At the Synchrotron
1. Download frames
On the MX windows CrysalisPro processing box, log in via these credientials:
User: mxuser
Password: Beam109Line
via filezilla or similar program, download the frames of the experiment. Instructions
They are in .h5 files, each of which contains 200 egier frames (20 degrees usually).
/data/mx/EPN/frames/$username/d
where $EPN and $username are the experiment number and the user name, respectively.
You will need each of the .h5 files, including the master file, for each experiment.
Make a new folder for each dataset you are processing. If you want to process more than one wedge of data at a time, put all of the frames in the same folder.
At Home
1. Download frames
Via filezilla or similar program, download the frames of the experiment. Instructions
Frames in folder: /data/mx/EPN/frames/$username/d
where $EPN and $username are the experiment number and the user name, respectively.
Frames are in .h5 files, each of which contains 200 eiger frames (20 degrees).
You will need each of the .h5 files, including the master file, for each experiment.
It is a good idea to make a new folder for each collection, if you didn't do this during data collection. If you want to process more than one wedge of data at a time, put all of the frames in the same folder.
2. Convert h5 files to cbf (on windows computer at MX1)
On the desktop, open the eiger2cbf_GUI.py shortcut
Fill in the boxes with information about your frames. If you are going to import more than one wedge of data into CAP, you will need to add the wedge number to the end of your output file prefix. Eg, for wedge 1, name the output “output_1” and for wedge 2, name it “output_2”. This means that CAP will read them in as runs 1 and 2 automatically.
Click start. The frames will start converting. When an info box pops up saying “Program completed successfully!”, your frames are ready to open with CrysalisPro. If you are doing more than one wedge/run, you will need to convert each one individually. You can click “Edit” to select the master file for the next run and give it the subsequent wedge name in the output prefix field.
Optional:
If you want to run eiger2cbf manually so you can select which frames to convert, eiger2cbf is in the PATH, so open a terminal and type eiger2cbf. See eiger2cbf GitHub for instructions.
2. Convert h5 files to cbf (at home)
Things you will need:
eiger2cbf_spawn.py script
eiger2cbf. Download directly from github, or get the exectuable from google drive.
Python 3.8 or above)
Option 1: Via terminal
In the folder for a collection/dataset:
Open a terminal
python eiger2cbf_spawn.py [name of master h5 file] [number of instances to spawn] [filename stem for CBF]
Unless eiger2cbf_spawn.py is in the same folder, you will need to include the path to it in the command.
In general, use 17 instances to spawn. If you add test to the end of the above command, it will tell you the fastest number of instances to spawn.
If you are going to import more than one wedge of data into CAP, you will need to add the wedge number to the end of the filename stem for CBF. Eg, for wedge 1, enter “output_1” and for wedge 2, name it “output_2”. This means that CAP will read them in as runs 1 and 2 automatically.
For example:
python "C:\Users\Documents\eiger2cbf\eiger2cbf_spawn.py" Thr_1_7s_Om180_K0_P0_0018_master.h5 17 Thr_1_7s_1
Option 2: Via GUI
You will also need a script which launches a GUI.
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For this GUI to work, you will also need:
The Gooey package for python, which you can download via pip:https://pypi.org/project/Gooey/
The eiger2cbf_spawn.py script saved to your C drive (or you can edit this in the eiger2cbf_GUI.py directly)
To run the GUI, run eiger2cbf_GUI.py and it should pop up with a GUI. If it doesn’t, there is an error with the script. See instructions for using the GUI to the left.