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Difference between revisions of "Linux installation from source (Ubuntu)"
 
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{{Note|These instructions are mostly complete, but the Java part does not compile due to it not finding <code>jni.h</code> [[User:P.nanda|P.nanda]] 17:04, 23 August 2013 (PDT)
+
Intallation notes to install micro-manager from source on Ubuntu systems. These instructions can also be used without modifications for installations on [http://debian.org Debian systems] (tested on Debian Wheezy and Debian Jessy).
−
<br />To allow the build to find jni.h, the --with-javaincl flag to ./configure can be used. I haven't tested it on Ubuntu. --[[User:Mark Tsuchida|Mark Tsuchida]] ([[User talk:Mark Tsuchida|talk]]) 17:56, 25 September 2013 (PDT)}}
+
  
−
== Preparation ==
+
{{Note|These instructions are for Micro-Manager 1.4 and needs updates for Micro-Manager 2.0 (which uses JDK 8 and has source code on [https://github.com/micro-manager/micro-manager github] rather than in a subversion repository.}}
  
−
=== Install ImageJ ===
+
{{Note|This page has been updated for the build system changes of r13120, based on testing on Ubuntu 12.04 LTS.}}
  
−
[http://rsb.info.nih.gov/ij/download.html Download the Linux version of ImageJ] from the NIH website. From a terminal, unzip to <code>/usr/local/</code> and test that it runs:
+
See also: <code>doc/how-to-build.md</code> in the source tree.
 +
 
 +
= Preparation =
 +
 
 +
 
 +
== Install JDK ==
 +
 
 +
If you are building the Micro-Manager Java GUI, Java 1.6 or 1.7 is recommended[http://imagej.1557.x6.nabble.com/Java-error-when-compiling-a-plugin-tp5004378p5004386.html]. The simplest way is to use OpenJDK:
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
−
cd ~/Downloads/
+
sudo apt-get install openjdk-6-jdk
−
sudo unzip ij*-linux*.zip -d /usr/local/
+
−
sudo chmod +r /usr/local/ImageJ
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−
cd /usr/local/ImageJ/
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−
./jre/bin/java -jar ij.jar
+
 
</pre>}}
 
</pre>}}
  
−
=== Install JDK ===
+
(You can also use <code>openjdk-7-jdk</code>.)
  
−
If you are building the Micro-Manager Java GUI, Java 1.6 is recommended[http://imagej.1557.x6.nabble.com/Java-error-when-compiling-a-plugin-tp5004378p5004386.html].  Download and run <code>jdk-6*-linux-*.bin</code> per the [https://help.ubuntu.com/community/Java#JDK_or_JRE JDK Ubuntu instructions].  This file has to be fetched from Oracle's website since their licensing prohibits redistribution in Linux repositories.  [http://www.oracle.com/technetwork/java/javasebusiness/downloads/java-archive-downloads-javase6-419409.html#jdk-6u45-oth-JPR Download the latest jdk-6*-linux-*.bin] from the archives (you must click "Accept License Agreement").  It may be worth using [[#OpenJDK instead of Sun JDK]]
+
== Install ImageJ ==
  
−
In spite of using Sun JDK, Micro-Manager fails to compile:
+
[http://rsb.info.nih.gov/ij/download.html Download the Linux version of ImageJ] from the NIH website.  From a terminal, unzip to <code>/usr/local/</code>, and remove the embedded JRE, as we already have one installed.
  
−
<code>
+
{{MessageBox|1=Commandline|2=<pre>
−
make[1]: Entering directory `/home/andor/mm/micro-manager1.4/MMCoreJ_wrap'
+
 
