diff --git a/css/customstyles.css b/css/customstyles.css index 70e85d68b..7c5181e5b 100644 --- a/css/customstyles.css +++ b/css/customstyles.css @@ -211,7 +211,6 @@ p.post-meta {font-size: 80%; color: #777;} border-left: 1px solid #dedede; } - ul#results-container a { background-color: transparent; } @@ -1236,6 +1235,33 @@ abbr[title]:after { content: "\f129"; } /* info */ padding-right: 2em; } +/* foldable-toggle */ +[data-toggle="foldable-tooltip"] > span { + color: var(--highlight); + cursor: pointer; +} + +[data-toggle="foldable-tooltip"] > div { + color: var(--text-grayed); + font-style: normal; +} + +/* team profile cards */ +.panel-profile-card { + display: flex; + box-shadow: none; + -webkit-box-shadow: none; + padding: 0; +} + +.panel-profile-card > .panel-heading { + width: 30%; +} + +.panel-profile-card > .panel-body { + width: 100%; +} + /* -------------------------- */ /* important / override rules */ /* -------------------------- */ @@ -1269,3 +1295,8 @@ a.no_icon:after { content: ""; padding-left: 0; } + +/* onyl for debugging */ +* { + /* outline: 1px solid red; */ +} diff --git a/images/profiles/bjorn-eske-soerensen.png b/images/profiles/bjorn-eske-soerensen.png new file mode 100644 index 000000000..f7d341145 Binary files /dev/null and b/images/profiles/bjorn-eske-soerensen.png differ diff --git a/images/profiles/david-mainprice.png b/images/profiles/david-mainprice.png new file mode 100644 index 000000000..ae0e98493 Binary files /dev/null and b/images/profiles/david-mainprice.png differ diff --git a/images/profiles/fabian-bartl.png b/images/profiles/fabian-bartl.png new file mode 100644 index 000000000..af93fef07 Binary files /dev/null and b/images/profiles/fabian-bartl.png differ diff --git a/images/profiles/felix-bartel.png b/images/profiles/felix-bartel.png new file mode 100644 index 000000000..53dc20c1a Binary files /dev/null and b/images/profiles/felix-bartel.png differ diff --git a/images/profiles/florian-bachmann.png b/images/profiles/florian-bachmann.png new file mode 100644 index 000000000..96a0d2445 Binary files /dev/null and b/images/profiles/florian-bachmann.png differ diff --git a/images/profiles/frank-niessen.png b/images/profiles/frank-niessen.png new file mode 100644 index 000000000..77385d666 Binary files /dev/null and b/images/profiles/frank-niessen.png differ diff --git a/images/profiles/oliver-kent-johnson.png b/images/profiles/oliver-kent-johnson.png new file mode 100644 index 000000000..2b3abf207 Binary files /dev/null and b/images/profiles/oliver-kent-johnson.png differ diff --git a/images/profiles/ralf-hielscher.png b/images/profiles/ralf-hielscher.png new file mode 100644 index 000000000..8ba6c6136 Binary files /dev/null and b/images/profiles/ralf-hielscher.png differ diff --git a/images/profiles/ruediger-kilian.png b/images/profiles/ruediger-kilian.png new file mode 100644 index 000000000..8ea381280 Binary files /dev/null and b/images/profiles/ruediger-kilian.png differ diff --git a/images/profiles/tuomo-nyyssoenen.png b/images/profiles/tuomo-nyyssoenen.png new file mode 100644 index 000000000..8bbea12cb Binary files /dev/null and b/images/profiles/tuomo-nyyssoenen.png differ diff --git a/index.md b/index.md index b7c831c19..1a4a6e5ef 100644 --- a/index.md +++ b/index.md @@ -7,14 +7,15 @@ permalink: index toc: false --- -MTEX is a free Matlab toolbox for analyzing and modeling crystallographic textures by means of EBSD or pole figure data. It is developed on a free and opensource basis by an interdisciplinary +MTEX is a free Matlab toolbox for analyzing and modeling crystallographic textures by means of EBSD or pole figure data. It is developed on a free and opensource basis by an interdisciplinary {% include reference.html link="people" content=' team' %} of material scientists, geologists and mathematicians.
-[![](https://badgen.net/badge/icon/github?icon=github&label)](https://github.com/mtex-toolbox/mtex) -[![ResearchGate Badge](https://img.shields.io/badge/Research-Gate-9cf)](https://www.researchgate.net/project/MTEX-free-crystallographic-texture-analysis-software) +[![](https://badgen.net/badge/icon/github?icon=github&label)](https://github.com/mtex-toolbox/mtex)  +[![](https://img.shields.io/badge/Research-Gate-9cf)](https://www.researchgate.net/project/MTEX-free-crystallographic-texture-analysis-software)  +  ![](https://img.shields.io/github/languages/top/mtex-toolbox/mtex)  ![](https://img.shields.io/github/downloads/mtex-toolbox/mtex/total)  ![](https://img.shields.io/github/contributors/mtex-toolbox/mtex)  diff --git a/js/customscripts.js b/js/customscripts.js index 9613c5fcb..a01511920 100644 --- a/js/customscripts.js +++ b/js/customscripts.js @@ -1,7 +1,10 @@ -$('#mysidebar').height($(".nav").height()); +// some small functions +const uniqId = (()=>{let i=0;return()=>{return i++;}})(); + +$('#mysidebar').height($(".nav").height()); -$( document ).ready(function() { +$(document).ready(function() { //this script says, if the height of the viewport is greater than 800px, then insert affix class, which makes the nav bar float in a fixed // position as your scroll. if you have a lot of nav items, this height may not work for you. @@ -36,6 +39,36 @@ $( document ).ready(function() { if (a_href.includes("://") && a_target === null) { a_tag.setAttribute("target", "_blank"); } } + + // add no_icon class to links with badges + $('a > img').each(function() { + $(this).parent().addClass("no_icon"); + }); + + // foldable tooltip + $('[data-toggle="foldable-tooltip"]').each(function() { + if ($(this).attr("data-icon") === null) { + $(this).attr("data-icon", "fa fa-info-circle"); + } + + $(this).html(" " + $(this).attr("data-title") + ""); + $(this).attr("unfolded", "false"); + }); + + $('[data-toggle="foldable-tooltip"]').click(function() { + let folded = " " + $(this).attr("data-title") + ""; + let unfolded = folded + "
" + $(this).attr("data-text") + "
"; + + if ($(this).attr("unfolded") === "false") { + $(this).html(unfolded); + $(this).attr("unfolded", "true"); + } else { + if (!$(this).children('div').is(':hover')) { + $(this).html(folded); + $(this).attr("unfolded", "false"); + } + } + }); }); // needed for nav tabs on pages. See Formatting > Nav tabs for more details. diff --git a/pages/download/Installation.md b/pages/download/Installation.md index 105f3d3eb..d61c5abef 100644 --- a/pages/download/Installation.md +++ b/pages/download/Installation.md @@ -1,20 +1,220 @@ --- -title: Installation -keywords: installation -last_updated: 14-Sep-2022 +title: Installation Issues for Mac OSX +keywords: installation issues, mac osx +last_updated: January 8, 2018 hide_sidebar: true -permalink: Installation +permalink: installation folder: download toc: false --- -In order to install MTEX onto your computer proceed as follows: +Since binaries are sometimes not compatible across different versions of +macOS and due to increasing security measures of Apple, some extra work might be +required to get MTEX running on macOS. -1. download and extract the zip file to an arbitrary folder -2. start Matlab -3. change the current folder in Matlab to the folder where MTEX is installed -4. type `startup_mtex` into the command window +## library load disallowed by system policy -In case you experience any problems, especiall on Mac OSX, have a look at our -{% include reference.html link="installationIssues" content=' trouble shooting page' %} +If you experience the following error message + +``` +Invalid MEX-file 'some path to +mtex/mtex-5.3/extern/nfft/nfsoftmex.mexmaci64': dlopen(some path to +mtex//mtex-5.3/extern/nfft/nfsoftmex.mexmaci64, 6): no suitable image +found. Did find: +some path to mtex/mtex-5.3/extern/nfft/nfsoftmex.mexmaci64: code +signature in (some path to +mtex/mtex-5.3/extern/nfft/nfsoftmex.mexmaci64) not valid for use in +process using Library Validation: library load disallowed by system policy +``` + +you can either download MTEX with a command line tool such as +[```curl```](https://www.youtube.com/watch?v=6pyVl3GdSuU) or ```wget``` +``` bash +curl -LJO --output mtex.zip https://github.com/mtex-toolbox/mtex/releases/download/mtex-5.3/mtex-5.3.zip +``` +or, if you have downloaded MTEX with a browser, type in Matlab + +``` matlab +!sudo xattr -r -d com.apple.quarantine /path/to/mtexfolder +``` + +## Unable to compile mex files during startup_mtex + +If you (still) get the following error, you will need to recompile the mex files +on your own. MTEX tries to perform the compilation automatically. However, in +some case you might experience error messages like + +``` +Error: unable to compile mex files during startup_mtex e.g.: + +Checking mex files failed! + > Trying now to recompile mex files. + > In mex_install (line 15) + In check_installation>check_mex (line 69) + In check_installation (line 33) + In startup_mtex (line 66) + In startup (line 7) +... compiling S1Grid_find.c +Building with 'Xcode with Clang'. +Compiling some path to mtex/mtex-5.3/mex/S1Grid_find.c failed! +``` +or +``` + > MTEX: Couldn't get the mex files working! + > The original error message was: + > Invalid MEX-file + > 'some path to mtex/mtex-5.3/mex/SO3Grid_dist_region.mexmaci64': + > dlopen(some path to mtex/mtex-5.3/mex/SO3Grid_dist_region.mexmaci64, + > 6): Library not loaded: @loader_path/libmex.dylib + > Referenced from: + > some path to mtex/mtex-5.3/mex/SO3Grid_dist_region.mexmaci64 + > Reason: image not found + > Contact author for help! +``` + +1. Make sure that after upgrading your system, to also upgrade ```xcode``` + (via appstore) and install the command line tools and accept the licence by +``` bash +sudo xcodebuild -license accept +xcode-select --install +``` +2. You might need to modify the compiler options used by Matlab. The configuration file can be found by the command +``` matlab +m = mex.getCompilerConfigurations +m.MexOpt +ans = + /Users/rk/Library/Application/MathWorks/MATLAB/R2019b/mex_C_maci64.xml +``` +The exact file name depends on the compiler installed on your system, e.g. ```/Applications/MATLAB_R2019a.app/bin/maci64/mexopts/clang_maci64.xml```. +Within the configuration file change the lines + +```xml + + + +``` + +to + +```xml + + + +``` + +and do from within Matlab +``` matlab +mex -setup C +``` +Now ```startup_mtex.m``` will hopefully run without any trouble. + +## Compiling the nfft + +### 1. Install gcc with openmp and libtools + +Using [homebrew](https://brew.sh/) is probably the easiest +``` bash +brew install gcc libtool +``` + +### 2. Get nfft source from github + +``` bash +git clone https://github.com/NFFT/nfft/ +cd nfft +./bootstrap.sh +``` + +### 3. Set the compilation parameters + +The path to gcc and matlab depends on your system and should be set accordingly. +If you uesd homebrew to install gcc, it should have ended up in some place called +`Cellar` typically found in `/usr/local/`. Check the right version and replace them +accordingly in the lines below. The same of coure applies to the Mathlab path and +version. If you are one an architecture other than x86_64, also set this one correctly +(e.g. or leave the option out completely and hope that automatic recognition will work). +For the ARMv8 from Apple this is currectly untested. + +``` bash +CC=/usr/local/Cellar/gcc/8.2.0/bin/gcc-8 +LDFLAGS=-Wl,-L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8 +./configure --with-matlab=/Applications/MATLAB_R2018b.app --enable-nfsoft\ + --enable-nfsft --enable-openmp --enable-portable-binary\ + --with-apple-gcc-arch=x86_64 - +``` +or if for some reason you can not use openMP +``` bash +CC=/usr/local/Cellar/gcc/8.2.0/bin/gcc-8 +LDFLAGS=-Wl,-L/usr/local/Cellar/gcc/8.2.0/lib/gcc/8 +./configure --with-matlab=/Applications/MATLAB_R2018b.app --enable-nfsoft\ + --enable-nfsft --enable-portable-binary --with-apple-gcc-arch=x86_64 +``` + +### 4. Compile the nfft + +``` bash +make +``` + +### 5. Link the nfft + +The easists way is to make out of the following lines an executable shell script. +Please do not forget to include the definitions of gcc and Matlab pathes from above. +Most likely you changed the exact version and path, so do this here accordingly. + +``` bash +#!/bin/bash +CC=/usr/local/Cellar/gcc/8.2.0/bin/gcc-8 +MATLABDIR=/Applications/MATLAB_R2018b.app + +for LIB in nfft nfsft nfsoft nnfft fastsum nfct nfst; do + cd matlab/"$LIB" + "$CC" -o .libs/lib"$LIB".mexmaci64 -bundle .libs/lib"$LIB"_la-"$LIB"mex.o \ + -Wl,-force_load,../../.libs/libnfft3_matlab.a \ + -Wl,-force_load,../../matlab/.libs/libmatlab.a \ + -L"$MATLABDIR"/bin/maci64 -lm -lmwfftw3 -lmx -lmex \ + -lmat -fopenmp -O3 -malign-double -march=core2 \ + -arch x86_64 -fopenmp -static-libgcc + cp .libs/lib"$LIB".mexmaci64 "$LIB"mex.mexmaci64 + cd ../.. +done +``` + +the vesion without ```openMP``` + +``` bash +#!/bin/bash +CC=/usr/local/Cellar/gcc/8.2.0/bin/gcc-8 +MATLABDIR=/Applications/MATLAB_R2018b.app + +for LIB in nfft nfsft nfsoft nnfft fastsum nfct nfst; do + cd matlab/"$LIB" + "$CC" -o .libs/lib"$LIB".mexmaci64 -bundle .libs/lib"$LIB"_la-"$LIB"mex.o \ + -Wl,-force_load,../../.libs/libnfft3_matlab.a \ + -Wl,-force_load,../../matlab/.libs/libmatlab.a \ + -L"$MATLABDIR"/bin/maci64 -lm -lmwfftw3 -lmx -lmex \ + -lmat -O3 -malign-double -march=core2 \ + -arch x86_64 -static-libgcc + cp .libs/lib"$LIB".mexmaci64 "$LIB"mex.mexmaci64 + cd ../.. +done +``` + +### 6. Copy the generated mex-files into the MTEX installation + +``` bash +make install +``` +for mtex, copy the two files +``` +matlab/nfsft/.libs/libnfsft.mexmaci64 +matlab/nfsoft/.libs/libnfsoft.mexmaci64 +``` +into your mtex installation into +``` +mtex/extern/nfft_openMP/ +``` +or +``` +mtex/extern/nfft/ +``` diff --git a/pages/people/people.md b/pages/people/people.md index 43e6b23f1..e3807bdad 100644 --- a/pages/people/people.md +++ b/pages/people/people.md @@ -8,223 +8,186 @@ folder: people toc: false --- -
-
- - - - - -
- {% include image.html file="profiles/ralf-hielscher.jpg" alt="Picture of Ralf Hielscher" max-width='120'%} - -

