Edited on 19-May-2023

4. Collect

4.1 Introduction

When pressing the "Collect"-button in the main window, the layout of the main window's buttons will be modified and you will obtain the following choices.

Menu Menu Choice Description
Collect Buttons Single Set Pops up the "Collect"-window for editing parameters of a single data set(see chapter 3.2)
Multiple Sets Pops up the "Collect"-window for editing parameters of multiple data sets(see chapter 3.3)
Index Crystal Pops up the "Collect"-window with data collection parameters specialized for indexing operations of single crystals(see chapter 3.4)
MAD Data Pops up the "Collect"-window with data collection parameters specialized for MAD data(see chapter 3.5)
Cancel Returns to the default layout of the main window

4.2 Single Set

Collect: Single Set

Most of the entries in this window should be self-explanatory and will be explained in the next chapters. When pushing the "Go"-button, the data collection will start using the programmed parameters. It is usually a good choice, to start the program with a clean imaging plate. Therefore, it is recommended to choose "Go/Erase first" if the imaging plate has not been scanned or erased for more than 60 minutes. The "Cancel"-button will bring you back to the default layout of the main window.

4.2.1 Directory, Image Root and Reference Image

With keyword "USE REFERENCE" in the configuration file, an additional field for "Reference image" is available starting with version 6.6 of the program. Here, you can enter the full name of a reference image. If the image resides in the directory given above, the full path is not required, but the entire image name, not just the root name, e.g. like shown in the figure:

Collect: Reference

When a valid reference image is given here, it will be applied to process images of the current data set as soon as they become available. Program mar345 for this purpose calls shell script "" which must be present in the executable search path. The script is called with parameters "-r reference_image" and "-i image_file", where reference_image is the name of the image entered here and image_file is the name of the image of the ongoing data collection. By default, the script calls program marreference which essentially subtracts the reference image from incoming images during the data collection. The original image is renamed to bck_image_file and kept in the data collection directory. The file processed by program marreference is called image_file and will be displayed automatically by program mar345 after processing has finished. This technique may play a role for special data collection situations. By subtracting reference images from diffraction images, the net diffraction of a sample will remain in the image assuming that the reference image is collected under EXACTLY the same conditions as the data collection image except for the presence of the sample. As is common for this technique, it is crucial that the reference image and the diffraction image to which it will be applied are on the same scale. If they are not, the resulting image may become useless. While it is possible to use special scaling algorithms to solve this problem, with program marreference we only supply only a simple program that will not do fancy scaling. Shell script may be edited to implement your own procedures that are potentially more clever than program marreference.

4.2.2 Scan Mode, Output Format and Collect Mode

4.2.3 Exposure Settings

Here is where you specify the parameters for controlling the exposures of the standard mar-goniostat.

An exposure consists of the following sequence of actions:

Please note, that when IGNORE BASE is set in the configuration file, a data collection is still possible. The mar345 controller will generate steps for the PHI motor and DISTANCE motor which does not interfere with the data collection. The motors do not need to be physically present. It is required, though, to provide an electrical feed back for the shutter. When the mar345 detector operates the local shutter, it sends a signal out but it watches the success of the operation. The controller needs to get a positive feedback that the shutter has successfully opened, otherwise it will generate an error. This can be done by shorting certain pins on the back of the scanner.

Instead of using the local shutter, it is possible to let the mar345 program cooperate with the MetalJet controller box manufactured by Marxperts. If there is no base attached (keyword IGNORE BASE), it is possible to use the MetalJet shutter directly for time controlled exposures (keywords METALJET ... and SHUTTER JET1). See 5.2.1 Input -> Configuration File -> Keywords for further details.

4.3 Multiple Sets

Collect: Multiple Sets

When using "Multiple Sets", the layout of the "Data collection parameters"-window will be slightly expanded by an area of buttons marked 1 to 4 and underneath those buttons a toggle button marked "Use". By pushing one of the numbered buttons of the "Selected sets", a complete set of parameters for a data collection may be programmed. Via the configuration file, the total number of programmable data sets may be modified. It defaults to 8 sets.

