Vista3d main (#30)

Fixes # .

### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] In-line docstrings updated.

---------

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: heyufan1995 <[email protected]>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <[email protected]>
Co-authored-by: mingxueg-nv <[email protected]>

.github/workflows/premerge-py-min.yml

@@ -0,0 +1,56 @@
+name: premerge-min
+
+on:
+  # quick tests for pull requests and the releasing branches
+  push:
+    branches:
+      - vista3d
+      - main
+  pull_request:
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: py-min-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  min-dep-py3:  # min dependencies installed tests for different python
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']
+    timeout-minutes: 40
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --user --upgrade pip setuptools wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install the dependencies
+      run: |
+        python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install "monai[all]"
+        python -m pip list
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        python -m unittest -v

.gitignore

@@ -108,6 +108,7 @@ temp/
 runs
 *.gz
 *.pth
+*.pt
 lib/
 pip-wheel-metadata/
 share/python-wheels/

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -27,23 +27,23 @@ repos:
       - id: end-of-file-fixer
       - id: mixed-line-ending
   - repo: https://github.com/psf/black
-    rev: "23.3.0"
+    rev: "24.4.2"
     hooks:
       - id: black
       - id: black-jupyter
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black"]
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.261
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
     hooks:
       - id: ruff
         args: ['--fix']
 
   - repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
       - id: yesqa
         name: Unused noqa
@@ -54,8 +54,7 @@ repos:
           - pep8-naming
         exclude: |
           (?x)^(
-              monai/__init__.py|
-              docs/source/conf.py|
+              .*/__init__.py|
               tests/utils.py
           )$
 

README.md

@@ -11,184 +11,5 @@ See the License for the specific language governing permissions and
 limitations under the License.
 -->
 
