serhii.net

Context: in a paper, using PDF graphics is much better than e.g. PNG, because antialiasing (230628-1313 Saving plots matplotlib seaborn plotly PDF). Assume you need to crop one, and taking a PNG screenshot won’t cut it, because it would defeat the entire purpose.

LaTeX

TL;DR: in \includegraphics, trim=left bottom right top (in cm)

positioning - How can I crop included PDF documents? - TeX - LaTeX Stack Exchange:

includegraphics[clip, trim=0.5cm 11cm 0.5cm 11cm, width=1.00\textwidth]{PDFFILE.pdf}

BUT! If I’m ever in this situation, inkscape can really nicely open a PDF and export only the selected things, also as PDF.

Inkscape (much better)

1. When importing, “Replace text with closest available font”
   • e.g. OpenSans gets matched to Open Sans and it works out usually
   • the full list of fonts is shown in the import window
2. Select the part I want to crop
   1. or create a shape over it and select that shape or something
3. Export selection only as PDF; play with export settings as well if needed but for me the defaults worked this time

And either way

… test the results by downloading the PDF from overleaf and opening it locally, because antialiasing w/ imported vector pictures can be broken from within the preview window.

Usual:

format: 
  revealjs:
    logo: logo.png
    theme: [default, custom.scss]

Adding after the first one, so no !important needed¹:

format: 
  revealjs:
    logo: logo.png
    header-includes: |
      <link href="custom.css" rel="stylesheet">      

Inline w/o declaring classes²:

Some [red words]{style="color:#cc0000"}

or:

::: {style="font-size: 1.5em; text-align: center"}
styling an entire div
:::

• Main Quarto Reveal SCSS: quarto-cli/src/resources/formats/revealjs/reveal/css/reveal.scss at 303c4bc9f52ea0b0c36c5eb5dfbade9cece2b100 · quarto-dev/quarto-cli
• Quarto footer css: quarto-cli/src/resources/formats/revealjs/plugins/support/footer.css at main · quarto-dev/quarto-cli

For yay, the cache is in

$HOME/.cache/yay/

If the package is there, then: sudo pacman -U ./quarto-cli-1.4.555-1-x86_64.pkg.tar.zst

Then pin the package in /etc/pacman.conf:

# Pacman won't upgrade packages listed in IgnorePkg and members of IgnoreGroup
IgnorePkg   = quarto-cli
#IgnoreGroup =

Then yay -Syu will ignore it as well:

:: Synchronizing package databases...
 endeavouros is up to date
 core is up to date
 extra is up to date
 multilib is up to date
:: Searching AUR for updates...
 -> quarto-cli: ignoring package upgrade (1.4.555-1 => 1.5.52-1)
:: Searching databases for updates...
 there is nothing to do

Refs: How do you downgrade an AUR package? : r/archlinux

For not-AUR, there’s the downgrade command: archlinux-downgrade/downgrade: Downgrade packages in Arch Linux

References

• Refs:
  • Revealjs Options – Quarto¹
  • Advanced Reveal – Quarto
  • Revealjs – Quarto
• Previously:
  • 240424-1923 Presentations with Quarto and Reveal.js has my list of tricks
• Code
  • Quarto reveal.scss: quarto-cli/src/resources/formats/revealjs/reveal/css/reveal.scss at 303c4bc9f52ea0b0c36c5eb5dfbade9cece2b100 · quarto-dev/quarto-cli
  • Quarto Reveal footer CSS: quarto-cli/src/resources/formats/revealjs/plugins/support/footer.css at main · quarto-dev/quarto-cli

Misc

Better preview at a specific port, handy for restarting after editing CSS. Similar to quarto project frontmatter preview: port: 4444 browser: false.

quarto preview slides.qmd --port 4444 --no-browser

Supported by default

In frontmatter:

• logo is in bottom-right+
  • footer-logo-link
• footer for all slides
  • overwrite with div of class footer
• Likely relevant for me: Numbering reveajs options for dynamic bits, shift-heading-level-by, number-offset, number-section, number-depth — will touch if I need this.

Headers

• Extension: shafayetShafee/reveal-header: A Quarto filter extension that helps to add header text and header logo in all pages of RevealJs slide²
  • Has absolutely awesome documentation!

In front matter:

• header: one header text for all presentation
• title-as-header,subtitle-as-header: if true, place the presentation frontmatter’s title/subtitle as header if one not provided (overwriting the header value)
  • use-case: I same repeating text everywhere w/o specifying it every time.
• hide-from-titleSlide: all/text/logo to hide it from title slide
• sc-sb-title: if true, h1/h2 slide titles will appear in the slide header automatically when slide-level is 2 or 3

Divs with classes:

• .header: slide-specific header

• Excellent example from its docu of dynamic per-(sub-)section headers:

  • code: reveal-header/example_all.qmd at main · shafayetShafee/reveal-header
  • demo: Quarto Presentations

Left/right/center blocks of text in header

³

• If one uses section/subsection titles, they go in the left third and right third of the header, with the normal header text in the middle. This is neat to have in general, w/o the section/subsection titles.
  • sc-title, on the left, is section title
  • sb-title, on the right, is subsection title
• How do I add arbitrary text there? And what would be a good interface for it?

