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mtex-toolbox · Oct 19, 2024 · bdd96c9 · bdd96c9
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diff --git a/images/BoundaryMisorientations_01.png b/images/BoundaryMisorientations_01.png
diff --git a/images/BoundaryMisorientations_02.png b/images/BoundaryMisorientations_02.png
diff --git a/images/BoundaryMisorientations_03.png b/images/BoundaryMisorientations_03.png
diff --git a/images/BoundaryMisorientations_04.png b/images/BoundaryMisorientations_04.png
diff --git a/images/BoundaryPlots_02.png b/images/BoundaryPlots_02.png
diff --git a/images/BoundaryPlots_03.png b/images/BoundaryPlots_03.png
diff --git a/images/BoundaryPlots_04.png b/images/BoundaryPlots_04.png
diff --git a/images/CrystalDirections_01.png b/images/CrystalDirections_01.png
diff --git a/images/CrystalDirections_02.png b/images/CrystalDirections_02.png
diff --git a/images/CrystalDirections_03.png b/images/CrystalDirections_03.png
diff --git a/images/CrystalDirections_04.png b/images/CrystalDirections_04.png
diff --git a/images/CrystalOperations_01.png b/images/CrystalOperations_01.png
diff --git a/images/CrystalOperations_02.png b/images/CrystalOperations_02.png
diff --git a/images/CrystalReferenceSystem_01.png b/images/CrystalReferenceSystem_01.png
diff --git a/images/CrystalReferenceSystem_02.png b/images/CrystalReferenceSystem_02.png
diff --git a/images/CrystalReferenceSystem_03.png b/images/CrystalReferenceSystem_03.png
diff --git a/images/EBSDFilling_06.png b/images/EBSDFilling_06.png
diff --git a/images/EBSDFilling_07.png b/images/EBSDFilling_07.png
diff --git a/images/EBSDTutorial_03.png b/images/EBSDTutorial_03.png
diff --git a/images/EBSDTutorial_04.png b/images/EBSDTutorial_04.png
diff --git a/images/EBSDTutorial_05.png b/images/EBSDTutorial_05.png
diff --git a/images/EBSDTutorial_07.png b/images/EBSDTutorial_07.png
diff --git a/images/GrainSpatialPlots.png b/images/GrainSpatialPlots.png
diff --git a/images/GrainSpatialPlots_01.png b/images/GrainSpatialPlots_01.png
diff --git a/images/GrainSpatialPlots_02.png b/images/GrainSpatialPlots_02.png
diff --git a/images/GrainSpatialPlots_03.png b/images/GrainSpatialPlots_03.png
diff --git a/images/GrainSpatialPlots_04.png b/images/GrainSpatialPlots_04.png
diff --git a/images/GrainSpatialPlots_05.png b/images/GrainSpatialPlots_05.png
diff --git a/images/GrainSpatialPlots_06.png b/images/GrainSpatialPlots_06.png
diff --git a/images/GrainSpatialPlots_07.png b/images/GrainSpatialPlots_07.png
diff --git a/images/GrainSpatialPlots_08.png b/images/GrainSpatialPlots_08.png
diff --git a/images/GrainSpatialPlots_09.png b/images/GrainSpatialPlots_09.png
diff --git a/images/GrainSpatialPlots_10.png b/images/GrainSpatialPlots_10.png
diff --git a/images/GrainSpatialPlots_11.png b/images/GrainSpatialPlots_11.png
diff --git a/images/MisorientationTheory_02.png b/images/MisorientationTheory_02.png
diff --git a/pages/documentation_matlab/BoundaryPlots.html b/pages/documentation_matlab/BoundaryPlots.html
@@ -63,17 +63,17 @@
 gB = grainBoundary
 
  Segments    length   mineral 1   mineral 2
-      883  27479 µm  notIndexed  Forsterite
-       35   1563 µm  notIndexed   Enstatite
+      875  27592 µm  notIndexed  Forsterite
+       37   1562 µm  notIndexed   Enstatite
        43   1361 µm  notIndexed    Diopside
-     1403  58204 µm  Forsterite  Forsterite
-      566  25123 µm  Forsterite   Enstatite
-      476  19543 µm  Forsterite    Diopside
-       23   1157 µm   Enstatite   Enstatite
-       89   3594 µm   Enstatite    Diopside
-       28   1250 µm    Diopside    Diopside
+     1398  56197 µm  Forsterite  Forsterite
+      654  26372 µm  Forsterite   Enstatite
+      522  20750 µm  Forsterite    Diopside
+       35   1296 µm   Enstatite   Enstatite
+      134   5802 µm   Enstatite    Diopside
+       23    951 µm    Diopside    Diopside
 {% endhighlight %}
-<p>We may use the <a href="grainBoundary.plot.html">plot</a> command to visualize the grain boundaries in the map</p>
+<p>We may use the <a href="grainBoundary.plot.html"><code class="language-plaintext highlighter-rouge">plot</code></a> command to visualize the grain boundaries in the map</p>
 {% highlight matlab %}
 % plot phases and grain boundaries
 plot(ebsd)
@@ -99,8 +99,9 @@ <h2 id="4">Specific boundaries</h2>
 ans = grainBoundary
 
