Merge pull request #14 from davidnabergoj/update

parallelization, new single_sample param, fix small bugs

Author: BernardaPetek

.github/workflows/build.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Build source and wheel distributions
         run: |

.github/workflows/release.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Build source and wheel distributions
         run: |

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

bootplot/backend/base.py

@@ -14,23 +14,38 @@ def __init__(self,
                  f: callable,
                  data: Union[np.ndarray, pd.DataFrame],
                  m: int,
-                 output_size_px: Tuple[int, int]):
+                 output_size_px: Tuple[int, int],
+                 single_sample: bool):
         self.output_size_px = output_size_px
         self.f = f
         self.data = data
         self.m = m
+        self.single_sample = single_sample
 
     @abstractmethod
     def create_figure(self):
         raise NotImplemented
 
     def plot(self):
-        indices = np.random.randint(low=0, high=len(self.data), size=len(self.data))
+        size = 1 if self.single_sample else len(self.data)
+        indices = np.random.randint(low=0, high=len(self.data), size=size)
         if isinstance(self.data, pd.DataFrame):
             return self.f(self.data.iloc[indices], self.data, *self.plot_args)
         elif isinstance(self.data, np.ndarray):
             return self.f(self.data[indices], self.data, *self.plot_args)
 
+    def sample_all_indices(self):
+        size = 1 if self.single_sample else len(self.data)
+        return np.random.randint(0, len(self.data), size=(self.m, size))
+
+
+    def plot_from_indices(self, indices):
+        if isinstance(self.data, pd.DataFrame):
+            subset = self.data.iloc[indices]
+        else:
+            subset = self.data[indices]
+        return self.f(subset, self.data, *self.plot_args)
+
     @abstractmethod
     def plot_to_array(self) -> np.ndarray:
         raise NotImplemented
@@ -50,8 +65,8 @@ def plot_args(self):
 
 
 class Basic(Backend):
-    def __init__(self, f: callable, data: Union[np.ndarray, pd.DataFrame], m: int, output_size_px: Tuple[int, int]):
-        super().__init__(f, data, m, output_size_px)
+    def __init__(self, f: callable, data: Union[np.ndarray, pd.DataFrame], m: int, output_size_px: Tuple[int, int], single_sample: bool):
+        super().__init__(f, data, m, output_size_px, single_sample)
         self.cached_image = None
 
     def plot(self):
@@ -79,10 +94,11 @@ def __init__(self,
                  f: callable,
                  data: Union[np.ndarray, pd.DataFrame],
                  m: int,
-                 output_size_px: Tuple[int, int] = (512, 512)):
+                 output_size_px: Tuple[int, int] = (512, 512),
+                 single_sample: bool = False):
         self.fig = None
         self.ax = None
-        super().__init__(f, data, m, output_size_px)
+        super().__init__(f, data, m, output_size_px, single_sample)
 
     def create_figure(self):
         self.fig, self.ax = bootplot.backend.matplotlib.create_figure(self.output_size_px)
@@ -106,8 +122,9 @@ def __init__(self,
                  f: callable,
                  data: Union[np.ndarray, pd.DataFrame],
                  m: int,
-                 output_size_px: Tuple[int, int] = (512, 512)):
-        super().__init__(f, data, m, output_size_px)
+                 output_size_px: Tuple[int, int] = (512, 512),
+                 single_sample: bool = False):
+        super().__init__(f, data, m, output_size_px, single_sample)
 
     def create_figure(self):
         raise NotImplemented
@@ -131,7 +148,8 @@ def __init__(self,
                  f: callable,
                  data: Union[np.ndarray, pd.DataFrame],
                  m: int,
-                 output_size_px: Tuple[int, int] = (512, 512)):
+                 output_size_px: Tuple[int, int] = (512, 512), 
+                 single_sample: bool = False):
         super().__init__(f, data, m, output_size_px)
 
     def create_figure(self):

bootplot/base.py

@@ -4,68 +4,88 @@
 import numpy as np
 import imageio
 import pandas as pd
-from matplotlib import pyplot as plt
+import matplotlib.pyplot as plt
 from scipy.ndimage import gaussian_filter
 from tqdm import tqdm
 from PIL import Image, ImageFilter
 from scipy.stats import beta
 
 from bootplot.backend.base import Backend, create_backend
 from bootplot.sorting import sort_images
-from collections import Counter
 
+import jax.numpy as jnp
+from jax import jit, vmap, device_get
+from jax.scipy.special import betainc
 
