nystrom-ncut 0.0.1__tar.gz

nystrom_ncut-0.0.1/LICENSE

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+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nystrom_ncut-0.0.1/MANIFEST.in

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+include ncut_pytorch/__init__.py
+include ncut_pytorch/ncut_pytorch.py
+include ncut_pytorch/backbone.py
+include ncut_pytorch/backbone_text.py
+include requirements.txt
+include MANIFEST.in
+include README.md
+include LICENSE
+include setup.py

nystrom_ncut-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: nystrom_ncut
+Version: 0.0.1
+Summary: Normalized Cut and Nyström Approximation
+Author-email: Huzheng Yang <huze.yann@gmail.com>, Wentinn Liao <wentinn.liao@gmail.com>
+Project-URL: Documentation, https://github.com/JophiArcana/Nystrom-NCUT/
+Project-URL: Github, https://github.com/JophiArcana/Nystrom-NCUT/
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+
+
+<div style="text-align: center;">
+  <img src="./docs/images/ncut.svg" alt="NCUT" style="width: 80%; filter: brightness(60%) grayscale(100%);"/>
+</div>
+
+### [🌐Documentation](https://ncut-pytorch.readthedocs.io/) | [🤗HuggingFace Demo](https://huggingface.co/spaces/huzey/ncut-pytorch)
+
+
+## NCUT: Nyström Normalized Cut
+
+**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.
+
+**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).  
+
+
+
+https://github.com/user-attachments/assets/f0d40b1f-b8a5-4077-ab5f-e405f3ffb70f
+
+
+
+<div align="center">
+  Video: NCUT applied to image encoder features from Segment Anything Model.
+</div>
+
+
+---
+
+## Installation
+
+#### 1. Install PyTorch
+
+<div style="text-align:">
+<pre><code class="language-shell">conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
+</code></pre>
+</div>
+
+#### 2. Install `nystrom-ncut`
+
+<div style="text-align:">
+    <pre><code class="language-shell">pip install nystrom-ncut</code></pre>
+</div>
+
+
+#### Trouble Shooting
+
+In case of `pip` install failed, please try install the build dependencies
+
+Option A:
+<div style="text-align:">
+    <pre><code class="language-shell">sudo apt-get update && sudo apt-get install build-essential cargo rustc -y</code></pre>
+</div>
+
+Option B:
+<div style="text-align:">
+    <pre><code class="language-shell">conda install rust -c conda-forge</code></pre>
+</div>
+
+Option C:
+<div style="text-align:">
+    <pre><code class="language-shell">curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh && . "$HOME/.cargo/env"</code></pre>
+</div>
+
+## Quick Start
+
+
+Minimal example on how to run NCUT:
+
+```py linenums="1"
+import torch
+from ncut_pytorch import NCUT, rgb_from_tsne_3d
+
+model_features = torch.rand(20, 64, 64, 768)  # (B, H, W, C)
+
+inp = model_features.reshape(-1, 768)  # flatten
+eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
+tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
+
+eigvectors = eigvectors.reshape(20, 64, 64, 100)  # (B, H, W, num_eig)
+tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3)  # (B, H, W, 3)
+```
+
+#### Load Feature Extractor Model
+
+Any backbone model works as plug-in feature extractor. 
+We have implemented some backbone models, here is a list of available models:
+
+```py
+from ncut_pytorch.backbone import list_models
+print(list_models())
+[
+  'SAM2(sam2_hiera_t)', 'SAM2(sam2_hiera_s)', 'SAM2(sam2_hiera_b+)', 'SAM2(sam2_hiera_l)', 
+  'SAM(sam_vit_b)', 'SAM(sam_vit_l)', 'SAM(sam_vit_h)', 'MobileSAM(TinyViT)', 
+  'DiNOv2reg(dinov2_vits14_reg)', 'DiNOv2reg(dinov2_vitb14_reg)', 'DiNOv2reg(dinov2_vitl14_reg)', 'DiNOv2reg(dinov2_vitg14_reg)', 
+  'DiNOv2(dinov2_vits14)', 'DiNOv2(dinov2_vitb14)', 'DiNOv2(dinov2_vitl14)', 'DiNOv2(dinov2_vitg14)', 
+  '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)',
+  'Diffusion(stabilityai/stable-diffusion-2)', 'Diffusion(CompVis/stable-diffusion-v1-4)', 'Diffusion(stabilityai/stable-diffusion-3-medium-diffusers)',
+  'CLIP(ViT-B-16/openai)', 'CLIP(ViT-L-14/openai)', 'CLIP(ViT-H-14/openai)', 'CLIP(ViT-B-16/laion2b_s34b_b88k)', 
+  '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)', 
+  'CLIP(eva02_base_patch14_448/mim_in22k_ft_in1k)', "CLIP(eva02_large_patch14_448/mim_m38m_ft_in22k_in1k)",
+  'MAE(vit_base)', 'MAE(vit_large)', 'MAE(vit_huge)', 
+  'ImageNet(vit_base)'
+]
+```
+
+#### Image model example:
+
+```py linenums="1"
+import torch
+from ncut_pytorch import NCUT, rgb_from_tsne_3d
+from ncut_pytorch.backbone import load_model, extract_features
+
+model = load_model(model_name="SAM(sam_vit_b)")
+images = torch.rand(20, 3, 1024, 1024)
+model_features = extract_features(images, model, node_type='attn', layer=6)
+# model_features = model(images)['attn'][6]  # this also works
+
+inp = model_features.reshape(-1, 768)  # flatten
+eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
+tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
+
+eigvectors = eigvectors.reshape(20, 64, 64, 100)  # (B, H, W, num_eig)
+tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3)  # (B, H, W, 3)
+```
+
+#### Text model example:
+
+```py linenums="1"
+import os
+from ncut_pytorch import NCUT, rgb_from_tsne_3d
+from ncut_pytorch.backbone_text import load_text_model
+
+os.environ['HF_ACCESS_TOKEN'] = "your_huggingface_token"
+llama = load_text_model("meta-llama/Meta-Llama-3.1-8B").cuda()
+output_dict = llama("The quick white fox jumps over the lazy cat.")
+
+model_features = output_dict['block'][31].squeeze(0)  # 32nd block output
+token_texts = output_dict['token_texts']
+eigvectors, eigvalues = NCUT(num_eig=5, device='cuda:0').fit_transform(model_features)
+tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
+# eigvectors.shape[0] == tsne_rgb.shape[0] == len(token_texts)
+```
+
+---
+
+> paper in prep, Yang 2024
+>
+> AlignedCut: Visual Concepts Discovery on Brain-Guided Universal Feature Space, Huzheng Yang, James Gee\*, Jianbo Shi\*,2024
+> 
+> Normalized Cuts and Image Segmentation, Jianbo Shi and Jitendra Malik, 2000

