nystrom-ncut 0.1.0__py3-none-any.whl → 0.1.1__py3-none-any.whl

nystrom_ncut/common.py

@@ -33,7 +33,7 @@ def to_euclidean(x: torch.Tensor, disttype: DistanceOptions) -> torch.Tensor:
         raise ValueError(f"to_euclidean not implemented for disttype {disttype}.")
 
 
-def quantile_min_max(x, q1=0.01, q2=0.99, n_sample=10000):
+def quantile_min_max(x: torch.Tensor, q1: float, q2: float, n_sample: int = 10000):
     if x.shape[0] > n_sample:
         np.random.seed(0)
         random_idx = np.random.choice(x.shape[0], n_sample, replace=False)
@@ -43,7 +43,7 @@ def quantile_min_max(x, q1=0.01, q2=0.99, n_sample=10000):
     return vmin, vmax
 
 
-def quantile_normalize(x, q=0.95):
+def quantile_normalize(x: torch.Tensor, q: float = 0.95):
     """normalize each dimension of x to [0, 1], take 95-th percentage, this robust to outliers
         </br> 1. sort x
         </br> 2. take q-th quantile

nystrom_ncut/visualize_utils.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Any, Callable, Dict, Literal, Tuple
+from typing import Any, Callable, Dict, Literal
 
 import numpy as np
 import torch
@@ -12,9 +12,6 @@ from .common import (
     quantile_min_max,
     quantile_normalize,
 )
-from .nystrom import (
-    DistanceRealization,
-)
 from .propagation_utils import (
     run_subgraph_sampling,
     extrapolate_knn,
@@ -334,14 +331,14 @@ def rgb_from_umap_3d(
     return rgb
 
 
-def flatten_sphere(X_3d):
-    x = np.arctan2(X_3d[:, 0], X_3d[:, 1])
-    y = -np.arccos(X_3d[:, 2])
-    X_2d = np.stack([x, y], axis=1)
+def flatten_sphere(X_3d: torch.Tensor) -> torch.Tensor:
+    x = torch.atan2(X_3d[:, 0], X_3d[:, 1])
+    y = -torch.acos(X_3d[:, 2])
+    X_2d = torch.stack((x, y), dim=1)
     return X_2d
 
 
-def rotate_rgb_cube(rgb, position=1):
+def rotate_rgb_cube(rgb: torch.Tensor, position: int = 1) -> torch.Tensor:
     """rotate RGB cube to different position
 
     Args:
@@ -365,7 +362,7 @@ def rotate_rgb_cube(rgb, position=1):
     return rgb
 
 
-def rgb_from_3d_rgb_cube(X_3d, q=0.95):
+def rgb_from_3d_rgb_cube(X_3d: torch.Tensor, q: float = 0.95) -> torch.Tensor:
     """convert 3D t-SNE to RGB color space
     Args:
         X_3d (torch.Tensor): 3D t-SNE embedding, shape (n_samples, 3)
@@ -383,6 +380,26 @@ def rgb_from_3d_rgb_cube(X_3d, q=0.95):
     return rgb
 
 
+def rgb_from_3d_lab_cube(X_3d: torch.Tensor, q: float = 0.95, full_range: bool = True) -> torch.Tensor:
+    from skimage import color
+    X_3d = X_3d - torch.mean(X_3d, dim=0)
+    U, S, VT = torch.linalg.svd(X_3d)
+    X_3d = torch.flip(U[:, :3] * S, dims=(1,))
+
+    AB_scale = 128.0 / torch.quantile(torch.linalg.norm(X_3d[:, 1:], dim=1), q=q, dim=0)
+    L_min, L_max = torch.quantile(X_3d[:, 0], q=torch.tensor(((1 - q) / 2, (1 + q) / 2)), dim=0)
+    L_scale = 100.0 / (L_max - L_min)
+
+    X_3d[:, 0] = X_3d[:, 0] - L_min
+    if full_range:
+        lab = X_3d * torch.tensor((L_scale, AB_scale, AB_scale))
+    else:
+        lab = X_3d * L_scale
+
+    rgb = torch.tensor(color.lab2rgb(lab.numpy(force=True)))
+    return rgb
+
+
 def convert_to_lab_color(rgb, full_range=True):
     from skimage import color
     import copy
@@ -401,7 +418,7 @@ def convert_to_lab_color(rgb, full_range=True):
     return lab_rgb
 
