serhii.net

• Main links

  • Extensions — 3D Slicer documentation¹
  • Extensions Manager — 3D Slicer documentation²

• slicerrc.py is a thing! sample: 3D-Slicer-Scripts/.slicerrc.py at master · jzeyl/3D-Slicer-Scripts · GitHub

• Slicer custom application deployment to many computers - Development - 3D Slicer Community

  • SlicerQReads.exe --python-code "folder='S:\SlicerQREADS\TestImages'; import os; slicer.util.loadVolume(folder + '/' + os.listdir(folder)[0], {'singleFile': False})"
  • alternatively: Slicer.exe --python-script "/full/path/to/myscript.py" --no-splash --no-main-window³

• Slicer can run in Docker⁴

• Slicer can run in webbrowser⁵

• Slicer can run in jupyter⁵, including partially (e.g. only a single view etc!)

Slicer --help:

  --testing                                     Activate testing mode. It implies --disable-settings and --ignore-slicerrc. (default: false)
  --disable-python                              Disable python support. This is equivalent to build the application with Slicer_USE_PYTHONQT=OFF.
  --python-script                               Python script to execute after slicer loads.
  --python-code                                 Python code to execute after slicer loads.
  -c                                            Python code to execute after slicer loads. By default, no modules are loaded and Slicer exits afterward.
  --ignore-slicerrc                             Do not load the Slicer resource file (~/.slicerrc.py).
  --additional-module-path                      Additional module path to consider when searching for modules to load.
  --additional-module-paths                     List of additional module path to consider when searching for modules to load.

• Slicer modules — todo, CLI things with easy arguments

  • Documentation/Nightly/Developers/Modules - Slicer Wiki

• Slicer extensions/modules creation

  • Developing extension in 3D Slicer - Google Slides presentation
    • 
    • Sharing extensions there: TL;DR use slicer publishing thing to publish to own repo, then PR to slicer main extensions index repo (GitHub - Slicer/ExtensionsIndex: Slicer extensions index)
      • Sample JSON: ExtensionsIndex/SurfaceWrapSolidify.json at main · Slicer/ExtensionsIndex · GitHub
      • Pull requests · Slicer/ExtensionsIndex has code for existing recent extensions that may be useful

• Extension manager

  • Extensions Manager — 3D Slicer documentation ²
  • Can have different extension server URI!
  • Updating:
    • Extensions Manager — 3D Slicer documentation
    • TL;D/R extension manager can do that incl. automatically

• CI/CD exists for extensions published officially

• Misc:

  • Script repository — 3D Slicer documentation has sample uses of slicer CLI!
  • 3D-Slicer-Scripts/.slicerrc.py at master · jzeyl/3D-Slicer-Scripts · GitHub

• Script repository — 3D Slicer documentation has this:

  • This code snippet can be useful for sharing code in development without requiring a restart of Slicer.

  • gist.githubusercontent.com/pieper/a9c0ba57de3833c9f5aea68247bda597/raw/82d73d85340ffd205b01fc339b096a8607cfe02b/InstallSlicerModuleFromGit.py
  • TODO, does this mean updating extensions without restart?
  • EDIT: I can reload the code of the extension as-is

• Fazit:

  • extensions can be built (C++) or not (python)
  • enabling:
    • add to CLI path to “additional module paths” path to place where .py extension is locally
      • git pull etc.?
      • get a .zip from the repo and use the python code to get it from there and update
    • make our own extension manager repo thing and use automatic updating functionality

• Other bits

  • Making Slicer simpler by hiding many things: Simple 3D Slicer based image viewer
  • And hiding a module UI: Slicer/Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py at 022a4f1a347ebb24509a50f6c8928ae26d3c5955 · Slicer/Slicer

inotifywait(1) - Linux man page

#!/bin/sh
while inotifywait --format '%:e %f' p.* *.bib; do
  sleep 1  # files get moved often
  echo "rsync!"
  rsync -avzirh --progress  p.* *.bib me@server.net:dir
done

boltctl monitor shows changes as they happens — nice when something breaks. I used to do a lot of watch boltctl list before in this exact scenario

(having a monitor subcommand in your thing says a lot about stuff, actually, — the best interpretation is that it’s written with developers in mind)

Very proud of this idea, haha :)

For absolute positioned elements one needs to “guess” the correct sizes etc., may not be trivial. Using a pixel ruler won’t help because the .absolute coords don’t map to the screen ones.

Solution:

.grid {
  // https://stackoverflow.com/questions/4191260/drawing-a-grid-using-css
  background-image:
    repeating-linear-gradient(lightblue 0 2px, transparent 2px 100%),
    repeating-linear-gradient(90deg, lightblue 0 2px, transparent 2px 100%);
  background-size: 50px 50px;
  //border: 2px solid red;
}

.smallgrid {
  background-image:
    repeating-linear-gradient(#ccc 0 1px, transparent 1px 100%),
    repeating-linear-gradient(90deg, #ccc 0 1px, transparent 1px 100%);
  background-size: 10px 10px;
  width: 100%;
  height: 100%;
}

::::: {.absolute left=0 right=0 top=0 bottom=0 .grid}
::: {.smallgrid}
:::
:::::

It’s not exactly aligned but close enough to judge the widths and heights involved!

