Command line interface

The library also includes a command line interface for easy access to some functionalities, and the convenience of using qim3d directly from your terminal.

This offers quick interactions, making it ideal for tasks that require efficiency or when certain functionalities need to run on a server.

Example

Command

qim3d gui --data-explorer

Graphical User Interfaces

qim3d gui

Reference

The GUIs available in qim3d are built using Gradio: https://github.com/gradio-app/gradio

@article{abid2019gradio,
title = {Gradio: Hassle-Free Sharing and Testing of ML Models in the Wild},
author = {Abid, Abubakar and Abdalla, Ali and Abid, Ali and Khan, Dawood and Alfozan, Abdulrahman and Zou, James},
journal = {arXiv preprint arXiv:1906.02569},
year = {2019},
}

Arguments	Description
--data-explorer	Starts the Data Explorer
--iso3d	Starts the 3D Isosurfaces visualization
--local-thickness	Starts the Local thickness tool
--anotation-tool	Starts the annotation tool
--layers	Starts the tool for segmenting layers
--host	Desired host for the server. By default runs on 0.0.0.0
--platform	Uses the Qim platform API for a unique path and port depending on the username

Example

Here's an example of how to open the Data Explorer

Command

qim3d gui --data-explorer

Output

Running on local URL:  http://127.0.0.1:7860

In this case, the GUI will be available at http://127.0.0.1:7860

Example

Or for the local thickness GUI:

Command

qim3d gui --local-thickness --host 127.0.0.1 --platform

Output

{'username': 'fima', 'jupyter_port': '57326', 'gradio_port': '47326'}


╭────────────────────────╮
│ Starting gradio server │
├────────────────────────╯
├ Gradio
├ Using port 47326
╰ Running at 10.52.0.158

http://127.0.0.1:47326/gui/fima/47326/
INFO:     Started server process [1534019]
INFO:     Waiting for application startup.
INFO:     Application startup complete.
INFO:     Uvicorn running on http://127.0.0.1:47326 (Press CTRL+C to quit)

In this case, the GUI will be available at http://127.0.0.1:47326/gui/fima/47326/

Data visualization

The command line interface also allows you to easily visualize data.

qim3d viz

Reference

Volumetric visualization uses itk-vtk-viewer and K3D.

You can launch volumetric visualizations directly from the command line. By default, it will launch the itk-vtk-viewer, but k3d can be selected by passing the argument --method k3d.

Info

If itk-vtk-viewer is not installed, you will be prompted for automatic installation via the qim3d library.

Argument	Description
source	Path to the volume file or OME-Zarr store (any image format supported by qim3d.io.load()).
--method	Visualization method: itk-vtk-viewer (default) or k3d.
--destination	Custom .html file to be saved when using k3d. By default, k3d.html is saved. An file is aways saved when calling k3d.
--no-browser	Prevent the file from opening automatically when finished.

Visualization of a OME-Zarr store

Command

qim3d viz Okinawa_Foram_1.zarr/

Output

itk-vtk-viewer
=> Serving /home/fima/Notebooks/Qim3d on port 3000

    enp0s31f6 => http://10.52.0.158:3000/
    wlp0s20f3 => http://10.197.104.229:3000/

Serving directory '/home/fima/Notebooks/Qim3d'
http://localhost:8042/

Visualization url:
http://localhost:3000/?rotate=false&fileToLoad=http://localhost:8042/Okinawa_Foram_1.zarr

A new tab in the default browser will be open with the visualization:

Example using k3d

Command

qim3d viz blobs_256x256x256.tif --method k3d

Output

Loading data from cement_128x128x128.tif
Loading: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.02MB/2.02MB  [00:00<00:00, 936MB/s]
Volume using 2.0 MB of memory

System memory:
• Total.: 31.0 GB
• Used..: 18.8 GB (60.8%)
• Free..: 12.1 GB (39.2%)
Done, volume shape: (128, 128, 128)

Generating k3d plot...
Done, plot available at <k3d.html>
Opening in default browser...

And a new tab will be opened in the default browser with the interactive k3d plot:

Or an specific path for destination can be used. We can also choose to not open the browser:

Example

qim3d viz cement_128x128x128.tif --destination my_plot.html --no-browser

Output

Loading data from cement_128x128x128.tif
Loading: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.02MB/2.02MB  [00:00<00:00, 909MB/s]
Volume using 2.0 MB of memory

System memory:
• Total.: 31.0 GB
• Used..: 18.9 GB (61.1%)
• Free..: 12.0 GB (38.9%)
Done, volume shape: (128, 128, 128)

Generating k3d plot...
Done, plot available at <my_plot.html>

This writes to disk the my_plot.html file.

File preview

Command line interface, which allows users to preview 3D structers or 2D images directly in command line.

qim3d preview

Arguments	Description
--axis	Specifies from which axis the slice will be taken. If the object is 2D image, then this is ignored. Defaults to 0.
--slice	Specifies which slice will be displayed. If the number exceeds number of slices, the last one is taken. Defaults to the middle slice.
--resolution	How many characters will be used to display the image in command line. Defaults to 80.
--absolute_values	If values are low the image might be just black square. By default maximum value is set to 255. This flag turns this behaviour off.

Example

Command

qim3d preview blobs_256x256x256.tif 

Example

Command

qim3d preview blobs_256x256x256.tif --resolution 30

Example

Command

qim3d preview blobs_256x256x256.tif --resolution 50 --axis 1

Example

Command

qim3d preview blobs_256x256x256.tif --resolution 50 --axis 2 --slice 0

Example

Command

qim3d preview qim_logo.png --resolution 40