-# MONAI VISTA
-
-MONAI **V**ersatile **I**maging **S**egmen**T**ation and **A**nnotation
-
-<div align="center"> <img src="./assets/imgs/demo_gif.gif" width="800"/> </div>
-
-*(We're seeking collaborators.
-If your institution is interested, please fill out the survey: https://forms.office.com/r/RedPQc9fmw)*
-
-### Table of Contents
-- [Overview](#overview)
-- [MONAI VISTA Training and FineTuning](training/)
-- [MONAI VISTA with MONAI Label](#monai-label-integration)
-  - [Step 1. Installation](#installation)
-  - [Step 2. MONAI Label monaivista app](#monai-vista-app)
-  - [Step 3. MONAI VISTA - Label Plugins](#monai-vista-viewer-plugins)
-  - [Step 4. Data Preparation](#sample-data)
-  - [Step 5. Start MONAI Label Server and Start Annotating!](#start-monai-label-server-with-vista-model)
-- [Video Demo](https://drive.google.com/file/d/1rEF1y9ZKo3Kj0Zms_gxkKwHlz75CYjwA/view?usp=sharing)
-- [Community](#community)
-- [License](#license)
-- [Reference](#reference)
-
-## Overview
-
-[MONAI Meetup presentation at MIDL 2023](https://docs.google.com/presentation/d/1evp8txCyTzkqLT0fVE_0eFlXL4hux5myb7ggFhokRFQ)
-
-MONAI VISTA provides domain-specific workflows for building and utilizing foundation models
-for medical image segmentation.
-It leverages state-of-the-art deep learning technology to establish a
-new collaborative approach for developing robust and versatile
- segmentation models and applications.
-
-This repository hosts the ongoing effort of building MONAI VISTA and
-is currently under active development.
-
-
-
-<div align="center"> <img src="./assets/imgs/montage.png" width="800"/> </div>
-
-
-## MONAI Label Integration
-This section provides MONAI Label integration and sample apps. The integration is a server-client
-system that facilitates interactive medical image segmentation using VISTA via the sample 3D slicer plugin.
-
-### Installation
-
-MONAI VISTA models are integrated based on [MONAI Label](https://docs.monai.io/projects/label/en/latest/index.html#).
-Start using MONAI Label locally and run the installation with your familiar visualization tools.
-Stable version software represents the currently tested and supported visualization tools with
-the latest release of MONAI Label.
-
-Refer to [MONAI Label installation](https://docs.monai.io/projects/label/en/latest/installation.html) page
-for details. For milestone releases, users can install from PyPl with the command:
-
-```bash
-pip install monailabel
-
-```
-
-For Docker and Github installation, refer to MONAI Label [Github](https://github.com/Project-MONAI/MONAILabel)
-
-### MONAI VISTA APP
-
-Based on MONAI Label, MONAI VISTA is developed as an app. This app has example models
-to do both interactive and "Everything" segmentation over medical images.
-Prompt-based segment experience is highlighted. Including class prompts and point click prompts, Segmentation with the latest deep learning architectures (e.g., Segmentation Anything Model (SAM)) for multiple lung, abdominal, and pelvis
-organs. Interactive tools include control points and class prompt check boxes developed with viewer plugins.
-
-Get the monaivista app with:
-
-```bash
-# Clone MONAI VISTA repo
-git clone [email protected]:Project-MONAI/VISTA.git
-# the sample monaivista app is in the monailabel folder
-cd VISTA/monailabel
-```
-
-For more details on `monaivista` app, see the [sample-app page](https://github.com/Project-MONAI/VISTA/tree/main/monailabel/monaivista).
-
-### MONAI VISTA Viewer Plugins
-
-The interactive annotation experience with prompt-based segmentation models needs the integration of medical image viewers.
-MONAI VISTA and MONAI Label support multiple open-sourced viewers, such as [3D Slicer](https://www.slicer.org/) and [OHIF](https://ohif.org/).
-
-Example of 3D Slicer integration:
-
-3D Slicer is a free, open-source software for visualization, processing, segmentation, registration,
-and other 3D images and meshes. 3D Slicer is a mature and well-tested viewer for radiology studies and algorithms.
-
-#### Installing 3D Slicer
-
-To use MONAI Label with 3D Slicer, you'll need to download and install 3D Slicer.
-MONAI Label supports stable and preview versions of 3D Slicer, version 5.0 or higher.
-For more information on installing 3D Slicer,
-check out the [3D Slicer Documentation](https://slicer.readthedocs.io/en/latest/user_guide/getting_started.html#installing-3d-slicer)
-
-#### Install MONAI VISTA-Label plugin of 3D Slicer
-
-The plugin needs to be added in developer mode. Please follow the below steps.
-
-##### Plugin in Developer Mode
-
-- `git clone [email protected]:Project-MONAI/VISTA.git`
-- Find the plugin folder: `plugins/slicer/MONAILabel`
-- Open 3D Slicer: Go to **Edit** -> **Application Settings** -> **Modules** -> **Additional Module Paths**
-- Add New Module Path: _<FULL_PATH>_/plugins/slicer/MONAILabel (You can drag the slicer/MONAILabel folder to the module panel.)
-- _**Restart**_ 3D Slicer
-
-<div align="center"> <img src="./assets/imgs/3dslicer_module.png" width="500"/> </div>
-
-<div align="center"> <img src="./assets/imgs/3dslicer_plugin.png" width="500"/> </div>
-
-### Sample Data
-
-Prepare some sample data to start with:
-
-Download MSD pancreas dataset as the sample dataset using monailabel API.
-The task is the volumetric (3D) segmentation of the pancreas from CT image.
-The dataset is from the 2018 MICCAI challenge.
-
-```bash
-monailabel datasets --download --name Task07_Pancreas --output .
-```
-
-### Start MONAI Label Server with VISTA Model
-
-Specify the sample app and sample datasets' path in the following command:
-
-```bash
-monailabel start_server --app monaivista --studies ./Task07_Pancreas/imagesTs --conf models vista_point_2pt5
-```
-
-- Open 3D Slicer and MONAI VISTA-Label plugin.
-<div align="center"> <img src="./assets/imgs/3dslicer_open.jpeg" width="800"/> </div>
-
-- Connect to the monailabel server, start annotating!
-<div align="center"> <img src="./assets/imgs/3dslicer_annotating.png" width="800"/> </div>
-
-## Community
-
-Join the conversation on Twitter [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join
-our [Slack channel](https://projectmonai.slack.com/archives/C031QRE0M1C).
-
-Ask and answer questions on [MONAI VISTA's GitHub discussions tab](https://github.com/Project-MONAI/VISTA/discussions).
-
-## License
-
-The model is licensed under the Apache 2.0 license.
-
-## Reference
-
-The current model is trained and developed based on [Segment Anything Model (SAM)](https://github.com/facebookresearch/segment-anything). Check the 3rd party license for reference.
-
-We greatly appreciate the authors of [`Segment Anything`](https://github.com/facebookresearch/segment-anything) and [`TotalSegmentator`](https://github.com/wasserth/TotalSegmentator) for releasing their work under a permissive license to the community.
-
-```
-@article{kirillov2023segany,
-      title={Segment Anything},
-      author={Kirillov, Alexander and Mintun, Eric and Ravi, Nikhila and Mao, Hanzi and Rolland, Chloe and Gustafson, Laura and Xiao, Tete and Whitehead, Spencer and Berg, Alexander C. and Lo, Wan-Yen and Doll{\'a}r, Piotr and Girshick, Ross},
-      journal={arXiv:2304.02643},
-      year={2023}
-    }
-@article{wasserthal2022totalsegmentator,
-      title={TotalSegmentator: robust segmentation of 104 anatomical structures in CT images},
-      author={Wasserthal, Jakob and Meyer, Manfred and Breit, Hanns-Christian and Cyriac, Joshy and Yang, Shan and Segeroth, Martin},
-      journal={arXiv preprint arXiv:2208.05868},
-      year={2022}
-    }
-```
-
-This integration is based on MONAI Label:
-
-```bash
-@article{diaz2022monai,
-  title={Monai label: A framework for ai-assisted interactive labeling of 3d medical images},
-  author={Diaz-Pinto, Andres and Alle, Sachidanand and Nath, Vishwesh and Tang, Yucheng and Ihsani, Alvin and Asad, Muhammad and P{\'e}rez-Garc{\'\i}a, Fernando and Mehta, Pritesh and Li, Wenqi and Flores, Mona and others},
-  journal={arXiv preprint arXiv:2203.12362},
-  year={2022}
-}
-```
+# MONAI VISTA Repository
+This is the repository for VISTA3D and VISTA2D For the older VISTA2.5d code, please checkout the vista2.5d branch