01/02/2023

How to get a matplotlib colormap into inkscape.

Inelegant, but works.

TL;DR: let python create an SVG file with a rectangle that uses the colormap as a gradient. Open, import or copy in inkscape.

Python code (this one gives coolwarm012.svg in your working directory):

ncol=12 #number of stops
grad='coolwarm' #name of matplotlib gradient
from matplotlib import colors, cm
import numpy as np

stopstr="""  <stop
    style="stop-color:%s;stop-opacity:1"
    offset="%.4f"
    id="stop%03d" />"""

init="""<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<svg
   width="1cm"
   height="1cm"
   viewBox="0 0 1 1"
   id="svg">   
  <defs id="defs">
    <linearGradient
       id="%s%03d">
"""%(grad,ncol)

exit="""
</linearGradient>
</defs>
<rect
       style="fill:url(#%s%03d)"
       id="rectangle"
       width="1"
       height="1"
       x="0"
       y="0"/>
</svg>"""%(grad,ncol)

cmap = cm.get_cmap(grad, ncol)   
spac=np.linspace(0,1,ncol)

#saves  <gradientname+numberofstops>.svg with a 1x1cm^2 rectangle using the gradient 
with open('%s%03d.svg'%(grad,ncol),'w') as f:
    f.write(init)
    for i in range(cmap.N):
        rgba = cmap(i)
        hexcol = colors.rgb2hex(rgba)
        f.write(stopstr%(hexcol,spac[i],i))
    f.write(exit)

Some code taken from https://stackoverflow.com/questions/33596491/extract-matplotlib-colormap-in-hex-format

18/02/2022

How to convert a LaTeX beamer presentation with videos to PPTX using Python

Update: The crash issue appears to be fixed in recent LibreOffice. So there is really no reason to do all of the below any more, hooray. See updated howto.

First, why on earth would you want to do that?

The American Physical Society insists that you upload PPTX slides to their conference server and LibreOffice crashes every time I try to import a movie. The developers on the LO forums say it's not their problem because it works with ODP. Glad you asked.

You'll need pdftoppm (or similar, comes with poppler) and the python-pptx and PIL modules. Also, FFMPEG if your movies still need conversion.

First, create page images, in bash:
pdftoppm mypresentation.pdf img -png -r 250

The output is a series of img-1.png, ...,img-n.png. Resolution is here 250.

If necessary, convert all movies to something PowerPoint will digest. Other containers and codecs might work as well, but my Windows failsafe is WMV2.

ffmpeg -i input.avi -codec:v wmv2 -b:v 2000k output.wmv

Batch conversion:

for m in *.avi; do ffmpeg -i $m -codec:v wmv2 -b:v 2000k ${m%avi}wmv; done

We'll assume that we have movie1.wmv and movie2.wmv on slide 2 and movie3.wmv on slide 5.

Now for the tedious bit - determine the bounding box (left, top, width, height, in px) for each movie on the img-1.png and img-5.png slide images. I just used gwenview's crop tool.

Now for the python script:

from pptx import Presentation
from pptx.util import Inches
from glob import glob
from PIL import Image

prs = Presentation()
prs.slide_width = Inches(16) #assuming 16:9 aspect ratio
prs.slide_height = Inches(9)

blank = prs.slide_layouts[6]

imgs = sorted(glob("img*.png"))
w,h=Image.open(imgs[0]).size
# conversion factor for pixel values to inches.
pxtoin=16./w
slides={}

# did the movie-slide attribution via some kind of messy dictionary/list construction. Use the top,left,width,height values determined above.
movies={4:[['movie3.wmv',[626,323,1263,708]]],
        1:[['movie1.wmv',[155,324,710,710]],['movie2.wmv',[1163,324,710,710]]]}

for i in range(len(imgs)):
   slides[i] = prs.slides.add_slide(blank)
   # add the slide contents as bitmaps
   pic = slides[i].shapes.add_picture(imgs[i], 0, 0, height=prs.slide_height)
   try:
      for it in movies[i]:
         movie = slides[i].shapes.add_movie(it[0],*[Inches(r*pxtoin) for r in it[1]])
   except KeyError: pass

prs.save("test.pptx")



This got me a minimum working presentation when I tested it on a remote Windows machine, apart from the fact that the movies had ugly speaker icons instead of poster images. There's a poster_frame_image keyword in add_movie where you can provide an image filename, but it didn't seem to change anything.

