matches the type of rendered content(e.g Cut I)
%
% _*Version 2.2* created on 2018-10-11 by Luca Della Santina_
%
% + 3D Rendering of reference points and fitted surfaces
% + MIP projections on the walls of the 3D scene
%
% _*Version 2.1* created on 2018-10-09 by Luca Della Santina_
%
% + Correct rendering of anisotropic voxels
% + New cut modes: Cut in Two/Three/Four parts
%
% _*Version 2.0* created on 2018-10-07 by Luca Della Santina_
%
% + Added Graphical interface using appdesigner
% + Packaged into a matlab App
% + Render the source and cut volumes using MATLAB's 3D renderer
% + Added custom smoothing of interpolated surfaces
% + Added custom Z offset for each individual surface
% + Added project website
%
% _*Version 1.5* created on 2018-09-19 by Luca Della Santina_
%
% + Offset1 and offset2 can nowbe appliedto all cutting modes
% + Both masks used to slice the volume are saved as -part1mask -part2mask
%
% _*Version 1.4.1* created on 2017-11-29 by Luca Della Santina_
%
% + Fixed bug in applying offset1 and offset2 to calculade midle plane
%
% _*Version 1.4* created on 2017-11-20 by Luca Della Santina_
%
% + Allows to cut at a custom distance from references planes when mode=1
% + Added progress bars and verbose output for all the processing steps
% + Added copyright statement
% % Exmplained the three cutting modes more clearly
%
% _*Version 1.3* created on 2017-10-01 by Luca Della Santina_
%
% % Fixed double extension inserted into filenames, i.e. ".tif-part1.tif"
% + Added new modes of slicing when using 2 set of coordinates
%
% Plane #1<->middle<->#2
% Part1: From beginning of plane #1 to halfway between planes
% Part2: From halfway between planes to plane #2
%
% Stack Start<->middle<->End mode:
% Part1: From beginning of volume to halfway between planes
% Part2: From halfway between planes to end of volume
%
% Inside/Outside planes mode:
% Part1: volume outside the planes delimited by the coordinate sets
% Part2: volume inside the planes delimited by the coordinate sets
%
% _*Version 1.2.1* created on 2017-09-07 by Luca Della Santina_
%
% + Reformatted documentation using proper MATLAB markup format
%
% _*Version 1.2* created on 2017-09-07 by Luca Della Santina_
%
% + When cutting with 2 set of reference points output stacks are:
% "-part1.tif" voxels between top and middle surfaces (g1<->g3)
% "-part2.tif" voxels between middle and bottom surfaces (g3<->g2)
% + Allow Surface 1 and Surface 2 to be loaded opposite than expected
%
% _*Version 1.1* created on 2017-09-01 by Luca Della Santina_
%
% % bug fixed the file selector for reference points
%
% _*Version 1.0* created on 2017-09-01 by Luca Della Santina_
%