The right way — extension code

• I could look at the extension, maybe fork it, and find a way to put text in these divs
• Relevant code:
  • This JS populates them in each slide: reveal-header/_extensions/reveal-header/resources/js/sc_sb_title.js at main · shafayetShafee/reveal-header
  • add_header js: reveal-header/_extensions/reveal-header/resources/js/add_header.js at main · shafayetShafee/reveal-header
  • Main lua: reveal-header/_extensions/reveal-header/reveal-header.lua at main · shafayetShafee/reveal-header

Ugly CSS hack

• (Learn sass in Y Minutes)
• CSS for the header bits: reveal-header/_extensions/reveal-header/resources/css/add_header.css at main · shafayetShafee/reveal-header

Since .s[c|b]-title is present always, text added that way will be present on the title slide regardless of settings. … and — adding text to a presentation through CSS is, well, ..

.reveal-header .sc-title {
  background-color: red;

	&::before {
		content: 'sc-title header content';
  }

}

Slightly better ugly hack: main header text split in three, with two aligned l/r correspondingly.

.header-right {
  // text-align: left;
  float: right;
  background-color: pink;
  display: inline-block;
}

.header-left {
  // text-align: left;
  float: left;
  background-color: yellow;
  display: inline-block;
}

::: header 
[left]{.header-left} and not left [and right]{.header-right}
:::

Result:

Extended ugly SCSS hack

Improved the above to support both footer and headers I have a hammer and everything is a nail SCSS can do mixins let’s use them

// L/R margins of the footer — if logo is wider than this, it may overlap right footer text.
// By default, logo max-height is 2.2em, width auto based on this.
$footer-margin: 5em;

// left or right column bits
%hfcol {
  display: inline-block;
}


/* L/R columns in header */
.reveal .reveal-header .rightcol {
  @extend %hfcol;
  float: right;
}

.reveal .reveal-header .leftcol {
  @extend %hfcol;
  float: left;
}

/* L/R columns in footer */
.reveal .footer .leftcol {
  @extend %hfcol;
  float: left;
  margin-left: $footer-margin;
}

.reveal .footer .rightcol {
  @extend %hfcol;
  float: right;
  margin-right: $footer-margin;
}

Usage:

## I am a slide  with custom headers

And With content 

::: footer 
[Left footer]{.leftcol} Center footer [Right footer]{.rightcol}
:::

::: header 
[Left header]{.leftcol} Center header [Right header]{.rightcol}
:::

Frontmatter usage works only for footer, likely header doesn’t support markup.

    footer: "Center footer [right]{.rightcol} [left]{.leftcol}"  # CHANGEME

Result:

PROBLEMS:

• asymmetrical if only one of the two is present. Likely fixable, but I don’t want to force any center div.

Footers through qmd cols

This works almost perfectly, including missing values:

::: footer 

::: {.columns}
:::: {.column width="20%"}
left
::::
:::: {.column width="50%"}
Center footer
::::
:::: {.column width="20%"}
right
::::
:::

:::

It even works inside frontmatter as multiline string (not that it’s a good idea):

    footer: | 
      ::: {.columns}
      :::: {.column width="20%"}
      left
      ::::
      :::: {.column width="50%"}
      FB5 – Informatik und Sprachen: Deep Learning (MDS)
      ::::
      :::: {.column width="20%"}

      ::::
      :::

This removes the margin placing it exactly in the same place as a normal footer:

.reveal .footer p {
  margin: 0 !important;
}

(but headers don’t work)

What is a good interface?

A filter that parses frontmatter and puts things in the correct places.

Misc

• Down the front-end rabbit hole | quartoand.me

For later.

• SenteraLLC/ulabel: A browser-based tool for image annotation is used by the KiTS23 | The 2023 Kidney Tumor Segmentation Challenge for annotation.