Sources:

The python-pptx documentation has a lot of basic use cases. https://python-pptx.readthedocs.io/










23/01/2020

Installing external python modules for Blender

Blender comes with its own Python, and it's not necessarily your system's, so just symlinking system packages like matplotlib is risky and cumbersome.
Some Googling Stackoverflow provided me with the following approach:
  • create a (temporary) virtual environment (VE) linking against Blender's python executable
  • within that VE, pip install the packages you need, but into a folder in Blender's Python path (e.g. the one in ~/.config)
  • I'd keep the VE, but Blender doesn't need it to be active to run.

In code (I keep Blender in ~/.local/bin, adapt to your setup), for matplotlib (You might have to run blender once at first to create the file structure in .config):
virtualenv --python=~/.local/bin/blender-2.81a/2.81/python/bin/python3.7m ve-blender
source ve-blender/bin/activate
mkdir -p ~/.config/blender/2.81/scripts/modules/
pip install --upgrade -t ~/.config/blender/2.81/scripts/modules/ matplotlib
deactivate


Run Blender.

Update: When I tried to do this with pickle5,  gcc failed via "Python.h: No such file or directory".

Fix: within the active VE, determine the Blender Python version (python -V).
Download the respective sources (e.g. 3.7.7) from www.python.org. and unpack.
Copy the contents of the Include directory to ~/.local/bin/blender-2.81/2.81/python/include/python3.7m/ (adapt versions and paths).

Next update:

Broken pip after initializing the virtual environment. Fixable via pip's bootstrap installer:
curl -sS https://bootstrap.pypa.io/get-pip.py | python3

Sources:
https://stackoverflow.com/questions/1534210/use-different-python-version-with-virtualenv
https://blender.stackexchange.com/questions/132278/how-to-make-use-of-custom-external-python-modules-in-blender-or-an-add-on-on-lin

https://blender.stackexchange.com/questions/81740/python-h-missing-in-blender-python 

https://stackoverflow.com/questions/49478573/pip3-install-not-working-no-module-named-pip-vendor-pkg-resources

26/10/2019

IcyBox IB-RD3621U3 RAID1 with Ubuntu 16.04

RAID is not backup, yeah, yeah, yeah…
Still, my laptop is bursting its 512GB SSD and anything is better than my current backup method of randomly distributing copies of important data on external USB drives in various states of health.

I settled on a mid price solution, two 4TB Seagate Barracuda and an IcyBox  IB-RD3621U3 RAID enclosure, for about 250€ in total.  Rsynced to a 4TB WD mobile drive I keep in daily use.
Setup procedure:
  1. S.M.A.R.T. self test. Note: the IcyBox board is not Smart capable. To do a full initial self test on the drives, plug them into a desktop SATA. (smartctl -d sat provides output, but the test will fail)
  2. Disk installation in the drive: note - there are handy stickers 'HDD1' and 'HDD2' in the box. Label your disks to correspond with the HDD1 and 2 labels on the front of the IcyBox.
  3. RAID mode:
    Switch the box off (1). Set the pins under MODE (2) to RAID1. Hold OK (3) pressed, switch the box on (1) and keep holding OK until the LED band at the front has stopped blinking in red (should take about 10 seconds)
     
  4. Connect to a computer. The box should now register as a single drive in GParted, which you can format at will.
  5. Note: GParted via the Dell XPS USB-C dongle hell didn't work too well, failed at creating the partition table.


