1-samples_selection.py

from Packages import *
st.set_page_config(page_title="NIRS Utils", page_icon=":goat:", layout="wide")
from Modules import *

# empty temp figures
for i in ['Report/figures','Report/datasets']:
    repertoire_a_vider = Path(i)
    if os.path.exists(repertoire_a_vider):
        for fichier in os.listdir(repertoire_a_vider):
            chemin_fichier = os.path.join(repertoire_a_vider, fichier)
            if os.path.isfile(chemin_fichier) or os.path.islink(chemin_fichier):
                os.unlink(chemin_fichier)
            elif os.path.isdir(chemin_fichier):
                shutil.rmtree(chemin_fichier)

# HTML pour le bandeau "CEFE - CNRS"
add_header()
#load specific model page css
local_css(css_file / "style_model.css")
add_sidebar(pages_folder)



# algorithms available in our app
dim_red_methods=['', 'PCA','UMAP', 'NMF']  # List of dimensionality reduction algos
cluster_methods = ['', 'Kmeans','HDBSCAN', 'AP', 'KS', 'RDM'] # List of clustering algos
selec_strategy = ['center','random']

match st.session_state["interface"]:
    case 'simple':
        st.write(':red[Automated Simple Interface]')
        # hide_pages("Predictions")
        if 37 not in st.session_state:
            default_reduction_option = 1
        else:
            default_reduction_option = dim_red_methods.index(st.session_state.get(37))
        if 38 not in st.session_state:
            default_clustering_option = 1
        else:
            default_clustering_option = cluster_methods.index(st.session_state.get(38))
        if 102 not in st.session_state:
            default_sample_selection_option = 1
        else:
            default_sample_selection_option = selec_strategy.index(st.session_state.get(102))
        
    case'advanced':
        default_reduction_option = 0
        default_clustering_option = 0
        default_sample_selection_option = 0

################################### I - Data Loading and Visualization ########################################
date_time = datetime.datetime.now().strftime('_%y_%m_%d_%H_%M_')
st.title("Calibration Subset Selection")
col2, col1 = st.columns([3, 1])
col2.image("./images/sample selection.png", use_column_width=True)
## Preallocation of data structure
spectra = pd.DataFrame()
meta_data = pd.DataFrame()
tcr=pd.DataFrame()
sam=pd.DataFrame()
sam1=pd.DataFrame()
selected_samples = pd.DataFrame()
non_clustered = None
l1 = []
labels = []
color_palette = None
dr_model = None # dimensionality reduction model
cl_model = None # clustering model
selection = None
selection_number = None

# loader for datafile
data_file = col1.file_uploader("Data file", type=["csv","dx"], help=" :mushroom: select a csv matrix with samples as rows and lambdas as columns", key=5)

if not data_file:
    col1.warning('⚠️ Please load data file !')
else:
    # Retrieve the extension of the file
    # test = data_file.name[data_file.name.find('.'):]
    
    
    extension = data_file.name.split(".")[-1]
    userfilename = data_file.name.replace(f".{extension}", '')

    match extension:
    ## Load .csv file
        case 'csv':
            with col1:
                # Select list for CSV delimiter
                psep = st.radio("Select csv separator - _detected_: " + str(find_delimiter('data/'+data_file.name)), options=[";", ","], index=[";", ","].index(str(find_delimiter('data/'+data_file.name))),horizontal=True, key=9)
                    # Select list for CSV header True / False
                phdr = st.radio("indexes column in csv? - _detected_: " + str(find_col_index('data/'+data_file.name)), options=["no", "yes"], index=["no", "yes"].index(str(find_col_index('data/'+data_file.name))),horizontal=True, key=31)
                if phdr == 'yes':
                    col = 0
                else:
                    col = False
                imp = pd.read_csv(data_file, sep=psep, index_col=col)
                imp.to_csv("./Report/datasets/"+data_file.name,sep = ';', encoding='utf-8', mode='a')
                
