documents:100922imagej_cluster
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| documents:100922imagej_cluster [2010/10/01 14:34] – kota | documents:100922imagej_cluster [2016/05/24 12:46] (current) – external edit 127.0.0.1 | ||
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| * headless.jar | * headless.jar | ||
| * This .jar file manages to work with ImageJ headlessly. | * This .jar file manages to work with ImageJ headlessly. | ||
| - | * download headless.jar file from [[http:// | + | * accessible by / |
| + | * Otherwise, | ||
| * blobs.tif | * blobs.tif | ||
| - | * You could download this by Normal ImageJ (with-head, or GUI). [File -> Open Samples -> Blob]. Save it in the current directory /home/miura/test | + | * You could download this by Normal ImageJ (with-head, or GUI). [File -> Open Samples -> Blob]. Save it in the current directory /home/<your username> |
| * headlesstest.ijm | * headlesstest.ijm | ||
| - | * You must created this ImageJ macro file and save it in the current directory. See below. | + | * You must write an ImageJ macro file and save it in the current directory. See below. |
| * testpbs.sh | * testpbs.sh | ||
| - | * You must created this ImageJ macro file and save it in the current directory. See below. | + | * You must write a shell script |
| **Write an ImageJ macro** that does the actual processing. | **Write an ImageJ macro** that does the actual processing. | ||
| Line 33: | Line 34: | ||
| #PBS -N TestPBS | #PBS -N TestPBS | ||
| #PBS -l walltime=1: | #PBS -l walltime=1: | ||
| - | / | + | / |
| </ | </ | ||
| Some more explanation: | Some more explanation: | ||
| Line 60: | Line 61: | ||
| Using plugin is a bit tricky. In case of desktop ImageJ, what you need to install plugin is simply drug and drop .class or .jar files to plugins folder within imageJ folder. With headless mode, you need to do the following: | Using plugin is a bit tricky. In case of desktop ImageJ, what you need to install plugin is simply drug and drop .class or .jar files to plugins folder within imageJ folder. With headless mode, you need to do the following: | ||
| * explicitly state where the plugins folder resides by setting -ijpath. | * explicitly state where the plugins folder resides by setting -ijpath. | ||
| - | * all plugins must not be in jar. They all have to be class files. | + | * <del>all plugins must not be in jar. They all have to be class files.</ |
| - | * if you only have jar file, then you should open it by zip archiver and extract all class files. File hierarchy should be maintained within the plugin folder. | + | * <del>if you only have jar file, then you should open it by zip archiver and extract all class files. File hierarchy should be maintained within the plugin folder.</ |
| - | ... so the java command would look like this: | + | ... so the java command would look like this: Macro file " |
| < | < | ||
| - | / | + | cd ~ |
| + | |||
| + | / | ||
| </ | </ | ||
| - | and the plugins folder resides within /home/miura/test. | + | and the plugins folder resides within /g/almf/software/ |
| ===== Spreading Jobs with qsub ===== | ===== Spreading Jobs with qsub ===== | ||
| Line 158: | Line 163: | ||
| </ | </ | ||
| - | |||
| - | |||
| - | |||
| - | |||
| ===== Automated Script (Only from within EMBL network) ===== | ===== Automated Script (Only from within EMBL network) ===== | ||
| - | Automated Script is available, | + | Automated Script is available |
| + | * arg[0]: full path to the directory containing image/stack files | ||
| + | * arg[1]: name of the imageJ | ||
| - | [[http:// | ||
| - | |||
| - | lines to be changed are | ||
| < | < | ||
| - | 64 IJMACROPATH=" | + | sh /g/almf/software/ij/ |
| - | ... | + | |
| - | 67 IJMACRONAME=" | + | |
| </ | </ | ||
| - | Path to the macro and name of the macro file should be replaced according to your situation. | ||
| - | rename and save the script, and do | + | argument < |
| + | |||
| + | argument <Name of ImageJ Macro> is the file name of ImageJ macro, and **this file should be placed under / | ||
| + | |||
| + | For example, your command could be | ||
| < | < | ||
| - | sh < | + | sh / |
| </ | </ | ||
| - | argument < | + | This script will create two new folders in the directory same as where the image directory is (*_job and *_proc). Processed |
| + | Besides, so-called job reports (text files containing output messages) will appear in your current directory where you executed the command. | ||
| + | |||
| + | The script could be viewed in the link below: [[http:// | ||
| ===== Example Scripts ===== | ===== Example Scripts ===== | ||
documents/100922imagej_cluster.1285943672.txt.gz · Last modified: 2016/05/24 12:46 (external edit)