From c0f3f8edc9dbc5cb81d0d307bfbe158e2dc5a788 Mon Sep 17 00:00:00 2001
From: DIANE <abderrahim.diane@cefe.cnrs.fr>
Date: Thu, 11 Jul 2024 16:04:22 +0200
Subject: [PATCH] report
---
src/Report/report.py | 103 ++++++++++++++++++++++++++++++-------------
1 file changed, 72 insertions(+), 31 deletions(-)
diff --git a/src/Report/report.py b/src/Report/report.py
index 78029e5..dfbdab5 100644
--- a/src/Report/report.py
+++ b/src/Report/report.py
@@ -40,7 +40,8 @@ def report(*args):
\usepackage{graphicx}
\usepackage{geometry}
\usepackage{changepage}
- \geometry{a4paper, left=2cm, right=2cm, top=1.5cm, bottom=3cm }
+ \geometry{a4paper, left=2cm, right=2cm, top=1.5cm, bottom=3cm,
+ headheight=0.05cm, footskip=1cm}
\usepackage{caption, subcaption}
\usepackage{hyperref}
\usepackage{hyphenat}
@@ -56,14 +57,30 @@ def report(*args):
\graphicspath{{images/}, {Figures/}}
\fancyhead[R]{\includegraphics[width=0.1\textwidth]{logo_cefe.png}}
\fancyhead[L]{PACE - NIRS Analysis Report}
-
\fancyfoot[L]{Project Name to fill}
\fancyfoot[C]{Plateforme d'Analyses Chimiques en Ecologie}
\fancyfoot[R]{\thepage}
-
\setlength{\headheight}{52pt}
\addtolength{\topmargin}{-9.2942pt}
\pagestyle{fancy}
+
+ \DeclareCaptionLabelFormat{myfigureformat}{\textbf{Fig. #2.}}
+ \captionsetup[figure]{
+ labelformat=myfigureformat, % Apply the custom format
+ justification=centering, % Justify the caption text
+ singlelinecheck=false, % Allow the caption to occupy multiple lines
+ labelsep=space, % Add a space after the label
+ }
+ \DeclareCaptionLabelFormat{mytableformat}{\textbf{Table #2}}
+ \captionsetup[table]{
+ labelformat=mytableformat, % Apply the custom format
+ justification=justified, % Justify the caption text
+ singlelinecheck=false, % Allow the caption to occupy multiple lines
+ skip=0pt, % Vertical space between caption and table
+ position=top % Position the caption at the top of the table
+ }
+
+
\begin{document}
\noindent
@@ -76,26 +93,33 @@ def report(*args):
\textbf{ENTERED INPUTS: }{"""+ re.sub(r'([_%])', r"\\\1", to_report[1])+ r"""}.\\"""
latex_report += r"""\section*{Results}"""
latex_report += r"""\subsection*{Spectral data visualization}"""
- latex_report += r"""Acquired spectra were visualized in fig1 by plotting the intensity
- of absorption, reflectance, transmission, etc, against the wavelengths or wavenumbers.
- This helps observe general patterns and trends in the spectra, and understand the
- variability within the data.
+ latex_report += r"""Acquired spectra were visualized in fig.\ref{raw_spectra} by plotting the signal of the samples captured in the specific spectral range
+ This helps observe general patterns and trends in the spectra, and understand the variability within the data.
\begin{figure}[h]
\centering
\includegraphics[width=1\linewidth]{spectra_plot.png}
\caption{Acquired spectra}
- \label{fig:raw_spectra}
+ \label{raw_spectra}
\end{figure}"""
if 'Representative subset selection' in to_report:
latex_report += r"""\subsection*{Multivariable Data Analysis}"""
- latex_report += r""" For optimal selection of subset of the samples to analyze through the
- reference method, a pipeline consisting of consecutively applying features extraction/dimensionality
+ latex_report += r"""\indent For optimal selection of subset of the samples to analyze through the \cite{Lesnoff2020}
+ reference method, a pipeline consisting of consecutively applying features extraction/dimensionality\cite{BellonMaurel2010,scikit-learn}
reduction and clustering analysis was developed. Features extraction was performed by means of {"""+dim_red_methods[to_report[2]] + r"""}
technique which helps represent the high dimensional spectra in a reduced perceptible 3D
subspace spanned by a few number of features (three features in our case), while clustering analysis was performed
using the {"""+cluster_methods[to_report[3]] + r"""} technique which
- helps group the data into groups of spectra that share the same carachteristics.\\*"""
+ helps group the data into groups of spectra that share the same carachteristics. """
+
+ latex_report += r"""After applying the pipeline, a subset sampling method, consisting of"""
+ if 'center' in to_report:
+ latex_report += r""" selecting {"""+to_report[7]+ r"""} samples, each from a distict cluster, with the least euclidian distance to the center of the cluster identified by {"""+to_report[3]+ r"""} and to which it the sample belongs."""
