nystrom-ncut 0.0.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- nystrom_ncut-0.0.1/LICENSE +19 -0
- nystrom_ncut-0.0.1/MANIFEST.in +9 -0
- nystrom_ncut-0.0.1/PKG-INFO +164 -0
- nystrom_ncut-0.0.1/README.md +150 -0
- nystrom_ncut-0.0.1/pyproject.toml +23 -0
- nystrom_ncut-0.0.1/requirements.txt +6 -0
- nystrom_ncut-0.0.1/setup.cfg +4 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut/__init__.py +22 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut/ncut_pytorch.py +561 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut/new_ncut_pytorch.py +241 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut/nystrom.py +170 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut/propagation_utils.py +371 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut/visualize_utils.py +655 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut.egg-info/PKG-INFO +164 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut.egg-info/SOURCES.txt +15 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut.egg-info/dependency_links.txt +1 -0
- nystrom_ncut-0.0.1/src/nystrom_ncut.egg-info/top_level.txt +1 -0
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Copyright (c) 2018 The Python Packaging Authority
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.1
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Name: nystrom_ncut
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Version: 0.0.1
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Summary: Normalized Cut and Nyström Approximation
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Author-email: Huzheng Yang <huze.yann@gmail.com>, Wentinn Liao <wentinn.liao@gmail.com>
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Project-URL: Documentation, https://github.com/JophiArcana/Nystrom-NCUT/
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Project-URL: Github, https://github.com/JophiArcana/Nystrom-NCUT/
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Classifier: Programming Language :: Python :: 3
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3
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Description-Content-Type: text/markdown
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License-File: LICENSE
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<div style="text-align: center;">
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<img src="./docs/images/ncut.svg" alt="NCUT" style="width: 80%; filter: brightness(60%) grayscale(100%);"/>
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</div>
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### [🌐Documentation](https://ncut-pytorch.readthedocs.io/) | [🤗HuggingFace Demo](https://huggingface.co/spaces/huzey/ncut-pytorch)
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## NCUT: Nyström Normalized Cut
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**Normalized Cut**, aka. spectral clustering, is a graphical method to analyze data grouping in the affinity eigenvector space. It has been widely used for unsupervised segmentation in the 2000s.
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**Nyström Normalized Cut**, is a new approximation algorithm developed for large-scale graph cuts, a large-graph of million nodes can be processed in under 10s (cpu) or 2s (gpu).
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https://github.com/user-attachments/assets/f0d40b1f-b8a5-4077-ab5f-e405f3ffb70f
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<div align="center">
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Video: NCUT applied to image encoder features from Segment Anything Model.
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</div>
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---
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## Installation
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#### 1. Install PyTorch
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<div style="text-align:">
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<pre><code class="language-shell">conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
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</code></pre>
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</div>
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#### 2. Install `nystrom-ncut`
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<div style="text-align:">
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<pre><code class="language-shell">pip install nystrom-ncut</code></pre>
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</div>
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#### Trouble Shooting
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In case of `pip` install failed, please try install the build dependencies
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Option A:
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<div style="text-align:">
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<pre><code class="language-shell">sudo apt-get update && sudo apt-get install build-essential cargo rustc -y</code></pre>
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</div>
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Option B:
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<div style="text-align:">
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<pre><code class="language-shell">conda install rust -c conda-forge</code></pre>
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</div>
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Option C:
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<div style="text-align:">
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<pre><code class="language-shell">curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh && . "$HOME/.cargo/env"</code></pre>
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</div>
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## Quick Start
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Minimal example on how to run NCUT:
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```py linenums="1"
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import torch
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from ncut_pytorch import NCUT, rgb_from_tsne_3d
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model_features = torch.rand(20, 64, 64, 768) # (B, H, W, C)
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inp = model_features.reshape(-1, 768) # flatten
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eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
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tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
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eigvectors = eigvectors.reshape(20, 64, 64, 100) # (B, H, W, num_eig)
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tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3) # (B, H, W, 3)
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```
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#### Load Feature Extractor Model
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Any backbone model works as plug-in feature extractor.
