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--- evaluation:extractgrainsizes [2021/04/20 15:19] – [2. Convert to absolute grain sizes] matthias
+++ evaluation:extractgrainsizes [2021/06/24 10:00] (current) – [2. Convert to absolute grain sizes] matthias
@@ Line 62: / Line 62: @@
 === List of relative grain volumes ===
-The command line will show a list of relative grain volumes. If you chose the option ''-o'', it will also save this list in a file. Note that this file is necessary if you want to convert the relative grain sizes to absolute ones later.
+The command line will show a list of relative grain volumes. If you set the histogram option ''-HR'' to ''True'', you can force the script to calculate grain radii instead of grain volumes (This goes not only for the histogram but also for the list of grain sizes itself.) If you chose the option ''-o'', it will save this list in a file. Note that this output file is necessary if you want to convert the relative grain sizes to absolute ones later.
 === Histogram ===
@@ Line 71: / Line 71: @@
 Try this:
-  timelessRelToAbsGrainSize.py
+  timelessRelToAbsGrainSize.py myoutputfile.txt -H 1.5 -V 1.8 -r 56 -t 20 -i 76.2 -hist 60 -prop 0.85
+This command will:
+  - Read the output file of ''timelessGrainSizes.py''
+  - Convert the relative grain volumes into absolute grain volumes (in µm)
+  - Save the absolute grain volumes in a new file ''myoutputfile_abs.txt'' and
+  - Plot a histogram similar to the one shown above
+The explanation of the individual parameters is given in the help:
+<code>
+# Explanation of the parameters:
+grainsizelist:                          An output file from the "timelessExtractGrainSizes.py" script. Should be a regular text document
+-H & -V # beamsize_H and beamsize_V:    Horizontal and vertical dimension of the X-ray beam in $\mu$m. Necessary to calculate the illuminated sample volume.
+-r      # rotationrange:                Full rotation range used in the experiment in micrometer. Necessary to calculate the illuminated sample volume more accurately.
+-t      # samplethickness:              Thickness of the sample in micrometer. Necessary to calculate the illuminated sample volume.
+-i      # indexquality:                 Quality of the previous indexing process in percent. Used to account for the fact that not all grains were found during the indexing.
+-rad    # radius:                       Boolean operator that determines if grainsizelist consists of grain volumes or grain radii. True means volumes, False means radii.
+-hist   # histogram_bins:               Number of histogram bins you want to use. By default, no histogram is plotted.
+-prop   # proportion:                   Defines how much of the sample is your phase of interest. Can be between 0 and 1.
+</code>
+=== Estimation of the illuminated volume ===
+The entire conversion is based on the correct estimation of the volume that is illuminated by the X-rays. Normally, this would be a simple cuboid:
+  V = a * b * c
+where a, b and c are the gasket thickness and the dimensions of the X-ray beam.
+However, because the sample is rotated, the actual volume is larger: The actual illuminated volume of a rotated sample chamber is:
+  V_r = v * [d * h * cos(ω/2) + 0.5 * h^2 * tan(ω/2)]
+with
+  * v = beamsize parallel to the rotation axis (usually vertical)
+  * d = beamsize orthogonal to the rotation axis (usually horizontal)
+  * h = gasket thickness
+For a graphical explanation, see the following sketch:
+{{:evaluation:illuminated_volume_new.png?400|}}
+A quick calculation example shows the difference:
+  v = 2 µm
+  d = 2 µm
+  h = 20 µm
+  ω = 56°
+  V = 80 µm^3
+  V_r = 283 µm^3
+The example shows that the volume, which is illuminated by the X-rays, can increase drastically when the sample is rotated. Therefore, the accurate estimation of the illuminated volume is crucial for the determination of the precise conversion factor.
+=== Error estimation ===
+While the dimensions of the X-ray beam and the rotation angle are usually well known, the thickness of the gasket in a diamond-anvil cell experiment is less constrained. This is due to the fact that the initial indentation thickness is getting thinner as the pressure is increased during the experiment. Usually, the rate, at which this happens, is unknown. Measuring the actual gasket thickness after the experiment can help to model the thickness evolution throughout the experiment. This can, however, still only be an approximation of the true thickness.
-To be continued ...