app.py

'''
an image processing tool that allows users to upload microscope images,
adjust the view with zoom and enhancement controls, and save the processed
image along with annotations. The tool uses OpenCV for image processing and
PIL for image enhancements. The processed image can be saved locally or
exported as a zip file containing the processed image, description, and
parameters. The tool also provides options to rename the processed image and
associated files.

The tool consists of the following components:
1. File Uploader: Allows users to upload microscope images in JPG or PNG format.
2. Image Controls: Provides sliders to adjust the zoom, contrast, brightness, and sharpness of the image.
3. Processed Image Display: Displays the processed image after applying the adjustments.
4. Original Image Display: Displays the original image uploaded by the user.
5. Save and Export Options: Allows users to add annotations, prepare a zip file for download, save the processed image locally, and rename the processed image and associated files.

To run the tool:
1. Save the script as `cell_exp_past.py`.
2. Run the script in a Python environment.
```python
streamlit run cell_exp_past.py
```
3. Open the provided local URL in a web browser.
4. Upload microscope images and adjust the image view.
5. Apply adjustments and save the processed image with annotations.
6. Download the processed image and annotations as a zip file.
7. Save the processed image locally or rename the processed image and
associated files.
'''

import streamlit as st
from PIL import Image, ImageEnhance
import pandas as pd
import numpy as np
import io
import os
import tempfile
import zipfile
import json

def zoom_at(img, x, y, zoom):
    w, h = img.size
    zoom2 = zoom * 2
    img = img.crop((x - w / zoom2, y - h / zoom2,
                    x + w / zoom2, y + h / zoom2))
    return img.resize((w, h), Image.LANCZOS)

st.title("Cell Explorer")

uploaded_files = st.file_uploader("Upload Images", accept_multiple_files=True, type="jpg")

if uploaded_files:
    img_index = st.selectbox("Select Image", range(len(uploaded_files)))
    x = st.slider("X Coordinate", 0, 500, 205)
    y = st.slider("Y Coordinate", 0, 500, 250)
    zoom = st.slider("Zoom", 1, 10, 0.5)
    contrast = st.slider("Contrast", 0.0, 5.0, 1.0)
    brightness = st.slider("Brightness", 0.0, 5.0, 1.0)
    sharpness = st.slider("Sharpness", 0.0, 2.0, 1.0)
    save_image = st.checkbox("Save Image")

    img_data = uploaded_files[img_index].read()
    img = Image.open(io.BytesIO(img_data)).resize((500, 500))
    img_zoomed = zoom_at(img, x, y, zoom)
    img_contrast = ImageEnhance.Contrast(img_zoomed).enhance(contrast)
    img_bright = ImageEnhance.Brightness(img_contrast).enhance(brightness)
    img_sharp = ImageEnhance.Sharpness(img_bright).enhance(sharpness)

    if save_image:
        processed_image_path = "image-processed.jpg"
        img_sharp.save(processed_image_path)
        st.session_state['processed_image_path'] = processed_image_path
        st.success(f"Image saved as {processed_image_path}")

    st.image(img_sharp, caption="Processed Image", use_container_width=True)

    description = st.text_area("Describe the image", "")
    if st.button("Save Description"):
        with tempfile.NamedTemporaryFile(delete=False, mode='w', suffix='.txt') as f:
            f.write(description)
            desc_file = f.name
        st.session_state['desc_file'] = desc_file
        st.success("Description saved.")

    if st.button("Save Image Parameters"):
        params = {
            "coordinates_x": x,
            "coordinates_y": y,
            "zoom": zoom,
            "contrast": contrast,
            "brightness": brightness,
            "sharpness": sharpness
        }
        with tempfile.NamedTemporaryFile(delete=False, mode='w', suffix='.json') as f:
            json.dump(params, f)
            params_file = f.name
        st.session_state['params_file'] = params_file
        st.success("Parameters saved.")

    if st.button("Rename Files"):
        file_ext = str(np.random.randint(100))
        processed_image_path = st.session_state.get('processed_image_path', None)
        desc_file = st.session_state.get('desc_file', None)
        params_file = st.session_state.get('params_file', None)

        if processed_image_path and os.path.exists(processed_image_path):
            try:
                new_image_name = f"img_processed{file_ext}.jpg"
                os.rename(processed_image_path, new_image_name)
            except FileNotFoundError:
                st.error(f"{processed_image_path} not found.")
        else:
            st.error("Processed image not found.")

        if params_file and os.path.exists(params_file):
            new_params_name = f"saved_image_parameters{file_ext}.json"
            os.rename(params_file, new_params_name)
        else:
            st.error("Saved image parameters file not found.")

        if desc_file and os.path.exists(desc_file):
            new_desc_name = f"saved_image_description{file_ext}.txt"
            os.rename(desc_file, new_desc_name)
        else:
            st.error("Saved image description file not found.")

        st.success("Files renamed successfully")

    if st.button("Export to ZIP"):
        with tempfile.NamedTemporaryFile(delete=False, suffix='.zip') as zipf:
            with zipfile.ZipFile(zipf.name, 'w') as z:
                if 'desc_file' in locals():
                    z.write(desc_file, os.path.basename(desc_file))
                if 'params_file' in locals():
                    z.write(params_file, os.path.basename(params_file))
        with open(zipf.name, 'rb') as f:
            st.download_button("Download ZIP", f, "annotations.zip")