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We have implemented some backbone models, here is a list of available models:
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```py
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from ncut_pytorch.backbone import list_models
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print(list_models())
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[
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'SAM2(sam2_hiera_t)', 'SAM2(sam2_hiera_s)', 'SAM2(sam2_hiera_b+)', 'SAM2(sam2_hiera_l)',
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'SAM(sam_vit_b)', 'SAM(sam_vit_l)', 'SAM(sam_vit_h)', 'MobileSAM(TinyViT)',
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'DiNOv2reg(dinov2_vits14_reg)', 'DiNOv2reg(dinov2_vitb14_reg)', 'DiNOv2reg(dinov2_vitl14_reg)', 'DiNOv2reg(dinov2_vitg14_reg)',
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'DiNOv2(dinov2_vits14)', 'DiNOv2(dinov2_vitb14)', 'DiNOv2(dinov2_vitl14)', 'DiNOv2(dinov2_vitg14)',
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'DiNO(dino_vits8_896)', 'DiNO(dino_vitb8_896)', 'DiNO(dino_vits8_672)', 'DiNO(dino_vitb8_672)', 'DiNO(dino_vits8_448)', 'DiNO(dino_vitb8_448)', 'DiNO(dino_vits16_448)', 'DiNO(dino_vitb16_448)',
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'Diffusion(stabilityai/stable-diffusion-2)', 'Diffusion(CompVis/stable-diffusion-v1-4)', 'Diffusion(stabilityai/stable-diffusion-3-medium-diffusers)',
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'CLIP(ViT-B-16/openai)', 'CLIP(ViT-L-14/openai)', 'CLIP(ViT-H-14/openai)', 'CLIP(ViT-B-16/laion2b_s34b_b88k)',
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'CLIP(convnext_base_w_320/laion_aesthetic_s13b_b82k)', 'CLIP(convnext_large_d_320/laion2b_s29b_b131k_ft_soup)', 'CLIP(convnext_xxlarge/laion2b_s34b_b82k_augreg_soup)',
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'CLIP(eva02_base_patch14_448/mim_in22k_ft_in1k)', "CLIP(eva02_large_patch14_448/mim_m38m_ft_in22k_in1k)",
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'MAE(vit_base)', 'MAE(vit_large)', 'MAE(vit_huge)',
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'ImageNet(vit_base)'
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]
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```
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#### Image model example:
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```py linenums="1"
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import torch
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from ncut_pytorch import NCUT, rgb_from_tsne_3d
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from ncut_pytorch.backbone import load_model, extract_features
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model = load_model(model_name="SAM(sam_vit_b)")
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images = torch.rand(20, 3, 1024, 1024)
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model_features = extract_features(images, model, node_type='attn', layer=6)
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# model_features = model(images)['attn'][6] # this also works
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inp = model_features.reshape(-1, 768) # flatten
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eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
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tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
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eigvectors = eigvectors.reshape(20, 64, 64, 100) # (B, H, W, num_eig)
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tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3) # (B, H, W, 3)
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```
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#### Text model example:
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```py linenums="1"
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import os
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from ncut_pytorch import NCUT, rgb_from_tsne_3d
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from ncut_pytorch.backbone_text import load_text_model
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os.environ['HF_ACCESS_TOKEN'] = "your_huggingface_token"
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llama = load_text_model("meta-llama/Meta-Llama-3.1-8B").cuda()
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output_dict = llama("The quick white fox jumps over the lazy cat.")
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model_features = output_dict['block'][31].squeeze(0) # 32nd block output
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token_texts = output_dict['token_texts']
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eigvectors, eigvalues = NCUT(num_eig=5, device='cuda:0').fit_transform(model_features)
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tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
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# eigvectors.shape[0] == tsne_rgb.shape[0] == len(token_texts)
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```
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---
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> paper in prep, Yang 2024
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>
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> AlignedCut: Visual Concepts Discovery on Brain-Guided Universal Feature Space, Huzheng Yang, James Gee\*, Jianbo Shi\*,2024
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>
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> Normalized Cuts and Image Segmentation, Jianbo Shi and Jitendra Malik, 2000
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<div style="text-align: center;">
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<img src="./docs/images/ncut.svg" alt="NCUT" style="width: 80%; filter: brightness(60%) grayscale(100%);"/>
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</div>
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### [🌐Documentation](https://ncut-pytorch.readthedocs.io/) | [🤗HuggingFace Demo](https://huggingface.co/spaces/huzey/ncut-pytorch)
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## NCUT: Nyström Normalized Cut
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**Normalized Cut**, aka. spectral clustering, is a graphical method to analyze data grouping in the affinity eigenvector space. It has been widely used for unsupervised segmentation in the 2000s.
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**Nyström Normalized Cut**, is a new approximation algorithm developed for large-scale graph cuts, a large-graph of million nodes can be processed in under 10s (cpu) or 2s (gpu).
