app.py

from pathlib import Path
from typing import List, Dict, Tuple
import matplotlib.colors as mpl_colors

import pandas as pd
import seaborn as sns
import shinyswatch

from shiny import App, Inputs, Outputs, Session, reactive, render, req, ui

import os
from transformers import SamModel, SamConfig, SamProcessor
import torch

from PIL import Image
import io
import numpy as np
import matplotlib.pyplot as plt

sns.set_theme()

dir = Path(__file__).resolve().parent
www_dir = Path(__file__).parent.resolve() / "www"

df = pd.read_csv(Path(__file__).parent / "penguins.csv", na_values="NA")
numeric_cols: List[str] = df.select_dtypes(include=["float64"]).columns.tolist()
species: List[str] = df["Species"].unique().tolist()
species.sort()

### UI ###
app_ui = ui.page_fillable(
    shinyswatch.theme.minty(),
    ui.layout_sidebar(
        ui.sidebar(
            ui.input_file("tile_image", "Choose TIFF File", accept=[".tif"], multiple=False),
            # Artwork by @allison_horst
            ui.input_selectize(
                "xvar",
                "X variable",
                numeric_cols,
                selected="Bill Length (mm)",
            ),
            ui.input_selectize(
                "yvar",
                "Y variable",
                numeric_cols,
                selected="Bill Depth (mm)",
            ),
            ui.input_checkbox_group(
                "species", "Filter by species", species, selected=species
            ),
            ui.hr(),
            ui.input_switch("by_species", "Show species", value=True),
            ui.input_switch("show_margins", "Show marginal plots", value=True),
        ),
        ui.output_image("uploaded_image"),  # display the uploaded TIFF sidewalk tile image
        ui.output_plot("prediction_plots"),
        ui.output_ui("value_boxes"),
        ui.output_plot("scatter", fill=True),
        ui.help_text(
            "Artwork by ",
            ui.a("@allison_horst", href="https://twitter.com/allison_horst"),
            class_="text-end",
        ),
    ),
)

### HELPER FUNCTIONS ###
def tif_bytes_to_pil_image(tif_bytes):
    # Create a BytesIO object from the TIFF bytes
    bytes_io = io.BytesIO(tif_bytes)
    
    # Open the BytesIO object as an Image, crop to square, resize to 256
    image = Image.open(bytes_io).convert("RGB")
    w, h = image.size
    dim = min(w, h)
    image = image.crop((0, 0, dim, dim))
    image = image.resize((256, 256))

    return image

def load_model():
    """ Get Model """
    # Load the model configuration
    model_config = SamConfig.from_pretrained("facebook/sam-vit-base")
    processor = SamProcessor.from_pretrained("facebook/sam-vit-base")
    
    # Create an instance of the model architecture with the loaded configuration
    model = SamModel(config=model_config)
    # Update the model by loading the weights from saved file
    model_state_dict = torch.load(str(dir / "checkpoint.pth"), map_location=torch.device('cpu'))
    model.load_state_dict(model_state_dict)
    
    # set the device to cuda if available, otherwise use cpu
    device = "cuda" if torch.cuda.is_available() else "cpu"
    model.to(device)

    return model, processor, device

def show_mask(mask, ax, random_color=False):
    if random_color:
        color = np.concatenate([np.random.random(3), np.array([0.6])], axis=0)
    else:
        color = np.array([30/255, 144/255, 255/255, 0.6])
    h, w = mask.shape[-2:]
    mask_image = mask.reshape(h, w, 1) * color.reshape(1, 1, -1)
    ax.imshow(mask_image, extent=(0, width, height, 0))  # Setting extent to match original image dimensions

### SERVER ###
def server(input: Inputs, output: Outputs, session: Session):

    # set model, processor, device once
    model, processor, device = load_model()
    
    @reactive.Calc
    def uploaded_image_path() -> str:
        """Returns the path to the uploaded image"""
        if input.tile_image() is not None:
            return input.tile_image()[0]['datapath']  # Assuming multiple=False
        else:
            return ""  # No image uploaded