+ if 'random' in to_report:
+ latex_report += r""" fitting a second clustering model, specifically kmeans, to each individual data cluster and selecting {"""+to_report[7]+ r"""}
+ samples or less from each subcluster (if a subcluster contains less than {"""+to_report[7]+ r"""} samples, then all samples included
+ in this subcluster are selected), was applied.\\"""
+
if "PCA" in to_report:
latex_report += r"""\indent To detect the presence of any spectral outliers, the influence and residuals plots were constructed,
with outlyingness limits established at the 95\% confidence level. Together, these plots helps distinguish regular observations,
@@ -104,10 +128,10 @@ def report(*args):
large residual distance to the subspace, but whose projection is on the subspace; and, finally, bad leverage
points, which have a large residual distance such that the projection on the subspace is away from regular observations.\\*"""
- latex_report += """\indent Results of applying this workflow are displayed in fig. 1. Based of the features extracted using
- {"""+to_report[2]+ r"""}, {"""+to_report[3]+ r"""} revealed the existance of {"""+to_report[5] + r"""}
+ latex_report += """\indent Results of applying this workflow are displayed in fig. 2. Based of the features extracted using
+ {"""+to_report[2]+ r"""}, {"""+to_report[3]+ r"""} revealed the existance of {"""+to_report[5] + r"""}
data clusters that are visualized with different colors.
- \begin{figure}[h]
+ \begin{figure}[h!]
\captionsetup{justification=centering}
\centering
\begin{minipage}[b]{0.33\textwidth}
@@ -123,13 +147,12 @@ def report(*args):
\caption{Illustration of the pairwise projection of spectra onto the reduced 3 dimensional subspace, clustering, and sample selection
results: data points with the same color belong to the same cluster and data points colored in black correspond to the samples to be
analyzed by a standard reference analytical procedure}
- \label{pcaplots}
- \end{figure}"""
- latex_report +=r""" """
+ \label{pcaplots}
+ \end{figure} """
if 'PCA' in to_report:
latex_report += r"""
- \begin{figure}[ht]
+ \begin{figure}[h!]
\centering
\begin{minipage}[b]{0.33\textwidth}
\centering
@@ -143,17 +166,9 @@ def report(*args):
\label{hotelling_and_influence}
\end{figure}
"""
-
- latex_report += r"""Following the exploratory data analysis, a subset sampling method, consisting of"""
- if 'center' in to_report:
- latex_report += r""" selecting {"""+to_report[7]+ r"""} samples, each from a distict cluster, with the least euclidian distance to the center of the cluster identified by {"""+to_report[3]+ r"""} and to which it the sample belongs."""
- if 'random' in to_report:
- latex_report += r""" fitting a second clustering model, specifically kmeans, to each individual data cluster and selecting {"""+to_report[7]+ r"""}
- samples or less from each subcluster (if a subcluster contains less than 3 samples, then all samples included
- in this subcluster are selected), was applied."""
-
- latex_report += r"""The subset of selected samples are identified to be representative and are suggested to be used for robust NIR calibration developement
- , i.e, to be analyzed by adequate reference analytical procedures (generally requiring destructive sample preparation)."""
+ latex_report += r"""A subset of {"""+to_report[8]+ r"""} samples were identified and selected to be representative and were suggested to be used for robust NIR calibration developement
+ , i.e, to be analyzed by adequate reference analytical procedures (generally requiring destructive sample preparation).
+ """
elif 'Predictive model development' in to_report:
latex_report += r"""\paragraph{}To develop a robust NIR calibration that formally correlates the spectral signature of the samples in the NIR region
@@ -186,6 +201,21 @@ def report(*args):
latex_report += r"""Predictive modelling development was performed using the {"""+reg_algo[to_report[6]]+ r"""} regression method."""
+ latex_report += r"""
+ For fig.\ref{fig:CV}
+ \begin{figure}[h]
+ \captionsetup{justification=centering}
+ \centering
+ \begin{minipage}[c]{0.5\textwidth}
+ \includegraphics[width=\linewidth]{meas_vs_pred_cv_onebyone.png}
+ \end{minipage}%
+ \begin{minipage}[c]{0.5\textwidth}
+ \includegraphics[width=\linewidth]{meas_vs_pred_cv_all.png}
+ \end{minipage}%
+ \caption{ Visualization of measured vs predicted values scatter plot for cross-validation }
+ \label{CV}
+ \end{figure}"""
+
if "Full-PLSR" in to_report:
latex_report += r"""the most important and influential spectral regions in the model, were visualized in fig.5"""
elif "Locally Weighted PLSR" in to_report:
@@ -207,15 +237,26 @@ def report(*args):
\begin{figure}[h]
\centering
\includegraphics[width=1\linewidth]{Variable_importance.png}
- \caption{Visualizing important spectral regions identifiedin the PLS model on the raw and preprocessed average spectrum}
+ \caption{Visualizing important spectral regions identified in the PLS model on the raw and preprocessed average spectrum}
\label{fig:Histogram}
\end{figure}
"""
latex_report += r"""After numerically analyzing the performance of the model, a visual investigation (figs 7 and 8) of goodness of model fit was performed to identify potential
issues such as a pattern, that has not been captured by the model, or outliers.\par.
- """
+ \begin{figure}[h]
+ \captionsetup{justification=centering}
+ \centering
+ \begin{minipage}[b]{0.5\textwidth}
+ \includegraphics[width=\linewidth]{measured_vs_predicted.png}
+ \end{minipage}%
+ \begin{minipage}[b]{0.5\textwidth}
+ \includegraphics[width=\linewidth]{residuals_plot.png}
+ \end{minipage}%
+ \caption{Post-hoc analysis of the developed predictive model; measured vs predicted values (a) and measured vs residuals (b) plots }
+ \label{pcaplots}
+ \end{figure}"""
latex_report += r"""
\fontsize{8}{9}\selectfont
\bibliographystyle{apalike}
--
GitLab