- Ralf Hielscher - invented MTEX in 2007 by implementing the pole figure to ODF inversion - algorithm and leads since than the development. -

-

- {% include reference.html link="mailto:Ralf.Hielscher@math.tu-freiberg.de" content="Ralf.Hielscher@math.tu-freiberg.de" %} -
- {% include reference.html link="https://tu-freiberg.de/fakult1/ana/hielscher" content="Institute of Applied Analysis, TU Bergakademie Freiberg" %} -

-
+
+
+
+ Picture of Ralf Hielscher +
+
+

+ Ralf Hielscher + invented MTEX in 2007 by implementing the pole figure to ODF inversion + algorithm and leads since than the development. +

+

+ {% include reference.html link="mailto:Ralf.Hielscher@math.tu-freiberg.de" + content="Ralf.Hielscher@math.tu-freiberg.de" %} +
+ {% include reference.html link="https://tu-freiberg.de/fakult1/ana/hielscher" content="Institute of + Applied Analysis, TU Bergakademie Freiberg" %} +

+
- -
- - - - - -
- {% include image.html file="profiles/ruediger-kilian.jpg" alt="Picture of Rüdiger Kilian" max-width='120'%} - -

- Rüdiger Kilian - joined the MTEX team in 2008 as a PhD student of - Rene Heilbronner, Basel. Since than he answered hundreds of questions in the - MTEX forum. Rüdiger spends much afford in continuously improving the EBSD - and grain analysis functionalities in MTEX. -