−
/bin/bash ../libtool --tag=CXX  --mode=compile g++ -DPACKAGE_NAME=\"Micro-Manager\" -DPACKAGE_TARNAME=\"micro-manager\" -DPACKAGE_VERSION=\"1.4\" -DPACKAGE_STRING=\"Micro-Manager\ 1.4\" -DPACKAGE_BUGREPORT=\"info@micro-manager.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"micro-manager\" -DVERSION=\"1.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_DATE_TIME=/\*\*/ -DHAVE__USR_INCLUDE_ZLIB_H=1 -DHAVE_LIBDL=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DSTDC_HEADERS=1 -DHAVE_MEMSET=1 -I.   -I/usr/include -g -O -MT MMCoreJ_wrap.lo -MD -MP -MF .deps/MMCoreJ_wrap.Tpo -c -o MMCoreJ_wrap.lo MMCoreJ_wrap.cxx
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cd ~/Downloads/
−
libtool: compile:  g++ -DPACKAGE_NAME=\"Micro-Manager\" -DPACKAGE_TARNAME=\"micro-manager\" -DPACKAGE_VERSION=\"1.4\" "-DPACKAGE_STRING=\"Micro-Manager 1.4\"" -DPACKAGE_BUGREPORT=\"info@micro-manager.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"micro-manager\" -DVERSION=\"1.4\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_DATE_TIME=/**/" -DHAVE__USR_INCLUDE_ZLIB_H=1 -DHAVE_LIBDL=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DSTDC_HEADERS=1 -DHAVE_MEMSET=1 -I. -I/usr/include -g -O -MT MMCoreJ_wrap.lo -MD -MP -MF .deps/MMCoreJ_wrap.Tpo -c MMCoreJ_wrap.cxx  -fPIC -DPIC -o .libs/MMCoreJ_wrap.o
+
sudo unzip ij*-linux*.zip -d /usr/local/
−
MMCoreJ_wrap.cxx:160:17: fatal error: jni.h: No such file or directory
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sudo rm -rf /usr/local/ImageJ/jre
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compilation terminated.
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sudo chmod a+Xr /usr/local/ImageJ
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make[1]: *** [MMCoreJ_wrap.lo] Error 1
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</pre>}}
−
make[1]: Leaving directory `/home/andor/mm/micro-manager1.4/MMCoreJ_wrap'
+
−
make: *** [all-recursive] Error 1
+
−
</code>
+
  
−
=== Install Build Programs and Libraries ===
+
== Install Build Programs and Libraries ==
  
 
You will need a subversion client to checkout the source code, several libraries, and build tools.  Install them with:
 
You will need a subversion client to checkout the source code, several libraries, and build tools.  Install them with:
Line 40: Line 39:
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
−
sudo apt-get install subversion build-essential automake libtool \
+
sudo apt-get install subversion build-essential autoconf automake libtool \
−
                     libboost-all-dev zlib1g-dev swig
+
                     libboost-all-dev zlib1g-dev swig ant
 
</pre>}}
 
</pre>}}
  
 
You may also need to install additional packages (for cameras and special hardware).  See the full list in [[#Dependencies]]
 
You may also need to install additional packages (for cameras and special hardware).  See the full list in [[#Dependencies]]
  
−
=== Fetch Source Repositories ===
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== Fetch Source Repositories ==
  
 
Create a directory for the the subversion repositories, such as <code>~/mm</code>.  Besides the source tree, additional binary dependencies are stored in the <code>3rdpartypublic</code> repository.  The build scripts in the source tree assume <code>3rdpartypublic</code> is in the same parent folder level:
 
Create a directory for the the subversion repositories, such as <code>~/mm</code>.  Besides the source tree, additional binary dependencies are stored in the <code>3rdpartypublic</code> repository.  The build scripts in the source tree assume <code>3rdpartypublic</code> is in the same parent folder level:
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
−
 
 
mkdir ~/mm
 
mkdir ~/mm
 
cd ~/mm
 
cd ~/mm
−
svn co https://valelab.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
+
svn co https://valelab4.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
−
svn co https://valelab.ucsf.edu/svn/3rdpartypublic/
+
svn co https://valelab4.ucsf.edu/svn/3rdpartypublic/
 
</pre>}}
 
</pre>}}
  
Line 64: Line 62:
 
</pre>
 
</pre>
  
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Add the Beanshell and SwingX to the ImageJ plugins directory:
+
Subversion (svn) will likely complain saying that it cannot verify the https certificate. Typing **t** to temporarily trust the certificate allows to retrieve the repository.
  
−
{{MessageBox|1=Commandline|2=<pre>
+
Also, when retrieving large repository (like the 3rdpartypublic/ repository), svn can hung in the middle of the process, with an error message:
  
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cd ~/mm/3rdpartypublic/classext
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<pre>
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sudo cp bsh-2.0b4.jar swingx-0.9.5.jar /usr/local/ImageJ/plugins/
+
svn: REPORT de '/svn/3rdpartypublic/!svn/vcc/default':
 +
Could not read chunk delimiter: Secure connection truncated (https://valelab4.ucsf.edu)
 +
</pre>
 +
 
 +
This can be [http://stackoverflow.com/questions/4031845/svn-resuming-aborted-checkout#13789596 solved] by typing:
 +
 
 +
{{MessageBox|1=Commandline|2=
 +
<pre>
 +
svn cleanup 3rdpartypublic/
 +
svn update 3rdpartypublic/ # This command might be executed several times
 
</pre>}}
 
</pre>}}
  
−
Create a new micro-manager directory in /usr/lib/
+
= Building Micro-Manager =
 +
 
 +
== Create the Autotools files ==
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
−
sudo mkdir /usr/lib/micro-manager
+
cd ~/mm/micro-manager1.4
 +
./autogen.sh
 +
./configure --enable-imagej-plugin=/usr/local/ImageJ
 
