diff --git a/Packages.py b/Packages.py
index ec7d83f23abc877b99e5eb07c3abc95a2280edba..fe21dcae4da468f573c90071dc6e646c642a9359 100644
--- a/Packages.py
+++ b/Packages.py
@@ -64,6 +64,8 @@ import joblib
from hyperopt import fmin, hp, tpe, Trials, space_eval, STATUS_OK, anneal
-
-
+import plotly.graph_objects as go
+import plotly.express as px
+import plotly.io as pio
+import streamlit as st
st.set_option('deprecation.showPyplotGlobalUse', False)
diff --git a/Report/figures/Elbow.png b/Report/figures/Elbow.png
new file mode 100644
index 0000000000000000000000000000000000000000..213645e6d6f619181e5ba2d285946ef481bac69a
Binary files /dev/null and b/Report/figures/Elbow.png differ
diff --git a/Report/figures/Influence_plot.png b/Report/figures/Influence_plot.png
new file mode 100644
index 0000000000000000000000000000000000000000..03f8edf8afc00a7e54349750c3c1b795902c519c
Binary files /dev/null and b/Report/figures/Influence_plot.png differ
diff --git a/Report/figures/Spectra_Plot.png b/Report/figures/Spectra_Plot.png
new file mode 100644
index 0000000000000000000000000000000000000000..b35f6dd6f5a24825054b640329f9dcb6f5747622
Binary files /dev/null and b/Report/figures/Spectra_Plot.png differ
diff --git a/Report/figures/graphe.png b/Report/figures/graphe.png
new file mode 100644
index 0000000000000000000000000000000000000000..3a7ad7924e3754459d2b9ab43f1515df6d201b19
Binary files /dev/null and b/Report/figures/graphe.png differ
diff --git a/Report/figures/graphe_hotelling.png b/Report/figures/graphe_hotelling.png
new file mode 100644
index 0000000000000000000000000000000000000000..31311510c2f3197203aee699a837ddb5c195992b
Binary files /dev/null and b/Report/figures/graphe_hotelling.png differ
diff --git a/Report/figures/graphe_loadings.png b/Report/figures/graphe_loadings.png
new file mode 100644
index 0000000000000000000000000000000000000000..b349077cfcd03696e8e42abdc810bac81d1aad33
Binary files /dev/null and b/Report/figures/graphe_loadings.png differ
diff --git a/Report/figures/scores_plot_2d_axis1_axis2.png b/Report/figures/scores_plot_2d_axis1_axis2.png
new file mode 100644
index 0000000000000000000000000000000000000000..1814cded91b834b285496cfa0140e417e1d9a8a0
Binary files /dev/null and b/Report/figures/scores_plot_2d_axis1_axis2.png differ
diff --git a/Report/figures/scores_plot_2d_axis1_axis3.png b/Report/figures/scores_plot_2d_axis1_axis3.png
new file mode 100644
index 0000000000000000000000000000000000000000..606d628e5f24e88504d90067efa6cd1335fbfea7
Binary files /dev/null and b/Report/figures/scores_plot_2d_axis1_axis3.png differ
diff --git a/Report/figures/scores_plot_2d_axis2_axis3.png b/Report/figures/scores_plot_2d_axis2_axis3.png
new file mode 100644
index 0000000000000000000000000000000000000000..1b9207f30458a794c2b94a28927f87ae81841199
Binary files /dev/null and b/Report/figures/scores_plot_2d_axis2_axis3.png differ
diff --git a/app.py b/app.py
index 027393b8079257a75cae2893f29cd52e15db1c8a..3ae15c08841d69be3ba72b75a3737d00269f65e6 100644
--- a/app.py
+++ b/app.py
@@ -6,6 +6,16 @@ from Modules import *
from Class_Mod.DATA_HANDLING import *
+# HTML pour le bandeau "CEFE - CNRS"