-

- {% include reference.html link="https://geodynamics.geo.uni-halle.de/ruediger-kilian" content="Martin-Luther-Universität Halle-Wittenberg" %} -

-
+
+
+ Picture of Rüdiger Kilian +
+
+

+ Rüdiger Kilian + joined the MTEX team in 2008 as a PhD student of + Rene Heilbronner, Basel. Since than he answered hundreds of questions in the + MTEX forum. Rüdiger spends much afford in continuously improving the EBSD + and grain analysis functionalities in MTEX. +

+

+ {% include reference.html link="https://geodynamics.geo.uni-halle.de/ruediger-kilian" + content="Martin-Luther-Universität Halle-Wittenberg" %} +

+
-
-
- - - - - -
- {% include image.html file="profiles/david-mainprice.jpg" alt="Picture of David Mainprice" max-width='120'%} - -

- David Mainprice - joined the MTEX team in 2009 by sharing his code - on tensorial properties and seismic velocities. Since than he is - continuously working on promoting MTEX to the world of geologists. -

-

- {% include reference.html link="http://www.gm.univ-montp2.fr/PERSO/mainprice/" content="Geosciences Montpellier, France" %} -

-
+
+
+
+ Picture of David Mainprice +
+
+

+ David Mainprice + joined the MTEX team in 2009 by sharing his code + on tensorial properties and seismic velocities. Since than he is + continuously working on promoting MTEX to the world of geologists. +

+

+ {% include reference.html link="http://www.gm.univ-montp2.fr/PERSO/mainprice/" content="Geosciences + Montpellier, France" %} +

+
- -
- - - - - -
- {% include image.html file="profiles/florian-bachmann.jpg" alt="Picture of Florian Bachmann" max-width='120'%} - -

- Florian Bachmann - started with MTEX during his diploma thesis at TU - Freiberg in 2008, when he implemented the MTEX grain reconstruction - algorithm. Furthermore, he was responsible for the import wizard and the - documentation center. -

-

- {% include reference.html link="https://xnovotech.com/" content="Xnovo Technology ApS, Denmark" %} -

-
+
+
+ Picture of Florian Bachmann +
+
+

+ Florian Bachmann + started with MTEX during his diploma thesis at TU + Freiberg in 2008, when he implemented the MTEX grain reconstruction + algorithm. Furthermore, he was responsible for the import wizard and the + documentation center. +

+

+ {% include reference.html link="https://xnovotech.com/" content="Xnovo Technology ApS, Denmark" %} +

+
-
- -
- - - - - -
- {% include image.html file="profiles/felix-bartel.jpg" alt="Picture of Felix Bartel" max-width='120'%} - -

- Felix Bartel - worked on MTEX during his master thesis at the TU Chemnitz in 2019. He - wrote the code for spherical function classes. -

-

- {% include reference.html link="https://www.tu-chemnitz.de/~febar" content="Institute of Mathematics, TU Chemnitz" %} -

-
+
+
+
+ Picture of Felix Bartel +
+
+

+ Felix Bartel + worked on MTEX during his master thesis at the TU Chemnitz in 2019. He + wrote the code for spherical function classes. +

+

+ {% include reference.html link="https://www.tu-chemnitz.de/~febar" content="Institute of + Mathematics, TU Chemnitz" %} +

+
- - - -
- - - - - -
- {% include image.html file="profiles/bjorn-eske-soerensen.jpg" alt="Picture of Bjoern Eske Soerensen" max-width='120'%} - -

- - {% include reference.html link="https://www.ntnu.edu/employees/bjorn.sorensen" content="Bjørn Eske Sørensen" %} - - contributes to spectral difraction and birefringence. -

-

- Department of Geoscience and Petroleum, -
- Norwegian University of Science and Technology -

-
+
+
+ Picture of Bjoern Eske Soerensen +
+
+

+ + {% include reference.html link="https://www.ntnu.edu/employees/bjorn.sorensen" + content="Bjørn Eske Sørensen" %} + + contributes to spectral difraction and birefringence. +

+

+ Department of Geoscience and Petroleum, +
+ Norwegian University of Science and Technology +

