Merge remote-tracking branch 'origin/master'

# Conflicts:
#	src/Report/report.log

src/Class_Mod/RegModels.py

@@ -4,7 +4,7 @@ from Class_Mod import metrics, Snv, No_transformation, KF_CV
 
 class Regmodel(object):
     
-    def __init__(self, train : [pd.DataFrame, pd.DataFrame], test : [pd.DataFrame, pd.DataFrame], n_iter, add_hyperparams = None, nfolds = 5, **kwargs):
+    def __init__(self, train, test, n_iter, add_hyperparams = None, nfolds = 5, **kwargs):
         self.SCORE = 100000000
         self._xc, self._xt, self._ytrain, self._ytest = train[0], test[0], train[1], test[1]
         self._nc, self._nt, self._p = train[0].shape[0], test[0].shape[0], train[0].shape[1]
@@ -60,7 +60,7 @@ class Regmodel(object):
         elif self._best['scatter'] == 'No_transformation':
             a = " No transformation was performed"
 
-        SG = f'- Savitzky-Golay derivative parameters (Window_length:{self._best['window_length']};  polynomial order: {self._best['polyorder']};  Derivative order : {self._best['deriv']})'
+        SG = f'- Savitzky-Golay derivative parameters \:(Window_length:{self._best['window_length']};  polynomial order: {self._best['polyorder']};  Derivative order : {self._best['deriv']})'
         Norm = f'- Spectral Normalization \: {a}'
         return SG+"\n"+Norm
     
@@ -88,7 +88,7 @@ class Regmodel(object):
   
 ###########################################    #########################################
 class Plsr(Regmodel):
-    def __init__(self, train: [pd.DataFrame, pd.DataFrame], test: [pd.DataFrame, pd.DataFrame], n_iter = 10):
+    def __init__(self, train, test, n_iter = 10):
         super().__init__(train, test, n_iter, add_hyperparams = {'n_components': hp.randint('n_components', 2,20)})
         ### parameters in common
         
@@ -132,7 +132,7 @@ class Plsr(Regmodel):
 
     ############################################    #########################################
 class TpeIpls(Regmodel):
-    def __init__(self, train: [pd.DataFrame, pd.DataFrame], test: [pd.DataFrame, pd.DataFrame], n_iter = 10, n_intervall = 5):
+    def __init__(self, train, test, n_iter = 10, n_intervall = 5):
         self.n_intervall = n_intervall
         self.n_arrets = self.n_intervall*2
         
@@ -204,6 +204,6 @@ class TpeIpls(Regmodel):
     ############################################    #########################################
 
 class Pcr(Regmodel):
-    def __init__(self, train: [pd.DataFrame, pd.DataFrame], test: [pd.DataFrame, pd.DataFrame], n_iter = 10, n_val = 5):
+    def __init__(self, train, test, n_iter = 10, n_val = 5):
         super.__init__()
         {f'pc{i}': hp.randint(f'pc{i+1}', 0, train[0].shape[1]) for i in range(self.n_val)}
\ No newline at end of file

