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--- processing:start [2019/06/07 17:18] – [Conversion of the file series to EDF] matthias
+++ processing:start [2019/06/07 18:00] (current) – [Workflow: Getting a list of grains and their orientations] matthias
@@ Line 5: / Line 5: @@
 {{ ::processing:workflow.jpg?nolink&600 |}}
-===== Workflow for getting grains and their orientations (outline) =====
+===== Data collection =====
-The goal of this workflow is to get a list of grains and their specific orientations. If you want to check your workflow you can start with a simulation (see [[workflow_training|here]]. This outline is for dealing with real diffraction data consisting of a series of 2D diffraction images which was acquired during a 3D scan. More info on the experimental setup can be found [[dac_experiments:geometry|here]].
+Usually, the data is collected in synchrotron facilities by stepwise rotating the sample while the detector is acquiring diffraction images. For more information, click [[dac_experiments:geometry|here]].
-  - Perform a calibration to obtain the exact sample-detector distance and the exact beam center. This calibration is crucial since all further processing depends on it. You can use Dioptas or fit2D and Maud, for example.
-  - If necessary, convert your series of images to //EDF// format (click [[xray_data:convertfileseries|here]] for further information on that).
-  - Have a closer look at your images (with [[software:fabian|Fabian]] or Dioptas, for example). Throw out all bad images and replace them with empty or average images.
-  - Create median and average images.
-  - Refine the average image with any refinement software (for example, [[software:maud|Maud]]) to obtain the exact cell parameters of your sample material.
-  - Remove diamond spots (and shadow).
-  - Perform a [[software:peaksearch|PeakSearch]].
-  - In [[software:imaged11|ImageD11]] the found peaks are fitted to the parameters of the sample and experiment, followed by the calculation of the g-vectors.
-  - With the calculated g-vectors the grains will now be indexed, using [[software:grainspotter|GrainSpotter]].
-===== Workflow for getting grains and their orientations (full) =====
+===== Workflow: Training with simulated data =====
-==== Calibration of the standard ====
+Starting with real data might be complicated if you are a beginner in MGC. Training the actual workflow with simulated data can help you to verify if your workflow is correct. It also makes you familiar with the software. Pitfalls are better visible with artificial data.
-...
-==== Conversion of the file series to EDF ====
+But even when you are working with real data, you can compare your results with the outcome of the simulation to prove if they are reasonable.
-Most of the used software can work only with [[fileformat:edf|EDF]] images. Unfortunately, most of the beamlines don't provide their data in this format but in MarCCD (//.mccd//) or Tiff (//.tif//). To convert them, you can use one of the [[software:timelesstools|TIMEleSS tools]].
-==== Remove bad images ====
+[[processing:workflow_training|Click here to train your workflow with a simulated dataset.]]
-The removal and exchange of bad images is not a process which is done once and then finished. During the processing it may happen several times that you have to throw out an image which you considered all right in a previous step.\\
-**What is a bad image and why do they have to be removed?**\\
-A bad image is one where you have artefacts which cannot be removed by any software. Frequent examples are :
-{{ :processing:diamonddoublediffraction_anotee.png?nolink&400 |}}
+===== Workflow: Find out the phases in your sample and their cell parameters =====
+This step is actually not part of the MGC but a normal Rietveld refinement. However, it is a necessary step for further processing workflows.
-While the simulation is running you can already look at the images, which are already created. For this, open a new tab in the Konsole and open Fabian:
+===== Workflow: Getting a list of grains and their orientations =====
-  fabian.py
+This workflow will provide you with a list of grains, as well as an orientation of each single grain in your sample. [[processing:workflow_dac_data|Click here when you feel ready to rock]]
-This is convenient because you can already see at this point if your simulation works. And in case it does not, you can stop the simulation process right now and you don't need to wait until all images are created, which can take very long time. While you're at it, check also the O-matrix. You find it in Fabian under //Image// --> //Orientation//. Choose the one which is the same as in your input file.
-==== Experimental parameters ====
-From these peaks you can now fit the experimental parameters. To do this, open [[software:imaged11|ImageD11]] by typing the following to the Konsole:
-  ImageD11_gui.py
-To load the PeakSearch file click on //Transformation// --> //Load filtered peaks// and choose the //.flt// file from the separate folder with the processed data. Although the image is loaded, it is not plotted automatically, because there are two different ways of plotting. One plotting option is the 2D diffraction image which is similar to Fabian (y/z plot). The other possibility is a cake plot (tth/eta plot). Both options can be accessed by clicking on //Transformation//. Note that plotting both options at once is not making sense because the software is using the same scale for both images (which makes it look weird). To switch from one plot to the other just click on the //Clear// button (bottom of the window) and then plot the other one. //Clear// does only erase the plot, the data is still there.
-Before you check the plots you should enter the measurement parameters. Go to //Transformation// --> //Edit parameters// and enter all parameters for your sample. Some of them can be found in the calbration files of the beamline (such as the [[fileformat:poni|poni file]]). Remove all check marks from the vary boxes and press //Ok//.
-Next you can have a look at the //tth/eta plot//. Most of the peaks should appear to be on imaginary vertical lines. Zoom in and check, if these lines are completely vertical. If not, you might have strain in your sample. If the line looks like a sinus curve of exactly one period this is due to a wrong beam center. To fix this, go back to //Edit parameters// and activate the check marks for the //y-position// and //z-position// of the detector. Press //Ok// and click on //Fit// for several times until the spots don't move anymore. The imaginary lines should now be completely straight (if you don't have strain). If they are not, you can try to fit other parameters.
-At some point you can click on //Transformation// --> //Add unit cell peaks//. Red tick marks will appear which indicate the expected positions of the vertical lines. With this you can check whether your input parameters (cell parameters, detector distance, ...) were correct.
+===== ... =====
+More to come ...