  Segments   length   mineral 1   mineral 2
-       78  2929 µm  Forsterite  Forsterite
-        8   505 µm  Forsterite   Enstatite
+       81  3365 µm  Forsterite  Forsterite
+       16   720 µm  Forsterite   Enstatite
+        9   386 µm  Forsterite    Diopside
 {% endhighlight %}
 <center>
 {% include inline_image.html file="BoundaryPlots_02.png" %}
@@ -160,7 +161,7 @@ <h2 id="8">The misorientation axes in crystal coordinates</h2>
 
 {% highlight plaintext %}
 axes = Miller (Forsterite)
- size: 1403 x 1
+ size: 1398 x 1
 {% endhighlight %}
 <center>
 {% include inline_image.html file="BoundaryPlots_06.png" %}
@@ -203,13 +204,13 @@ <h2 id="10">The misorientation axes in specimen coordinates</h2>
 gB_red = grainBoundary
 
  Segments    length   mineral 1   mineral 2
-      281  11571 µm  Forsterite  Forsterite
+      280  11373 µm  Forsterite  Forsterite
 
 ori = orientation (Forsterite → xyz)
-  size: 281 x 2
+  size: 280 x 2
 
 axes = vector3d
- size: 281 x 1
+ size: 280 x 1
 {% endhighlight %}
 <center>
 {% include inline_image.html file="BoundaryPlots_08.png" %}

diff --git a/pages/documentation_matlab/CrystalDirections.html b/pages/documentation_matlab/CrystalDirections.html
@@ -69,7 +69,18 @@ <h2 id="1">Crystal Lattice Directions</h2>
 <center>
 {% include inline_image.html file="CrystalDirections_01.png" %}
 </center>
-<p>Note that MTEX by default aligns spherical projections of crystal directions such that the b-axis points towards east and the z-axis points out of the plane. This behaviour can be changed by the commands <code class="language-plaintext highlighter-rouge">plota2east</code>, <code class="language-plaintext highlighter-rouge">plota2north</code>, <code class="language-plaintext highlighter-rouge">plota2west</code>, <code class="language-plaintext highlighter-rouge">plota2south</code>, <code class="language-plaintext highlighter-rouge">plotb2east</code>, <code class="language-plaintext highlighter-rouge">plotb2north</code>, <code class="language-plaintext highlighter-rouge">plotb2west</code>, <code class="language-plaintext highlighter-rouge">plotb2south</code>, or <code class="language-plaintext highlighter-rouge">plotaStar2East</code>.</p>
+<p>Note that for triclinic and monoclinic symmetries MTEX aligns spherical projections of crystal directions such that the b-axis points towards east and c* points out of the plane. This behavior can be changed by altering the <a href="plottingConvention.plottingConvention.html">plotting convention</a> stored in <code class="language-plaintext highlighter-rouge">cs.how2plot</code>. E.g. we might want to have the a-axis to point to east</p>
+{% highlight matlab %}
+% change the plotting convention
+cs.how2plot.east = cs.aAxis;
+
+plot(m,'labeled','grid')
+
+annotate([a,b,c],'label',{'a','b','c'},'backgroundcolor','w','textAboveMarker')
+{% endhighlight %}
+<center>
+{% include inline_image.html file="CrystalDirections_02.png" %}
+</center>
 <h2 id="6">Crystal Lattice Planes</h2>
 <p>A crystal lattice plane \((hkl)\) is commonly described by its normal vector \(\vec n = h \cdot \vec a^* + k \cdot \vec b^* + \ell \cdot \vec c^*\) where \(\vec a^*\), \(\vec b^*\) and \(\vec c^*\) describe the reciprocal crystal coordinate system. In MTEX a lattice plane is defined by</p>
 {% highlight matlab %}
@@ -92,7 +103,7 @@ <h2 id="6">Crystal Lattice Planes</h2>
 hold off
 {% endhighlight %}
 <center>
-{% include inline_image.html file="CrystalDirections_02.png" %}
+{% include inline_image.html file="CrystalDirections_03.png" %}
 </center>
 <p>Note that for non Euclidean crystal frames uvw and hkl notations usually lead to different directions.</p>
 <h2 id="9">Trigonal and Hexagonal Convention</h2>
@@ -123,7 +134,7 @@ <h2 id="9">Trigonal and Hexagonal Convention</h2>
   1  1 -2  3
 {% endhighlight %}
 <center>
-{% include inline_image.html file="CrystalDirections_03.png" %}
+{% include inline_image.html file="CrystalDirections_04.png" %}
 </center>
 <p>In order to switch the output format, e.g. from UVTW to uvw do</p>
 {% highlight matlab %}

