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| from sklearn.preprocessing import OrdinalEncoder | |
| import xgboost as xgb | |
| import numpy as np | |
| import matplotlib.pyplot as plt | |
| import argparse, h5py, os, re, zipfile | |
| import streamlit as st | |
| def append_cale_to_name(name): | |
| if name.startswith("icsd"): | |
| return name + "cale" | |
| return name | |
| def get_POMFinder(): | |
| # Get file paths | |
| load_files = "Backend/" | |
| DataBase_path = "Backend/POMFinder_443structures_100Dataset_per_Structure_xPDF_hypercube_sampling_Grmax_Name.h5" | |
| POMFinder_path = "Backend/XGBoost_443structures_100PDFperStructure_xPDF_hypercube_sampling_Grmax.model" | |
| # Import the Database | |
| hf_name = h5py.File(DataBase_path, "r") | |
| y = hf_name.get('y') | |
| enc = OrdinalEncoder() | |
| y_onehotenc_cat = enc.fit(np.array(y)) | |
| y_onehotenc_values = enc.fit_transform(np.array(y)) | |
| # Import POMFinder | |
| POMFinder = xgb.XGBClassifier() | |
| POMFinder.load_model(POMFinder_path) | |
| return y, y_onehotenc_cat, y_onehotenc_values, POMFinder | |
| def PDF_Preparation(Your_PDF_Name, Qmin, Qmax, Qdamp, rmax, nyquist): | |
| for i in range(1000): | |
| with open(Your_PDF_Name, "r") as file: | |
| data = file.read().splitlines(True) | |
| if len(data[0]) == 0: | |
| with open(Your_PDF_Name, 'w') as fout: | |
| fout.writelines(data[1:]) | |
| break | |
| first_line = data[0] | |
| if len(first_line) > 3 and re.match(r'^-?\d+(?:\.\d+)?$', first_line[0]) != None and re.match(r'^-?\d+(?:\.\d+)?$', first_line[1]) == None and re.match(r'^-?\d+(?:\.\d+)?$', first_line[2]) != None: | |
| PDF = np.loadtxt(Your_PDF_Name) | |
| break | |
| else: | |
| with open(Your_PDF_Name, 'w') as fout: | |
| fout.writelines(data[1:]) | |
| r, Gr = PDF[:,0], PDF[:,1] | |
| if r[0] != 0: # In the case that the Data not start at 0. | |
| Gr = Gr[np.where(r==1)[0][0]:] # Remove Data from 0 to 0.5 AA | |
| Gr = Gr[::10] # Nyquist sample the rest of the Data | |
| Gr = np.concatenate(([0,0,0,0,0,0,0,0,0,0], Gr), axis=0) # Concatenate 0 - 0.5 AA on the Gr. | |
| if not nyquist: | |
| Gr = Gr[::10] # Pseudo Nyquist sample Data | |
| if len(Gr) >= (rmax*10+1): | |
| Gr = Gr[:(rmax*10+1)] # In the case Data is up to more than 30 AA, we do not use it. | |
| else: | |
| Gr = np.concatenate((Gr, np.zeros((101-len(Gr),))), axis=0) # In case Data is not going to 30 AA, we add 0's. | |
| Gr[:10] = np.zeros((10,)) | |
| r = np.arange(0, (rmax+0.1), 0.1) | |
| # Normalise it to the data from the database | |
| Gr /= np.max(Gr) | |
| # Add experimental parameters to the Gr | |
| Gr = np.expand_dims(np.concatenate((np.expand_dims(Qmin, axis=0), np.expand_dims(Qmax, axis=0), np.expand_dims(Qdamp, axis=0), Gr), axis=0), axis=0) | |
| # Create a new figure object | |
| fig, ax = plt.subplots() | |
| # Plot the transformation to make sure everything is alright | |
| ax.plot(PDF[:,0], PDF[:,1], label="Original Data") | |
| ax.plot(r, Gr[0,3:], label="Gr ready for ML") | |
| ax.legend() | |
| ax.set_title("Original Data vs. normalised Data") | |
| ax.set_xlabel("r (AA)") | |
| ax.set_ylabel("Gr") | |
| st.pyplot(fig) | |
| return r, Gr | |
| def POMPredicter(POMFinder, Gr, y_onehotenc_cat): | |
| y_pred_proba = POMFinder.predict_proba(Gr); | |
| y_pred_proba = y_pred_proba[:,1]; | |
| res = sorted(range(len(y_pred_proba)), key = lambda sub: y_pred_proba[sub]); | |
| res.reverse(); | |
| name = str(y_onehotenc_cat.categories_[0][res[0]])[2:-2] | |
| if name.startswith("icsd"): | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[0]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[0]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| else: | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[0]])[2:-2]+".xyz"}</b> with a probability of {100*y_pred_proba[res[0]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| name = str(y_onehotenc_cat.categories_[0][res[1]])[2:-2] | |
