1. Remove default OpenJDK

   1	sudo apt-get purge openjdk-\*

2. download jdk(containing jre) and tar.

3. add into /etc/profile

   1 2	JAVA_HOME="/home/newly/Program_Files/Java/jdk1.8.0_65" PATH="$PATH:$JAVA_HOME/jre/bin:$JAVA_HOME/bin"

4. set newly installed jdk as default jdk.

   1 2 3

   sudo update-alternatives --install "/usr/bin/java" "java" "$JAVA_HOME/bin/java" 1 sudo update-alternatives --install "/usr/bin/javac" "javac" "$JAVA_HOME/bin/javac" 1 sudo update-alternatives --install "/usr/bin/javaws" "javaws" "$JAVA_HOME/bin/javaws" 1

Locate OpenCV:

1
2
3

pkg-config --modversion opencv //version
pkg-config --cflags opencv //include file path
pkg-config --libs opencv //library path

Uninstall OpenCV:

1. go to the compile package and make uninstall
2. if cannot find the compile package, sudo find / -name "*opencv*" -exec rm -i {} \;

Install OpenCV:

For Windows: C++(Visual Studio)

1. Download latest OpenCV from http://sourceforge.net/projects/opencvlibrary/?source=typ_redirect.
2. Make a dir named build. Use cmake to generate OpenCV.sln in build.
3. Click OpenCV.sln and CMakeTargets->INSTALL->build. You can build it in both debug and release modes.
4. In the environmental variables, add D:\Program Files\OpenCV_3.0.0\build\install\x64\vc11 as OPENCV_DIR, add Path with %OPENCV_DIR%\bin.
5. Create a OpenCV project. C/C++->General->Additional Include Directories: $(OPENCV_DIR)\..\..\include
6. Linker->General->Additional Library Directories: $(OPENCV_DIR)\lib
7. Linker->Input->Additional Dependencies: copy all the lib files. *d.lib means debug mode.

Note that there may be some problems for visual studio to recognize the updated environmental variable. Try to restart the visual studio or recreate the project.

For Linux: install for C++

1. pre-install packages
   [compiler] sudo apt-get install build-essential
   [required] sudo apt-get install cmake git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev
   [optional] sudo apt-get install python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev
2. download the required version on https://sourceforge.net/projects/opencvlibrary/
3. make and install

   1 2 3 4 5

   mkdir build cd build cmake .. //cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local .. make sudo make install

Tips: if you want to install multiple versions of OpenCV, set CMAKE_INSTALL_PREFIX differently for different versions of OpenCV.

cmake -D CMAKE_BUILD_TYPE=RELEASE \
    -D CMAKE_INSTALL_PREFIX=/usr/local \
    -D INSTALL_PYTHON_EXAMPLES=ON \
    -D INSTALL_C_EXAMPLES=ON \
    -D OPENCV_EXTRA_MODULES_PATH=../opencv_contrib/modules \
    -D PYTHON_EXECUTABLE=/usr/bin/python \
    -D BUILD_EXAMPLES=ON ..

If want to turn off some modules, use -D BUILD_opencv_xfeatures2d=OFF

Switch between different versions of OpenCV:

switch from version 3.2 to version 2.4 shell

switch from version 2.4 to version 3.2 shell

For Linux: Python(Anaconda)

source activate tgt_env
conda install -c https://conda.binstar.org/menpo opencv
spyder

Then try import cv2

• Install gst-plugin

  1 2	sudo add-apt-repository ppa:ddalex/gstreamer sudo apt-get install gstreamer0.10-*

• Install gstffmpeg

  1 2 3

  sudo add-apt-repository ppa:mc3man/gstffmpeg-keep sudo apt-get update sudo apt-get install gstreamer0.10-ffmpeg

Remote-SSH: Open SSH Configuration File ~/.ssh/config

Host jump-box
HostName
User
Port

Host target-box
HostName
User
Port 22
ProxyCommand ssh -q -W %h:%p jump-box

Remote Explorer

For Windows

1. Download Java JDK from http://www.oracle.com/technetwork/java/javase/downloads/index.html and install. Note that JDK contains JRE. Modify the following environment variables:

   • add JAVAHOME D:\Program Files (x86)\Java\jdk1.7.051
   • add Path %JAVA_HOME%\bin;\%JAVA_HOME%\jre\bin;
   • add CLASSPATH %JAVA_HOME%\lib\tools.jar;%JAVA_HOME%\jre\lib\rt.jar

2. Download Eclipse from http://www.eclipse.org/downloads/ and click eclipse.exe

For Linux

1. Install JDK

   1 2 3 4

   sudo add-apt-repository ppa:webupd8team/java sudo apt-get update // depending on the needed java version sudo apt-get install openjdk-7-jdk or sudo apt-get install openjdk-8-jre openjdk-8-jdk