-def plot(plot_function: callable,
-         data: Union[np.ndarray, pd.DataFrame],
-         indices: np.ndarray,
-         backend: Backend,
-         **kwargs):
-    if isinstance(data, pd.DataFrame):
-        plot_function(data.iloc[indices], data, *backend.plot_args, kwargs)
-    else:
-        plot_function(data[indices], data, *backend.plot_args, **kwargs)
-
-def symmetric_transformation_new(x, 
-                                 k, 
-                                 threshold):
-    y = beta.cdf(x, k, k)
-    return (1-2*threshold) * y + threshold
-
-def adjust_relative_frequencies_opt(relative_frequencies, 
-                                    k, 
-                                    threshold):
-    dominant_color = max(relative_frequencies, key=relative_frequencies.get)
-    transformed_dominant = symmetric_transformation_new(relative_frequencies[dominant_color], k, threshold)
-    sum_other = 1-relative_frequencies[dominant_color]
-    transformed_other = 1-transformed_dominant
-    return {
-        color: transformed_other * rel_freq / sum_other if color != dominant_color else 
-               transformed_dominant
-        for color, rel_freq in relative_frequencies.items()
-    }
-
-def merge_images(images: np.ndarray, 
-                 k: int, 
-                 threshold: int) -> np.ndarray:
-    num_images, rows, cols, _ = images.shape
-    new_image = np.zeros((rows, cols, 3), dtype=np.uint8)
-
-    # Iterate over each pixel location
-    for i in range(rows):
-        for j in range(cols):
-            # Extract the colors at the current pixel location across all images
-            pixel_colors = [tuple(images[img, i, j]) for img in range(num_images)]
-            # Count the occurrence of each color in this list of colors
-            color_counts = Counter(pixel_colors)
-            percentages_old = {color: count / sum(color_counts.values()) for color, count in color_counts.items()}
-            if len(percentages_old) > 1:
-                percentages = adjust_relative_frequencies_opt(percentages_old, k, threshold)
-                new_color = np.sum([np.array(c) * p for c, p in percentages.items()], axis=0)
-                new_color = np.clip(new_color, 0, 255).astype(np.uint8)
-                new_image[i, j] = new_color
-            else:
-                new_image[i,j] = list(percentages_old.keys())[0]
-    return new_image
+
+def symmetric_transformation_new(x: float,
+                                 k: float,
+                                 threshold: float) -> float:
+    y = betainc(k, k, x)
+    return (1 - 2 * threshold) * y + threshold
+
+def adjust_freqs(freqs: jnp.ndarray,
+                 k: float,
+                 threshold: float) -> jnp.ndarray:
+    dom_idx = jnp.argmax(freqs)
+    dom = freqs[dom_idx]
+
+    t_dom = symmetric_transformation_new(dom, k, threshold)
+    sum_other = 1.0 - dom
+    scale = (1.0 - t_dom) / sum_other
+
+    out = freqs * scale
+    return out.at[dom_idx].set(t_dom)
+
+
+def process_pixel(pixel_stack: jnp.ndarray,
+                  k: float,
+                  threshold: float) -> jnp.ndarray:
+    mn = pixel_stack.shape[0]
+
+    r = pixel_stack[:, 0].astype(jnp.int32)
+    g = pixel_stack[:, 1].astype(jnp.int32)
+    b = pixel_stack[:, 2].astype(jnp.int32)
+
+    idx = (r << 16) + (g << 8) + b
+
+    uniq, counts = jnp.unique(idx, size=mn, fill_value=0, return_counts=True)
+
+    n_unique = jnp.sum(counts > 0)
+
+    ur = ((uniq >> 16) & 255).astype(jnp.float32)
+    ug = ((uniq >> 8) & 255).astype(jnp.float32)
+    ub = (uniq & 255).astype(jnp.float32)
+    
+    colors = jnp.stack([ur, ug, ub], axis=1)
+
+    freqs = counts.astype(jnp.float32) / mn
+
+    only_one = (n_unique == 1)
+    one_color = colors[0].astype(jnp.uint8)
+
+    freqs_adj = adjust_freqs(freqs, k, threshold)
+
+    rgb = jnp.sum(colors * freqs_adj[:, None], axis=0)
+    rgb = jnp.clip(rgb, 0, 255).astype(jnp.uint8)
+
+    return jnp.where(only_one, one_color, rgb)
+
+
+    
+@jit
+def merge_images(images: np.ndarray,
+                 k: float,
+                 threshold: float) -> jnp.ndarray:
+    mn, rows, cols, _ = images.shape 
+
+    pixels = images.transpose(1, 2, 0, 3)
+    
+    #each of the rows * cols elements is a list of RGB pixels from all images at the same location:
+    pixels = pixels.reshape(rows * cols, mn, 3)
+
+    fused = vmap(process_pixel, in_axes=(0, None, None))(pixels, k, threshold)
+    return fused.reshape(rows, cols, 3)
 
