grain3d docu

pages/documentation_matlab/Grains3D.html

@@ -23,39 +23,34 @@
 <div>
 <!--introduction-->
 <!--/introduction-->
-<p>grain3d is a structure to store 3D grain data. At the moment 3d data is usually obtained from <a href="NeperInterface.html">Neper tessellations</a> or triangulated Dream3d data sets.</p>
+<p>Variables of type <a href="grain3d.grain3d.html">grain3d</a> store 3D grain data. At the moment 3d grains can be imported from &lt;NeperInterface.html Neper% &gt; or from Dream3d.</p>
 <h2 id="2">Grain sets from Dream3d</h2>
 {% highlight matlab %}
 grains = grain3d.load(fullfile(mtexDataPath,'EBSD','SmallIN100_MeshStats.dream3d'));
 
 % for triangulated data sets it may be useful to plot them without lines
 plot(grains,grains.meanOrientation,'LineStyle','none')
+
+how2plot = plottingConvention;
+how2plot.outOfScreen = vector3d(-10,-5,2);
+how2plot.east = vector3d(1,-2,0);
+setCamera(how2plot)
 {% endhighlight %}
 <center>
 {% include inline_image.html file="Grains3D_01.png" %}
 </center>
-<h2 id="3">Plot the normal directions of one grain</h2>
+<p>Similarly as with two dimensional grains we can select individual grains by arbitrary constraints. For instance we can find the largest grain by</p>
 {% highlight matlab %}
-grains = grains(1)
-dir = grains.I_GF(1,:)' .* grains.boundary.N % flip according to I_GF
-quiver(grains.boundary,dir)
-plot(grains)
+% index of the grain with the largest volume
+[~,id] = max(grains.volume)
+
+plot(grains(id),grains(id).meanOrientation)
+setCamera(how2plot)
 {% endhighlight %}
 
 {% highlight plaintext %}
-grains = grain3d
-
- Phase  Grains  Volume  Mineral  Symmetry  Crystal reference frame
-     2       1      16  unknown       622       X||a*, Y||b, Z||c*
-
- boundary faces: 748
-
- Id   Phase   Pixels      meanRotation
-  1       2        1   (207°,35°,319°)
-
-
-dir = vector3d
- size: 748 x 1
+id =
+   146
 {% endhighlight %}
 <center>
 {% include inline_image.html file="Grains3D_02.png" %}
@@ -67,16 +62,19 @@ <h2 id="4">Grain sets from Neper</h2>
 % set up the communication with Neper
 job = neperInstance
 
-% define crystal symmetry
-cs = loadCIF('Cu-Copper.cif');
+% define a texture
+cs = crystalSymmetry.load('quartz.cif','color','lightblue');
+odf = fibreODF(cs.cAxis,vector3d(1,1,1));
 
-% some odf in brass orientation
-odf = unimodalODF(orientation.brass(cs));
 numGrains=100;
+grains = job.simulateGrains(odf,numGrains,'silent')
 
-grains3 = job.simulateGrains(odf,numGrains)
 % or you can load an existing tessellation file
 %grains3 = grain3d.load('allgrains.tess','CS',cs)
+
+% colorize by mean orientation
+plot(grains,grains.meanOrientation,'micronbar','off')
+setCamera(how2plot)
 {% endhighlight %}
 