    @render.image
    def uploaded_image():
        """Displays the uploaded image"""
        img_src = uploaded_image_path()
        if img_src:
            img: ImgData = {"src": str(dir / uploaded_image_path()), "width": "100px"}
            return img
        else:
            return None  # Return an empty string if no image is uploaded

    def generate_input_points(image, grid_size=10):
        """
        input_points (torch.FloatTensor of shape (batch_size, num_points, 2)) —
        Input 2D spatial points, this is used by the prompt encoder to encode the prompt.
        Generally yields to much better results. The points can be obtained by passing a
        list of list of list to the processor that will create corresponding torch tensors
        of dimension 4. The first dimension is the image batch size, the second dimension
        is the point batch size (i.e. how many segmentation masks do we want the model to
        predict per input point), the third dimension is the number of points per segmentation
        mask (it is possible to pass multiple points for a single mask), and the last dimension
        is the x (vertical) and y (horizontal) coordinates of the point. If a different number
        of points is passed either for each image, or for each mask, the processor will create
        “PAD” points that will correspond to the (0, 0) coordinate, and the computation of the
        embedding will be skipped for these points using the labels.
        
        """

        # Get the dimensions of the image
        array_size = max(image.width, image.height)
        
        # Generate the grid points
        x = np.linspace(0, array_size-1, grid_size)
        y = np.linspace(0, array_size-1, grid_size)
        
        # Generate a grid of coordinates
        xv, yv = np.meshgrid(x, y)
        
        # Convert the numpy arrays to lists
        xv_list = xv.tolist()
        yv_list = yv.tolist()
        
        # Combine the x and y coordinates into a list of list of lists
        input_points = [[[int(x), int(y)] for x, y in zip(x_row, y_row)] for x_row, y_row in zip(xv_list, yv_list)]
        
        #We need to reshape our nxn grid to the expected shape of the input_points tensor
        # (batch_size, point_batch_size, num_points_per_image, 2),
        # where the last dimension of 2 represents the x and y coordinates of each point.
        #batch_size: The number of images you're processing at once.
        #point_batch_size: The number of point sets you have for each image.
        #num_points_per_image: The number of points in each set.
        input_points = torch.tensor(input_points).view(1, 1, grid_size*grid_size, 2)
        
        return input_points
        
    def process_image():
        """Processes the uploaded image, loads the model, and evaluates to get predictions"""

        """ Get Image """
        img_src = uploaded_image_path()
        
        # Read the image bytes from the file
        with open(img_src, 'rb') as f:
            image_bytes = f.read()
        
        # Convert the image bytes to a PIL Image
        image = tif_bytes_to_pil_image(image_bytes)

        """ Prepare Inputs """
        # get input points prompt (grid of points)
        input_points = generate_input_points(image)
        
        # prepare image and prompt for the model
        inputs = processor(image, input_points=input_points, return_tensors="pt")
        
        # # remove batch dimension which the processor adds by default
        # inputs = {k:v.squeeze(0) for k,v in inputs.items()}

        # Move the input tensor to the GPU if it's not already there
        inputs = {k: v.to(device) for k, v in inputs.items()}
        
        """ Get Predictions """
        # forward pass
        with torch.no_grad():
            outputs = model(**inputs, multimask_output=False)
        
        # apply sigmoid
        prob = torch.sigmoid(outputs.pred_masks.squeeze(1))
        # convert soft mask to hard mask
        prob = prob.cpu().numpy().squeeze()
        prediction = (prob > 0.5).astype(np.uint8)
        
        # Return the processed result 
        return image, prob, prediction

    @reactive.Calc
    def get_predictions():
        """Processes the image when uploaded to get predictions"""
        if input.tile_image() is not None:
            return process_image()
        else:
            return None, None, None

    @output
    @render.plot
    def prediction_plots():
        # get prediction results when image is uploaded
        image, prob, prediction = get_predictions()

