v1.3.1

New feature

Raw output probabilities

It is now possible to output the raw probability map. Simply do:

lungtumormask input_path output_path --threshold -1

Setting threshold -1 simply ignores the post-processing all together and stores the raw float32 output as a NIfTI file.

Web demo application

A very simple gradio web application was developed, which now has been deployed on HF spaces.

You can access the demo by clicking here.

What's Changed

• macOS-11 CI bump by @andreped in #28
• Replaced gdown with wget for test CI using GitHub for data hosting instead of Google Drive by @andreped in #29
• Developed gradio demo + HF Space integration and continuous deployment by @andreped in #30
• Added missing Dockerfile for HF space deployment by @andreped in #31
• Fixed demo + added demo README + new Dockerfile by @andreped in #33
• Added demo snapshot by @andreped in #34
• Added option to output probability map from CLI by @andreped in #35
• bump v1.3.1 [no ci] by @andreped in #37

Full Changelog: v1.3.0...v1.3.1

v1.3.0

Summary

Main feature include an option to disable the GPU for computation. Other fixes were mostly documentation improvements.

What's Changed

• Docs: README fixes by @andreped in #20
• Add training pipeline by @VemundFredriksen in #21
• Added info regarding training code to README [no ci] by @andreped in #22
• Refactored training README [no ci] by @andreped in #23
• Minor training readme refactor [no ci] by @andreped in #24
• Added training code disclaimer [no ci] by @andreped in #25
• Added CLI arg to disable GPU + bump v1.3.0 by @andreped in #27

New Contributors

• @VemundFredriksen made their first contribution in #21

Full Changelog: v1.2.2...v1.3.0

v1.2.1

What's Changed

• Docs: Resized figures + added info on custom argument usage in CLI to README by @andreped in #15
• Added fraxinus application update to README by @andreped in #17
• Fixed lungmask filtering + set batch size through args + bump v1.2.1 by @andreped in #18

New API

Ability to set batch size, which is especially relevant to accelerate GPU inference:

lungtumormask samples/lung_001.nii.gz mask_001.nii.gz --batch-size 16

Full Changelog: v1.2.0...v1.2.1

v1.2.0

Minor release which should result in more robust and smoothing 3D segmentations, with reduced fragmentation post-interpolation.

What's Changed

• Enable running CI from dispatch by @andreped in #12
• v1.1.3 doc update by @andreped in #13
• Improved morphological post-processing by @andreped in #14

New API

Lungmask filtering is not done by default and there has been added post-processing methods to refine the segmentations.

Example use case:

lungtumormask samples/lung_001.nii.gz mask_001.nii.gz --lung-filter --threshold 0.3 --radius 3

Here we filter tumor candidates outside the lungs, use a lower tumor probability threshold to boost recall, and use a kernel radius of 3 for 2D morhological post-processing.

For more information, see:

lungtumormask -h

Full Changelog: v1.1.3...v1.2.0

v1.1.3

What's Changed

• Support for setting prediction threshold as arg in CLI by @andreped in #9
• Fixed interpolation artifact + added morphological post-processing by @andreped in #10
• Release v1.1.3 by @andreped in #11

Full Changelog: v1.1.2...v1.1.3

v1.1.2

What's Changed

• Fixed model unzipping issues + dependency versioning + Python 3.6-3.10 support by @andreped in #7
• Updated license copyright to include all software authors
• Stricter versioning: torch>=1.10.2,<=1.11 and numpy<=1.23.2

Full Changelog: v1.1.1...v1.1.2

v1.1.1

What's changed

• Fixed dependency versioning - more strict and thus more stable for lungtumormask install
• Removed Python 3.9 for now
• Used older, fixed version of MONAI
• Use lungmask fork - fixed versioning
• Reduced numpy version
• Fixed postprocessing typo in lungmask postprocessing after upgrade
• Use Ubuntu 20.04 in CIs as Ubuntu 18.04 is deprecated
• Ignore .nii files in commits

Full Changelog: v1.1.0...v1.1.1

v1.1.0

What's changed

• Added lung mask postprocessing (removes predicted tumor candidates outside the lung)

Full Changelog: v1.0.0...v1.1.0

v1.0.0

First release of the LungTumorMask command line tool, introduced in the paper "Teacher-student approach for lung tumor segmentation from mixed-supervised datasets" published in PLOS ONE.

The release includes precompiled binaries and source code.

What's Changed

• update README to include arXiv-paper stuff by @andreped in #1
• Update journal by @andreped in #2
• Minor refactoring by @andreped in #3

New Contributors

• @andreped made their first contribution in #1

Full Changelog: 0.0...v1.0.0

Sample Images

Dummy release for sample images