nystrom_ncut-0.0.1/README.md

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+
+
+<div style="text-align: center;">
+  <img src="./docs/images/ncut.svg" alt="NCUT" style="width: 80%; filter: brightness(60%) grayscale(100%);"/>
+</div>
+
+### [🌐Documentation](https://ncut-pytorch.readthedocs.io/) | [🤗HuggingFace Demo](https://huggingface.co/spaces/huzey/ncut-pytorch)
+
+
+## NCUT: Nyström Normalized Cut
+
+**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.
+
+**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).  
+
+
+
+https://github.com/user-attachments/assets/f0d40b1f-b8a5-4077-ab5f-e405f3ffb70f
+
+
+
+<div align="center">
+  Video: NCUT applied to image encoder features from Segment Anything Model.
+</div>
+
+
+---
+
+## Installation
+
+#### 1. Install PyTorch
+
+<div style="text-align:">
+<pre><code class="language-shell">conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
+</code></pre>
+</div>
+
+#### 2. Install `nystrom-ncut`
+
+<div style="text-align:">
+    <pre><code class="language-shell">pip install nystrom-ncut</code></pre>
+</div>
+
+
+#### Trouble Shooting
+
+In case of `pip` install failed, please try install the build dependencies
+
+Option A:
+<div style="text-align:">
+    <pre><code class="language-shell">sudo apt-get update && sudo apt-get install build-essential cargo rustc -y</code></pre>
+</div>
+
+Option B:
+<div style="text-align:">
+    <pre><code class="language-shell">conda install rust -c conda-forge</code></pre>
+</div>
+
+Option C:
+<div style="text-align:">
+    <pre><code class="language-shell">curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh && . "$HOME/.cargo/env"</code></pre>
+</div>
+
+## Quick Start
+
+
+Minimal example on how to run NCUT:
+
+```py linenums="1"
+import torch
+from ncut_pytorch import NCUT, rgb_from_tsne_3d
+
+model_features = torch.rand(20, 64, 64, 768)  # (B, H, W, C)
+
+inp = model_features.reshape(-1, 768)  # flatten
+eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
+tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
+
+eigvectors = eigvectors.reshape(20, 64, 64, 100)  # (B, H, W, num_eig)
+tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3)  # (B, H, W, 3)
+```
+
+#### Load Feature Extractor Model
+
+Any backbone model works as plug-in feature extractor. 
+We have implemented some backbone models, here is a list of available models:
+
+```py
+from ncut_pytorch.backbone import list_models
+print(list_models())
+[
+  'SAM2(sam2_hiera_t)', 'SAM2(sam2_hiera_s)', 'SAM2(sam2_hiera_b+)', 'SAM2(sam2_hiera_l)', 
+  'SAM(sam_vit_b)', 'SAM(sam_vit_l)', 'SAM(sam_vit_h)', 'MobileSAM(TinyViT)', 
+  'DiNOv2reg(dinov2_vits14_reg)', 'DiNOv2reg(dinov2_vitb14_reg)', 'DiNOv2reg(dinov2_vitl14_reg)', 'DiNOv2reg(dinov2_vitg14_reg)', 
+  'DiNOv2(dinov2_vits14)', 'DiNOv2(dinov2_vitb14)', 'DiNOv2(dinov2_vitl14)', 'DiNOv2(dinov2_vitg14)', 
+  '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)',
+  'Diffusion(stabilityai/stable-diffusion-2)', 'Diffusion(CompVis/stable-diffusion-v1-4)', 'Diffusion(stabilityai/stable-diffusion-3-medium-diffusers)',
+  'CLIP(ViT-B-16/openai)', 'CLIP(ViT-L-14/openai)', 'CLIP(ViT-H-14/openai)', 'CLIP(ViT-B-16/laion2b_s34b_b88k)', 
+  '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)', 