diff --git a/pages/documentation_matlab/EBSDKAM.html b/pages/documentation_matlab/EBSDKAM.html
@@ -45,11 +45,7 @@ <h2 id="2">A Deformed Ferrite Specimen</h2>
 {% highlight matlab %}
 mtexdata ferrite
 
-[grains,ebsd.grainId] = calcGrains(ebsd('indexed'));
-% remove one-three pixel grains
-ebsd(grains(grains.grainSize <= 3)) = [];
-[grains,ebsd.grainId] = calcGrains(ebsd('indexed'));
-
+[grains,ebsd.grainId] = calcGrains(ebsd('indexed'),'minPixel',3);
 grains = smooth(grains,5);
 
 plot(ebsd('indexed'),ebsd('indexed').orientations)

diff --git a/pages/documentation_matlab/GND.html b/pages/documentation_matlab/GND.html
@@ -49,13 +49,7 @@
 <p>In the next step we reconstruct grains, remove all grains with less then 5 pixels and smooth the grain boundaries.</p>
 {% highlight matlab %}
 % reconstruct grains
-[grains,ebsd.grainId] = calcGrains(ebsd,'angle',5*degree);
-
-% remove small grains
-ebsd(grains(grains.grainSize<=5)) = [];
-
-% redo grain reconstruction
-[grains,ebsd.grainId] = calcGrains(ebsd,'angle',2.5*degree);
+[grains,ebsd.grainId] = calcGrains(ebsd,'angle',2.5*degree,'minPixel',6);
 
 % smooth grain boundaries
 grains = smooth(grains,5);
@@ -86,9 +80,9 @@ <h2 id="3">Data cleaning</h2>
 <center>
 {% include inline_image.html file="GND_03.png" %}
 </center>
-<p>We observe that the data are quite noisy. As noisy orientation data lead to overestimate the GND density we apply sime denoising techniques to the data.</p>
+<p>We observe that the data are quite noisy. As noisy orientation data lead to overestimating the GND density we first have to denoise the orientation data.</p>
 {% highlight matlab %}
-% denoise orientation data
+% define the denoising filter
 F = halfQuadraticFilter;
 