                # spectra = col_cat(imp)[0]
                # meta_data = col_cat(imp)[1]
                spectra, md_df_st_ = col_cat(imp)
                meta_data = md_df_st_
                st.success("The data have been loaded successfully", icon="✅")
        ## Load .dx file
        case 'dx':
            # Create a temporary file to save the uploaded file
            with NamedTemporaryFile(delete=False, suffix=".dx") as tmp:
                tmp.write(data_file.read())
                with open(tmp.name, 'r') as dd:
                    dxdata = dd.read()
                with open('Report/datasets/'+data_file.name, 'w') as dd:
                    dd.write(dxdata)
                tmp_path = tmp.name
                with col1:
                    _, spectra, meta_data, md_df_st_ = read_dx(file = tmp_path)
                    st.success("The data have been loaded successfully", icon="✅")
            os.unlink(tmp_path)


    
## Visualize spectra
st.header("I - Spectral Data Visualization", divider='blue')
if not spectra.empty:
    n_samples = spectra.shape[0]
    nwl = spectra.shape[1]
    # retrieve columns name and rows name of spectra
    colnames = list(spectra.columns)
    rownames = [str(i) for i in list(spectra.index)]
    spectra.index = rownames
    col2, col1 = st.columns([3, 1])
    with col2:
        fig, ax = plt.subplots(figsize = (30,7))
        if extension =='dx':
            lab = ['Wavenumber (1/cm)' if meta_data.loc[:,'xunits'][0] == '1/cm' else 'Wavelength (nm)']
            if lab[0] =='Wavenumber (1/cm)':
                spectra.T.plot(legend=False, ax = ax).invert_xaxis()
            else :
                spectra.T.plot(legend=False, ax = ax)
            ax.set_xlabel(lab[0], fontsize=18)
        else:
            spectra.T.plot(legend=False, ax = ax)
            ax.set_xlabel('Wavelength/Wavenumber', fontsize=18)
        
        ax.set_ylabel('Signal intensity', fontsize=18)
        plt.margins(x = 0)
        plt.tight_layout()
        st.pyplot(fig)
        
        # update lines size
        for line in ax.get_lines():
            line.set_linewidth(0.8)  # Set the desired line width here

        # Update the size of plot axis for exprotation to report
        l, w = fig.get_size_inches()
        fig.set_size_inches(8, 3)
        for label in (ax.get_xticklabels()+ax.get_yticklabels()):
            ax.xaxis.label.set_size(9.5)
            ax.yaxis.label.set_size(9.5)
        plt.tight_layout()
        fig.savefig("./Report/figures/spectra_plot.png", dpi=400) ## Export report
        fig.set_size_inches(l, w)# reset the plot size to its original size
        data_info = pd.DataFrame({'Name': [data_file.name],
                                'Number of scanned samples': [n_samples]},
                                  index = ['Input file'])
    with col1:
        st.info('Information on the loaded data file')
        st.write(data_info) ## table showing the number of samples in the data file

############################## Exploratory data analysis ###############################
st.header("II - Exploratory Data Analysis-Multivariable Data Analysis", divider='blue')

###### 1- Dimensionality reduction ######
t = pd.DataFrame # scores
p = pd.DataFrame # loadings
if not spectra.empty:
    bb1, bb2, bb3, bb4, bb5, bb6, bb7 = st.columns([1,1,0.6,0.6,0.6,1.5,1.5])
    dim_red_method = bb1.selectbox("Dimensionality reduction techniques: ", options = dim_red_methods, index = default_reduction_option, key = 37)
    clus_method = bb2.selectbox("Clustering/sampling techniques: ", options = cluster_methods, index = default_clustering_option, key = 38)
    xc = standardize(spectra, center=True, scale=False)
    
    match dim_red_method:
        case "":
                bb1.warning('⚠️ Please choose an algorithm !')
        
        case "PCA":
            @st.cache_data
            def dr_model_(change):
                dr_model = LinearPCA(xc, Ncomp=8)
                return dr_model
            dr_model = dr_model_(change = hash_data(xc))

        case "UMAP":
            if not meta_data.empty:
                filter = md_df_st_.columns
                filter = filter.insert(0, 'Nothing')
                col = bb1.selectbox('Supervised UMAP by:', options= filter, key=108)
                if col == 'Nothing':
                    supervised = None
                else:
                    supervised = md_df_st_[col]
            else:
                supervised = None
            @st.cache_data
            def dr_model_(change):
                dr_model = Umap(numerical_data = MinMaxScale(spectra), cat_data = supervised)
                return dr_model
            dr_model = dr_model_(change = hash_data(spectra))
                

        case 'NMF':
            @st.cache_data
            def dr_model_(change):
                dr_model = Nmf(spectra, Ncomp= 3)
                return dr_model
            dr_model = dr_model_(change = hash_data(spectra))
        

    if dr_model:
        axis1 = bb3.selectbox("x-axis", options = dr_model.scores_.columns, index=0)
        axis2 = bb4.selectbox("y-axis", options = dr_model.scores_.columns, index=1)
        axis3 = bb5.selectbox("z-axis", options = dr_model.scores_.columns, index=2)

        t = pd.concat([dr_model.scores_.loc[:,axis1], dr_model.scores_.loc[:,axis2], dr_model.scores_.loc[:,axis3]], axis = 1)



