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Tuesday, October 6, 2015

Friday, September 18, 2015

pdfcrop with margins



http://askubuntu.com/questions/124692/command-line-tool-to-crop-pdf-files

If you wish to crop a pdf with left, top, right and bottom margins of 5, 10, 20, and 30 pt (points), then run
pdfcrop --margins '5 10 20 30' input.pdf output.pdf
in terminal. To actually crop something away, use negative values in the argument for crop. For example,
pdfcrop --margins '-50 -50 -50 -50' input.pdf output.pdf
crops 50 pts from the left, top, right, bottom (in this order).
If you run only the command pdfcrop input, it will output a file titled input-crop.pdf with zero margins. I find this very handy when including pdf illustrations in documents.
Cropping multiple files
Unfortunately, pdfcrop cannot crop multiple files at the time. It is however easy to write a script that will crop all pdfs in the folder the script is located in.
Create a new empty file, and call it something.sh. Open it with a text editor and insert the following:
#!/bin/bash

for FILE in ./*.pdf; do
  pdfcrop "${FILE}"
done
Save it, and close. Then right click the file, go to Properties > Permissions and check the field Allow executing file as program. Now close the dialog. Run the script by double clicking it and choosingRun in Terminal. And new, zero-margin cropped version of all pdfs with suffix -crop will now be printed in the folder. If you want margins or other things, you can of course just open the script and add arguments after pdfcrop.

Saturday, September 12, 2015

linear regression matlab script

function [p,Rsq] = LinearRegression (Xin,Yin)
% LinearRegression example
% x=0:1:9;
% y=3.0 * x + 7 + rand(1,length(x)) ;
% [p,Rsq] = LinearRegression (x,y) ;
% yfit = p(1)*x + p(2) ;
% plot(x,y,"o",x,yfit) ;
p = polyfit(Xin,Yin,1);
Yfit =  p(1) * Xin + p(2);
Yresid = Yin - Yfit;
SSresid = sum(Yresid.^2);
SStotal = (length(Yin)-1) * var(Yin);
Rsq = 1 - SSresid/SStotal;

Wednesday, September 9, 2015

lyx shortcuts


https://pepebioinformatics.wordpress.com/2014/03/06/lyx-keyboard-shortcuts/

LyX Keyboard Shortcuts

  1. ⇧ + ⌘ + L -> Insert Label (label-insert);
  2. ⌘ + L -> Insert ERT (ert-insert);
  3. ⇧ + ⌘ + G -> Insert Graphic (dialog-show-new-inset graphics);
  4. ⇧ + ⌘ + FF -> Insert FloatFigure (float-insert figure);
  5. ⇧ + ⌘ + FT -> Insert FloatTable (float-insert table);
  6. ⇧ + ⌘ + P -> Typewriter font;
  7. ⇧ + ⌘ + C -> Insert Cross-reference (dialog-show-new-inset ref);
  8. ^ + A + [C, L or R] -> paragraph-params \align Center, Left or Right;
  9. ⌘ + E -> Italic (font-emph);
  10. ⌘ + B -> Bold (font-bold);
  11. ⌘ + M -> Insert Math (math-mode);
  12. ⌘ + ⇧ + R -> Refresh Run
  13. ⌘ + R -> Run
  14. ^ + P + [*] + [234]; layout [without numbers] [S/SubS/SubSubS]

Thursday, August 20, 2015

Netgen on Mac

Netgen installation on Mac is hopeless.
It is better to use Ubuntu virtual machine or Windows laptop.

Tuesday, August 18, 2015

Netgen command line approach

This works for version 4.9 but does not for 5.3.1 (only GUI mode).

$  netgen -batchmode  -geofile=cone.geo -meshfile=cone.ng -coarse

$  netgen -batchmode  -geofile=cone.geo -meshfile=cone.ngn  -meshfiletype="Neutral Format"

The possible mesh size options are
-verycoarse
-coarse
-moderate
-fine
-veryfine

Wednesday, July 29, 2015

Compilation with NETGEN Ubuntu 14.04

Compilation with NETGEN Ubuntu 14.04


http://forum.freecadweb.org/viewtopic.php?t=6702


=== Mon Aug 17 22:47:36 HST 2015
OpenGL library is located in /usr/lib/x86_64-linux-gnu/
The netgen compilation did not give any error after installing libxmu-dev library. This will also install Togl1.7 library so that no separate installation of Togl 1.7 is necessary.
 
$ apt-get install libxmu-dev 

After installation, execution of 'netgen' in ng directory gave:
 
symbol lookup error: /usr/lib/libTogl.so: undefined symbol: tkStubsPtr
 

-ltcl8.6 -ltk8.6  -ltkstub8.5


=== Mon Aug 17 10:00:36 HST 2015 ===
The next error came out of 'netgen' compiling. Togl cannot call XmuLookupStandardColormap function in OpenGL, which need to be fixed.

### error message ### 
/bin/bash ../libtool --tag=CXX   --mode=link g++  -g -O2 -fopenmp -export-dynamic  -o netgen demoview.o ngappinit.o onetcl.o parallelfunc.o ngpkg.o ../libsrc/visualization/libvisual.la ../libsrc/csg/libcsgvis.la ../libsrc/csg/libcsg.la ../libsrc/interface/libinterface.la ../libsrc/meshing/libmesh.la -L/usr/lib/Togl1.7  -lTogl -lGLU -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6    -lGL -lXmu -lX11   

libtool: link: g++ -g -O2 -fopenmp -o .libs/netgen \

demoview.o ngappinit.o onetcl.o parallelfunc.o ngpkg.o \
-Wl,--export-dynamic  \
../libsrc/visualization/.libs/libvisual.a \
../libsrc/csg/.libs/libcsgvis.so \
../libsrc/csg/.libs/libcsg.so \
../libsrc/interface/.libs/libinterface.so \
../libsrc/meshing/.libs/libmesh.so \
-L/usr/lib/Togl1.7 -lTogl -lGLU \
-L/usr/lib/x86_64-linux-gnu -ltk8.6 -ltcl8.6 -lGL -lXmu -lX11 \
-fopenmp -Wl,-rpath -Wl,/opt/netgen/lib

/usr/lib/Togl1.7/libTogl.so: undefined reference to `XmuLookupStandardColormap'


collect2: error: ld returned 1 exit status
make: *** [netgen] Error 1


=== Sun Aug 16 23:37:50 HST 2015
Difficulties of compiling netgen source package is purely from Togl library.
In "configure" file of netgen, Togl version is specified as 1.7, but it does require functions included in Togl 2.0.


To overcome this issue, install Togl1.7 in
/opt/Togl1.7
make a link to it in /usr/lib
$ cd /usr/lib
ln -s /opt/Togl-1.7  /usr/lib/Togl1.7

Go do /opt/Togl-1.7 and make a link of Togl library:
$ ln  -s  libTogl1.7.so  libTogl.so

Then the next is OpenGL:
http://xed.ch/help/opengl.html#check

 

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