+bandeau_html = """
+<div style="width: 100%; background-color: #4682B4; padding: 10px; margin-bottom: 10px;">
+ <h1 style="text-align: center; color: white;">CEFE - CNRS</h1>
+</div>
+"""
+
+# Injecter le code HTML du bandeau
+st.markdown(bandeau_html, unsafe_allow_html=True)
+
# # TOC menu on the left
show_pages(
[Page("app.py", "Home"),
@@ -18,6 +28,7 @@ hide_pages("Samples Selection")
hide_pages("Models Creation")
hide_pages("Predictions")
+
with st.sidebar:
interface = st.selectbox(label="Interface", options=['simple', 'advanced'], key='interface')
st.page_link('pages\\1-samples_selection.py')
@@ -35,17 +46,35 @@ with st.sidebar:
st.page_link('pages\\2-model_creation.py')
st.page_link('pages\\3-prediction.py')
+
# Page header
with st.container():
- st.subheader("Plateforme d'Analyses Chimiques pour l'Ecologie-PACE :goat:")
- st.title("NIRS Utils")
- st.write("Samples selection (PCA, [UMAP](https://umap-learn.readthedocs.io/en/latest/how_umap_works.html), ...), Predictive Modelling ([Pinard](https://github.com/GBeurier/pinard), [LWPLSR](https://doi.org/10.1002/cem.3209), ...), and Predictions using your data (CSV or DX files) and/or PACE NIRS Database.")
- #st.image(img_general)
- st.markdown("### We could add documentation here ###")
+
+ # Centrer les boutons
+ st.markdown(
+ """
+ <style>
+ .stButton>button {
+ display: block;
+ margin: 0 auto;
+ width: 200px;
+ height: 50px;
+ font-size: 16px;
+ }
+ </style>
+ """,
+ unsafe_allow_html=True
+ )
+
header1, header2, header3 = st.columns(3)
if header1.button("Samples Selection"):
st.switch_page('pages\\1-samples_selection.py')
if header2.button("Model Creation"):
st.switch_page('pages\\2-model_creation.py')
if header3.button("Predictions"):
- st.switch_page('pages\\3-prediction.py')
\ No newline at end of file
+ st.switch_page('pages\\3-prediction.py')
+ st.subheader("Plateforme d'Analyses Chimiques pour l'Ecologie-PACE :goat:")
+ st.title("NIRS Utils")
+ st.write("Samples selection (PCA, [UMAP](https://umap-learn.readthedocs.io/en/latest/how_umap_works.html), ...), Predictive Modelling ([Pinard](https://github.com/GBeurier/pinard), [LWPLSR](https://doi.org/10.1002/cem.3209), ...), and Predictions using your data (CSV or DX files) and/or PACE NIRS Database.")
+ #st.image(img_general)
+ st.markdown("### We could add documentation here ###")
\ No newline at end of file
diff --git a/pages/1-samples_selection.py b/pages/1-samples_selection.py
index 08d8cb6e364ee4b7a55b00dbab272583e1ab2c4e..035240caa8996c5571ca58b0bc38c910b90d0b8e 100644
--- a/pages/1-samples_selection.py
+++ b/pages/1-samples_selection.py
@@ -3,6 +3,19 @@ st.set_page_config(page_title="NIRS Utils", page_icon=":goat:", layout="wide")
from Modules import *
from Class_Mod.DATA_HANDLING import *
+
+
+# HTML pour le bandeau "CEFE - CNRS"
+bandeau_html = """
+<div style="width: 100%; background-color: #4682B4; padding: 10px; margin-bottom: 10px;">
+ <h1 style="text-align: center; color: white;">CEFE - CNRS</h1>
+</div>
+"""
+
+
+# Injecter le code HTML du bandeau
+st.markdown(bandeau_html, unsafe_allow_html=True)
+