###### II - clustering #######
if not t.empty:
    clustered = np.arange(n_samples)
    non_clustered = None

    if dim_red_method == 'UMAP':
        scores = st.container()
    else:
        scores, loadings= st.columns([3,3])

    tcr = standardize(t)
    
    # Clustering
    match clus_method:
        case '':
            bb2.warning('⚠️ Please choose an algothithm !')
        case 'Kmeans':
            cl_model = Sk_Kmeans(tcr, max_clusters = 25)
            ncluster = scores.number_input(min_value=2, max_value=25, value=cl_model.suggested_n_clusters_, label = 'Select the desired number of clusters')  
            data, labels, clu_centers = cl_model.fit_optimal(nclusters = ncluster)

        # 2- HDBSCAN clustering
        case 'HDBSCAN':
            optimized_hdbscan = Hdbscan(np.array(tcr))
            all_labels, clu_centers = optimized_hdbscan.HDBSCAN_scores_
            labels = [f'cluster#{i+1}' if i !=-1 else 'Non clustered' for i in all_labels]
            ncluster = len(clu_centers)
            non_clustered = np.where(np.array(labels) == 'Non clustered')[0]

        # 3- Affinity propagation
        case 'AP':
            cl_model = AP(X = tcr)
            data, labels, clu_centers = cl_model.fit_optimal_
            ncluster = len(clu_centers)

        case 'KS':
            rset = scores.number_input(min_value=0, max_value=100, value=20, label = 'The ratio of data to be sampled (%)')
            cl_model = KS(x = tcr, rset = rset)
            calset = cl_model.calset
            labels = ["ind"]*n_samples
            ncluster = "1"
            selection_number = 'None'

        case 'RDM':
            rset = scores.number_input(min_value=0, max_value=100, value=20, label = 'The ratio of data to be sampled (%)')
            cl_model = RDM(x = tcr, rset = rset)
            calset = cl_model.calset
            labels = ["ind"]*n_samples
            ncluster = "1"
            selection_number = 'None'            

    new_tcr = tcr.iloc[clustered,:]    
    

#################################################### III - Samples selection using the reduced data preentation ######
samples_df_chem = pd.DataFrame
selected_samples = []
selected_samples_idx = []

if not labels:
    custom_color_palette = px.colors.qualitative.Plotly[:1]
elif labels:
    num_clusters = len(np.unique(labels))
    custom_color_palette = px.colors.qualitative.Plotly[:num_clusters]
    if clus_method:
        if clus_method in ['KS', 'RDM']:
            selected_samples_idx = calset[1]
            selection = 'None'
        else:
            selection = scores.radio('Select samples selection strategy:',
                                        options = selec_strategy, index = default_sample_selection_option, key=102)
        
        match selection:
        # Strategy 0
            case 'center':
                # list samples at clusters centers - Use sklearn.metrics.pairwise_distances_argmin if you want more than 1 sample per cluster
                closest, _ = pairwise_distances_argmin_min(clu_centers, new_tcr)
                selected_samples_idx = np.array(new_tcr.index)[list(closest)]
                selected_samples_idx = selected_samples_idx.tolist()
                
            #### Strategy 1
            case 'random':
                selection_number = scores.number_input('How many samples per cluster?',
                                                        min_value = 1, step=1, value = 3)
                s = np.array(labels)[np.where(np.array(labels) !='Non clustered')[0]]
                for i in np.unique(s):
                    C = np.where(np.array(labels) == i)[0]
                    if C.shape[0] >= selection_number:
                        # scores.write(list(tcr.index)[labels== i])
                        km2 = KMeans(n_clusters = selection_number)
                        km2.fit(tcr.iloc[C,:])
                        clos, _ = pairwise_distances_argmin_min(km2.cluster_centers_, tcr.iloc[C,:])
                        selected_samples_idx.extend(tcr.iloc[C,:].iloc[list(clos)].index)
                    else:
                        selected_samples_idx.extend(new_tcr.iloc[C,:].index.to_list())
                    # list indexes of selected samples for colored plot    