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https://github.com/user-attachments/assets/f0d40b1f-b8a5-4077-ab5f-e405f3ffb70f
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<div align="center">
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Video: NCUT applied to image encoder features from Segment Anything Model.
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</div>
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---
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## Installation
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#### 1. Install PyTorch
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<div style="text-align:">
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<pre><code class="language-shell">conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
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</code></pre>
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</div>
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#### 2. Install `nystrom-ncut`
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<div style="text-align:">
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<pre><code class="language-shell">pip install nystrom-ncut</code></pre>
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</div>
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#### Trouble Shooting
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In case of `pip` install failed, please try install the build dependencies
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Option A:
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<div style="text-align:">
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<pre><code class="language-shell">sudo apt-get update && sudo apt-get install build-essential cargo rustc -y</code></pre>
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</div>
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Option B:
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<div style="text-align:">
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<pre><code class="language-shell">conda install rust -c conda-forge</code></pre>
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</div>
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Option C:
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<div style="text-align:">
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<pre><code class="language-shell">curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh && . "$HOME/.cargo/env"</code></pre>
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</div>
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## Quick Start
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Minimal example on how to run NCUT:
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```py linenums="1"
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import torch
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from ncut_pytorch import NCUT, rgb_from_tsne_3d
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model_features = torch.rand(20, 64, 64, 768) # (B, H, W, C)
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inp = model_features.reshape(-1, 768) # flatten
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eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
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tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
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eigvectors = eigvectors.reshape(20, 64, 64, 100) # (B, H, W, num_eig)
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tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3) # (B, H, W, 3)
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```
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#### Load Feature Extractor Model
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Any backbone model works as plug-in feature extractor.
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We have implemented some backbone models, here is a list of available models:
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```py
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from ncut_pytorch.backbone import list_models
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print(list_models())
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[
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'SAM2(sam2_hiera_t)', 'SAM2(sam2_hiera_s)', 'SAM2(sam2_hiera_b+)', 'SAM2(sam2_hiera_l)',
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'SAM(sam_vit_b)', 'SAM(sam_vit_l)', 'SAM(sam_vit_h)', 'MobileSAM(TinyViT)',
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'DiNOv2reg(dinov2_vits14_reg)', 'DiNOv2reg(dinov2_vitb14_reg)', 'DiNOv2reg(dinov2_vitl14_reg)', 'DiNOv2reg(dinov2_vitg14_reg)',
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'DiNOv2(dinov2_vits14)', 'DiNOv2(dinov2_vitb14)', 'DiNOv2(dinov2_vitl14)', 'DiNOv2(dinov2_vitg14)',
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'DiNO(dino_vits8_896)', 'DiNO(dino_vitb8_896)', 'DiNO(dino_vits8_672)', 'DiNO(dino_vitb8_672)', 'DiNO(dino_vits8_448)', 'DiNO(dino_vitb8_448)', 'DiNO(dino_vits16_448)', 'DiNO(dino_vitb16_448)',
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'Diffusion(stabilityai/stable-diffusion-2)', 'Diffusion(CompVis/stable-diffusion-v1-4)', 'Diffusion(stabilityai/stable-diffusion-3-medium-diffusers)',
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'CLIP(ViT-B-16/openai)', 'CLIP(ViT-L-14/openai)', 'CLIP(ViT-H-14/openai)', 'CLIP(ViT-B-16/laion2b_s34b_b88k)',
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'CLIP(convnext_base_w_320/laion_aesthetic_s13b_b82k)', 'CLIP(convnext_large_d_320/laion2b_s29b_b131k_ft_soup)', 'CLIP(convnext_xxlarge/laion2b_s34b_b82k_augreg_soup)',
|
100
|
+
'CLIP(eva02_base_patch14_448/mim_in22k_ft_in1k)', "CLIP(eva02_large_patch14_448/mim_m38m_ft_in22k_in1k)",
|
101
|
+
'MAE(vit_base)', 'MAE(vit_large)', 'MAE(vit_huge)',
|
102
|
+
'ImageNet(vit_base)'
|
103
|
+
]
|
104
|
+
```
|
105
|
+
|
106
|
+
#### Image model example:
|
107
|
+
|
108
|
+
```py linenums="1"
|
109
|
+
import torch
|
110
|
+
from ncut_pytorch import NCUT, rgb_from_tsne_3d
|
111
|
+
from ncut_pytorch.backbone import load_model, extract_features
|
112
|
+
|
113
|
+
model = load_model(model_name="SAM(sam_vit_b)")
|
114
|
+
images = torch.rand(20, 3, 1024, 1024)
|
115
|
+
model_features = extract_features(images, model, node_type='attn', layer=6)
|
116
|
+
# model_features = model(images)['attn'][6] # this also works
|
117
|
+
|
118
|
+
inp = model_features.reshape(-1, 768) # flatten
|
119
|
+
eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
|
120
|
+
tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
|
121
|
+
|
122
|
+
eigvectors = eigvectors.reshape(20, 64, 64, 100) # (B, H, W, num_eig)
|
123
|
+
tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3) # (B, H, W, 3)
|
124
|
+
```
|
125
|
+
|
126
|
+
#### Text model example:
|
127
|
+
|
128
|
+
```py linenums="1"
|
129
|
+
import os
|
130
|
+
from ncut_pytorch import NCUT, rgb_from_tsne_3d
|
131
|
+
from ncut_pytorch.backbone_text import load_text_model
|
132
|
+
|
133
|
+
os.environ['HF_ACCESS_TOKEN'] = "your_huggingface_token"
|
134
|
+
llama = load_text_model("meta-llama/Meta-Llama-3.1-8B").cuda()
|
135
|
+
output_dict = llama("The quick white fox jumps over the lazy cat.")
