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--- software:imagemath [2018/06/23 12:38] – created matthias
+++ software:imagemath [2019/09/05 14:54] (current) – smerkel
@@ Line 1: / Line 1: @@
-====== Image Math ======
+====== ImageMath ======
-Image Math is a tool to calculate the average and the median of all the diffractograms.
+===== What does the program do? =====
-For this, navigate to the folder where the [[file:edf|.edf]] images are saved and type the following to the Konsole:
+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.
-    image_math_petra 'name stem' 'first number (usually 0)' 'last number' median
+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 =====
+From the command line in the folder with the //.edf// files type image_math_petra [stem name] [first file] [last file] [operation] \\ \\
+Example:
+  image_math_petra fcc_1_ 0 111 median
+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.
+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)
+===== Visualizing images with the background removed =====
+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 | }}
-The program will create three new files, which are named the same as your previous .edf images, just with an 'm' in the middle.