Recent changes to Linux

Linux modified by Lam Son

Lam Son — Thu, 26 Feb 2015 21:15:10 -0000

--- v5
+++ v6
@@ -4,6 +4,8 @@
     gcc
     boost-dev
     fftw3-dev
+    tinyXML
+    openCV
     subversion
     beautifull soup 4
     numpy
@@ -14,7 +16,7 @@
 On Debian, Ubuntu, etc. this can be done via

     :::sh
-    sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion python-bs4 python-numpy python-scipy python-numexpr python-pygraph
+    sudo apt-get install build-essential libboost-all-dev libfftw3-dev libtinyxml-dev libopencv-dev subversion python-bs4 python-numpy python-scipy python-numexpr python-pygraph

 For the C++ implementation, you will also need CImg.h in your include path.

Linux modified by Lam Son

Lam Son — Thu, 26 Feb 2015 09:21:07 -0000

--- v4
+++ v5
@@ -9,11 +9,12 @@
     numpy
     scipy
     numexpr
+    pygraph

 On Debian, Ubuntu, etc. this can be done via

     :::sh
-    sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion python-bs4 python-numpy python-scipy python-numexpr
+    sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion python-bs4 python-numpy python-scipy python-numexpr python-pygraph

 For the C++ implementation, you will also need CImg.h in your include path.

@@ -25,7 +26,7 @@
     :::sh
     svn co https://colloids.svn.sourceforge.net/svnroot/colloids/trunc ~/src/colloids

-Optimized C++ code can be compiled via
+Optimized C++ code can be compiled via.

     :::sh
     cd ~/src/colloids
@@ -33,13 +34,17 @@
     make
     make install

-The multiscale tracker  can be compiled via
+Note that most of it is rather old code, before I knew Python, and is now superseded by much lighter python implementation where only the critical parts are compiled. However, the implementation of the Crocker and Grier tracking algorithm is still of interest.
+
+The C++ version of the multiscale tracker can be compiled via

     :::sh
     cd ~/src/colloids/multiscale/Release
     make all
     make install

+It is much more recent code, highly optimized and required for most practical 3D tracking purposes (except if you have hundred of Gb of RAM and time to spare).
+
 To use the python implementation, you will need to set the PYTHONPATH environment variable so that it points to ~/src/colloids/python. On Ubuntu you can edit (or create) the file ~/.pam_environement and add (or edit) the line

     PYTHONPATH DEFAULT=${PYTHONPATH}:${HOME}/src/colloids/python

Linux modified by Lam Son

Lam Son — Thu, 26 Feb 2015 09:07:53 -0000

--- v3
+++ v4
@@ -20,13 +20,26 @@
 Setup and install
 ------------------

+You can obtain the last version of the code via subversion
+
     :::sh
     svn co https://colloids.svn.sourceforge.net/svnroot/colloids/trunc ~/src/colloids
+
+Optimized C++ code can be compiled via
+
+    :::sh
     cd ~/src/colloids
     ./configure --prefix=$HOME --with-boost --with-boost_program_options
     make
     make install

+The multiscale tracker  can be compiled via
+
+    :::sh
+    cd ~/src/colloids/multiscale/Release
+    make all
+    make install
+
 To use the python implementation, you will need to set the PYTHONPATH environment variable so that it points to ~/src/colloids/python. On Ubuntu you can edit (or create) the file ~/.pam_environement and add (or edit) the line

     PYTHONPATH DEFAULT=${PYTHONPATH}:${HOME}/src/colloids/python

Linux modified by Lam Son

Lam Son — Wed, 25 Feb 2015 18:29:37 -0000

--- v2
+++ v3
@@ -1,4 +1,5 @@
 Prerequisite
+------------------

     gcc
     boost-dev
@@ -14,8 +15,10 @@
     :::sh
     sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion python-bs4 python-numpy python-scipy python-numexpr

-You will also need CImg.h in your include path.
+For the C++ implementation, you will also need CImg.h in your include path.
+
 Setup and install
+------------------

     :::sh
     svn co https://colloids.svn.sourceforge.net/svnroot/colloids/trunc ~/src/colloids

Linux modified by Lam Son

Lam Son — Wed, 25 Feb 2015 18:27:46 -0000

--- v1
+++ v2
@@ -5,11 +5,14 @@
     fftw3-dev
     subversion
     beautifull soup 4
+    numpy
+    scipy
+    numexpr

 On Debian, Ubuntu, etc. this can be done via

     :::sh
-    sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion
+    sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion python-bs4 python-numpy python-scipy python-numexpr

 You will also need CImg.h in your include path.
 Setup and install

Linux modified by Lam Son

Lam Son — Wed, 25 Feb 2015 18:24:47 -0000

Prerequisite

gcc
boost-dev
fftw3-dev
subversion
beautifull soup 4

On Debian, Ubuntu, etc. this can be done via

sudo apt-get install build-essentials libboost-all-dev libfftw3-dev subversion

You will also need CImg.h in your include path.
Setup and install

svn co https://colloids.svn.sourceforge.net/svnroot/colloids/trunc ~/src/colloids
cd ~/src/colloids
./configure --prefix=$HOME --with-boost --with-boost_program_options
make
make install

To use the python implementation, you will need to set the PYTHONPATH environment variable so that it points to ~/src/colloids/python. On Ubuntu you can edit (or create) the file ~/.pam_environement and add (or edit) the line

PYTHONPATH DEFAULT=${PYTHONPATH}:${HOME}/src/colloids/python