src/Report/report.log

+This is pdfTeX, Version 3.141592653-2.6-1.40.25 (MiKTeX 24.1) (preloaded format=pdflatex 2024.6.4)  4 JUN 2024 17:10
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+**./report.tex
+(report.tex
+LaTeX2e <2023-11-01> patch level 1
+L3 programming layer <2024-01-04>
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/base\article.cls
+Document Class: article 2023/05/17 v1.4n Standard LaTeX document class
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/base\size10.clo
+File: size10.clo 2023/05/17 v1.4n Standard LaTeX file (size option)
+)
+\c@part=\count187
+\c@section=\count188
+\c@subsection=\count189
+\c@subsubsection=\count190
+\c@paragraph=\count191
+\c@subparagraph=\count192
+\c@figure=\count193
+\c@table=\count194
+\abovecaptionskip=\skip48
+\belowcaptionskip=\skip49
+\bibindent=\dimen140
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/fancyhdr\fancyhdr.sty
+Package: fancyhdr 2024/04/23 v4.2 Extensive control of page headers and footers
+
+\f@nch@headwidth=\skip50
+\f@nch@O@elh=\skip51
+\f@nch@O@erh=\skip52
+\f@nch@O@olh=\skip53
+\f@nch@O@orh=\skip54
+\f@nch@O@elf=\skip55
+\f@nch@O@erf=\skip56
+\f@nch@O@olf=\skip57
+\f@nch@O@orf=\skip58
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics\graphicx.sty
+Package: graphicx 2021/09/16 v1.2d Enhanced LaTeX Graphics (DPC,SPQR)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics\keyval.sty
+Package: keyval 2022/05/29 v1.15 key=value parser (DPC)
+\KV@toks@=\toks17
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics\graphics.sty
+Package: graphics 2022/03/10 v1.4e Standard LaTeX Graphics (DPC,SPQR)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics\trig.sty
+Package: trig 2021/08/11 v1.11 sin cos tan (DPC)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics-cfg\graphics.c
+fg
+File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration
+)
+Package graphics Info: Driver file: pdftex.def on input line 107.
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics-def\pdftex.def
+File: pdftex.def 2022/09/22 v1.2b Graphics/color driver for pdftex
+))
+\Gin@req@height=\dimen141
+\Gin@req@width=\dimen142
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/geometry\geometry.sty
+Package: geometry 2020/01/02 v5.9 Page Geometry
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/iftex\ifvtex.sty
+Package: ifvtex 2019/10/25 v1.7 ifvtex legacy package. Use iftex instead.
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/iftex\iftex.sty
+Package: iftex 2022/02/03 v1.0f TeX engine tests
+))
+\Gm@cnth=\count195
+\Gm@cntv=\count196
+\c@Gm@tempcnt=\count197
+\Gm@bindingoffset=\dimen143
+\Gm@wd@mp=\dimen144
+\Gm@odd@mp=\dimen145
+\Gm@even@mp=\dimen146
+\Gm@layoutwidth=\dimen147
+\Gm@layoutheight=\dimen148
+\Gm@layouthoffset=\dimen149
+\Gm@layoutvoffset=\dimen150
+\Gm@dimlist=\toks18
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/geometry\geometry.cfg))
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/caption\caption.sty
+Package: caption 2023/08/05 v3.6o Customizing captions (AR)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/caption\caption3.sty
+Package: caption3 2023/07/31 v2.4d caption3 kernel (AR)
+\caption@tempdima=\dimen151
+\captionmargin=\dimen152
+\caption@leftmargin=\dimen153
+\caption@rightmargin=\dimen154
+\caption@width=\dimen155
+\caption@indent=\dimen156
+\caption@parindent=\dimen157
+\caption@hangindent=\dimen158
+Package caption Info: Standard document class detected.
+)
+\c@caption@flags=\count198
+\c@continuedfloat=\count199
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/caption\subcaption.sty
+Package: subcaption 2023/07/28 v1.6b Sub-captions (AR)
+Package caption Info: New subtype `subfigure' on input line 238.
+\c@subfigure=\count266
+Package caption Info: New subtype `subtable' on input line 238.
+\c@subtable=\count267
+) (C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hyperref\hyperref.sty
+Package: hyperref 2023-11-26 v7.01g Hypertext links for LaTeX
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/infwarerr\infwarerr.s
+ty
