serhii.net

EDIT: this may be all wrong, in the debugger I can just edit the code and it gets automatically used by slicer — logical, since it’s just a CLI script.

It’s the .xml with the interface that’s problematic and it can’t be reloaded using the method below, or at least I couldn’t.

A scriptedcli module imported to Slicer doesn’t show for me the usual “reload” buttons as seen in scripted modules in dev. mode. To develop, I need my changes I need to reload it w/o restarting 3dslicer.

Based on this more complete example¹ linked in the script repository²

>>> mpath = "/full/path/to/the/my_module.py"
>>> factoryManager = slicer.app.moduleManager().factoryManager()
>>> factoryManager.registerModule(qt.QFileInfo(mpath))
>>> factoryManager.loadModules(["my_module"])
True

BONUS:

• To debug such a module using pycharm, adding the pydev lines inside it works (and official slicer debug extension doesn’t):

import pydevd_pycharm
pydevd_pycharm.settrace('localhost', port=5678, stdoutToServer=True, stderrToServer=True)

Links

• GUI
  • XML reference Documentation/Nightly/Developers/SlicerExecutionModel - Slicer Wiki

Debugging

TL;DR Pycharm Professional instructions work

• These instructions: SlicerRt/SlicerDebuggingTools: Extension for 3D Slicer containing various tools for module development and debugging¹
  • No need to change anything in module code
• During debugging everything freezes
• You can use pycharm python CLI to look around etc. — neat!

not TL;DR

• SlicerRt/SlicerDebuggingTools: Extension for 3D Slicer containing various tools for module development and debugging¹
  • needs pycharm Pro
  • SlicerDebuggingTools/PyDevRemoteDebug/PyDevRemoteDebug.py at master · SlicerRt/SlicerDebuggingTools
  • source of the 3dslicer bits
• pdb-attach · PyPI can attach to random programs,
  • os.getpid() is my friend
• Documentation/4.5/Developers/FAQ/Python Scripting - Slicer Wiki at some point it was possible to use python-remote-pdb
• ionelmc/python-remote-pdb: Remote vanilla PDB (over TCP sockets). 2y ago last commit
• I can use these same instructions mostly for pdb-attach, I see no reason it shouldn’t work, python is python
• it Kiiiinda works but breaks after the first button
• Giving up for now
• Update: installed Pycharm Pro, works!
  • Pycharm Pro egg was in /opt/pycharm-professional/debug-eggs/pydevd-pycharm.egg

Basics

Starting Slicer

Loads the module automatically (for some reason doing it manually doesn’t preserve it across restarts?..)

Slicer  --additional-module-path /path/to/my/extension/one/lower/than/what/i/would/pick/in/Slicer/GUI

Logging

• Not directly mentioned in the help because they state it’s always better to use the debugger²
• Slicer/Base/Python/slicer/slicerqt.py at main · Slicer/Slicer has the slicer setup
• I can do logging.warning("test") in the python console and it works
• Slicer settings allow changing the loglevel of its python console!

Module types: CLI modules

Different types of modules exist: Module Overview — 3D Slicer documentation

In the first tests there was a lot of latency.

Solution: CLI modules (not extensions) that can run in the background and whose status can be queried, which can be added to new extension from extension editor.

Now I understad this better:

• CLI modules are simple I/O, non-blocking, that’s where the networkig logic should go to
• scripted are python scripts with GUIs

• This bit about running CLI in the backgroundPython FAQ — 3D Slicer documentation

Looking into the sample code

Module of type scripted

• Created an extension of type cmake, to which I added a module of type scripted. It’s the sample thresholding extension
  • Base class: Slicer/Base/Python/slicer/ScriptedLoadableModule.py at main · Slicer/Slicer
• Sample data
  • It shows how to add sample data to the extension for testing
  • It can then be found in the Sample Data module, named after the extension itself!

Module of type scriptedCLI

• I hope it’s the same as type CLI, but only with python

• I think it’s lassoan/SlicerPythonCLIExample: Example extension for 3D Slicer that demonstrates how to make a Python script available as a CLI module

• Is a CLI script w/ an XML that has module metadata + examples

  • CLI module goes in the same examles menu
  • and a basic UI has been generated for it? Wow
  • Running it from the UI actually shows a progress bar and it doesn’t block the interface! Woohoo!

• Adding it added it to CMakeLists.xml: add_subdirectory(my_scripted_cli)

• python dev tools actually show the CLI used to run a CLI module!

  • the input arguments are filepaths, and slicer automatically generates and then deletes temporary files for this when running

• can’t debug it the usual way, I guess I’ll have to add the pydevd-pycharm things to the code

[VTK] /opt/3dslicer/bin/python-real /home/.../cli_model_service.py /tmp/Slicer-sh/IACHCI_vtkMRMLScalarVolumeNodeD.nrrd 1 /tmp/Slicer-sh/IACHCI_vtkMRMLScalarVolumeNodeF.nrrd 

(Auto-creating) GUI

• Slicer/Docs/developer_guide/parameter_nodes/gui_creation.md at main · Slicer/Slicer seems interesting

• CLI modules have an interface specified by the .xml file, and the interface is generated based on it

  • couldn’t find any documentation on how to write the XML: Documentation/Nightly/Developers/SlicerExecutionModel - Slicer Wiki

• Bits about the XML

  • channel is either input or output, and only for pics.
  • No parameter names, just their index

• If I read the volume as volume, it uses the .nrrd file extension by default — and I want .nii

  • Script repository deals with these settings, but I can’t use them from within a CLI module Script repository — 3D Slicer documentation

Auto-loading the module at startup

Module from console with arguments - Support - 3D Slicer Community

Slicer.exe --python-code "selectModule('SampleData'); getModuleGui('SampleData').setCategoryVisible('BuiltIn', False)"

File operations

Script repository — 3D Slicer documentation:

# Create a new directory where the scene will be saved into
import time
sceneSaveDirectory = slicer.app.temporaryPath + "/saved-scene-" + time.strftime("%Y%m%d-%H%M%S")
if not os.access(sceneSaveDirectory, os.F_OK):
  os.makedirs(sceneSaveDirectory)

Inspiration

• User_Manual.md · develop · OpenDose / SlicerOpenDose3D · GitLab
  • openDose3D is a cool example extension that shows many things
• SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py at main · lassoan/SlicerTotalSegmentator

  		outputSegmentation.AddDefaultStorageNode()
  		outputSegmentation.GetStorageNode().SetFileName(output_segmentation_path)
  		outputSegmentation.GetStorageNode().ReadData(outputSegmentation)
  

Useful bits from documentation

• There’s a node type for tables
  • statistics become a table
  • also: many modules exist
    • Documentation/Nightly/Extensions/MeshStatistics - Slicer Wiki / DCBIA-OrthoLab/MeshStatisticsExtension
      • does a lot including creating a table GUI programmatically and CSV export etc.
• Colors: are not just colors, but class/label names as well

• 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.