Rectangle in the pic is:

:::: {.redrect .absolute right=200 top=130 width=200 height=100}
::::

(And the small grid can be omitted if not needed by removing the div in the middle. )

For bonus points, can be saved as a file and included if needed:

{\{< include ../_shared/smallgrid.qmd >}\}

ALSO:

// show the border of the slide
.reveal .slides {
  border: 1px dashed red;
}

DAMN.

Figures – Quarto:

:::: {layout="1,1,1],[1],[1,1,1" layout-valign="center"}

if it’s a layout I do get a valign thing. I just have to use layouts, not columns. Damn.

This doesn’t work on SVGs for me:

![](images/02/svgs/02_seqsiii.svg){.absolute top=0 left=0}

This does:

::: {.absolute top=0 left=0}
![](images/02/svgs/02_seqsiii.svg)
:::

SO.

One can literally generate a plot w/ graphviz, export as svg, open and edit in inkscape, save as optimized svg, paste into quarto, and manually add the correct class="fragment" data-fragment-index=4 bits to the relevant groups.

Insert with the usual {=html} thing.

Damn.

LeaderLine

almost works with quarto, except that line.position needs to be called on slide change — ergo likely won’t work in pdf export mode.

maurosilber/pyfragments: Animated figures for Quarto installs as-is

IT WORKS FOR PDF MODE TOO! And uses fragments

# | fig-width: 15
# | fig-height: 10
# | output: asis
import matplotlib.pyplot as plt
from pyfragments import AnimatedFigure

with AnimatedFigure() as ani:
# Data for plotting
  train_loss = [1.0, 0.6, 0.3, 0.2, 0.1]
  val_loss = [1.2, 0.8, 0.5, 0.4, 0.6]
  iterations = [1, 2, 3, 4, 5]

  plt.xlim(0, 6)
  plt.ylim(0, 1.5)

# Labels and legend
  plt.xlabel('Trainingsiterationen', fontsize=14)
  plt.ylabel('Loss', fontsize=14)
  plt.legend(loc='upper right', fontsize=12)

# Plot
  for x in range(len(train_loss)+1):
    with ani.fragment():
      plt.plot(iterations[:x], train_loss[:x], 'bo-', label='Training', linewidth=2)
      plt.plot(iterations[:x], val_loss[:x], 'go-', label='Validation', linewidth=2)

# Add a dashed vertical line in the middle
  mid_iteration = (iterations[0] + iterations[-1]) / 2

  with ani.fragment():
    plt.axvline(x=mid_iteration, color='r', linestyle='--', linewidth=1.5)

I couldn’t make a graph large enough to fill the screen, increasing fig-width didn’t help.

Solution: increase both fig-width and fig-height!

{dot}
//| fig-width: 12
//| fig-height: 9
digraph G {
    rankdir=LR;
	..

Execution Options – Quarto has figure options that lists the default sizes of figures based on output formats. Couldn’t find them because was looking in figures/graphviz etc. pages, not execution. …

For reveal slides, it’s 9 x 5.

Apparently it didn’t want to increase the 5 till I explicitly told it to, then width started increasing as well.

Both superscripts and subscripts

… are hard and you have to use a table.

digraph Neural_Network {
    rankdir=LR;
    ranksep=1.3;
    
    node [shape=circle, style=filled, fontcolor=white, fontsize=25, fillcolor="blue", color="black"];

    subgraph cluster_0 {
        node [fillcolor="#2c3e50", style="filled"];
        x1 [label=<
        <TABLE border="0" cellborder="0" cellspacing="0">
        <TR><TD rowspan="2" style="...">X</TD><TD style="...">1</TD></TR>
        <TR>                                  <TD style="...">1</TD></TR>
        </TABLE>>];
        x2 [label=<
        <TABLE border="0" cellborder="0" cellspacing="0">
        <TR><TD rowspan="2" style="...">X</TD><TD style="...">1</TD></TR>
        <TR>                                  <TD style="...">2</TD></TR>
        </TABLE>>];
    }

    sum [label=<∑<FONT color="yellow" point-size="10">(⎰)</FONT>>,  fillcolor="#27ae60", width=0.8, height=0.8, fixedsize=true];
    y [label=<y<sup>1</sup>>];
    
    edge [style=solid, color="#2c3e50"];
    x2 -> sum;
    x1 -> sum;

    edge [style=solid, color="#27ae60"];
    sum -> y;

    {rank=same; x1; x2;}
}