+Package: infwarerr 2019/12/03 v1.5 Providing info/warning/error messages (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/kvsetkeys\kvsetkeys.sty
+Package: kvsetkeys 2022-10-05 v1.19 Key value parser (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/kvdefinekeys\kvdefine
+keys.sty
+Package: kvdefinekeys 2019-12-19 v1.6 Define keys (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/pdfescape\pdfescape.s
+ty
+Package: pdfescape 2019/12/09 v1.15 Implements pdfTeX's escape features (HO)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/ltxcmds\ltxcmds.sty
+Package: ltxcmds 2023-12-04 v1.26 LaTeX kernel commands for general use (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/pdftexcmds\pdftexcmds
+.sty
+Package: pdftexcmds 2020-06-27 v0.33 Utility functions of pdfTeX for LuaTeX (HO
+)
+Package pdftexcmds Info: \pdf@primitive is available.
+Package pdftexcmds Info: \pdf@ifprimitive is available.
+Package pdftexcmds Info: \pdfdraftmode found.
+))
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hycolor\hycolor.sty
+Package: hycolor 2020-01-27 v1.10 Color options for hyperref/bookmark (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/letltxmacro\letltxmacro
+.sty
+Package: letltxmacro 2019/12/03 v1.6 Let assignment for LaTeX macros (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/auxhook\auxhook.sty
+Package: auxhook 2019-12-17 v1.6 Hooks for auxiliary files (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hyperref\nameref.sty
+Package: nameref 2023-11-26 v2.56 Cross-referencing by name of section
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/refcount\refcount.sty
+Package: refcount 2019/12/15 v3.6 Data extraction from label references (HO)
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/gettitlestring\gettit
+lestring.sty
+Package: gettitlestring 2019/12/15 v1.6 Cleanup title references (HO)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/kvoptions\kvoptions.sty
+Package: kvoptions 2022-06-15 v3.15 Key value format for package options (HO)
+))
+\c@section@level=\count268
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/etoolbox\etoolbox.sty
+Package: etoolbox 2020/10/05 v2.5k e-TeX tools for LaTeX (JAW)
+\etb@tempcnta=\count269
+)
+\@linkdim=\dimen159
+\Hy@linkcounter=\count270
+\Hy@pagecounter=\count271
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hyperref\pd1enc.def
+File: pd1enc.def 2023-11-26 v7.01g Hyperref: PDFDocEncoding definition (HO)
+Now handling font encoding PD1 ...
+... no UTF-8 mapping file for font encoding PD1
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/intcalc\intcalc.sty
+Package: intcalc 2019/12/15 v1.3 Expandable calculations with integers (HO)
+)
+\Hy@SavedSpaceFactor=\count272
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hyperref\puenc.def
+File: puenc.def 2023-11-26 v7.01g Hyperref: PDF Unicode definition (HO)
+Now handling font encoding PU ...
+... no UTF-8 mapping file for font encoding PU
+)
+Package hyperref Info: Hyper figures OFF on input line 4181.
+Package hyperref Info: Link nesting OFF on input line 4186.
+Package hyperref Info: Hyper index ON on input line 4189.
+Package hyperref Info: Plain pages OFF on input line 4196.
+Package hyperref Info: Backreferencing OFF on input line 4201.
+Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
+Package hyperref Info: Bookmarks ON on input line 4448.
+\c@Hy@tempcnt=\count273
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/url\url.sty
+\Urlmuskip=\muskip16
+Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
+)
+LaTeX Info: Redefining \url on input line 4786.
+\XeTeXLinkMargin=\dimen160
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/bitset\bitset.sty
+Package: bitset 2019/12/09 v1.3 Handle bit-vector datatype (HO)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/bigintcalc\bigintcalc
+.sty
+Package: bigintcalc 2019/12/15 v1.5 Expandable calculations on big integers (HO
+)
+))
+\Fld@menulength=\count274
+\Field@Width=\dimen161
+\Fld@charsize=\dimen162
+Package hyperref Info: Hyper figures OFF on input line 6065.
