Wednesday, December 31, 2014

Scalar or vector field on structured, uniform grid - Create VTK file for loading into Paraview

Thanks to Joe Yeh for having created a Matlab function, vtkwrite(...), to create a file where scalar and/or vector fields defined on a structured, uniform and regular grid can be saved according to the VTK format needed to be imported in Paraview.
It's a very handy function. To create scalar and vector fields defined on a structured, uniform and regular grid is easy in Matlab. To be able to load the dataset into Paraview is fantastic because one can exploit the powerful visualization and analysis tools of that software.
The Matlab function can be downloaded from this URL.

Load a 3D image in Paraview

How to import a stack of 2D images (3D image) in Paraview?
It may seem a trivial question ... but without knowing some details it may take some time the first time one tries doing that.
See some useful tips at this URL.
Thanks to the Univ. of Manchester, IT Services Group and Computational Science Community Wiki administrators for posting these tips.

Update (14. January 2019)

From version 5.6.0, it's possible to import into Paraview stacks of 2D TIFF image files interpreting them not as a time series of 2D images but as a 3D volume. See the 4.4 version release notes here (point 15.13). Search for "tomography" or for "image stack" as a keyword.
ATTENTION: compared with opening the stack in, say, ImageJ and one of its 3D rendering plugins, e.g., VolumeViewer, the images in the stack are mirrored along the vertical (Y-)axis. Be careful about that!

Wednesday, July 30, 2014

Create a new shortcut to a command in ImageJ/Fiji

Very useful when you frequently call a command and you want to avoid wandering around/through the command menu trees.
Go to the Plugins menu. Choose Shortcuts, then the Create shortcut... command.

Thursday, June 12, 2014

Extract data from a Matlab plot

Very useful instructions about how to extract the data plotted in a figure saved as a Matlab figure (.fig format file), in order to be able to re-plot the data in a different way.

http://www.mathworks.com/matlabcentral/answers/100687-how-do-i-extract-data-from-matlab-figures

Thursday, June 5, 2014

7-Zip unavailable for 64-bit Cygwin

7-Zip is one of the most used programs for compression/decompression of files and archives.
p7zip is the porting of 7-Zip for GNU-Linux/POSIX-based systems.
It is not yet available for the 64-bit version of Cygwin.
In this post by Michael Hirsch, there are the instructions for running the 64-bit version of 7-Zip from the Cygwin terminal, which is of fundamental importance if you want to use 7-Zip in scripts for batch backing up of data.

Tuesday, January 14, 2014

User's session ID under MS Windows 7 and Server 2008 R2

This may be needed sometimes under MS Windows 7 or Server 2008 R2, for any reason ...
find which session ID is associated to a user logged to the machine, interactively or by a Remote Desktop Connection (RDP).

There is a built-in command that you can run from the DOS shell or by the MS PowerShell which is called qwinsta and provides you with all the details about any user session at the moment.

More than 2 Remote Desktop Connections on a MS Windows Server 2008 R2

On a server running on MS Windows Server 2008 R2, by default configuration, only 2 Remote Desktop Connections (RDPs) are allowed. If you need to change that setup, read the following instructions at

http://technet.microsoft.com/en-us/library/cc753380.aspx