By pushing the "Go"-button, the data collections are going to start, but only those data collection sets will be carried out that have been explicitely marked as "Use". This feature allows you to keep parameters for typically used data collections, but select on-the-fly wether you actually want to use them now.

4.4 Index Crystal

Collect: Index Crystal

Index Crystal is a special way of collecting data with a PHI movement inbetween each image. This PHI movement is denominated "PHI increment". The purpose is to collect a small number of images at different positions in PHI. This is beneficial for determining accurate cell parameters when indexing single crystal data.

When using "Index Crystal", the layout of the "Data collection parameters"-window will be slightly changed. The text field "First image no." is replaced by the text field "PHI increment". The first image no. will always be 1. Before doing the next exposure, the PHI axis drives to a new value that is "PHI increment" degrees away from the previous image. The image no. for the new image is calculated as: previous image no. + PHI increment/Delta PHI. As an example, to collect 2 images that are 90 degrees apart from each other with a PHI oscillation of 1 degree each one will have to use a PHI increment of 89 degrees.

4.5 MAD Data

Collect: MAD Data

MAD Data is a special way of collecting data for maximizing anomalous signals. In this mode, the data collection is actually 2 blocks of data marked "A" and "B". Each block of data is a series of images that are contiguous in PHI. Inbetween set A and set B there is a PHI movement of 180 degrees.

Set A starts at "Starting PHI", set B at "Starting PHI" + 180 deg.. The first PHI-block of images will be in set A, the second one in set B, the third one also in set B, but at "Starting PHI + (images/block)* Delta-PHI + 180 deg.", the fourth one again in set A at "Starting PHI + (images/block)*Delta-PHI", etc..

When using "MAD Data", the layout of the "Data collection parameters"-window will be slightly changed. The text field "No. of images" is replaced by the text field "No. of PHI blocks". For each PHI-block the number of images has to be given in the field on the right. To obtain the total number of images to be collected, just multiply the number of PHI-blocks by the number of images per PHI-block. To alternate between both sets, use 1 image per block. Note, that the smaller the number of images per PHI-block the more PHI movements are required. For further illustration, use the Help-button in the window.

Collect: MAD Data: Help

4.6 Load, Save & Copy Parameters

4.6.1 Load Parameters

Collect: Load Parameters

The "Load Parameters"-window can be accessed by pushing the button "Load" in the upper left corner of the "Data collection parameters"-window.

Within this window, you may select a file with data collection parameters. The format of this file is described in chapter Parameter File of section Input. This feature comes handy for loading parameters typically used for collecting data of a certain sample and saves you lots of typing.

The default place where to store and to load parameter files from is $MARLOGDIR/sets

4.6.2 Save Parameters

Collect: Save Parameters

The "Save Parameters"-window can be accessed by pushing the button "Save" in the upper right corner of the "Data collection parameters"-window.

This window is used to store parameters from your current program session. You may may either save only the set that is currently in work or all sets at once. The format of this file is described in chapter Parameter File of section Input.

The default place where to store and to load parameter files from is $MARLOGDIR/sets

4.6.3 Copy Parameters

Edit: Copy Parameters

You may copy parameters from one data set into another data set. You may either copy parameters from current set into any other or copy parameters from any set into the current. This methods allows for quickly program multiple data sets with almost identical conditions. For this purpose, select from the option menu at the top of the "Data collection parameters"-window either "Copy params from" or "Copy params into" and then either one of sets 1 to 8 of multiple data sets or the single data set. Please note that at the time where you make your choice the data will immediately copied from the origin window to the destination window.

4.7 IuS Options

Edit: IuS options

The program version that supports Incoatec's IuS generator offers an additional choice in the "Single Set" and "Multiple Set" windows underneath the field for setting the distance. You have a choice for telling the X-ray source to lower power and go into STANDBY mode or turn the generator off alltogether at the end of the data collection. The default is to keep the X-ray source as is.