11/06/2019

KCM Wacom settings on (K)ubuntu 16.04

There's a handy KDE System Settings module for configuring Wacom tablets - calibration, screen areas, you name it. I was rather keen to have it handle my old Graphire4 on a multi screen setup on my work desktop (Ubuntu 16.05).
Sadly, the wacomtablet package (https://github.com/KDE/wacomtablet) seems to have been dropped from the repos between 14.04 and 19.04 due to ongoing bugfixes in dependencies. They do offer instructions for manual compiling - with dire warnings that there'd there be no easy uninstall. 'make uninstall' worked nicely, though.
However, I kept running into missing headers etc., until I found the one version that worked, 2.9.82.

Command line log:
wget https://github.com/KDE/wacomtablet/archive/v2.9.82.zip 
unzip v2.9.82.zip 
cd wacomtablet-2.9.82 
mkdir build 
cd build  
cmake ../ -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DKDE_INSTALL_USE_QT_SYS_PATHS=ON 
make 
sudo make install

Et voilĂ !

23/04/2019

XPS13 webcam doesn't wake up (BIOS fix)

The XPS13 9370 (summer 2018's model) webcam is horrible anyway (still stuck at the bottom of the display). However, it didn't help that it stopped working when the laptop resumed after suspend (all Kubuntu versions I used from 18.04 upwards).
According to this Dell support discussion, it was a BIOS problem that was fixed in BIOS 1.5.0 - I had 1.3.3. Updating seems to have fixed the problem.
Steps:
Get the current BIOS installer from here.
Put it on a flash drive (unless you've got a USB-C one, the Dell dongle works. MicroSDs don't)
Plug in your power supply.
Press F12 during re-boot, select BIOS Flash Update. There should be a drop-down menu top left on the next screen that lets you select and browse the flash drive. Pick the EXE installer. Install. Reboot.

do-release-upgrade or don't

I couldn't resist the lure of the Dingo, but it took me some time to get there. Long story short: do-release-upgrade is a picky bitch. It kept and kept and kept coming up with a "Your python3 install is corrupted. Please fix the '/usr/bin/python3' symlink." message. That message is produced by a script downloaded into /tmp during the installation process and IMO *should* just make sure that the /usr/bin/python3 symlink points to a correct python binary (might have to be 3.6). After all, the update scripts have a "#!/usr/bin/python3" header.
However, over the years, people have had to resort to the weirdest workarounds:
  • Make sure /usr/bin/python and /usr/bin/python3 point to python3.6
  • Reinstall default python3 
  • Purge anything done by update-alternatives (sudo update-alternatives --remove-all python)
  • Purge python2.x
Reader, I tried all of them.
update-alternatives --display python
sudo update-alternatives --remove-all python
sudo apt install --reinstall ubuntu-release-upgrader-core
sudo apt install --reinstall python3
sudo ln -sf /usr/bin/python3.6 /usr/bin/python
sudo ln -sf /usr/bin/python3.6 /usr/bin/python3
sudo apt-get remove --purge python2.7-minimal
In the end, purging python2.7 did the trick. That involved uninstalling inkscape and bits of TeXlive, but it was a small list of dependencies that could be reinstalled after the update. Still, a mess. Serves me right for not bothering to do a clean reinstall.

11/04/2019

articletitle, article-title, gnah!

Joseph Wright is an awesome person who provides handy biblatex styles for numerous journals.
Some of those require article titles in the submission reference list which are later removed for publication, so it makes sense to put in a switch when you load the package:
\usepackage[style=science,articletitle=true]{biblatex}
(the switch is defined in the science.bbx file, btw.) All hunky dory,  except for the fact that the most recent texlive shipping with ubuntu (TeXLive 2018.20180824) still provides biblatex-science from 2016, where the switch is called article-title. I hope the newest versions get into TexLive soon, apparently he's done quite a bit of cleanup.
https://github.com/josephwright/biblatex-science/issues/1
Update: Fixed in the TeXlive 2018.20190227 that came with the Dingo upgrade. Gnah. Now my work desktop and laptop have different versions of the script.