app.py

from matplotlib import cm 
import matplotlib.pyplot as plt
# from mpl_toolkits.axes_grid1 import make_axes_locatable

import numpy as np

# import onnx
import onnxruntime as ort
# from onnx import helper
from optimum.onnxruntime import ORTModel

import pandas as pd

from scipy import special

# import torch
# import torch.utils.data

import gradio as gr
# from transformers import pipeline


model_path = 'chlab/planet_detection_models/'

# plotting a prameters
labels = 20
ticks = 14
legends = 14
text = 14
titles = 22
lw = 3
ps = 200
cmap = 'magma'

def normalize_array(x: list):

    '''Makes array between 0 and 1'''
    
    x = np.array(x)
    
    return (x - np.min(x)) / np.max(x - np.min(x))

def load_model(model: str, activation: bool=True):
    
    if activation:
        model += '_w_activation'
    
    options = ort.SessionOptions()
    options.intra_op_num_threads = 1
    options.graph_optimization_level = ort.GraphOptimizationLevel.ORT_ENABLE_ALL
    provider = "CPUExecutionProvider"
    ort_session = ort.InferenceSession(model_path + '%s.onnx' % (model), options, providers=[provider])
    # ort_session = ORTModel.load_model(model_path + '%s.onnx' % (model))
    
    return ort_session

def get_activations(intermediate_model, image: list,
                               layer=None, vmax=2.5, sub_mean=True):
    
    '''Gets activations for a given input image'''
    
    
    input_name = intermediate_model.get_inputs()[0].name
    outputs = intermediate_model.run(None, {input_name: image})
    # outputs = intermediate_model(image)
    
    output_1 = outputs[1]
    output_2 = outputs[2]
    
    output = outputs[0]
    output = special.softmax(output)
    
    # origin = 'lower'
    
    # plt.rcParams['xtick.labelsize'] = ticks
    # plt.rcParams['ytick.labelsize'] = ticks
    
    # fig, axs = plt.subplots(nrows=1, ncols=3, figsize=(28, 8))
    
    # ax1, ax2, ax3 = axs[0], axs[1], axs[2]
    
    in_image = np.sum(image[0, :, :, :], axis=0)
    in_image = normalize_array(in_image)
    
    
    # im1 = ax1.imshow(in_image, cmap=cmap, vmin=0, vmax=vmax, origin=origin)
    if layer is None:
        activation_1 = np.sum(output_1[0, :, :, :], axis=0)
        activation_2 = np.sum(output_2[0, :, :, :], axis=0)
    else:
        activation_1 = output_1[0, layer, :, :]
        activation_2 = output_2[0, layer, :, :]
    
    if sub_mean:
        activation_1 -= np.mean(activation_1)
        activation_1 = np.abs(activation_1)
        
        activation_2 -= np.mean(activation_2)
        activation_2 = np.abs(activation_2)
    
    
    # im2 = ax2.imshow(activation_1, cmap=cmap, #vmin=0, vmax=1, 
    #                  origin=origin)
    # im3 = ax3.imshow(activation_2, cmap=cmap, #vmin=0, vmax=1, 
    #                  origin=origin) 
    # ims = [im1, im2, im3]
        
    # for (i, ax) in enumerate(axs):
    #     divider = make_axes_locatable(ax)
    #     cax = divider.append_axes('right', size='5%', pad=0.05)
    #     fig.colorbar(ims[i], cax=cax, orientation='vertical')
        
    # ax1.set_title('Input', fontsize=titles)
    
    # plt.show()
    
    return in_image, activation_1, activation_2


def predict_and_analyze(model_name, num_channels, dim, image):
    
    '''Loads a model with activations, passes through image and shows activations
    
    The image must be a pandas dataframe that can be made from a (C, W, H) numpy array
    using
    
    m,n,r = X.shape
    X = np.column_stack((np.repeat(np.arange(C), W), 
                               X.reshape(C * W, -1)))
    df = pd.DataFrame(X)
    
    then get the image back with 
    
    X = df.values
    X = X[:, 1:]
    X = X.reshape((C, W, W))
    
    image = 2d numpy array in shape (C, W*W)
    i.e. take a C,W,W array and reshape into (C, W*W)
    
    '''
    
    num_channels = int(num_channels)
    W = int(dim)
    
    # image = image.read()
    
    # with open(image, 'rb') as f:
    #     im = f.readlines()
    # image = np.frombuffer(image)
    
    print("Loading data")
    image = np.load(image.name, allow_pickle=True)
    
    # image = image.reshape((num_channels, W, W))
    
    # W = int(np.sqrt(image.shape[1]))
    
    # image = image.reshape((num_channels, W, W))
    
    if len(image.shape) != 4:
        image = image[np.newaxis, :, :, :]
        
    assert image.shape == (1, num_channels, W, W), "Data is the wrong shape"
        
    input_image = np.sum(image[0, :, :, :], axis=0)
    
    model_name += '_%i' % (num_channels)
        
        
    print("Loading model")
    model = load_model(model_name, activation=True)
    
    print("Looking at activations")
    output, activation_1, activation_2 = get_activations(model, image, sub_mean=True)
    
    output = 'Planet prediction with %f percent confidence' % (100*output)
    
    return output, input_image, activation_1, activation_2


demo = gr.Interface(
    fn=predict_and_analyze,
    inputs=[gr.Dropdown(["regnet", "efficientnet"], 
                        value="efficientnet",
                        label="Model Selection",
                        show_label=True), 
            gr.Dropdown(["45", "61", "75"], 
                        value="61",
                        label="Number of Velocity Channels",
                        show_label=True), 
            gr.Dropdown(["600"], 
                        value="600",
                        label="Image Dimensions",
                        show_label=True), 
            gr.File(label="Input Data", show_label=True)],
    outputs=[gr.Textbox(lines=1, label="Prediction", show_label=True), 
             gr.Image(label="Input Image", show_label=True), 
             gr.Image(label="Activation 1", show_label=True), 
             gr.Image(label="Actication 2", show_label=True)],
    title="Kinematic Planet Detector"
)
demo.launch()