Download GitHub directory: paste an URI to the directory, get .zip of that directory only. Handy for downloading only parts of datasets

• nnU-Net Revisited paper lists the following, in bold the ones it considers the best:
  • ACDC, KiTS, AMOS “most suitable for benchmarking”
  • BTCV, LiTS, BraTS

Datasets

ACDC

• Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved? | IEEE Journals & Magazine | IEEE Xplore
• cardiac diagnosis
• 150 (Cardiac) MRI recordings/patients from 5 different diagnosis groups
• 3 classes: LV+RV heart cavities and myocardium
• 4D (3D+time)
• 100/50 patients train/test split
• nifti/.nii
• For each patient:
  • raw+ground truth data for two frames
  • 4d beating raw heart
  • age etc.
• links:
  • Website: ACDC Challenge
  • Dataset official download link: Human Heart Project
  • Their python code to load/save images to nifti (nii) format and compute metrics: https://www.creatis.insa-lyon.fr/Challenge/acdc/code/metrics_acdc.py
• Dataset structure
  • nifti (.nii)
  • sample: https://humanheart-project.creatis.insa-lyon.fr/database/#collection/637218c173e9f0047faa00fb/folder/6372204873e9f0047faa160b
  • folders: training/patient101/ containing
    • Info.cfg
      • metadata about the patient
    • MANDATORY_CITATION.md
    • patient101_4d.nii.gz
      • 3d of the beating heart (+time), viewable animated in the brainbrowser viewer¹
    • patient101_frame01_gt.nii.gz
      • ground truth data only for frame 01
    • patient101_frame01.nii.gz
      • raw data only for frame 01
    • patient101_frame14_gt.nii.gz
    • patient101_frame14.nii.gz

KiTS-23

• existed in 2019 2021 and 2023
  • KiTS23 | The 2023 Kidney Tumor Segmentation Challenge²
  • The main proceedings of the conference/challenge: Kidney and Kidney Tumor Segmentation: MICCAI 2023 Challenge, KiTS 2023, Held … - Google Books
  • The latest publication is from the 2021 challenge
  • // (Interesting anno startegy: professional places markers around the region, non-professional makes it into a pretty segmentation shape)
• KITS2023 dataset repo: neheller/kits23: The official repository of the 2023 Kidney Tumor Segmentation Challenge (KiTS23)
  • they use postprocessing after annotations
  • Sample: kits23/dataset/case_00194 at main · neheller/kits23
  • annotating etc. was done online and the webapp is still live: Annotate | KiTS23
    • They used the ulabel anno tool: SenteraLLC/ulabel: A browser-based tool for image annotation
• Structure
  • raw images must be separately downloaded from servers!
  • nifti/nii
  • 489 train set instances released³ — mostly similar to the files from older challenges
  • 3 classes: kidney, tumor, cyst
  • main metadata for all patients in kits23.json: kits23/dataset/kits23.json at main · neheller/kits23
  • directories are case00000-case00588
    • segmentation.nii.gz is the ground truth as used in the challenge, after postprocessing, the one we need.
    • ./instances/ has annotations — are the raw things annotated by humans.⁴
      • break brainviewer but not brainbrowser
      • [kidney|tumor|cyst]_instance-[1|2|..?]_annotation-[1|2|3].nii.gz
      • N instances — e.g. most people have two kidneys — all annotations done by 3 diff annotators, then merged into the main segmentation file.

TL;DR use Chromium

PDF, PS and DjVu - ArchWiki has a table, but it lies, in my tests:

• zathura explicitly no support
• evince didn’t work
• gnome document viewer didn’t work

And for the Nth time, I end up remembering about Chrome/Chromium PDF viewer, that does this reliably.

• TIL Arch has no cron by default, and uses systemd timers¹.
• cron - ArchWiki

sudo pacman -S cronie
sudo systemctl enable cronie.service

# many minutes were lost due to me forgetting to start it as well...
sudo systemctl start cronie.service

• I like this website to generate stuff:Crontab Generator - Generate crontab syntax
• cronie - Timed Tasks - Documentation as good as any
• the script has to be executable
• crontab -e edits your own crontab, then you can omit the username.

Cron git backup script

#!/bin/bash

# https://stackoverflow.com/posts/1482133/
# get the directory where this file is located
DIRNAME="$( dirname -- "$( readlink -f -- "$0"; )"; )"

cd $DIRNAME &&
git add -A &&
git commit -m "Automatic backup at `date`" &&
git push origin master &&
echo "Done"

# and this is the crontab
# odd hours:
# * 1-23/2 * * *  /bin/bash $HOME/this-script-location.sh > /tmp/cronlog

EDIT: sometimes if git crashes an index file stays and then nothing runs — so the cronjob must be somehow monitored manually, todo.

TL;DR: fish easy version below works, but needs quotes when expression is complex: cc 2+2 but cc 'floor(2.3)'.

I’m continuing to move my useful snippets from zsh to fish (240620-2109 Fish shell bits), and the most challenging one was the CLI python calculator I really love and depend on, since it contained arguments with parentheses (which are fish expressions as well).

Basically: cc WHATEVER runs WHATEVER inside python, can do both easy math a la 2+2 and more casual statistics-y mean([2,33,28]).