+Package hyperref Info: Link nesting OFF on input line 6070.
+Package hyperref Info: Hyper index ON on input line 6073.
+Package hyperref Info: backreferencing OFF on input line 6080.
+Package hyperref Info: Link coloring OFF on input line 6085.
+Package hyperref Info: Link coloring with OCG OFF on input line 6090.
+Package hyperref Info: PDF/A mode OFF on input line 6095.
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/base\atbegshi-ltx.sty
+Package: atbegshi-ltx 2021/01/10 v1.0c Emulation of the original atbegshi
+package with kernel methods
+)
+\Hy@abspage=\count275
+\c@Item=\count276
+\c@Hfootnote=\count277
+)
+Package hyperref Info: Driver (autodetected): hpdftex.
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hyperref\hpdftex.def
+File: hpdftex.def 2023-11-26 v7.01g Hyperref driver for pdfTeX
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/base\atveryend-ltx.sty
+Package: atveryend-ltx 2020/08/19 v1.0a Emulation of the original atveryend pac
+kage
+with kernel methods
+)
+\Fld@listcount=\count278
+\c@bookmark@seq@number=\count279
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/rerunfilecheck\rerunfil
+echeck.sty
+Package: rerunfilecheck 2022-07-10 v1.10 Rerun checks for auxiliary files (HO)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/generic/uniquecounter\uniquec
+ounter.sty
+Package: uniquecounter 2019/12/15 v1.4 Provide unlimited unique counter (HO)
+)
+Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
+85.
+)
+\Hy@SectionHShift=\skip59
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/hyphenat\hyphenat.sty
+Package: hyphenat 2009/09/02 v2.3c hyphenation utilities
+\langwohyphens=\language79
+LaTeX Info: Redefining \_ on input line 43.
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/booktabs\booktabs.sty
+Package: booktabs 2020/01/12 v1.61803398 Publication quality tables
+\heavyrulewidth=\dimen163
+\lightrulewidth=\dimen164
+\cmidrulewidth=\dimen165
+\belowrulesep=\dimen166
+\belowbottomsep=\dimen167
+\aboverulesep=\dimen168
+\abovetopsep=\dimen169
+\cmidrulesep=\dimen170
+\cmidrulekern=\dimen171
+\defaultaddspace=\dimen172
+\@cmidla=\count280
+\@cmidlb=\count281
+\@aboverulesep=\dimen173
+\@belowrulesep=\dimen174
+\@thisruleclass=\count282
+\@lastruleclass=\count283
+\@thisrulewidth=\dimen175
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/xcolor\xcolor.sty
+Package: xcolor 2023/11/15 v3.01 LaTeX color extensions (UK)
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics-cfg\color.cfg
+File: color.cfg 2016/01/02 v1.6 sample color configuration
+)
+Package xcolor Info: Driver file: pdftex.def on input line 274.
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/graphics\mathcolor.ltx)
+Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1350.
+Package xcolor Info: Model `hsb' substituted by `rgb' on input line 1354.
+Package xcolor Info: Model `RGB' extended on input line 1366.
+Package xcolor Info: Model `HTML' substituted by `rgb' on input line 1368.
+Package xcolor Info: Model `Hsb' substituted by `hsb' on input line 1369.
+Package xcolor Info: Model `tHsb' substituted by `hsb' on input line 1370.
+Package xcolor Info: Model `HSB' substituted by `hsb' on input line 1371.
+Package xcolor Info: Model `Gray' substituted by `gray' on input line 1372.
+Package xcolor Info: Model `wave' substituted by `hsb' on input line 1373.
+) (C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/psnfss\times.sty
+Package: times 2020/03/25 PSNFSS-v9.3 (SPQR) 
+)
+LaTeX Font Info:    Trying to load font information for OT1+ptm on input line 3
+2.
+
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/psnfss\ot1ptm.fd
+File: ot1ptm.fd 2001/06/04 font definitions for OT1/ptm.
+)
+(C:\Users\diane\AppData\Local\Programs\MiKTeX\tex/latex/l3backend\l3backend-pdf
+tex.def
+File: l3backend-pdftex.def 2024-01-04 L3 backend support: PDF output (pdfTeX)
+\l__color_backend_stack_int=\count284
+\l__pdf_internal_box=\box51
+) (report.aux
+
+LaTeX Warning: Label `fig:frog' multiply defined.
+
+
+LaTeX Warning: Label `fig:frog' multiply defined.
+
+)
+\
\ No newline at end of file