2. Download Eclipse and unpack

3. Create a new file eclipse.desktop in /usr/share/applications/ and add the below code

   1 2 3 4 5 6 7 8

   [Desktop Entry] Name=Eclipse Comment=Eclipse IDE Exec=/home/liniu/Program_Files/Eclipse/eclipse/eclipse Icon=/home/ivan/Eclipse/icon.xpm Categories=Application;Development;Java;IDE Type=Application Terminal=0

   and then run

   1	sudo desktop-file-install /usr/share/applications/eclipse.desktop

4. Add to the path: sudo ln -s /opt/eclipse/eclipse /usr/local/bin/

1. install by running the sh file
2. refer to the crack folder
3. After installation, create a shortcut
   a) sudo ln -s /usr/local/MATLAB/R2012a/bin/matlab /usr/bin/matlab
   b) copy the matlab.desktop to /usr/share/applications and matlab.png to /usr/share/icons.

Problem:

1. /tmp/mathworks……. permission denied

   1 2	$cd /Matlab.R2012a.UNIX/sys/java/jre/glnxa64/jre/bin chmod +x ./java

2. warning: usr/local/MATLAB/R2012a/bin/util/oscheck.sh: /lib/libc.so.6: not found

   1	sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6

Format

1. DICOM: (Digital Imaging and COmmunications in Medicine) meta info + raw data
2. nrrd: meta info (e.g., sizes, dimension, encoding, endian) + raw data

The meta info in nrrd mainly consists of the format of raw data while the meta info in DICOM contains the detailed information of patient, study, and series.
There exist matlab and python functions to read DICOM and nrdd files.

• MATLAB
  • DICOM: dicominfo, dicomread
  • nrrd: nrrdread
  • conversion from DICOM to nrrd: Dicom2nrrd

DICOM is generally a directory containing a sequence of slices while nrrd is a single file. The meta info of DICOM is more complicated and thus more error-prone than that of nrrd. Use DICOMPatcher to fix up DICOM files if errors occur when loading them to 3D Slicer.

Software

1. 3D Slicer: cross-platform, compatible with different formats (e.g., DICOM and nrrd), and convert between them.

2. Other softwares to view medical images: http://www.cabiatl.com/mricro/dicom/#links

1. run MATLAB using shellscript

   1	matlab -nodisplay -r "vid2frames('../data/regular_videos/', 'RiceCam106.MP4', '../data/frames/', '.png');exit"

2. VideoReader: NumberOfFrames is 0, cannot read frames.

   something is wrong with gstreamer, first get the right version of gstreamer (0.10 for MATLAB R2015b)

   • install gst-plugins

     1 2	sudo add-apt-repository ppa:ddalex/gstreamer sudo apt-get install gstreamer0.10-*

   • install gstffmpeg

     1 2 3

     sudo add-apt-repository ppa:mc3man/gstffmpeg-keep sudo apt-get update sudo apt-get install gstreamer0.10-ffmpeg

1. Problem: HTML cannot be rendered: the view has crashed awesomium: Awesomium.Windows.Controls.WebControl
   solution: Win+R to open regedit: change the following value from 1 to 0
   HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Lsa\FipsAlgorithmPolicy\Enabled

2. Problem: How to suppport Latex: MathJax?
   solution: tools > Options > Advanced > HTML Head Editor, add the following:

   1 2 3

   <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> </script>

   After adding the above, a simple example in the MarkDownPad: When $a \ne 0$, there are two solutions to $ax^2 + bx + c = 0$ and they are:

   $$x = {-b \pm \sqrt{b^2-4ac} \over 2a}$$

Tips:

1. insert image: <center><img src="http://....jpg" width=50% border="0"></center>

Installation:

• Ubuntu

  1 2	sudo apt-get install texlive-full sudo apt-get install texmaker

• Windows

  1. Install Miktex: https://miktex.org/download
  2. Install texmaker or texstudio

Extension:

1. Latexdiff
   • Install perl: http://www.perl.org/get.html
   • Download latexdiff.zip package from https://ctan.org/pkg/latexdiff
   • Unzip the latexdiff files and copy them to the Perl\perl\bin folder
   • latexdiff draft.tex revision.tex > diff.tex

Math input:

1. Include the definition.tex file with macro definition. \input{definition} in the main text.

2. Mathpix Snip can convert images to LaTeX.

3. IguanaTex allows you to insert LaTeX formulations in PowerPoint.

Tips:

1. Refer to this for commonly used symbols

2. Set color: \usepackage{xcolor} and \textcolor{red}{}

3. Setlength: set the indentation in paragraphs \setlength\parindent{0pt}; set the separation between paragraphs \setlength{\parskip}{10pt}; set column width in table \setlength{\tabcolsep}{12pt}; set the space below table/figure \setlength{\textfloatsep}{2pt}

4. Math annotation: expectation \usepackage{amsfonts} and \mathbb{E}; not imply: \usepackage{amssymb} and \nRightarrow

5. Encoding error: try adding \UseRawInputEncoding or \usepackage[utf8x]{inputenc} or \usepackage{newunicodechar} \newunicodechar{fi}{fi}