

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 Warning! foxtrot is only compatible with 64bits systems. 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!




 ---------
| Windows |
 ---------
Requirements: 
    Java (Oracle or OpenJDK) 8 64bits

STEP 0:
If you installed a too recent version of Java (9, 10, 11, etc.), foxtrot might not work properly.
Since Java 9, a lot of things changed in Java, and backward compatibility is no more fully assured.
Moreover, Oracle changed its licences concerning classic distributions of Java, so we advise you to download OpenJDK 8 64bits.
There are 2 possibilities:
- either foxtrot is your only Java application (see "Windows Installed Java case"),
- or you might have other Java application(s) that might need a more recent version of Java (see "Windows Standalone Java case")

If you have a doubt about your Java installed version, just launch foxtrot.bat.
It will tell you if your Java version is not the right one, or just work as expected if your Java is correct (unless your OS is too old).


=== Windows Installed Java case ===
STEP 1: If you have a too recent version of Java, first uninstall Java.

STEP 2:
- If you have a valid Oracle licence, download Java 8 64bits installer from Oracle website: https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html
- If you don't have a valid Oracle licence, download OpenJDK 8 installer from this website: https://adoptopenjdk.net/
You can use any JVM version, but OpenJ9 might give foxtrot better performances.

STEP 3: Execute the installer you just downloaded and install Java/OpenJDK 8.

STEP 4: Launch foxtrot.bat
===================================


=== Windows Standalone Java case ===
STEP 1: Download OpenJDK 8 64bits JRE (click on "Download JRE" button) from this website: https://adoptopenjdk.net/releases.html?variant=openjdk8#x64_win
You can use any JVM version, but OpenJ9 might give foxtrot better performances.

STEP 2: Unzip the downloaded file in a folder of your choice.

STEP 3: Edit foxtrot.bat with a good text editor, like Notepad++.
Search for the line containing REM SET JAVA_PATH=path\to\java\standalone\directory\bin
Uncomment the line by removing REM.
Replace path\to\java\standalone\directory by the path of the folder containing java. You must keep the final \bin.
Do not surround this path with double quotes (").
If your path is correct (bin included), you should find java.exe in matching directory.

STEP 4: Do the same modification in all .bat files in the resources\tools folder (you can copy and paste the modified line).

STEP 5: launch foxtrot.bat
====================================




 -------
| Linux |
 -------
Requirements:
 - Java 8 64bits
 - Python 2.7 with recent enough h5py module (tested with python 2.7.16 and h5py 2.9)
 - tifffile python module through line commande : pip install tifffile (tested with tifffile-2019.7.26)

STEP 0:
If you installed a too recent version of Java (9, 10, 11, etc.), foxtrot might not work properly.
Since Java 9, a lot of things changed in Java, and backward compatibility is no more fully assured.
Moreover, Oracle changed its licences concerning classic distributions of Java, so we advise you to download OpenJDK 8 64bits.
There are 2 possibilities:
- either foxtrot is your only Java application (see "Linux Installed Java case"),
- or you might have other Java application(s) that might need a more recent version of Java (see "Linux Standalone Java case")
In all cases:
- you will have to install Python 2.7 with recent enough h5py module (tested with python 2.7.16 and h5py 2.9).
  Debian/Ubuntu:
    sudo apt-get install python-h5py
- Please, make sure that foxtrot.sh, extractor.sh (located in python folder), and any ".sh" file in resources/tools folder, are executable.
If that's not the case: chmod +x <filename>

If you have a doubt about your Java installed version, just launch foxtrot.sh.
It will tell you if your Java version is not the right one, or just work as expected if your Java is correct (unless your OS is too old).


=== Linux Installed Java case ===
STEP 1: If you have a too recent version of Java, first uninstall Java.

STEP 2: Install java 8
  Debian/Ubuntu:
    sudo apt-get install openjdk-8-jre
  If, for some reason, you didn't get java 8, or previous step didn't work, update your distribution:
    sudo apt-get update
    sudo apt-get upgrade
  And then download required libraries again

STEP 3: Launch foxtrot.sh
=================================


=== Linux Standalone Java case ===
STEP 1: Download OpenJDK 8 64bits JRE (click on "Download JRE" button) from this website: https://adoptopenjdk.net/releases.html?variant=openjdk8#x64_linux
You can use any JVM version, but OpenJ9 might give foxtrot better performances.