+
-
- -
- - - - - -
- {% include image.html file="profiles/tuomo-nyyssoenen.jpg" alt="Picture of Tuomo Nyyssoenen" - max-width='120'%} - -

- - {% include reference.html link="https://www.researchgate.net/profile/Tuomo-Nyyssoenen" content="Tuomo Nyyssoenen" %} - - worked on parent austenite reconstruction during his PhD at Tampere University of Technology. He wrote the initial MTEX code for the reconstruction of parent grain structures and the determination of the parent to child orientation relationship. -

-
+
+
+
+ Picture of Tuomo Nyyssoenen +
+
+

+ + {% include reference.html link="https://www.researchgate.net/profile/Tuomo-Nyyssoenen" + content="Tuomo Nyyssoenen" %} + + worked on parent austenite reconstruction during his PhD at Tampere University of Technology. He + wrote the initial MTEX code for the reconstruction of parent grain structures and the determination + of the parent to child orientation relationship. +

+
- -
- - - - - -
- {% include image.html file="profiles/frank-niessen.jpg" alt="Picture of Frank Niessen" max-width='120'%} - -

- - {% include reference.html link="https://www.researchgate.net/profile/Frank_Niessen4" content="Frank Niessen" %} - - generalized and optimized the orientation relationship analysis and parent grain reconstruction algorithm in towards arbitrary phase combinations. He is also the author of export functions for ctf and ang files. -

-

- {% include reference.html link="https://www.dtu.dk/english/service/phonebook/person?id=74988&tab=3&qt=dtuprojectquery" content="Department of Mechanical Engineering,
Technical University of Denmark" %} -

-
+
+
+ Picture of Frank Niessen +
+
+

+ + {% include reference.html link="https://www.researchgate.net/profile/Frank_Niessen4" + content="Frank Niessen" %} + + generalized and optimized the orientation relationship analysis and parent grain reconstruction + algorithm in towards arbitrary phase combinations. He is also the author of export functions for ctf + and ang files. +

+

+ {% include reference.html + link="https://www.dtu.dk/english/service/phonebook/person?id=74988&tab=3&qt=dtuprojectquery" + content="Department of Mechanical Engineering,
Technical University of Denmark" %} +

+
-
- -
- - - - - -
- {% include image.html file="profiles/oliver-kent-johnson.jpg" alt="Picture of Oliver kent Johnson" - max-width='120'%} - -

- Oliver Kent Johnson - finished his PhD in 2015 under the supervision of Christopher A. Schuh at the Massachusetts Institute of Technology. He implemented the misorientation color key. -

-
+
+
+
+ Picture of Oliver kent Johnson +
+
+

+ Oliver Kent Johnson + finished his PhD in 2015 under the supervision of Christopher A. Schuh at the Massachusetts + Institute of Technology. He implemented the misorientation color key. +

+
- -
- - - - - -
- {% include image.html file="profiles/fabian-bartl.jpg" alt="Picture of Fabian Bartl" max-width='120'%} - -

- Fabian Bartl - is responsible for the webpage since 2021. -

-

- {% include reference.html link="https://tu-freiberg.de/" content="TU Bergakademie Freiberg" %} -

-
+
+
+ Picture of Fabian Bartl +
+
+

+ Fabian Bartl + is responsible for the webpage since 2021. +

+

+ {% include reference.html link="https://tu-freiberg.de/" content="TU Bergakademie Freiberg" %} +

+
-
\ No newline at end of file +
diff --git a/pages/workshops/workshop23.md b/pages/workshops/workshop23.md index aeb5b0b23..2ecb4b2d3 100644 --- a/pages/workshops/workshop23.md +++ b/pages/workshops/workshop23.md @@ -309,12 +309,11 @@ The second week will consist of lectures by invited experts that explain in deta - **{% include reference.html link="https://lightform.org.uk/people/dr-adam-plowman" content="Adam - Plowman" %}** (University of Manchester): *Using MTEX with MatFlow for crystal plasticity and phase field modeling* + Plowman" %}** (University of Manchester): - **{% include reference.html link="https://scholar.google.co.uk/citations?hl=en&user=GvwErjEAAAAJ&view_op=list_works&sortby=pubdate" content="Vivian Tong" %}** (National Physical Laboratory UK): *Characterising microstructural shapes using EBSD and correlative SEM imaging techniques* -