################################      Plots visualization          ############################################


    ## Scores
if not t.empty:
    with scores:
        fig1, ((ax1, ax2),(ax3,ax4)) = plt.subplots(2,2)
        st.write('Scores plot')
        # scores plot with clustering
        if list(labels) and meta_data.empty:
            fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3, color=labels ,color_discrete_sequence= custom_color_palette)
            sns.scatterplot(data = tcr, x = axis1, y =axis2 , hue = labels, ax = ax1)
        # scores plot with metadata
        elif len(list(labels)) == 0 and not meta_data.empty:
            filter = md_df_st_.columns
            col = st.selectbox('Color by:', options= filter)
            if col == 0:
                fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3)
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , ax = ax1)
                sns.scatterplot(data = tcr, x = axis2, y =axis3 , ax = ax2)
                sns.scatterplot(data = tcr, x = axis1, y =axis3 , hue = list(map(str.lower,md_df_st_[col])), ax = ax3)


            else:
                fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3, color = list(map(str.lower,md_df_st_[col])) )
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , hue = list(map(str.lower,md_df_st_[col])), ax = ax1)
                sns.scatterplot(data = tcr, x = axis2, y =axis3 , hue = list(map(str.lower,md_df_st_[col])), ax = ax2)
                sns.scatterplot(data = tcr, x = axis1, y =axis3 , hue = list(map(str.lower,md_df_st_[col])), ax = ax3)

        # color with scores and metadata
        elif len(list(labels)) > 0  and not meta_data.empty:
            if clus_method in cluster_methods[1:]:
                filter = ['None', clus_method]
                filter.extend(md_df_st_.columns)
            else:
                filter = md_df_st_.columns.insert(0,'None')

            col = st.selectbox('Color by:', options= filter)
            if col == "None":
                fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3)
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , ax = ax1)
            elif col == clus_method:
                fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3, color = labels)
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , ax = ax1)
            else:
                fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3, color = list(map(str.lower,md_df_st_[col])))
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , hue = list(map(str.lower,md_df_st_[col])), ax = ax1)
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , hue = list(map(str.lower,md_df_st_[col])), ax = ax2)
                sns.scatterplot(data = tcr, x = axis1, y =axis2 , hue = list(map(str.lower,md_df_st_[col])), ax = ax3)

        else:
            fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3, color=labels if list(labels) else None,color_discrete_sequence= custom_color_palette)
            sns.scatterplot(data = tcr, x = axis1, y =axis2 , ax = ax1)
        fig.update_traces(marker=dict(size=4))

        if selected_samples_idx:
            tt = tcr.iloc[selected_samples_idx,:]
            fig.add_scatter3d(x = tt.loc[:,axis1], y = tt.loc[:,axis2],z = tt.loc[:,axis3],
                               mode ='markers', marker = dict(size = 5, color = 'black'),
                              name = 'selected samples')        
        st.plotly_chart(fig, use_container_width = True)

        if labels:
            # export 2D scores plot
            comb = [i for i in combinations([1,2,3], 2)]
            subcap = ['a','b','c']
            for i in range(len(comb)):
                fig_export = px.scatter(tcr, x = eval(f'axis{str(comb[i][0])}'), y=eval(f'axis{str(comb[i][1])}'),
                                            color = labels if list(labels) else None,
                                            color_discrete_sequence = custom_color_palette)
                fig_export.add_scatter(x = tt.loc[:,eval(f'axis{str(comb[i][0])}')], y = tt.loc[:,eval(f'axis{str(comb[i][1])}')],
                               mode ='markers', marker = dict(size = 5, color = 'black'),
                              name = 'selected samples')
                fig_export.update_layout(font=dict(size=23))
                fig_export.add_annotation(text= f'({subcap[i]})', align='center', showarrow= False, xref='paper', yref='paper', x=-0.13, y= 1,
                                             font= dict(color= "black", size= 35), bgcolor ='white', borderpad= 2, bordercolor= 'black', borderwidth= 3)
                fig_export.update_traces(marker=dict(size= 10), showlegend= False)
                fig_export.write_image(f'./Report/Figures/scores_pc{str(comb[i][0])}_pc{str(comb[i][1])}.png')



