User Tools
software:imagemath
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
software:imagemath [2018/06/23 14:06] matthias |
software:imagemath [2019/09/05 12:54] (current) smerkel |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== Evaluation of the background (Image Math) ====== | + | ====== ImageMath ====== |
| ===== What does the program do? ===== | ===== What does the program do? ===== | ||
| - | Image Math is a tool to calculate the average and the median of all the diffractograms. | + | ImageMath is a set of script to work on diffraction images. We use it to calculate the average and the median of all the diffractograms. |
| + | |||
| + | It was written by Gavin Vaughan at ESRF and is available on the old fable website: [[https://sourceforge.net/p/fable/code/HEAD/tree/ImageTools/trunk/Image/code/image_math.c]]. You have to install the whole //image// package to get it working. | ||
| + | |||
| + | In fact there is a small issue with it. S. Merkel did find a fix some years ago but does not remember what he did. He has a binary called image_math_petra that works. This should be fixed at some point... | ||
| + | |||
| + | ===== Installing Image Math ===== | ||
| + | |||
| + | ==== Necessary Hardware and Software ==== | ||
| + | First of all, you will need Linux, either as a separate harddrive (with lots of memory space) or as a virtual machine on your Windows/Apple computer. In case you are not familiar with Linux, ask your administrator for help and maybe do an online crash course to learn basic navigation and so on. | ||
| + | |||
| + | The next thing to do is to ask [[people:sebastienmerkel|S. Merkel]] for the binary file. It is called //image_math_petra.bin//. Sometimes //.bin// files are stopped by the firewall of the mailing program. In this case, try out another mailing program or use a cloud. | ||
| + | |||
| + | ==== Installation ==== | ||
| + | Save the binary file in the directory ///usr/local/bin//. To save the file there, type the following to the Konsole (You usually need root/administrator permission for this so make sure you have the password nearby): | ||
| + | sudo cp ../Downloads/image_math_petra.bin /usr/local/bin/ | ||
| + | and type in the root/admin password. Afterwards, check if the copying process worked by looking at the target directory /usr/local/bin/ (it is somewhere in the basis directory). | ||
| + | |||
| + | Next thing to do is to make the file executable. This works by typing the following to the Konsole (you have to be in the /usr/local/bin/ directory): | ||
| + | sudo chmod u+x image_math_petra.bin | ||
| + | If it looks like nothing happened, everything worked fine. | ||
| ===== Working with Image Math ===== | ===== Working with Image Math ===== | ||
| - | From the command line in the folder with the .edf files type image_math_petra [stem name] [first file] [last file] [operation] \\ \\ | + | From the command line in the folder with the //.edf// files type image_math_petra [stem name] [first file] [last file] [operation] \\ \\ |
| Example: | Example: | ||
| image_math_petra fcc_1_ 0 111 median | image_math_petra fcc_1_ 0 111 median | ||
| - | | ||
| - | The program will create three new files, which are named the same as your previous .edf images, just with an 'm' in the middle. | + | In case you have only the //.bin// file this won't work. You have to go to the folder where //image_math_petra.bin// is stored and type this to the Konsole: |
| + | sudo ./image_math_petra.bin /'directory'/.../'directory'/fcc_1_ 0 111 median | ||
| + | Make sure you get the path of the //.edf// images right. Otherwise //image_math_petra// will not find it. This second way is a bit inconvenient since you need the root password every time you want to perform the calculation. | ||
| - | fcc_1_m10000.edf (average) | + | The program will create three new files, which are named the same as your previous //.edf// images, just with an **m** in the middle. |
| + | * fcc_1_m10000.edf (average image) | ||
| + | * fcc_1_m20000.edf (median image) | ||
| + | * fcc_1_m30000.edf (trimean image) | ||
| - | fcc_1_m20000.edf (median) | + | ===== Visualizing images with the background removed ===== |
| - | + | ||
| - | fcc_1_m30000.edf (some other more sophisticated median) | + | |
| We proceed with the "normal" median (file no. 2). In [[software:fabian|Fabian]] go to //Image//, then to //Correction//, then to //Background Correction// and load the median file (in this example **fcc_1_m20000.edf**) | We proceed with the "normal" median (file no. 2). In [[software:fabian|Fabian]] go to //Image//, then to //Correction//, then to //Background Correction// and load the median file (in this example **fcc_1_m20000.edf**) | ||
| - | + | {{ :backgrouundsubstraction.png?400 | }} | |
| - | {{:backgrouundsubstraction.png?400|}} | + | |
software/imagemath.1529762802.txt.gz · Last modified: 2019/02/18 10:11 (external edit)
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: GNU Free Documentation License 1.3