st.session_state["interface"] = st.session_state.get('interface')
if st.session_state["interface"] == 'simple':
hide_pages("Predictions")
@@ -54,13 +67,12 @@ if data_file:
st.success("The data have been loaded successfully", icon="✅")
os.unlink(tmp_path)
-
## Visualize spectra
if not spectra.empty:
with col2:
fig = plot_spectra(spectra)
st.pyplot(fig)
-
+ fig.savefig("./Report/figures/Spectra_Plot.png")
############################## Exploratory data analysis ###############################
container2 = st.container(border=True)
@@ -102,8 +114,13 @@ if not t.empty:
if clus_method == cluster_methods[1]:
ncluster = scores.number_input(min_value=2, max_value=30, value=3, label = 'Select the desired number of clusters')
cl_model = Sk_Kmeans(tcr, max_clusters = 30)
- fig2 = px.scatter(cl_model.inertia_.T, y = 'inertia')
+ fig2 = px.scatter(cl_model.inertia_.T, y = 'inertia')
scores.plotly_chart(fig2)
+ img = pio.to_image(fig2, format="png")
+ with open("./Report/figures/Elbow.png", "wb") as f:
+ f.write(img)
+
+
data, labels = cl_model.fit_optimal(nclusters = ncluster)
elif clus_method == cluster_methods[2]:
@@ -119,7 +136,7 @@ if not t.empty:
# scores plot with clustering
if list(labels) and meta_data.empty:
fig = px.scatter_3d(tcr, x=axis1, y=axis2, z = axis3, color = labels)
-
+
# scores plot with metadata
elif len(list(labels)) == 0 and not meta_data.empty:
filter = meta_data.columns[1:]
@@ -151,26 +168,63 @@ if not t.empty:
st.plotly_chart(fig)
+## Export en 2d Axe1..Axe3
+if not t.empty:
+ if dim_red_method == dim_red_methods[1]:
+
+ # nombre de clusters
+ num_clusters = len(np.unique(labels))
+
+ # Une couleur par cluster
+ custom_color_palette = px.colors.qualitative.Plotly[:num_clusters]
+
+ # Graphique pour les dimensions (axis1, axis2)
+ fig_2d_axis1_axis2 = px.scatter(t, x=axis1, y=axis2, color=labels, color_discrete_sequence=custom_color_palette)
+ img_2d_axis1_axis2 = pio.to_image(fig_2d_axis1_axis2, format="png")
+ with open("./Report/figures/scores_plot_2d_axis1_axis2.png", "wb") as f:
+ f.write(img_2d_axis1_axis2)
+
+ # Graphique pour les dimensions (axis1, axis3)
+ fig_2d_axis1_axis3 = px.scatter(t, x=axis1, y=axis3, color=labels, color_discrete_sequence=custom_color_palette)
+ img_2d_axis1_axis3 = pio.to_image(fig_2d_axis1_axis3, format="png")
+ with open("./Report/figures/scores_plot_2d_axis1_axis3.png", "wb") as f:
+ f.write(img_2d_axis1_axis3)
+
+ # Graphique pour les dimensions (axis2, axis3)
+ fig_2d_axis2_axis3 = px.scatter(t, x=axis2, y=axis3, color=labels, color_discrete_sequence=custom_color_palette)
+ img_2d_axis2_axis3 = pio.to_image(fig_2d_axis2_axis3, format="png")
+ with open("./Report/figures/scores_plot_2d_axis2_axis3.png", "wb") as f:
+ f.write(img_2d_axis2_axis3)
if not spectra.empty:
if dim_red_method == dim_red_methods[1]:
+
with loadings:
st.write('Loadings plot')
p = dr_model.loadings_
- pp = pd.concat([p, pd.DataFrame(np.arange(p.shape[0]), index=p.index, columns=['wl'])], axis =1)
+ pp = pd.concat([p, pd.DataFrame(np.arange(p.shape[0]), index=p.index, columns=['wl'])], axis=1)
df1 = pp.melt(id_vars="wl")
- fig = px.line(df1, x = 'wl', y = 'value', color='variable')
