and back.

Like S. Herbert did.

Now we work more like a class with methods.

Small enough to be committed.
Images by Leo Valon, Institut Pasteur, Levayer lab.

- We smooth the height-map by a scale automatically determined by
object scales -> avoid jagged edges.
- We prune effectively regions where Z = 0.
- Compute and display de-project area.

- Directly permute X & Y to have boundary coordinates in the proper
referential, like junctions.
- Reduce the number of vertices in the polygon, using reducepoly.
With this setting (0.005) reducepoly is very conservative, but
effectively decimate useless vertices. This has a positive impact
on the area calculation (fewer, larger triangles), and on all
performance.

Computing a mesh for the height-map is difficult and takes forever
as soon as we have images of a sgnificant size. Here we will simply
use the height map to assign a Z value to all location on request.
And see whether this still works.

Follow grosso-modo a maven repo.

Douglas Schwarz (2020). uipickfiles: uigetfile on steroids
(https://www.mathworks.com/matlabcentral/fileexchange/
10867-uipickfiles-uigetfile-on-steroids), MATLAB Central File
Exchange. Retrieved June 29, 2020.

Mask to objects: Accept B&W contour images as input for cells.

This reverts commit a71c1fe2.

Adds a the following command as a GUI StartupFcn which switches MATLAB to use Java file dialogs instead of native file dialogs (i.e. those of your operating system):

>> com.mathworks.mwswing.MJFileChooserPerPlatform.setUseSwingDialog(1)

Error introduced in commit 46c3e745 about parallelization

Produced with R2017b.
New error at usage of the main method to be fixed, but GUI is running as is with relevant parameters accessible to user

GUI was made with the app designer of MATLAB R2019a (or R2017a for the temp version).
It has not been tested again under Ubuntu because of freezing issues when interacting with the GUI. Mathworks has been contacted

Signed-off-by: sebherbert <sherbert@pasteur.fr>

improved speed but only by a marginal value (~20%)

Signed-off-by: sebherbert <sherbert@pasteur.fr>

Now accepts a 2D elevation map in .tif format (z is the height of the tissue)

Signed-off-by: sebherbert <sherbert@pasteur.fr>

Signed-off-by: sebherbert <sherbert@pasteur.fr>

This file must be updated regularly to stay up to date with the different commits

Added the angular transformation of the ellipses to create a 3D orientation of the ellipses
Refactoring the code for new variable names easier to handle.
Last non nuclear commit!

Signed-off-by: sebherbert <sherbert@pasteur.fr>