src/Report/report.py

@@ -65,7 +65,7 @@ def report(*args):
         """
 
     if 'model' in to_report:
-        latex_report += r"""\subsection*{Data Visualization}
+        latex_report += r"""\subsection{Data Visualization}
 
         Here we have a sub-heading. There is no blank line after the sub-heading. You can have one level of subheadings but not a third i.e. you cannot have Section 1.1.1 as a subheading.
         \begin{center}
@@ -424,6 +424,7 @@ def report(*args):
 
 def compile_latex():
     # path to pdflatex
+    pdflatex_path = Path("C:/Users/diane/AppData/Local/Programs/MiKTeX/miktex/bin/x64/")
     # pdflatex_path = Path("C:/Users/maimouni/AppData/Local/Programs/MiKTeX/miktex/bin/x64/")
     from config.config import pdflatex_path
     import os

src/pages/2-model_creation.py

@@ -14,7 +14,7 @@ import matplotlib.pyplot as plt, mpld3
 import streamlit.components.v1 as components
 
 repertoire_a_vider = 'D:/Mouhcine/nirs_workflow/src/Report/figures'
-
+import shutil
 if os.path.exists(repertoire_a_vider):
     for fichier in os.listdir(repertoire_a_vider):
         chemin_fichier = os.path.join(repertoire_a_vider, fichier)
@@ -48,7 +48,7 @@ st.header("I - Data visualization", divider='blue')
 M0, M00 = st.columns([1, .4])
 st.header("II - Model creation", divider='blue')
 M1, M2 = st.columns([2 ,4])
-st.header("Cross-Validation")
+st.header("Cross-Validation results")
 cv1, cv2 = st.columns([2,2])
 cv3 = st.container()
 
@@ -344,8 +344,7 @@ if not spectra.empty and not y.empty:
 ##########
         M1.write("-- Model performance --")
         M1.dataframe(metrics(c = [y_train, yc], t = [y_test, yt], method='regression').scores_)
-        M2.write("-- Model performance --")
-        M2.dataframe(metrics(c = [y_train, yc], t = [y_test, yt], method='regression').scores_)
+
         model_per=pd.DataFrame(metrics(c = [y_train, yc], t = [y_test, yt], method='regression').scores_)
         #from st_circular_progress import CircularProgress
         #my_circular_progress = CircularProgress(label = 'Performance',value = 50, key = 'my performance',
@@ -362,7 +361,7 @@ if not spectra.empty and not y.empty:
         M8.pyplot(residual_plot)
         plt.savefig('./Report/figures/residual_plot.png')
 
-        # rega = Reg.important_features_  ##### ADD FEATURES IMPORTANCE PLOT
+        rega = Reg.important_features_  ##### ADD FEATURES IMPORTANCE PLOT
             
             #model_export = M1.selectbox("Choose way to export", options=["pickle", "joblib"], key=20)
         model_name = M9.text_input('Give it a name')
@@ -411,8 +410,7 @@ if not spectra.empty and not y.empty:
 ## Load .dx file
 Ac_Km = ['histo.png', 'Spectre_mod.png','Predictions_V.png','Allinone.png','Predictedvs.png','residual_plot.png']
 with st.container():
-    header3, header4 = st.columns(2)
-    if header3.button("Exporter le RR"):
+    if st.button("Download the report"):
         if regression_algo == reg_algo[1]:
                 latex_report = report.report(LoDaSum, 'model',Ac_Km,a_Test,json_sp,model_per,'full_plsr',cv99)
                 report.compile_latex()