+  'CLIP(eva02_base_patch14_448/mim_in22k_ft_in1k)', "CLIP(eva02_large_patch14_448/mim_m38m_ft_in22k_in1k)",
+  'MAE(vit_base)', 'MAE(vit_large)', 'MAE(vit_huge)', 
+  'ImageNet(vit_base)'
+]
+```
+
+#### Image model example:
+
+```py linenums="1"
+import torch
+from ncut_pytorch import NCUT, rgb_from_tsne_3d
+from ncut_pytorch.backbone import load_model, extract_features
+
+model = load_model(model_name="SAM(sam_vit_b)")
+images = torch.rand(20, 3, 1024, 1024)
+model_features = extract_features(images, model, node_type='attn', layer=6)
+# model_features = model(images)['attn'][6]  # this also works
+
+inp = model_features.reshape(-1, 768)  # flatten
+eigvectors, eigvalues = NCUT(num_eig=100, device='cuda:0').fit_transform(inp)
+tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
+
+eigvectors = eigvectors.reshape(20, 64, 64, 100)  # (B, H, W, num_eig)
+tsne_rgb = tsne_rgb.reshape(20, 64, 64, 3)  # (B, H, W, 3)
+```
+
+#### Text model example:
+
+```py linenums="1"
+import os
+from ncut_pytorch import NCUT, rgb_from_tsne_3d
+from ncut_pytorch.backbone_text import load_text_model
+
+os.environ['HF_ACCESS_TOKEN'] = "your_huggingface_token"
+llama = load_text_model("meta-llama/Meta-Llama-3.1-8B").cuda()
+output_dict = llama("The quick white fox jumps over the lazy cat.")
+
+model_features = output_dict['block'][31].squeeze(0)  # 32nd block output
+token_texts = output_dict['token_texts']
+eigvectors, eigvalues = NCUT(num_eig=5, device='cuda:0').fit_transform(model_features)
+tsne_x3d, tsne_rgb = rgb_from_tsne_3d(eigvectors, device='cuda:0')
+# eigvectors.shape[0] == tsne_rgb.shape[0] == len(token_texts)
+```
+
+---
+
+> paper in prep, Yang 2024
+>
+> AlignedCut: Visual Concepts Discovery on Brain-Guided Universal Feature Space, Huzheng Yang, James Gee\*, Jianbo Shi\*,2024
+> 
+> Normalized Cuts and Image Segmentation, Jianbo Shi and Jitendra Malik, 2000

nystrom_ncut-0.0.1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nystrom_ncut"
+version = "0.0.1"
+authors = [
+    { name = "Huzheng Yang", email = "huze.yann@gmail.com" },
+    { name = "Wentinn Liao", email = "wentinn.liao@gmail.com" },
+]
+description = "Normalized Cut and Nyström Approximation"
+readme = "README.md"
+requires-python = ">=3"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+Documentation = "https://github.com/JophiArcana/Nystrom-NCUT/"
+Github = "https://github.com/JophiArcana/Nystrom-NCUT/"

nystrom_ncut-0.0.1/requirements.txt

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+einops
+scikit-learn
+umap-learn
+fpsample>=0.3.2
+pycolormap-2d
+tqdm

nystrom_ncut-0.0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

nystrom_ncut-0.0.1/src/nystrom_ncut/__init__.py

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+from .ncut_pytorch import NCUT
+from .propagation_utils import (
+    affinity_from_features,
+    propagate_eigenvectors,
+    propagate_knn,
+    quantile_normalize,
+)
+from .visualize_utils import (
+    eigenvector_to_rgb,
+    rgb_from_tsne_3d,
+    rgb_from_umap_sphere,
+    rgb_from_tsne_2d,
+    rgb_from_umap_3d,
+    rgb_from_umap_2d,
+    rgb_from_cosine_tsne_3d,
+    rotate_rgb_cube,
+    convert_to_lab_color,
+    propagate_rgb_color,
+    get_mask,
+)
+from .ncut_pytorch import nystrom_ncut, ncut
+from .ncut_pytorch import kway_ncut, axis_align