- fig.update_layout(legend=dict(x=1, y=0,font=dict(family="Courier", size=12, color="black"),
- bordercolor="Black", borderwidth=2))
- st.plotly_chart(fig, use_container_width = True)
+ fig = px.line(df1, x='wl', 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))
+ st.plotly_chart(fig, use_container_width=True)
+
+ # Export du graphique
+ img = pio.to_image(fig, format="png")
+ with open("./Report/figures/graphe_loadings.png", "wb") as f:
+ f.write(img)
with influence:
st.write('Influence plot')
ax1 = st.selectbox("Component", options=dr_model.scores_.columns, index=3)
leverage = dr_model.leverage_
residuals = dr_model.residuals_
- fig = px.scatter(x=leverage[ax1], y=residuals[ax1], color = leverage[ax1]*residuals[ax1]).update_layout(xaxis_title="Leverage",yaxis_title="Residuals")
+ fig = px.scatter(x=leverage[ax1], y=residuals[ax1], color=leverage[ax1]*residuals[ax1], color_continuous_scale='Blues')
+ fig.update_layout(xaxis_title="Leverage", yaxis_title="Residuals")
st.plotly_chart(fig)
+ img = pio.to_image(fig, format="png")
+ with open("./Report/figures/Influence_plot.png", "wb") as f:
+ f.write(img)
with hotelling:
st.write('T²-Hotelling vs Q residuals plot')
@@ -179,4 +233,5 @@ if not spectra.empty:
hotelling = dr_model.hotelling_
fig = px.scatter(t, x=hotelling[ax2], y=residuals[ax2]).update_layout(xaxis_title="T²",yaxis_title="Residuals")
- st.plotly_chart(fig)
\ No newline at end of file
+ st.plotly_chart(fig)
+ fig.write_image("./Report/figures/graphe_hotelling.png", format="png")
diff --git a/pages/2-model_creation.py b/pages/2-model_creation.py
index 3f506ea752eda5ebf0460f6b53ca8a24015225ec..9fac8a2212a53a02f7b9ea0f26bc9cc033f39432 100644
--- a/pages/2-model_creation.py
+++ b/pages/2-model_creation.py
@@ -2,7 +2,15 @@ from Packages import *
st.set_page_config(page_title="NIRS Utils", page_icon=":goat:", layout="wide")
from Modules import *
from Class_Mod.DATA_HANDLING import *
-
+# HTML pour le bandeau "CEFE - CNRS"
+bandeau_html = """
+<div style="width: 100%; background-color: #4682B4; padding: 10px; margin-bottom: 10px;">
+ <h1 style="text-align: center; color: white;">CEFE - CNRS</h1>
+</div>
+"""
+
+# Injecter le code HTML du bandeau
+st.markdown(bandeau_html, unsafe_allow_html=True)
st.session_state["interface"] = st.session_state.get('interface')
if st.session_state["interface"] == 'simple':
diff --git a/pages/3-prediction.py b/pages/3-prediction.py
index 65130fd1dfcdde9f491dc7f8eaee4e19817ddc55..16fe404830d28abe22a98d822d72b391da909583 100644
--- a/pages/3-prediction.py
+++ b/pages/3-prediction.py
@@ -2,7 +2,15 @@ from Packages import *
st.set_page_config(page_title="NIRS Utils", page_icon=":goat:", layout="wide")
from Modules import *
from Class_Mod.DATA_HANDLING import *
+# HTML pour le bandeau "CEFE - CNRS"
+bandeau_html = """
+<div style="width: 100%; background-color: #4682B4; padding: 10px; margin-bottom: 10px;">
+ <h1 style="text-align: center; color: white;">CEFE - CNRS</h1>
+</div>
+"""
+# Injecter le code HTML du bandeau
+st.markdown(bandeau_html, unsafe_allow_html=True)
st.session_state["interface"] = st.session_state.get('interface')