</pre>}}
 
</pre>}}
  
−
== Building Micro-Manager ==
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== Download build dependencies ==
−
 
+
−
=== Create the Autotools files ===
+
−
 
+
−
<code>configure</code> uses the bundled version of ImageJ:
+
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
−
cd ~/mm/micro-manager1.4
+
make fetchdeps  # Required since SVN r14001-r14016
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./mmUnixBuild.sh
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−
./configure --with-imagej=/usr/local/ImageJ
+
 
</pre>}}
 
</pre>}}
  
−
=== Compile ===
+
== Compile ==
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
Line 99: Line 104:
 
</pre>}}
 
</pre>}}
  
−
=== Install ===
+
== Install ==
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
 
sudo make install
 
sudo make install
−
sudo ldconfig
 
 
</pre>}}
 
</pre>}}
  
−
== Post Install ==
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= Post Install =
  
−
=== Create the startup script ===
+
== Editing the startup script ==
  
−
Micro-Manager requires the path to <code>/usr/lib/micro-manager</code>. Create the 4 line Bash script below in <code>/usr/local/ImageJ</code> and save it as, say, <code>mmscript</code>.
+
A script named <code>mmimagej</code> will have been installed in <code>/usr/local/ImageJ</code>. You might want to edit its contents to pass extra flags to Java. You may also want to put this script in your <code>PATH</code>.
  
−
{{MessageBox|1=File: mmscript|2=<pre>
+
= Running Micro-Manager =
  
−
#!/bin/bash
+
Start Micro-Manager by typing:
−
cd /usr/local/ImageJ
+
−
export LD_LIBRARY_PATH=.:/usr/local/lib:/usr/lib/micro-manager:/usr/local/ImageJ
+
−
java -mx1200m \
+
−
    -Djava.library.path=/usr/lib/micro-manager:/usr/local/ImageJ \
+
−
    -Dplugins.dir=/usr/local/ImageJ \
+
−
    -cp /usr/local/ImageJ/ij.jar:usr/local/jdk1.5.0_04/lib/tools.jar \
+
−
      ij.ImageJ
+
−
</pre>}}
+
−
 
+
−
Make the script executable:
+
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
−
sudo chmod +x mmscript
+
/usr/local/ImageJ/mmimagej 2>&1 >/dev/null &
 
</pre>}}
 
</pre>}}
  
−
== Running Micro-Manager ==
+
To view the Core logging in the terminal while Micro-Manager is running, start simply as:
−
 
+
−
Start ImageJ with your new script:
+
  
 
{{MessageBox|1=Commandline|2=<pre>
 
{{MessageBox|1=Commandline|2=<pre>
  
−
./mmscript &
+
/usr/local/ImageJ/mmimagej
 
</pre>}}
 
</pre>}}
  
−
Run <code>Plugins > Micro-Manager > Micro-Manager Studio</code>
+
= Appendix =
−
 
+
−
== Appendix ==
+
  
−
=== Dependencies ===
+
== Dependencies ==
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 157: Line 147:
 
| GNU C++ || <code>build-essential</code>
 
| GNU C++ || <code>build-essential</code>
 
|-
 
|-
−
| GNU Autotools || <code>automake</code>
+
| GNU Autotools || <code>autoconf</code>, <code>automake</code>
 
|-
 
|-
 
| GNU Libtool || <code>libtool</code>
 
| GNU Libtool || <code>libtool</code>
Line 167: Line 157:
 
| Simplified Wrapper and Interface Library || <code>swig</code>
 
| Simplified Wrapper and Interface Library || <code>swig</code>
 
|-
 
|-
−
| Sun Java SDK || N/A - manually fetch from Oracle website
+
| OpenJDK || <code>openjdk-6-jdk</code> or <code>openjdk-7-jdk</code>
 
|-
 
|-
 
|colspan="2"  style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"| Optional Dependencies:
 
|colspan="2"  style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"| Optional Dependencies:
 +
|-
 +
| Python || <code>python-dev</code>, <code>python-numpy-dev</code>
 
|-
 
|-
 
| Firewire Camera Library || <code>libdc1394-*-dev</code>
 
| Firewire Camera Library || <code>libdc1394-*-dev</code>
 
|-
 
|-
 
| Open Source Computer Vision Library || <code>libopencv-dev</code>
 
| Open Source Computer Vision Library || <code>libopencv-dev</code>
 +
|-
 +
| GPhoto2 || <code>libgphoto2-2-dev</code>
 +
|-
 +
| FreeImagePlus (used by GPhoto device adapter) || <code>libfreeimage-dev</code>
 +
|-
 +
| libusb 0.1 || <code>libusb-dev</code>
 +
|-
 +
| Andor SDK 2/3 || N/A - request from Andor website
 
|}
 
|}
−
 
−
=== OpenJDK instead of Sun JDK ===
 
−
 
−
It may be possible to also use the distro-friendly OpenJDK (<code>default-jdk</code>) without too much effort. To start, you would have to patch the Micro-Manager <code>configure.in</code> file to find <code>jni.h</code>[https://bugzilla.redhat.com/show_bug.cgi?id=498964#c2] and possibly apply other fixes.
 