| if name.startswith("icsd"): | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[1]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[1]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| else: | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[1]])[2:-2]+".xyz"}</b> with a probability of {100*y_pred_proba[res[1]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| name = str(y_onehotenc_cat.categories_[0][res[2]])[2:-2] | |
| if name.startswith("icsd"): | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[2]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[2]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| else: | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[2]])[2:-2]+".xyz"}</b> with a probability of {100*y_pred_proba[res[2]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| name = str(y_onehotenc_cat.categories_[0][res[3]])[2:-2] | |
| if name.startswith("icsd"): | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[3]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[3]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| else: | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[3]])[2:-2]+".xyz"}</b> with a probability of {100*y_pred_proba[res[3]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| name = str(y_onehotenc_cat.categories_[0][res[4]])[2:-2] | |
| if name.startswith("icsd"): | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[4]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[4]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| else: | |
| st.markdown(f'<span style="font-size: 24px; color: green;">The 1st guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[4]])[2:-2]+".xyz"}</b> with a probability of {100*y_pred_proba[res[4]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| # st.markdown(f'<span style="font-size: 24px; color: green;">The 2nd guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[1]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[1]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| # st.markdown(f'<span style="font-size: 24px; color: green;">The 3rd guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[2]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[2]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| # st.markdown(f'<span style="font-size: 24px; color: green;">The 4th guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[3]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[3]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| # st.markdown(f'<span style="font-size: 24px; color: green;">The 5th guess from the model is: <b>{str(y_onehotenc_cat.categories_[0][res[4]])[2:-2]+"cale.xyz"}</b> with a probability of {100*y_pred_proba[res[4]]:.2f} %</span> <hr/>',unsafe_allow_html=True) | |
| return res, y_pred_proba | |
| # Define a download button to download the file | |
| def download_button(file_name, button_text): | |
| with open(file_name, "rb") as f: | |
| bytes = f.read() | |
| st.download_button( | |
| label=button_text, | |
| data=bytes, | |
| file_name=file_name, | |
| mime="text/xyz",) | |
| def create_zip_with_txt(y_onehotenc_cat, res, y_pred_proba): | |
| """ | |
| Create a zip file containing specific .xyz files and a txt file with model guesses. | |
| Parameters: | |
| y_onehotenc_cat: The one-hot encoder categories object. | |
| res: The result index for selecting the appropriate file. | |
| y_pred_proba: The probability associated with each prediction. | |
| Returns: | |
| None. A zip file is created in the current directory. | |
| """ | |
| zip_file_name = "POMFinder_results.zip" | |
| # Create a zip file | |
| with zipfile.ZipFile(zip_file_name, 'w') as zipf: | |
| # Add the .xyz files | |
| for i in range(5): | |
| name = str(y_onehotenc_cat.categories_[0][res[i]])[2:-2] | |
| if name.startswith("icsd"): | |
