app.py

import gradio as gr

from fastmri.data.subsample import create_mask_for_mask_type
from fastmri.data.transforms import apply_mask, to_tensor, center_crop
import skimage
import fastmri

import numpy as np
import pandas as pd
import torch

import matplotlib.pyplot as plt
import uuid

# st.title('FastMRI Kspace Reconstruction Masks')
# st.write('This app allows you to visualize the masks and their effects on the kspace data.')


def main_func(
    mask_name: str,
    mask_center_fractions: int,
    accelerations: int,
    seed: int,
    slice_index: int,
    # input_image: str,
):
    
    # file_dict = {
    #     "knee singlecoil": "data/knee1_kspace.npy",
    #     "knee multicoil": "data/knee2_kspace.npy",
    #     "brain multicoil 1": "data/brain1_kspace.npy",
    #     "brain multicoil 2": "data/brain2_kspace.npy",
    #     "prostate multicoil 1": "data/prostate1_kspace.npy",
    #     "prostate multicoil 2": "data/prostate2_kspace.npy",
    # }
    # input_file_path = file_dict[input_image]
    
    # kspace = np.load(input_file_path)
    kspace = np.load("data/prostate1_kspace.npy")
    kspace = to_tensor(kspace)
    mask_func = create_mask_for_mask_type(
        mask_name, center_fractions=[mask_center_fractions], accelerations=[accelerations]
    )
    subsampled_kspace, mask, num_low_frequencies  = apply_mask(
        kspace,
        mask_func,
        seed=seed,
    )
    
    print(mask.shape)
    print(subsampled_kspace.shape)
    print(kspace.shape)

    mask = mask.squeeze() # 451
    mask = mask.unsqueeze(0) # 1, 451
    mask = mask.repeat(subsampled_kspace.shape[-3], 1).cpu().numpy()

    print(mask.shape)
    print()

    subsampled_kspace = fastmri.rss(fastmri.complex_abs(fastmri.ifft2c(subsampled_kspace)), dim=1)
    kspace = fastmri.rss(fastmri.complex_abs(fastmri.ifft2c(kspace)), dim=1)
    
    print(subsampled_kspace.shape)
    print(kspace.shape)

    subsampled_kspace = subsampled_kspace[slice_index]
    kspace = kspace[slice_index]

    print(subsampled_kspace.shape)
    print(kspace.shape)


    subsampled_kspace = center_crop(subsampled_kspace, (320, 320))
    kspace = center_crop(kspace, (320, 320))

    # now that we have the reconstructions, we can calculate the SSIM and psnr
    kspace = kspace.cpu().numpy()
    subsampled_kspace = subsampled_kspace.cpu().numpy()



    ssim = skimage.metrics.structural_similarity(subsampled_kspace, kspace, data_range=kspace.max() - kspace.min())
    psnr = skimage.metrics.peak_signal_noise_ratio(subsampled_kspace, kspace, data_range=kspace.max() - kspace.min())

    df = pd.DataFrame({"SSIM": [ssim], "PSNR": [psnr], "Num Low Frequencies": [num_low_frequencies]})
    print(df)

    # create a plot
    fig, ax = plt.subplots(1, 3, figsize=(15, 5))
    ax[0].imshow(mask, cmap="gray")
    ax[0].set_title("Mask")
    ax[0].axis("off")

    ax[1].imshow(subsampled_kspace, cmap="gray")
    ax[1].set_title("Reconstructed Image")
    ax[1].axis("off")

    ax[2].imshow(kspace, cmap="gray")
    ax[2].set_title("Original Image")
    ax[2].axis("off")

    plt.tight_layout()
    plot_filename = f"data/{uuid.uuid4()}.png"
    plt.savefig(plot_filename)

    return df, plot_filename


demo = gr.Interface(
    fn=main_func,
    inputs=[
        gr.Radio(['random', 'equispaced', "equispaced_fraction", "magic", "magic_fraction"], label="Mask Type", value="equispaced"),
        gr.Slider(minimum=0.0, maximum=1.0, value=0.4, label="Center Fraction"),
        gr.Number(value=4, label="Acceleration"),
        gr.Number(value=42, label="Seed"),
        gr.Number(value=15, label="Slice Index"),
#         gr.Radio(["knee singlecoil", "knee multicoil", "brain multicoil 1", "brain multicoil 2", "prostate multicoil 1", "prostate multicoil 2"], label="Input Image")
    ],
    outputs=[
        gr.Dataframe(headers=["SSIM", "PSNR", "Num Low Frequencies"]),
        gr.Image(type="filepath", label="Plot"),
        # gr.Image(type="numpy", image_mode="L", label="Mask",),
        # gr.Image(type="numpy", image_mode="L", label="Reconstructed Image", height=320, width=320),
        # gr.Image(type="numpy", image_mode="L", label="Original Image", height=320, width=320),
    ],
    title="FastMRI Kspace Reconstruction Masks",
    description="This app allows you to visualize the masks and their effects on the kspace data."
)

demo.launch()