if not spectra.empty:
    if dim_red_method in ['PCA','NMF']:
        with loadings:
            st.write('Loadings plot')
            p = dr_model.loadings_
            freq = pd.DataFrame(colnames, index=p.index)
            if extension =='dx':
                if meta_data.loc[:,'xunits'][0] == '1/cm':
                    freq.columns = ['Wavenumber (1/cm)']
                    xlab = "Wavenumber (1/cm)"
                    inv = 'reversed'
                else:
                    freq.columns = ['Wavelength (nm)']
                    xlab = 'Wavelength (nm)'
                    inv = None
            else:
                freq.columns = ['Wavelength/Wavenumber']
                xlab = 'Wavelength/Wavenumber'
                inv = None
                
            pp = pd.concat([p, freq], axis=1)
            #########################################
            df1 = pp.melt(id_vars=freq.columns)
            fig = px.line(df1, x=freq.columns, y='value', color='variable', color_discrete_sequence=px.colors.qualitative.Plotly)
            fig.update_layout(legend=dict(x=1, y=0, font=dict(family="Courier", size=12, color="black"),
                                        bordercolor="black", borderwidth=2))
            fig.update_layout(xaxis_title = xlab,yaxis_title = "Intensity" ,xaxis = dict(autorange= inv))

            
            st.plotly_chart(fig, use_container_width=True)
            

            # Export du graphique
            img = pio.to_image(fig, format="png")
            with open("./Report/figures/loadings_plot.png", "wb") as f:
                f.write(img)
#############################################################################################################
    if dim_red_method == 'PCA':
        influence, hotelling = st.columns([3, 3])
        with influence:
            st.write('Influence plot')
            # Laverage
            Hat =  t.to_numpy() @ np.linalg.inv(np.transpose(t.to_numpy()) @ t.to_numpy()) @ np.transpose(t.to_numpy())
            leverage = np.diag(Hat) / np.trace(Hat)
            tresh3 = 2 * tcr.shape[1]/n_samples
            # Loadings
            p = pd.concat([dr_model.loadings_.loc[:,axis1], dr_model.loadings_.loc[:,axis2], dr_model.loadings_.loc[:,axis3]], axis = 1)
            # Matrix reconstruction
            xp = np.dot(t,p.T)
            # Q residuals: Q residuals represent the magnitude of the variation remaining in each sample after projection through the model
            residuals = np.diag(np.subtract(xc.to_numpy(), xp)@ np.subtract(xc.to_numpy(), xp).T)
            tresh4 = sc.stats.chi2.ppf(0.05, df = 3)

            # color with metadata
            if not meta_data.empty and clus_method:
                if col == "None":
                    l1 = ["Samples"]* n_samples

                elif col == clus_method:
                    l1 = labels
                
                else:
                    l1 = list(map(str.lower,md_df_st_[col]))

            elif meta_data.empty and clus_method:                        
                l1 = labels

            elif meta_data.empty and not clus_method:
                l1 = ["Samples"]* n_samples
            
            elif not meta_data.empty and not clus_method:
                l1 = list(map(str.lower,md_df_st_[col]))

            fig = px.scatter(x = leverage, y = residuals, color=labels if list(labels) else None,
                                            color_discrete_sequence= custom_color_palette)
            fig.add_vline(x = tresh3, line_width = 1, line_dash = 'solid', line_color = 'red')
            fig.add_hline(y=tresh4, line_width=1, line_dash='solid', line_color='red')
            fig.update_layout(xaxis_title="Leverage", yaxis_title = "Q-residuals", font=dict(size=20), width=800, height=600)

            out3 = leverage > tresh3
            out4 = residuals > tresh4

            for i in range(n_samples):
                if out3[i]:
                    if not meta_data.empty:
                        ann =  meta_data.loc[:,'name'][i]
                    else:
                        ann = t.index[i]
                    fig.add_annotation(dict(x = leverage[i], y = residuals[i], showarrow=True, text = ann,font= dict(color= "black", size= 15),
                                xanchor = 'auto', yanchor = 'auto'))
            
            fig.update_traces(marker=dict(size= 6), showlegend= True)
            fig.update_layout(font=dict(size=23), width=800, height=500)
            st.plotly_chart(fig, use_container_width=True)


