differences for PR #328

files/source-code/blur-animation/README.md

@@ -0,0 +1,24 @@
+# Simple blur animation of image
+## Installation
+Use the provided `env.yml` environment file to install dependencies:
+```bash
+$ conda env install -f env.yml
+```
+
+## Usage
+1. Navigate to script directory:
+```bash
+$ cd ./image-processing/episodes/files/source-code/blur-animation
+```
+
+2. Run the script using the installed virtual environment:
+```bash
+$ conda activate anim-env
+$ python create_blur_animation.py
+```
+
+3. Follow prompt (choose kernel size) and press Enter.
+
+
+## Author
+@marcodallavecchia

files/source-code/blur-animation/create_blur_animation.py

@@ -0,0 +1,147 @@
+### METADATA
+# author: Marco Dalla Vecchia
+# description: Simple blurring animation of simple image
+# data-source: A.tif was created using ImageJ (https://imagej.net/ij/)
+###
+
+### POTENTIAL IMPROVEMENTS
+# - Change colors for rectangular patches in animation
+# - Ask for image input instead of hard-coding it
+# - Ask for FPS as input
+# - Ask for animation format output
+
+
+# Import packages
+# Use associated requirements file to make sure you have all dependencies installed
+from matplotlib import pyplot as plt
+from matplotlib import patches as p
+from matplotlib.animation import FuncAnimation
+import numpy as np
+from scipy.ndimage import convolve
+from tqdm import tqdm
+
+# Fix image path depending from where you run this script -> this should run as is, from the repo structure
+img_path = "../../../data/A.tif"
+# Change here colors to improve accessibility
+kernel_color = "tab:red"
+center_color = "tab:olive"
+
+### ANIMATION FUNCTIONS
+def init():
+    """
+    Initialization function
+    - Set image array data
+    - Autoscale image display
+    - Set XY coordinates of rectangular patches
+    """
+    im.set_array(img_convolved)
+    im.autoscale()
+    k_rect.set_xy((-0.5, -0.5))
+    c_rect1.set_xy((kernel_size / 2 - 1, kernel_size / 2 - 1))
+    return [im, k_rect, c_rect1]
+
+def update(frame):
+    """
+    Animation update function. For every frame do the following:
+    - Update X and Y coordinates of rectangular patch for kernel
+    - Update X and Y coordinates of rectangular patch for central pixel
+    - Update blurred image frame
+    """
+    pbar.update(1)
+    row = (frame % total_frames) // (img_pad.shape[0] - kernel_size + 1)
+    col = (frame % total_frames) % (img_pad.shape[1] - kernel_size + 1)
+
+    k_rect.set_x(col - 0.5)
+    c_rect1.set_x(col + (kernel_size/2 - 1))
+    k_rect.set_y(row - 0.5)
+    c_rect1.set_y(row + (kernel_size/2 - 1))
+
+    im.set_array(all_frames[frame])
+    im.autoscale()
+
+    return [im, k_rect, c_rect1]
+
+# MAIN PROGRAM
+if __name__ == "__main__":
+    # simple input to ask for kernel size
+    print("Please provide kernel size for mean filter blur animation")
+    kernel_size = int(input("> "))
+
+    while kernel_size % 2 == 0:
+        print("Please use an odd kernel size")
+        kernel_size = int(input("> "))
+
+    print("Creating blurred animation with kernel size:", kernel_size)
+
+    # Load image
+    img = plt.imread(img_path)
+
+    ### HERE WE USE THE CONVOLVE FUNCTION TO GET THE FINAL BLURRED IMAGE
+    # I chose a simple mean filter (equal kernel weights)
+    kernel = np.ones(shape=(kernel_size, kernel_size)) / kernel_size ** 2 # create kernel
+    # convolve the image i.e. apply mean filter
+    img_convolved = convolve(img, kernel, mode='constant', cval=0) # pad borders with zero like below for consistency
+
+
+    ### HERE WE CONVOLVE MANUALLY STEP-BY-STEP TO CREATE ANIMATION
+    img_pad = np.pad(img, (int(np.ceil(kernel_size/2) - 1), int(np.ceil(kernel_size/2) - 1))) # Pad image to deal with borders
+    new_img = np.zeros(img.shape, dtype=np.uint16) # this will be the blurred final image
+
+    # add first frame with complete blurred image for print version of GIF
+    all_frames = [img_convolved]
+
+    # precompute animation frames and append to the list
+    total_frames = (img_pad.shape[0] - kernel_size + 1) * (img_pad.shape[1] - kernel_size + 1) # total frames if by change image is not squared
+    for frame in range(total_frames):
+        row = (frame % total_frames) // (img_pad.shape[0] - kernel_size + 1) # row index
+        col = (frame % total_frames) % (img_pad.shape[1] - kernel_size + 1) # col index
+        img_chunk = img_pad[row : row + kernel_size, col : col + kernel_size] # get current image chunk inside the kernel
+        new_img[row, col] = np.mean(img_chunk).astype(np.uint16) # calculate its mean -> mean filter
+        all_frames.append(new_img.copy()) # append to animation frames list
+
+    # We now have an extra frame
+    total_frames += 1 
+
+    ### FROM HERE WE START CREATING THE ANIMATION
+    # Initialize canvas
+    f, (ax1, ax2) = plt.subplots(1,2, figsize=(10,5))
+
+    # Display the padded image -> this one won't change during the animation
+    ax1.imshow(img_pad, cmap='gray')
+    # Initialize the blurred image -> this is the first frame with already the final result
+    im = ax2.imshow(img_convolved, animated=True, cmap='gray')
+
+    # Define rectangular patches to identify moving kernel
+    k_rect = p.Rectangle((-0.5,-0.5), kernel_size, kernel_size, linewidth=2, edgecolor=kernel_color, facecolor='none', alpha=0.8) # kernel rectangle
+    c_rect1 = p.Rectangle(((kernel_size/2 - 1), (kernel_size/2 - 1)), 1, 1, linewidth=2, edgecolor=center_color, facecolor='none') # central pixel rectangle
+    # Add them to the figure
+    ax1.add_patch(k_rect)
+    ax1.add_patch(c_rect1)
+
+    # Fix limits to the right image (without padding) is the same size as the left image (with padding)
+    ax2.set(
+        ylim=((img_pad.shape[0] - kernel_size / 2), -kernel_size / 2), 
+        xlim=(-kernel_size / 2, (img_pad.shape[1] - kernel_size / 2))
+    )
+
+    # We don't need to see the ticks
+    ax1.axis("off")
+    ax2.axis("off")
+
+    # Create progress bar to visualize animation progress
+    pbar = tqdm(total=total_frames)
+
+    ### HERE WE CREATE THE ANIMATION
+    # Use FuncAnimation to create the animation
+    ani = FuncAnimation(
+        f, update, 
+        frames=range(total_frames), 
+        interval=50, # we could change the animation speed
+        init_func=init,
+        blit=True
+    )
+
+    # Export animation
+    plt.tight_layout()
+    ani.save('../../../fig/blur-demo.gif')
+    print("Animation exported")

files/source-code/blur-animation/env.yml

@@ -0,0 +1,11 @@
+name: anim-env
+channels:
+  - defaults
+dependencies:
+  - python=3.11
+  - pandas
+  - scikit-image
+  - seaborn
+  - pooch
+  - jupyterlab
+  - tqdm