Scientific Computing

Disable text wrapping in nano

Word wrapping in nano text editor can make scripts and files fail to run/parse properly. A simple edit can goof up a config or script by adding unwanted newlines. These settings are in general good for nano on any operating system.

Disable text wrap in nano by adding to ~/.nanorc

set nowrap

A suggested ~/.nanorc contains the following for good defaults including Python coding:

set constantshow
set tabsize 4
set nowrap
set tabstospaces
  • constantshow: show line and column of cursor position (on old nano version as in Red Hat 7, this option may not be recognized)
  • tabsize 4, tabstospaces: make tabs into 4 spaces
  • nowrap: disable long-line text wrapping

Nano syntax highlighting is enabled with include statements in ~/.nanorc.

WINE serial port links

WINE creates serial port softlinks( automatically.

Serial port mapping is managed via

WINEPREFIX=~/.wine wine regedit

Be sure to include the WINEPREFIX (default is ~/.wine)

Which WINE serial port to use: find the WINE serial port corresponding to the Linux serial port device name by watch log output from:

dmesg -w

when plugging in the serial ↔ USB adapter.

Using WINEPREFIX, start the WINE registry editor:

WINEPREFIX=~/.wine wine regedit

Configure the port–if the device is seen at /dev/ttyUSB0, and you want it to appear to WINE on COM1, edit HKEY_LOCAL_MACHINE\Software\Wine\Ports to have a new string entry named COM1 with value /dev/ttyUSB0.

Verify this setting (but do not edit) by:

ls ~/.wine/dosdevices

where again ~/.wine is the location of your WINEPREFIX.

64-bit Irfanview in WINE on Ubuntu

Irfanview is a popular Windows image viewing/editing program that works well on Linux via WINE. IrfanView requires MFC42, install by:

winetricks mfc42

Download and install IrfanView:

wine iview*x64_setup.exe

For more complex setups using winecfg, it’s best to use a separate WINEPREFIX.

Map coordinate convert Python, Matlab, Fortran

Over the past few years we have created and refined open-source map coordinate conversion programs that are independently available for:

These programs use syntax similar to the $1000 Matlab Mapping and Aerospace Toolboxes, while being independently developed as open-source software. We use continuous integration on each package to help ensure quality results.

The functions available include

aer2ecef  aer2enu  aer2geodetic  aer2ned
ecef2aer  ecef2enu  ecef2enuv  ecef2geodetic  ecef2ned  ecef2nedv
ecef2eci  eci2ecef  eci2aer  aer2eci
enu2aer  enu2ecef   enu2geodetic
geodetic2aer  geodetic2ecef  geodetic2enu  geodetic2ned
ned2aer  ned2ecef   ned2geodetic
azel2radec radec2azel
vreckon vdist
lookAtSpheroid
track2

Extracting raw images from PDF

Instead of low-quality screen-shots a PDF to get the images, use Poppler to extract the original high-resolution images from the PDF. Note: only raster images can be exported with Poppler.

Examples of PDF image extraction tasks:

List all PDF images:

pdfimages -list in.pdf

Extract PDF images from all pages, dumping all images in mydoc.pdf to the same directory. Filenames start with out-. There might be a lot of images.

pdfimages -all in.pdf out

Extract PDF images from specific pages: example is for page 3 only:

pdfimages -all -f 3 -l 3 in.pdf out
-f
first page to extract
-l
last page to extract

Install Poppler:

  • Linux: apt install poppler-utils
  • macOS / Linux (Homebrew): brew install poppler
  • Windows: use WSL poppler

Related: extracting a page(s) from PDF

Joining PDF files into one

Join multiple PDF files into one:

pdfunite one.pdf two.pdf three.pdf joined.pdf

pdfunite is obtained by installing Poppler:

  • Linux: apt install poppler-utils
  • macOS: brew install poppler
  • Windows: WSL poppler

recursive convert DOC, DOCX to PDF

We have created Python scripts in LibreOffice Utils that recursively search for files matching a glob pattern (such as *.docx) and convert or print these input documents. They use LibreOffice in headless (console) mode, just a single Terminal command.

  • doc2pdf.py: recursively converts directories containing DOC, DOCX, RTF or other word processing files to PDF.
  • doc2print.py: recursively print documents to the default printer

xarray NetCDF LRU cache replaced autoclose

Python code using xarray.open_dataset() or xarray.open_dataarray() or similar functions reading from NetCDF4 use an LRU cache that automatically closes unneeded files.

As of xarray 0.11.0, the obsolete autoclose=True option should no longer be used.

Problems fixed by LRU cache: the LRU cache used to open NetCDF4 files with xarray fixes these problems, and gives high performance:

  • random segmentation fault while reading NetCDF4 .nc files, where the same file is reopened in the program.
  • OSError from too many open files, where even increasing ulimit doesn’t help

Animate imagesc movies in Matlab

The pause() Matlab / Octave statement causes figures to refresh.

%% create data, 25 frames of 512x512 pixels
data = rand(512,512,25);

%% create blank image
h = imagesc(data(:,:,1));

%% for loop to play "movie"
for i = 1:size(data,3)
  set(h, cdata=data(:,:,i)) % update latest frame
  pause(0.01) % feel free to reduce, but keep greater than 0 to ensure redraw
end

Related: animate plots in Matplotlib