documents:100922imagej_cluster
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| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
| documents:100922imagej_cluster [2010/10/05 10:22] – kota | documents:100922imagej_cluster [2010/11/16 09:00] – kota | ||
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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 160: | Line 161: | ||
| ===== Automated Script (Only from within EMBL network) ===== | ===== Automated Script (Only from within EMBL network) ===== | ||
| - | Automated Script is available in ALMF server (clust5fullp.sh). With this script, you only need to invoke the script with two arguments. | + | Automated Script is available in the ALMF server (clust5fullp.sh). With this script, you only need to invoke the script with two arguments. |
| * arg[0]: full path to the directory containing image/stack files | * arg[0]: full path to the directory containing image/stack files | ||
| * arg[1]: name of the imageJ macro you want to apply. | * arg[1]: name of the imageJ macro you want to apply. | ||
| Line 177: | Line 178: | ||
| </ | </ | ||
| - | This script will create two new folders in the directory same as where the image directory is (*_job and *_proc). Processed images or stacks will be saved under *_proc. job reports will appear in your current directory where you executed the command. | + | This script will create two new folders in the directory same as where the image directory is (*_job and *_proc). Processed images or stacks will be saved under *_proc. |
| + | Besides, so-called | ||
| - | The script could be viwed in the link below: [[http:// | + | The script could be viewed |
| ===== Example Scripts ===== | ===== Example Scripts ===== | ||
documents/100922imagej_cluster.txt · Last modified: 2016/05/24 12:46 by 127.0.0.1