Update app.py

app.py

@@ -1,151 +1,88 @@
-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
-
-sns.set_theme()
-
-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()
-
-app_ui = ui.page_fillable(
-    shinyswatch.theme.minty(),
+from shiny import App, ui, render, reactive
+
+import os
+import numpy as np
+import torch
+from PIL import Image
+from transformers import SamModel, SamProcessor
+
+# Load the processor and the finetuned model
+processor = SamProcessor.from_pretrained("facebook/sam-vit-base")
+model_path = "SAM/mito_model_checkpoint.pth"
+model = SamModel.from_pretrained("facebook/sam-vit-base")
+model.load_state_dict(torch.load(model_path, map_location=torch.device('cpu')))
+device = "cuda" if torch.cuda.is_available() else "cpu"
+model.to(device)
+model.eval()
+
+def process_image(image_path):
+    # Open and prepare the image
+    image = Image.open(image_path).convert("RGB")  # Ensure RGB format for consistency
+    image_np = np.array(image)
+
+    # Prepare the image for the model using the processor
+    inputs = processor(images=image_np, return_tensors="pt")
+    inputs = {k: v.to(device) for k, v in inputs.items()}
+
+    # Perform inference
+    with torch.no_grad():
+        outputs = model(**inputs, multimask_output=False)
+    
+    # Process the prediction to create a binary mask
+    pred_masks = torch.sigmoid(outputs.pred_masks).cpu().numpy()
+    segmented_image = (pred_masks[0] > .99).astype(np.uint8) * 255
+    print(segmented_image)
+    # Save the segmented image
+    root, ext = os.path.splitext(image_path)
+    output_path = f"{root}_segmented.png"
+    segmented_image_pil = Image.fromarray(segmented_image.squeeze(), mode="L")
+    segmented_image_pil.save(output_path)
+
+    return output_path
+
+# Define the Shiny app UI layout
+app_ui = ui.page_fluid(
     ui.layout_sidebar(
-        ui.sidebar(
-            # 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_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",
+        ui.panel_sidebar(
+            ui.input_file("image_upload", "Upload Satellite Image", accept=".jpg,.jpeg,.png,.tif")
         ),
-    ),
+        ui.panel_main(
+            ui.output_image("uploaded_image", "Uploaded Image"),
+            ui.output_image("segmented_image", "Segmented Image")
+        )
+    )
 )
 
-
-def server(input: Inputs, output: Outputs, session: Session):
-    @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())]
-
+def server(input, output, session):
     @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,
-        )
+    @render.image
+    def uploaded_image():
+        file_info = input.image_upload()
+        if file_info:
+            if isinstance(file_info, list):
+                file_path = file_info[0].get('datapath')
+                if file_path:
+                    return {'src': file_path}
+            else:
+                file_path = file_info.get('datapath')
+                if file_path:
+                    return {'src': file_path}
+        return None
 
     @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),
-)
+    @render.image
+    def segmented_image():
+        file_info = input.image_upload()
+        if file_info:
+            try:
+                file_path = file_info[0].get('datapath') if isinstance(file_info, list) else file_info.get('datapath')
+                if file_path:
+                    segmented_path = process_image(file_path)
+                    return {'src': segmented_path}
+            except Exception as e:
+                print(f"Error processing image: {e}")
+        return None
+
+# Create and run the Shiny app
+app = App(app_ui, server)
+app.run(port=8000)