 
-def rgb_from_2d_colormap(X_2d, q=0.95):
+def rgb_from_2d_colormap(X_2d: torch.Tensor, q: float = 0.95):
     xy = X_2d.clone()
     for i in range(2):
         xy[:, i] = quantile_normalize(xy[:, i], q=q)

{nystrom_ncut-0.1.0.dist-info → nystrom_ncut-0.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nystrom_ncut
-Version: 0.1.0
+Version: 0.1.1
 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/

{nystrom_ncut-0.1.0.dist-info → nystrom_ncut-0.1.1.dist-info}/RECORD

@@ -1,14 +1,14 @@
 __init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nystrom_ncut/__init__.py,sha256=ffExLdGTaPsUweHcYc61Ose6a5A5Tfo9hm48zjEl6ho,441
-nystrom_ncut/common.py,sha256=l5kjF6neukdtbMrt5bE69pN0JM9r-93JYltLlYJuBik,2227
+nystrom_ncut/common.py,sha256=2nffH0I2UrE6-7gQV6NlA7xSXeAl2GPR5F_5Or1yMt4,2275
 nystrom_ncut/propagation_utils.py,sha256=79M61iJfp_RWj_xLOn51PHiextWcEWTQ7NWl2T51-3Y,10907
-nystrom_ncut/visualize_utils.py,sha256=uGfBBkETQ8uRJ-UXPWpiXT8KEYMLmEHXPKJMLvN0c34,16543
+nystrom_ncut/visualize_utils.py,sha256=EQKsNTfCssLYJv7HhwHxAyI18GLrkwbnOIrIKVoYZ1w,17344
 nystrom_ncut/nystrom/__init__.py,sha256=4EpxD3Cmc8Fif4vo8DG-6FpTfCnNanD5zCZxK3WrMwQ,121
 nystrom_ncut/nystrom/distance_realization.py,sha256=FGH7VjbtRrSROH0d8OPuCUxLQy5j7Z8BuE4hrSGGZG4,6031
 nystrom_ncut/nystrom/normalized_cut.py,sha256=s9ZS3-tQbWnxAlPc01v9l7fqBhl28lvOalaCO2y-Gd8,7175
 nystrom_ncut/nystrom/nystrom.py,sha256=OV5o9UL9fkrz9HdsD6rXh7MTsenPKrtCNRIczMuDS_4,12779
-nystrom_ncut-0.1.0.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
-nystrom_ncut-0.1.0.dist-info/METADATA,sha256=wAhGONU0ZM1VWoLqEwtfAs3_GUAt4CItkHq3ISuFyVE,6058
-nystrom_ncut-0.1.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-nystrom_ncut-0.1.0.dist-info/top_level.txt,sha256=gM8IWWHYysIRTCvCTcdS4RShOyl9pxpylgSwPUZR2XM,22
-nystrom_ncut-0.1.0.dist-info/RECORD,,
+nystrom_ncut-0.1.1.dist-info/LICENSE,sha256=2bm9uFabQZ3Ykb_SaSU_uUbAj2-htc6WJQmS_65qD00,1073
+nystrom_ncut-0.1.1.dist-info/METADATA,sha256=XQymsKFQrtzWDKjwUbyVv8KiWwdbsMSCGIKPS9WcBGk,6058
+nystrom_ncut-0.1.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+nystrom_ncut-0.1.1.dist-info/top_level.txt,sha256=gM8IWWHYysIRTCvCTcdS4RShOyl9pxpylgSwPUZR2XM,22
+nystrom_ncut-0.1.1.dist-info/RECORD,,