|
136
|
+
|
137
|
+
model_features = output_dict['block'][31].squeeze(0) # 32nd block output
|
138
|
+
token_texts = output_dict['token_texts']
|
139
|
+
eigvectors, eigvalues = NCUT(num_eig=5, device='cuda:0').fit_transform(model_features)
|
140
|
+
tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
|
141
|
+
# eigvectors.shape[0] == tsne_rgb.shape[0] == len(token_texts)
|
142
|
+
```
|
143
|
+
|
144
|
+
---
|
145
|
+
|
146
|
+
> paper in prep, Yang 2024
|
147
|
+
>
|
148
|
+
> AlignedCut: Visual Concepts Discovery on Brain-Guided Universal Feature Space, Huzheng Yang, James Gee\*, Jianbo Shi\*,2024
|
149
|
+
>
|
150
|
+
> Normalized Cuts and Image Segmentation, Jianbo Shi and Jitendra Malik, 2000
|
@@ -0,0 +1,23 @@
|
|
1
|
+
[build-system]
|
2
|
+
requires = ["setuptools>=61.0"]
|
3
|
+
build-backend = "setuptools.build_meta"
|
4
|
+
|
5
|
+
[project]
|
6
|
+
name = "nystrom_ncut"
|
7
|
+
version = "0.0.1"
|
8
|
+
authors = [
|
9
|
+
{ name = "Huzheng Yang", email = "huze.yann@gmail.com" },
|
10
|
+
{ name = "Wentinn Liao", email = "wentinn.liao@gmail.com" },
|
11
|
+
]
|
12
|
+
description = "Normalized Cut and Nyström Approximation"
|
13
|
+
readme = "README.md"
|
14
|
+
requires-python = ">=3"
|
15
|
+
classifiers = [
|
16
|
+
"Programming Language :: Python :: 3",
|
17
|
+
"License :: OSI Approved :: MIT License",
|
18
|
+
"Operating System :: OS Independent",
|
19
|
+
]
|
20
|
+
|
21
|
+
[project.urls]
|
22
|
+
Documentation = "https://github.com/JophiArcana/Nystrom-NCUT/"
|
23
|
+
Github = "https://github.com/JophiArcana/Nystrom-NCUT/"
|
@@ -0,0 +1,22 @@
|
|
1
|
+
from .ncut_pytorch import NCUT
|
2
|
+
from .propagation_utils import (
|
3
|
+
affinity_from_features,
|
4
|
+
propagate_eigenvectors,
|
5
|
+
propagate_knn,
|
6
|
+
quantile_normalize,
|
7
|
+
)
|
8
|
+
from .visualize_utils import (
|
9
|
+
eigenvector_to_rgb,
|
10
|
+
rgb_from_tsne_3d,
|
11
|
+
rgb_from_umap_sphere,
|
12
|
+
rgb_from_tsne_2d,
|
13
|
+
rgb_from_umap_3d,
|
14
|
+
rgb_from_umap_2d,
|
15
|
+
rgb_from_cosine_tsne_3d,
|
16
|
+
rotate_rgb_cube,
|
17
|
+
convert_to_lab_color,
|
18
|
+
propagate_rgb_color,
|
19
|
+
get_mask,
|
20
|
+
)
|
21
|
+
from .ncut_pytorch import nystrom_ncut, ncut
|
22
|
+
from .ncut_pytorch import kway_ncut, axis_align
|