| file_path = "Backend/COD_ICSD_XYZs_POMs_unique99/" + str(y_onehotenc_cat.categories_[0][res[i]])[2:-2] + "cale.xyz" | |
| zipf.write(file_path, arcname=str(y_onehotenc_cat.categories_[0][res[i]])[2:-2] + "cale.xyz") | |
| else: | |
| file_path = "Backend/COD_ICSD_XYZs_POMs_unique99/" + str(y_onehotenc_cat.categories_[0][res[i]])[2:-2] + ".xyz" | |
| zipf.write(file_path, arcname=str(y_onehotenc_cat.categories_[0][res[i]])[2:-2] + ".xyz") | |
| # Create and add the txt file with model guesses | |
| with zipf.open("model_guesses.txt", "w") as f: | |
| for i in range(5): | |
| name = str(y_onehotenc_cat.categories_[0][res[i]])[2:-2] | |
| if name.startswith("icsd"): | |
| guess_text = f'The {i+1}st guess from the model is: {str(y_onehotenc_cat.categories_[0][res[i]])[2:-2]+"cale.xyz"} with a probability of {y_pred_proba[res[i]]:.2f} %\n' | |
| f.write(guess_text.encode('utf-8')) | |
| else: | |
| guess_text = f'The {i+1}st guess from the model is: {str(y_onehotenc_cat.categories_[0][res[i]])[2:-2]+".xyz"} with a probability of {y_pred_proba[res[i]]:.2f} %\n' | |
| f.write(guess_text.encode('utf-8')) | |
| st.title('POMFinder') | |
| st.write('Welcome to POMFinder which is a tree-based supervised learning algorithm that can predict the polyoxometalate cluster from a Pair Distribution Function.') | |
| st.write('Upload a PDF to use POMFinder to predict the structure.') | |
| # Define the file upload widget | |
| pdf_file = st.file_uploader("Upload PDF file in .gr format", type=["gr"]) | |
| # Define the form to get the other parameters | |
| Qmin = 0.7 #st.number_input("Qmin value of the experimental PDF", min_value=0.0, max_value=2.0, value=0.7) | |
| Qmax = 30 #st.number_input("Qmax value of the experimental PDF", min_value=15.0, max_value=40.0, value=30.0) | |
| Qdamp = 0.04 #st.number_input("Qdamp value of the experimental PDF", min_value=0.00, max_value=0.08, value=0.04) | |
| nyquist = st.checkbox("Is the data nyquist sampled", value=False) | |
| parser = argparse.ArgumentParser(prog='POMFinder', formatter_class=argparse.ArgumentDefaultsHelpFormatter) | |
| args = parser.parse_args() | |
| args.data = "uploaded_file.gr" | |
| args.nyquist = nyquist | |
| args.Qmin = Qmin | |
| args.Qmax = Qmax | |
| args.Qdamp = Qdamp | |
| args.file_name = "POMFinder_results.txt" | |
| if pdf_file is None: | |
| st.warning("Please upload a PDF file.") | |
| else: | |
| # Get the contents of the file as bytes | |
| file_bytes = pdf_file.read() | |
| # Save the contents of the file to disk | |
| with open("uploaded_file.gr", "wb") as f: | |
| f.write(file_bytes) | |
| #Predict with POMFinder | |
| y, y_onehotenc_cat, y_onehotenc_values, POMFinder = get_POMFinder() | |
| r, Gr = PDF_Preparation(args.data, args.Qmin, args.Qmax, args.Qdamp, rmax=10, nyquist=args.nyquist) | |
| res, y_pred_proba = POMPredicter(POMFinder, Gr, y_onehotenc_cat); | |
| # Download the structural database | |
| #download_button("COD_ICSD_XYZs_POMs_unique99.zip", "Download structural database") | |
| create_zip_with_txt(y_onehotenc_cat, res, y_pred_proba) | |
| download_button("POMFinder_results.zip", "Download top-5 predictions") | |
| st.subheader('Cite') | |
| st.write('If you use POMFinder, our code or results, please consider citing our paper. Thanks in advance!') | |
| st.write('POMFinder: Identifying polyoxometalate cluster structures from pair distribution function data using explainable machine learning **2023** (https://chemrxiv.org/engage/chemrxiv/article-details/64e5fef7dd1a73847f5951b9)') | |
| st.subheader('LICENSE') | |
| st.write('This project is licensed under the Apache License Version 2.0, January 2004 - see the LICENSE file at https://github.com/AndySAnker/POMFinder/blob/master/LICENSE.txt for details.') | |
| st.write("") | |
| st.subheader('Github') | |
| st.write('https://github.com/AndySAnker/POMFinder') | |
| st.subheader('Questions') | |
| st.write('ansoan@dtu.dk or etsk@chem.ku.dk') | |