 ebsd = smooth(ebsd('indexed'),F,'fill',grains);
@@ -134,7 +128,7 @@ <h2 id="5">The incomplete curvature tensor</h2>
  -11.952  17.293     NaN
 {% endhighlight %}
 <h2 id="6">The components of the curvature tensor</h2>
-<p>As expected the curvature tensor is NaN in the third column as this column corresponds to the directional derivative in z-direction which is usually unknown for 2d EBSD maps.</p>
+<p>As expected the curvature tensor is NaN in the third column as this column corresponds to the directional derivative in z-direction which is usually unknown for 2d-EBSD maps.</p>
 <p>We can access the different components of the curvature tensor with</p>
 {% highlight matlab %}
 kappa12 = kappa{1,2};
@@ -196,7 +190,7 @@ <h2 id="8">The incomplete dislocation density tensor</h2>
      NaN     NaN  -2.649
 {% endhighlight %}
 <h2 id="10">Crystallographic Dislocations</h2>
-<p>The central idea of Pantleon is that the dislocation density tensor is build up by single dislocations with different densities such that the total energy is minimum. Depending on the attomic lattice different dislocattion systems have to be considered. In present case of a body centered cubic (bcc) material 48 edge dislocations and 4 screw dislocations have to be considered. Those principle dislocations are defined in MTEX either by their Burgers and line vectors or by</p>
+<p>The central idea of Pantleon is that the dislocation density tensor is build up by single dislocations with different densities such that the total energy is minimum. Depending on the atomic lattice different dislocattion systems have to be considered. In present case of a body centered cubic (bcc) material 48 edge dislocations and 4 screw dislocations have to be considered. Those principle dislocations are defined in MTEX either by their Burgers and line vectors or by</p>
 {% highlight matlab %}
 dS = dislocationSystem.bcc(ebsd.CS)
 {% endhighlight %}
@@ -327,7 +321,7 @@ <h2 id="12">The Energy of Dislocations</h2>
   1.1717  0.5858 -0.5858
  -1.1717 -0.5858  0.5858
 {% endhighlight %}
-<p>Note that the unit of this tensors is the same as the unit used for describing the length of the unit cell, which is in most cases Angstrom (au). Furthremore, we observe that the tensor is given with respect to the crystal reference frame while the dislocation densitiy tensors are given with respect to the specimen reference frame. Hence, to make them compatible we have to rotate the dislocation tensors into the specimen reference frame as well. This is done by</p>
+<p>Note that the unit of this tensors is the same as the unit used for describing the length of the unit cell, which is in most cases Angstrom (au). Furthermore, we observe that the tensor is given with respect to the crystal reference frame while the dislocation density tensors are given with respect to the specimen reference frame. Hence, to make them compatible we have to rotate the dislocation tensors into the specimen reference frame as well. This is done by</p>
 {% highlight matlab %}
 dSRot = ebsd.orientations * dS
 {% endhighlight %}
@@ -338,7 +332,7 @@ <h2 id="12">The Energy of Dislocations</h2>
  screw dislocations: 5144 x 4
 {% endhighlight %}
 <h2 id="15">Fitting Dislocations to the incomplete dislocation density tensor</h2>
-<p>Now we are ready for fitting the dislocation tensors to the dislocation densitiy tensor in each pixel of the map. This is done by the command <a href="curvatureTensor.fitDislocationSystems.html">fitDislocationSystems</a>.</p>
+<p>Now we are ready for fitting the dislocation tensors to the dislocation density tensor in each pixel of the map. This is done by the command <a href="curvatureTensor.fitDislocationSystems.html"><code class="language-plaintext highlighter-rouge">fitDislocationSystems</code></a>.</p>
 {% highlight matlab %}
 [rho,factor] = fitDislocationSystems(kappa,dSRot);
 {% endhighlight %}
@@ -351,13 +345,13 @@ <h2 id="15">Fitting Dislocations to the incomplete dislocation density tensor</h
 % the restored dislocation density tensors
 alpha = sum(dSRot.tensor .* rho,2);
 
-% we have to set the unit manualy since it is not stored in rho
+% we have to set the unit manually since it is not stored in rho
 alpha.opt.unit = '1/um';
 
 % the restored dislocation density tensor for pixel 2
 alpha(2)
 
-% the dislocation density dervied from the curvature in pixel 2
+% the dislocation density derived from the curvature in pixel 2
 kappa(2).dislocationDensity
 {% endhighlight %}
 
@@ -413,7 +407,7 @@ <h2 id="15">Fitting Dislocations to the incomplete dislocation density tensor</h
 {% include inline_image.html file="GND_06.png" %}
 </center>
 <h2 id="19">The total dislocation energy</h2>
-<p>The unit of the densities <code class="language-plaintext highlighter-rouge">h</code> in our example is 1/um * 1/au where 1/um comes from the unit of the curvature tensor an 1/au from the unit of the Burgers vector. In order to transform <code class="language-plaintext highlighter-rouge">h</code> to SI units, i.e., 1/m^2 we have to multiply it with 10^16. This is exactly the values returned as the second output <code class="language-plaintext highlighter-rouge">factor</code> by the function <a href="curvatureTensor.fitDislocationSystems.html">fitDislocationSystems</a>.</p>
+<p>The unit of the densities <code class="language-plaintext highlighter-rouge">h</code> in our example is 1/um * 1/au where 1/um comes from the unit of the curvature tensor an 1/au from the unit of the Burgers vector. In order to transform <code class="language-plaintext highlighter-rouge">h</code> to SI units, i.e., 1/m^2 we have to multiply it with 10^16. This is exactly the values returned as the second output <code class="language-plaintext highlighter-rouge">factor</code> by the function <a href="curvatureTensor.fitDislocationSystems.html"><code class="language-plaintext highlighter-rouge">fitDislocationSystems</code></a>.</p>
 {% highlight matlab %}
 factor
 {% endhighlight %}
@@ -439,9 +433,6 @@ <h2 id="19">The total dislocation energy</h2>
 <center>
 {% include inline_image.html file="GND_07.png" %}
 </center>
-{% highlight matlab %}
-plotx2east
-{% endhighlight %}
 </div>
 </body>
 </html>