 {% highlight plaintext %}
@@ -91,255 +89,82 @@ <h2 id="4">Grain sets from Neper</h2>
       fileName2d: '2dslice'
       fileName3d: 'allgrains'
         filePath: '/tmp/neper/'
-
-========================    N   e   p   e   r    =======================
-Info   : A software package for polycrystal generation and meshing.
-Info   : Version 4.9.1-4
-Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
-Info   : Running on 12 threads.
-Info   : <https://neper.info>
-Info   : Copyright (C) 2003-2022, and GNU GPL'd, by Romain Quey.
-Info   : No initialization file found (`/home/hielscher/.neperrc').
-Info   : ---------------------------------------------------------------
-Info   : MODULE  -T loaded with arguments:
-Info   : [ini file] (none)
-Info   : [com line] -n 100 -id 1 -morpho graingrowth -domain cube(1,1,1)
-         -morphooptistop itermax=1000 -oricrysym m-3m -ori
-         file(/tmp/neper/ori_in.txt) -statpoly faceeqs -o
-         /tmp/neper/allgrains -oridescriptor rodrigues -oriformat plain
-         -format tess,ori
-Info   : ---------------------------------------------------------------
-Info   : Reading input data...
-Warning:   - Option `-oricrysym' will be removed in a future version.  Use `-crysym` instead.
-Info   : Creating domain...
-Info   : Creating tessellation...
-Info   :   - Setting seeds... 100%
-Info   :   - Running tessellation...
-Info   :     > Initial solution: f   =2.806198409
-Info   :     > Iteration   1000: fmin=0.566500872 f=0.566500872
-Info   :     > Final   solution: f   =0.566500872
-Info   :     > Final solution  : f   =0.566500872 (1001 iterations)
-Info   :     > Reached `itermax' criterion.
-Info   : Generating crystal orientations...
-Info   :     [i] Parsing file `/tmp/neper/ori_in.txt'...
-Info   :     [i] Parsed file `/tmp/neper/ori_in.txt'.
-Info   : Writing results...
-Info   :     [o] Writing file `/tmp/neper/allgrains.tess'...
-Info   :     [o] Wrote file `/tmp/neper/allgrains.tess'.
-Info   :     [o] Writing file `/tmp/neper/allgrains.ori'...
-Info   :     [o] Wrote file `/tmp/neper/allgrains.ori'.
-Info   : Writing statistics...
-Info   :     [o] Writing file `/tmp/neper/allgrains.stpoly'...
-Info   :     [o] Wrote file `/tmp/neper/allgrains.stpoly'.
-Info   : Elapsed time: 2.958 secs.
-========================================================================
-
-
-========================    N   e   p   e   r    =======================
-Info   : A software package for polycrystal generation and meshing.
-Info   : Version 4.9.1-4
-Info   : Built with: gsl|muparser|opengjk|openmp|nlopt|libscotch (full)
-Info   : Running on 12 threads.
-Info   : <https://neper.info>
-Info   : Copyright (C) 2003-2022, and GNU GPL'd, by Romain Quey.
-Info   : No initialization file found (`/home/hielscher/.neperrc').
-Info   : ---------------------------------------------------------------
-Info   : MODULE  -V loaded with arguments:
-Info   : [ini file] (none)
-Info   : [com line] /tmp/neper/allgrains.tess
-Info   : ---------------------------------------------------------------
-Info   :   - Reading arguments...
-Info   : Elapsed time: 0.001 secs.
-========================================================================
-
 
-grains3 = grain3d
+grains = grain3d
 
  Phase  Grains  Volume  Mineral  Symmetry  Crystal reference frame
-     2     100       1   Copper      m-3m                         
+     2     100       1   Quartz       321       X||a*, Y||b, Z||c*
 
  boundary faces: 650
 
  <strong>Properties</strong>: meanRotation
 {% endhighlight %}
-<h2 id="5">Plotting Grains</h2>
-{% highlight matlab %}
-% set camera
-how2plot = plottingConvention;
-how2plot.outOfScreen = vector3d(-10,-5,2);
-how2plot.east = vector3d(1,-2,0);
-
-% colorize by mean orientation
-plot(grains3,grains3.meanOrientation)
-setCamera(how2plot)
-{% endhighlight %}
 <center>
 {% include inline_image.html file="Grains3D_03.png" %}
 </center>
-<h2 id="6">Rotation</h2>
-<p>rotate 180 degrees about the x-axis</p>
-{% highlight matlab %}
-rot = rotation.byAxisAngle(xvector,180*degree);
-grains3_rot = rot * grains3;   % or rotate(grains3,rot)
-
-% plotting
-plot(grains3_rot,grains3_rot.meanOrientation)
-{% endhighlight %}
-<center>
-{% include inline_image.html file="Grains3D_04.png" %}
-</center>
-<p>colorize by volume</p>
-{% highlight matlab %}
-plot(grains3,grains3.volume)
-setCamera(how2plot)
-{% endhighlight %}
-<center>
-{% include inline_image.html file="Grains3D_05.png" %}
-</center>
-<p>plot single grains, color by phase</p>
-{% highlight matlab %}
-figure
-grains = grains3(1:5)
-plot(grains)
-{% endhighlight %}
-
-{% highlight plaintext %}
-grains = grain3d
-
- Phase  Grains  Volume  Mineral  Symmetry  Crystal reference frame
-     2       5   0.045   Copper      m-3m                         
-
- boundary faces: 56
-
- Id   Phase   Pixels            meanRotation
-  1       2        1    (34.7°,42.2°,355.5°)
-  2       2        1    (26.2°,40.1°,352.1°)
-  3       2        1   (192.7°,31.1°,202.9°)
-  4       2        1   (203.7°,32.5°,173.5°)
-  5       2        1   (216.3°,46.1°,172.4°)
-{% endhighlight %}
-<center>
-{% include inline_image.html file="Grains3D_06.png" %}
-</center>
-<h2 id="9">Triangulation</h2>
-<p>Some functions are much faster on triangulated meshes. Therefore you can triangulate your grains with the following command.</p>
-{% highlight matlab %}
-grainsTri = grains3.triangulate
-{% endhighlight %}
-
-{% highlight plaintext %}
-grainsTri = grain3d
-
- Phase  Grains  Volume  Mineral  Symmetry  Crystal reference frame
-     2     100       1   Copper      m-3m                         
-
- boundary faces: 2608
-
- <strong>Properties</strong>: meanRotation
-{% endhighlight %}
-<h2 id="10">Slicing</h2>
+<h2 id="5">Slicing</h2>
 <p>To get the usually used 2d grain data, it is possible to slice 3d grains by different methods.</p>
 {% highlight matlab %}
-% make all slices passing through this point
+% make all slices passing through the center point of the cube
 P0 = vector3d(0.5,0.5,0.5);
+% with normal (1,-1,1)
+N = vector3d(1,-1,1);
 