 
 def merge_images_original(images: np.ndarray) -> np.ndarray:
@@ -84,6 +104,7 @@ def merge_images_original(images: np.ndarray) -> np.ndarray:
     return merged
 
 
+
 def decay_images(images: np.ndarray,
                  m: int,
                  decay_length: int) -> np.ndarray:
@@ -107,12 +128,16 @@ def decay_images(images: np.ndarray,
     return decayed_images
 
 
+
+
+
 def bootplot(f: callable,
              data: Union[np.ndarray, pd.DataFrame],
              m: int = 100,
              k: int = 2.5,
              threshold: int = 0.3,
              output_size_px: Tuple[int, int] = (512, 512),
+             single_sample: bool = False,
              output_image_path: Union[str, Path] = None,
              transformation: bool = True,
              output_animation_path: Union[str, Path] = None,
@@ -147,9 +172,12 @@ def bootplot(f: callable,
     :param threshold: input transformation parameter. Controls the codomain of the transformation. It lies between 0 and 0.5. Default: ``0,3``.
     :type threshold: int
 
-    :param output_size_px: output size (height, width) in pixels. Default: ``(512, 512)``.
+    :param output_size_px: output size (width, heigth) in pixels. Default: ``(512, 512)``.
     :type output_size_px: tuple[int, int]
 
+    :param single_sample: if true data_subset consists of a single sample. Default: ``False``.
+    :type single_sample: bool
+
     :param output_image_path: path where the image should be stored. The image format is inferred from the filename
         extension. If None, the image is not stored. Default: ``None``.
     :type output_image_path: str or pathlib.Path
@@ -223,28 +251,36 @@ def bootplot(f: callable,
         >>> image.shape
         (512, 512, 3)
     """
+
+    
     if isinstance(backend, str):
-        backend = create_backend(backend, f, data, m, output_size_px=output_size_px)
+        backend_class = create_backend(backend, f, data, m, output_size_px=output_size_px, single_sample=single_sample)
 
-    backend.create_figure()
+    backend_class.create_figure()
     images = []
     for _ in tqdm(range(m), desc='Generating plots', disable=not verbose):
-        backend.plot()
-        image = backend.plot_to_array()
+        backend_class.plot()
+        image = backend_class.plot_to_array()
         images.append(image)
-        backend.clear_figure()
-    backend.close_figure()
+        backend_class.clear_figure()
+    backend_class.close_figure()
     images = np.stack(images)
 
+
     if transformation:
-        merged_image = merge_images(images[..., :3], k, threshold)
+        merged_image = np.array(merge_images(images[..., :3], k, threshold))
+
     else:
         merged_image = merge_images_original(images[..., :3])
 
     if output_image_path is not None:
         if verbose:
             print(f'> Saving bootstrapped image to {output_image_path}')
-        Image.fromarray(merged_image).save(output_image_path)
+        if isinstance(backend, str) and backend.lower() == "matplotlib":
+            dpi = plt.rcParams['figure.dpi']
+            Image.fromarray(merged_image).save(output_image_path, dpi=(dpi, dpi))
+        else:
+            Image.fromarray(merged_image).save(output_image_path)
     if output_animation_path is not None:
         sort_kwargs = dict() if sort_kwargs is None else sort_kwargs
         order = sort_images(images, sort_type, verbose=verbose, **sort_kwargs)

requirements.txt

@@ -1,12 +1,13 @@
-numpy>=1.3,<2
-imageio~=2.9.0
-imageio-ffmpeg==0.4.7
+numpy>=1.3
+imageio>=2.9.0
+imageio-ffmpeg>=0.4.7
 matplotlib>=3
-tqdm~=4.64.0
+tqdm>=4.64.0
 pillow>=8
 scipy>=1.5
 scikit-image>=0.17
 networkx>=2.7.1
 scikit-learn>=0.24
-opencv-python~=4.5.5
-pandas~=1.4.3
+opencv-python>=4.5.5
+pandas>=1.4.3
+jax>=0.8.1