            
            for annotation in fig.layout.annotations:
                annotation.font.size = 35
            fig.update_layout(font=dict(size=23), width=800, height=600)
            fig.update_traces(marker=dict(size= 10), showlegend= False)
            fig.add_annotation(text= '(a)', align='center', showarrow= False, xref='paper', yref='paper', x=-0.125, y= 1,
                                             font= dict(color= "black", size= 35), bgcolor ='white', borderpad= 2, bordercolor= 'black', borderwidth= 3)
            fig.write_image('./Report/figures/influence_plot.png', engine = 'kaleido')
        
        
        with hotelling:
            st.write('T²-Hotelling vs Q-residuals plot')
            # Hotelling
            hotelling  = t.var(axis = 1)
            # Q residuals: Q residuals represent the magnitude of the variation remaining in each sample after projection through the model
            residuals = np.diag(np.subtract(xc.to_numpy(), xp)@ np.subtract(xc.to_numpy(), xp).T)

            fcri = sc.stats.f.isf(0.05, 3, n_samples)
            tresh0 = (3 * (n_samples ** 2 - 1) * fcri) / (n_samples * (n_samples - 3))
            tresh1 = sc.stats.chi2.ppf(0.05, df = 3)
            
            fig = px.scatter(t, x = hotelling, y = residuals, color=labels if list(labels) else None,
                                            color_discrete_sequence= custom_color_palette)
            fig.update_layout(xaxis_title="Hotelling-T² distance",yaxis_title="Q-residuals")
            fig.add_vline(x=tresh0, line_width=1, line_dash='solid', line_color='red')
            fig.add_hline(y=tresh1, line_width=1, line_dash='solid', line_color='red')

            out0 = hotelling > tresh0
            out1 = residuals > tresh1

            
            for i in range(n_samples):
                if out0[i]:
                    if not meta_data.empty:
                        ann =  meta_data.loc[:,'name'][i]
                    else:
                        ann = t.index[i]
                    fig.add_annotation(dict(x = hotelling[i], y = residuals[i], showarrow=True, text = ann, font= dict(color= "black", size= 15),
                                xanchor = 'auto', yanchor = 'auto'))
                    
            fig.update_traces(marker=dict(size= 6), showlegend= True)
            fig.update_layout(font=dict(size=23), width=800, height=500)
            st.plotly_chart(fig, use_container_width=True)


            for annotation in fig.layout.annotations:
                annotation.font.size = 35
            fig.update_layout(font=dict(size=23), width=800, height=600)
            fig.update_traces(marker=dict(size= 10), showlegend= False)
            fig.add_annotation(text= '(b)', align='center', showarrow= False, xref='paper', yref='paper', x=-0.125, y= 1,
                                             font= dict(color= "black", size= 35), bgcolor ='white', borderpad= 2, bordercolor= 'black', borderwidth= 3)
            fig.write_image("./Report/figures/hotelling_plot.png", format="png")

st.header('III - Selected Samples for Reference Analysis', divider='blue')
if labels:
    sel, info = st.columns([3, 1])
    sel.write("Tabular identifiers of selected samples for reference analysis:")
    if selected_samples_idx:
        if meta_data.empty:
            sam1 = pd.DataFrame({'name': spectra.index[clustered][selected_samples_idx],
                                'cluster':np.array(labels)[clustered][selected_samples_idx]},
                                index = selected_samples_idx)
        else:
            sam1 = meta_data.iloc[clustered,:].iloc[selected_samples_idx,:]
            sam1.insert(loc=0, column='index', value=selected_samples_idx)
            sam1.insert(loc=1, column='cluster', value=np.array(labels)[selected_samples_idx])
        sam1.index = np.arange(len(selected_samples_idx))+1
        info.info(f'Information !\n - The total number of samples: {n_samples}.\n- The number of samples selected for reference analysis: {sam1.shape[0]}.\n - The proportion of samples selected for reference analysis: {round(sam1.shape[0]/n_samples*100)}%.')
        sam = sam1
        # if clus_method == cluster_methods[2]:
        #     unclus = sel.checkbox("Include non clustered samples (for HDBSCAN clustering)", value=True)