  
 
{{Programming_Sidebar}}
 
{{Programming_Sidebar}}

Latest revision as of 15:08, 12 March 2020

Intallation notes to install micro-manager from source on Ubuntu systems. These instructions can also be used without modifications for installations on Debian systems (tested on Debian Wheezy and Debian Jessy).

Note
These instructions are for Micro-Manager 1.4 and needs updates for Micro-Manager 2.0 (which uses JDK 8 and has source code on github rather than in a subversion repository.
Note
This page has been updated for the build system changes of r13120, based on testing on Ubuntu 12.04 LTS.

See also: doc/how-to-build.md in the source tree.

Preparation

Install JDK

If you are building the Micro-Manager Java GUI, Java 1.6 or 1.7 is recommended[1]. The simplest way is to use OpenJDK:

Commandline

sudo apt-get install openjdk-6-jdk

(You can also use openjdk-7-jdk.)

Install ImageJ

Download the Linux version of ImageJ from the NIH website. From a terminal, unzip to /usr/local/, and remove the embedded JRE, as we already have one installed.

Commandline

cd ~/Downloads/
sudo unzip ij*-linux*.zip -d /usr/local/
sudo rm -rf /usr/local/ImageJ/jre
sudo chmod a+Xr /usr/local/ImageJ

Install Build Programs and Libraries

You will need a subversion client to checkout the source code, several libraries, and build tools. Install them with:

Commandline

sudo apt-get install subversion build-essential autoconf automake libtool \
                     libboost-all-dev zlib1g-dev swig ant

You may also need to install additional packages (for cameras and special hardware). See the full list in #Dependencies

Fetch Source Repositories

Create a directory for the the subversion repositories, such as ~/mm. Besides the source tree, additional binary dependencies are stored in the 3rdpartypublic repository. The build scripts in the source tree assume 3rdpartypublic is in the same parent folder level:

Commandline
mkdir ~/mm
cd ~/mm
svn co https://valelab4.ucsf.edu/svn/micromanager2/trunk/ micro-manager1.4
svn co https://valelab4.ucsf.edu/svn/3rdpartypublic/

This creates 2 new folders in the mm directory: 

    ~/mm/micro-manager1.4
    ~/mm/3rdpartypublic

Subversion (svn) will likely complain saying that it cannot verify the https certificate. Typing **t** to temporarily trust the certificate allows to retrieve the repository.

Also, when retrieving large repository (like the 3rdpartypublic/ repository), svn can hung in the middle of the process, with an error message: 

svn: REPORT de '/svn/3rdpartypublic/!svn/vcc/default': 
Could not read chunk delimiter: Secure connection truncated (https://valelab4.ucsf.edu)

This can be solved by typing:

Commandline
svn cleanup 3rdpartypublic/
svn update 3rdpartypublic/ # This command might be executed several times

Building Micro-Manager

Create the Autotools files

Commandline

cd ~/mm/micro-manager1.4
./autogen.sh
./configure --enable-imagej-plugin=/usr/local/ImageJ

Download build dependencies

Commandline

make fetchdeps   # Required since SVN r14001-r14016

Compile

Commandline

make

Install

Commandline

sudo make install

Post Install

Editing the startup script

A script named mmimagej will have been installed in /usr/local/ImageJ. You might want to edit its contents to pass extra flags to Java. You may also want to put this script in your PATH.

Running Micro-Manager

Start Micro-Manager by typing:

Commandline

/usr/local/ImageJ/mmimagej 2>&1 >/dev/null &

To view the Core logging in the terminal while Micro-Manager is running, start simply as:

Commandline

/usr/local/ImageJ/mmimagej

Appendix

Dependencies

You need the following packages:
Name Equivalent Synaptic package name
Required Dependencies:
Subversion subversion
GNU C++ build-essential
GNU Autotools autoconf, automake
GNU Libtool libtool
Boost libraries libboost-all-dev
zlib compression library zlib1g-dev
Simplified Wrapper and Interface Library swig
OpenJDK openjdk-6-jdk or openjdk-7-jdk
Optional Dependencies:
Python python-dev, python-numpy-dev
Firewire Camera Library libdc1394-*-dev
Open Source Computer Vision Library libopencv-dev
GPhoto2 libgphoto2-2-dev
FreeImagePlus (used by GPhoto device adapter) libfreeimage-dev
libusb 0.1 libusb-dev
Andor SDK 2/3 N/A - request from Andor website
programming

APIs

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