        # Check if there are no predictions (i.e., no uploaded image)
        if image is None or prob is None or prediction is None:
            # Return a placeholder plot or message
            fig, ax = plt.subplots()
            ax.text(0.5, 0.5, "Upload a square image to see predictions. If the image is not a square, the image will be cropped to a square, taking the top left portion of the image. Predictions will take a few moments to load.", fontsize=12, ha="center")
            ax.axis("off")  # Hide axis
            plt.tight_layout()
            return fig
        
        fig, axes = plt.subplots(1, 4, constrained_layout=True)
        
        # Extract the image data
        #image_data = image.cpu().detach().numpy()
        
        # Plot the first image on the left
        axes[0].imshow(image)  
        axes[0].set_title("Image")
        
        # Plot the probability map on the right
        axes[1].imshow(prob)
        axes[1].set_title("Probability Map")
        
        # Plot the prediction image on the right
        axes[2].imshow(prediction) 
        axes[2].set_title("Prediction")
        
        # Plot the predicted mask on the right
        axes[3].imshow(image) 
        show_mask(prediction, axes[3])
        axes[3].set_title("Predicted Mask")
        
        # Hide axis ticks and labels
        for ax in axes:
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            
        plt.tight_layout()
        
        return fig
    



    
    
    @reactive.Calc
    def filtered_df() -> pd.DataFrame:
        """Returns a Pandas data frame that includes only the desired rows"""

        # This calculation "req"uires that at least one species is selected
        req(len(input.species()) > 0)

        # Filter the rows so we only include the desired species
        return df[df["Species"].isin(input.species())]

    @output
    @render.plot
    def scatter():
        """Generates a plot for Shiny to display to the user"""

        # The plotting function to use depends on whether margins are desired
        plotfunc = sns.jointplot if input.show_margins() else sns.scatterplot

        plotfunc(
            data=filtered_df(),
            x=input.xvar(),
            y=input.yvar(),
            palette=palette,
            hue="Species" if input.by_species() else None,
            hue_order=species,
            legend=False,
        )

    @output
    @render.ui
    def value_boxes():
        df = filtered_df()

        def penguin_value_box(title: str, count: int, bgcol: str, showcase_img: str):
            return ui.value_box(
                title,
                count,
                {"class_": "pt-1 pb-0"},
                showcase=ui.fill.as_fill_item(
                    ui.tags.img(
                        {"style": "object-fit:contain;"},
                        src=showcase_img,
                    )
                ),
                theme_color=None,
                style=f"background-color: {bgcol};",
            )

        if not input.by_species():
            return penguin_value_box(
                "Penguins",
                len(df.index),
                bg_palette["default"],
                # Artwork by @allison_horst
                showcase_img="penguins.png",
            )

        value_boxes = [
            penguin_value_box(
                name,
                len(df[df["Species"] == name]),
                bg_palette[name],
                # Artwork by @allison_horst
                showcase_img=f"{name}.png",
            )
            for name in species
            # Only include boxes for _selected_ species
            if name in input.species()
        ]

        return ui.layout_column_wrap(*value_boxes, width = 1 / len(value_boxes))


# "darkorange", "purple", "cyan4"
colors = [[255, 140, 0], [160, 32, 240], [0, 139, 139]]
colors = [(r / 255.0, g / 255.0, b / 255.0) for r, g, b in colors]

palette: Dict[str, Tuple[float, float, float]] = {
    "Adelie": colors[0],
    "Chinstrap": colors[1],
    "Gentoo": colors[2],
    "default": sns.color_palette()[0],  # type: ignore
}

bg_palette = {}
# Use `sns.set_style("whitegrid")` to help find approx alpha value
for name, col in palette.items():
    # Adjusted n_colors until `axe` accessibility did not complain about color contrast
    bg_palette[name] = mpl_colors.to_hex(sns.light_palette(col, n_colors=7)[1])  # type: ignore


app = App(
    app_ui,
    server,
    static_assets=str(www_dir),
)