-% Slice by plane normal and point
-N = vector3d(1,-1,0);
-grains1_10 = grains3.slice(N,P0)
+grains_2d = grains.slice(N,P0)
 
+% plot the slice and adjust the plotting convention such that N points out
+% of screen
+plot(grains_2d,grains_2d.meanOrientation,'micronbar','off')
 how2plot = plottingConvention;
 how2plot.outOfScreen = N;
-plot(grains1_10,grains1_10.meanOrientation)
 setCamera(how2plot)
 {% endhighlight %}
 
 {% highlight plaintext %}
-grains1_10 = grain2d
+grains_2d = grain2d
 
  Phase  Grains  Pixels  Mineral  Symmetry  Crystal reference frame
-     2      39      39   Copper      m-3m                         
+     2      41      41   Quartz       321       X||a*, Y||b, Z||c*
 
- boundary segments: 118 (16 µm)
+ boundary segments: 126 (16 µm)
  inner boundary segments: 0 (0 µm)
- triple points: 59
+ triple points: 64
 
  <strong>Properties</strong>: meanRotation
 {% endhighlight %}
 <center>
-{% include inline_image.html file="Grains3D_07.png" %}
+{% include inline_image.html file="Grains3D_04.png" %}
 </center>
+<h2 id="6">Grains intersecting a slice</h2>
+<p>Lets plot the grains intersecting the plane in 3d</p>
 {% highlight matlab %}
-% Slice by matgeom plane
-N3 = vector3d(2,2,4);
-plane = createPlane(P0.xyz, N3.xyz);     % consider the different order
-grains224 = grains3.slice(plane);
-
-% Slice going through 3 points
-A = vector3d(0,0,0.5);
-B = vector3d(0,1,0.5);
-grains001 = grains3.slice(P0,A,B);
-
-% plot the slices
-plot(grains001,grains001.meanOrientation);
+isInter = grains.intersected(N,P0);
 hold on
-plot(grains1_10,grains1_10.meanOrientation);
-hold on
-plot(grains224,grains224.meanOrientation);
-
-% set camera
-how2plot = plottingConvention;
-how2plot.outOfScreen = vector3d(-10,-5,2);
-how2plot.east = vector3d(1,-2,0);
-setCamera(how2plot)
-{% endhighlight %}
-
-{% highlight plaintext %}
-Warning: still can not concatenate grains on different slices 
-Warning: still can not concatenate grains on different slices
-{% endhighlight %}
-<center>
-{% include inline_image.html file="Grains3D_08.png" %}
-</center>
-<p>Plot single 3D grains together with slices</p>
-{% highlight matlab %}
-grains = grains3(1:5)
+plot(grains(isInter),grains(isInter).meanOrientation)
+hold off
 
-plot(grains,grains.meanOrientation)
-how2plot.outOfScreen = vector3d(-10,-4,1);
-how2plot.east = vector3d(2,-5,0);
+how2plot.north = N;
+how2plot.outOfScreen = vector3d(1,-1,-1)
 setCamera(how2plot)
 {% endhighlight %}
 
 {% highlight plaintext %}
-grains = grain3d
-
- Phase  Grains  Volume  Mineral  Symmetry  Crystal reference frame
-     2       5   0.045   Copper      m-3m                         
-
- boundary faces: 56
+how2plot = plottingConvention
 
- Id   Phase   Pixels            meanRotation
-  1       2        1    (34.7°,42.2°,355.5°)
-  2       2        1    (26.2°,40.1°,352.1°)
-  3       2        1   (192.7°,31.1°,202.9°)
-  4       2        1   (203.7°,32.5°,173.5°)
-  5       2        1   (216.3°,46.1°,172.4°)
+  outOfScreen: (1,-1,-1)
+  north      : (5,-3,8) 
+  east       : (6,7,-1)
 {% endhighlight %}
 <center>
-{% include inline_image.html file="Grains3D_09.png" %}
+{% include inline_image.html file="Grains3D_05.png" %}
 </center>
-<h2 id="13">Slice Dream3d Grains</h2>
-<p>still inefficient, expensive</p>
+<h2 id="7">Plot the normal directions of one grain</h2>
 {% highlight matlab %}
-N = vector3d(1,1,1);
-P0 = vector3d(0.5,0.5,0.5);
-
-slice = grains.slice(N,P0);
-plot(slice,slice.meanOrientation);
+%grains = grains(1)
+%dir = grains.I_GF(1,:)' .* grains.boundary.N % flip according to I_GF
+%quiver(grains.boundary,dir)
+%plot(grains)
 {% endhighlight %}
-<center>
-{% include inline_image.html file="Grains3D_10.png" %}
-</center>
 </div>
 </body>
 </html>