STEP 2: Uncompress (tar xzvf) the downloaded .tar.gz file in a folder of your choice.

STEP 3: Edit foxtrot.sh.
Search for the line containing #JAVA_PATH=/path/to/java/standalone/directory/bin.
Uncomment the line by removing #.
Replace /path/to/java/standalone/directory by the path of the folder containing java. You must keep the final /bin.
If your path is correct (bin included), you should find executable java in matching directory.

STEP 4: Do the same modification in all .sh files in the resources/tools folder (you can copy and paste the modified line).

STEP 5: Launch foxtrot.sh
==================================




 -----
| Mac |
 -----
Requirements:
 - Java 8 (see STEP 3)
 - Python 2.7 with recent enough h5py module (tested with python 2.7.16 and h5py 2.9) (see STEP 1)
 - tifffile python module through line commande : pip install tifffile (tested with tifffile-2019.7.26)
 


STEP 0:
If you installed a too recent version of Java (9, 10, 11, etc.), foxtrot might not work properly.
Since Java 9, a lot of things changed in Java, and backward compatibility is no more fully assured.
Moreover, Oracle changed its licences concerning classic distributions of Java, so we advise you to download OpenJDK 8.
There are 2 possibilities:
- either foxtrot is your only Java application (see "Mac Installed Java case"),
- or you might have other Java application(s) that might need a more recent version of Java (see "Mac Standalone Java case")

In all cases:
STEP 1:
In order to have the python extractor working:
Install Anaconda (python 2.7) as suggested here: http://docs.h5py.org/en/latest/build.html

STEP 2: Please, make sure that foxtrot.command, extractor.sh (located in python folder), and any ".command" file in resources/tools folder, are executable.
If that's not the case: chmod +x <filename>

If you have a doubt about your Java installed version, just launch foxtrot.command.
It will tell you if your Java version is not the right one, or just work as expected if your Java is correct (unless your OS is too old).


=== Mac Installed Java case ===
STEP 3: If you have a too recent version of Java, first uninstall Java.
To do so, you will have to follow instructions detailed at these pages (follow both instructions):
- Uninstall Java/JRE: https://www.java.com/en/download/help/mac_uninstall_java.xml (section "Uninstall Oracle Java using the Terminal")
- Uninstall Java/JDK: https://docs.oracle.com/javase/8/docs/technotes/guides/install/mac_jdk.html#A1096903 (section "Uninstalling the JDK")

STEP 4:
- If you have a valid Oracle licence, download Java JDK 8 (not JRE) 64bits installer from Oracle website: https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
- If you don't have a valid Oracle licence, download OpenJDK JDK 8 (not JRE) installer from this website: https://adoptopenjdk.net/
You can use any JVM version, but OpenJ9 might give foxtrot better performances.

STEP 5: Execute the installer you just downloaded and install Java/OpenJDK 8.

STEP 6:
-> Launch foxtrot.command
===============================


=== Mac Standalone Java case ===
STEP 3: Download OpenJDK 8 64bits JRE (click on "Download JRE" button) from this website: https://adoptopenjdk.net/releases.html?variant=openjdk8#x64_mac
You can use any JVM version, but OpenJ9 might give foxtrot better performances.

STEP 4: Uncompress (tar xzvf) the downloaded .tar.gz file in a folder of your choice.

STEP 5: Edit foxtrot.command.
Search for the line containing #JAVA_PATH=/path/to/java/standalone/directory/bin.
Uncomment the line by removing #.
Replace /path/to/java/standalone/directory by the path of the folder containing java. You must keep the final /bin.
If your path is correct (bin included), you should find executable java in matching directory.

STEP 6: Do the same modification in all .command files in the resources/tools folder (you can copy and paste the modified line).

STEP 7: Launch foxtrot.command
================================




 -----
| All |
 -----
- To activate 2Theta, edit the python script (python/extractor.py) and comment lines 156 and 157
- You can customize your application parameters (like the context data folder), by changing the values in "User Parameters" section