        if clus_method == cluster_methods[2]:
            unclus = sel.checkbox("Include non clustered samples (for HDBSCAN clustering)", value=True)

            if selected_samples_idx:
                if unclus:
                    if meta_data.empty:
                        sam2 = pd.DataFrame({'name': spectra.index[non_clustered],
                                            'cluster':['Non clustered']*len(spectra.index[non_clustered])},
                                            index = spectra.index[non_clustered])
                    else :
                        sam2 = meta_data.iloc[non_clustered,:]
                        sam2.insert(loc=0, column='index', value= spectra.index[non_clustered])
                        sam2.insert(loc=1, column='cluster', value=['Non clustered']*len(spectra.index[non_clustered]))
                    
                    sam = pd.concat([sam1, sam2], axis = 0)
                    sam.index = np.arange(sam.shape[0])+1
                    info.info(f'- The number of Non-clustered samples: {sam2.shape[0]}.\n - The proportion of Non-clustered samples: {round(sam2.shape[0]/n_samples*100)}%')
        else:
            sam = sam1
        sel.write(sam)
        

# st.write(hash_data(change = './Report/report.tex'))
with open('./Report/report.tex') as myfile:
    filehash = hash_data(myfile.read())

# figs_list = os.listdir("./Report/figures")
if data_file:
    Nb_ech = str(n_samples)
    nb_clu = str(sam1.shape[0])
    ###################################################
    ## generate report
    latex_report = report.report('Representative subset selection', data_file.name, dim_red_method,
                                  clus_method, Nb_ech, ncluster, selection, selection_number, nb_clu,tcr, sam)
    
    @st.cache_data
    def download_res(file,sam):
        zipname = f'results{date_time}subset_selection_{file.name.split('.')[0]}.zip' # name of the zipfile
        with open('./temp/fname.json', 'w') as f: # dump filename and save it as a .json file
            json.dump(zipname, f)
        shutil.make_archive(base_name = zipname.split('.')[0],format = "zip",root_dir = "./Report", base_dir = "figures")# create zip containing figures and report
        
        file_path = Path("./temp/"+zipname)
        sam.to_csv("./"+zipname,sep = ';',
          encoding='utf-8', mode='a',
          compression=dict(method='zip',archive_name=f"selected subset for reference analysis_{userfilename}_{date_time}_.csv")) 
        
        with zipfile.ZipFile("./"+zipname, 'a') as newzip:
                newzip.write("./Report/report.pdf", arcname="report.pdf")
                newzip.write("./Report/datasets/"+os.listdir("./Report/datasets")[0], arcname=os.listdir("./Report/datasets")[0])
                

        # #### add data to zip
        # match data_file.name:
        #     case 'csv':
        #         with open(data_file.name, 'wb') as cs:
        #             st.write(data_file.getbuffer())
        #     case 'dx':
        #         st.write(4)
                
        ### move the .zip file to the temp directory
        shutil.move('./'+zipname,'./temp/'+ zipname)

    a =''
    for i in (data_file.name, dim_red_method,clus_method, Nb_ech, tcr.astype(str)):
        a += str(i)

    myfilepdf = Path("./Report/report.pdf")
    if 'htest' not in st.session_state:
        st.session_state.htest = '0'
        report.compile_latex(change =hash_data(a))
        st.write(hash_data(a))
        if myfilepdf.is_file():
            download_res(file = data_file, sam = sam)

    elif st.session_state['htest'] != hash_data(a):
        st.session_state['htest'] = hash_data(a)
        report.compile_latex(change =hash_data(a))
        st.write(hash_data(a))
        if myfilepdf.is_file():
            download_res(file = data_file, sam = sam)
    else:
        pass

    
    list_of_files = glob.glob(r"./temp/*.zip")
    if len(list_of_files) >3:
        oldest_file = min(list_of_files, key=os.path.getctime)
        os.remove(oldest_file)
    list_of_files = glob.glob(r"./temp/*.zip")
    recent_file = max(list_of_files, key=os.path.getctime)

    with open('./temp/fname.json', 'r') as f:
        zipname = json.load(f)
    if os.path.split(recent_file)[1] == os.path.split(zipname)[1]:
        with open("./temp/"+zipname, "rb") as fp:
                st.download_button('Download', data = fp, file_name=zipname, mime="application/zip",
                                args=None, kwargs=None,type="primary",use_container_width=True)