Before in zsh this was the magic function:

cc() python3 -c "from math import *; from statistics import *; print($*);"
alias cc='noglob cc'

Fish, easy version:

function cc
  command python3 -c "from math import *; from statistics import *; print($argv);"
end

Works for easy cc 2+2 bits, but as soon as functions and therefore parentheses get involved (cc floor(2.3)) it starts to error out.

[I] sh@nebra~/t $ cc mean([2,4])
fish: Unknown command: '[2,4]'
in command substitution
fish: Unknown command
cc mean([2,4])
       ^~~~~~^
[I] sh@nebra~/t $ cc mean\([2,4]\)

>>> mean([2,4])
3
[I] sh@nebra~/t $

(But I REALLY don’t want to do cc mean\([2, 3]\))

In the zsh snippet, noglob meant basically “take this literally w/o expanding anything”, and it passed everything as-is to python, and this is what fails in my fish solution.

Noglob in fish is fun:

• The fish language — fish-shell 3.7.0 documentation on escaping characters
• Implement the noglob modifier · Issue #3504 · fish-shell/fish-shell:

  If you wish to use arguments that may be expanded somehow literally, quote them. echo ‘’ and echo “” both will print the literal.

• The fish language on quotes:
  • single quotes = no expansion of any kind
    • \' for literals inside single
  • double quotes = variable exp. ($TERM) & command substitution ($(command))
    • \" for literal "s inside double
  • within each other, no special meaning
  • Let’s test:
    • echo (ls) = ls output, one line
    • echo "$(ls)" = ls output, multiline
    • echo '(ls)' = (ls)
    • echo "(ls)" = "(ls)"

THEN

• command python3 -c "from math import *; from statistics import *; print($argv);"

  • cc ceil\(2\) +
  • cc ceil(2) -

• `command python3 -c “from math import *; from statistics import *; print(’$argv’);”

  • literally prints the passed thing w/o python eval, w/ same rules

• OK can I do a variable then?

  set pyc $argv
  echo $pyc
  command python3 -c "from math import *; from statistics import *; print($pyc);"

nope.

Bruteforcing the solution

(and learning to use fish loops mainly, of course there are better ways to do this.)

# list of simple, brackets, and parentheses + no, single, double quotes 
# no space between nums in brackets, python interpreter would add them. [2,3] — literal, [2, 3] — parsed by python
set cmds \
'2+2' \
'\'2+2\'' \
'"2+2"' \
'[2,3]' \
'\'[2,3]\'' \
'"[2,3]"' \
'floor(2.3)' \
'\'floor(2.3)\'' \
'"floor(2.3)"' 

function tcc
  set pyc $argv
  # command python3 -c "from math import *; from statistics import *; print" '(' "$pyc" ');'
  # command python3 -c "from math import *; from statistics import *; print($pyc);"
  command python3 -c "from math import *; from statistics import *; print($pyc);"
end


# loop through all test cases to see sth that works for all
for i in $cmds
  echo $i:
  echo "   $(tcc $i)"
end

At the end, no additional literal quotes + initial command didn’t error out, and we came full circle:

set cmds \
'2+2' \
'[2,3]' \
'floor(2.3)' 

# winner command!
function tcc
  command python3 -c "from math import *; from statistics import *; print($argv);"
end

[I] sh@nebra~/t $ ./test_cc.sh
2+2:
   4
[2,3]:
   [2, 3]
floor(2.3):
   2

• Double quotes in the python command mean only $pyc gets expanded
• $pyc in the working versions have no hard-coded quotes
• in CLI tcc floor(2.3) still fails — because like that it’s a command, not a string. In the file it was inside single quotes, as a string. So I can do this in the CLI as well.

So simple and logical at the end.

Final solution

function cc
  echo ">>> $argv"
  command python3 -c "from math import *; from statistics import *; print($argv);"
end

When using, quotes are needed only for complex bits (parentheses, * etc.).

[I] sh@nebra~/t $ cc 2+2
>>> 2+2
4

[I] sh@nebra~/t $ cc [2,3,4]
>>> [2,3,4]
[2, 3, 4]

# no quotes
[I] sh@nebra~/t $ cc mean([2,3,4])
fish: Unknown command: '[2,3,4]'
in command substitution
fish: Unknown command
cc mean([2,3,4])
       ^~~~~~~~^

# with quotes
[I] sh@nebra~/t $ cc 'mean([2,3,4])'
>>> mean([2,3,4])
3

So I literally had to follow the advice from the first link I found and used single quotes in my initial command:

If you wish to use arguments that may be expanded somehow literally, quote them. echo ‘’ and echo “” both will print the literal.

Still, I learned a lot about fish in the process and honestly am loving it.