Merge pull request #29 from baldonib/0.5

rameau modifications for v0.5
charlesll · Jul 6, 2023 · facef6c · facef6c
2 parents 1c34064 + bbd7861
commit facef6c
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diff --git a/NEWS.md b/NEWS.md
@@ -12,8 +12,6 @@ Licence: see LICENCE.md
 
 - Classification via 1D CNN and other algorithms using Keras or Pytorch
 
-- Addition of external calibration method in rameau
-
 - peak fitting for maps
 
 # 0.5.0 (stable)
@@ -24,6 +22,10 @@ Licence: see LICENCE.md
 
 - add a despiking() function
 
+- add external calibration in rameau
+
+- add the posibility to calibrate K coefficient(s) on another dataset of spectra
+
 # 0.4.9
 
 - quick fix of a bug in read_horiba function (from rampy.maps) 

diff --git a/examples/README.md b/examples/README.md
@@ -22,6 +22,8 @@ The following folders contain codes related to publications using Rampy:
 
   Di Genova, D., Sicola, S., Romano, C., Vona, A., Fanara, S., & Spina, L. (2017). *Effect of iron and nanolites on Raman spectra of volcanic glasses: A reassessment of existing strategies to estimate the water content.* Chemical Geology, 475, 76-86.
 
+  S.-M. Thomas, R. Thomas, P. Davidson, P. Reichart, M. Koch-Muller, G. Dollinger, Application of Raman Spectroscopy to Quantify Trace Water Concentrations in Glasses and Garnets. American Mineralogist 2008, 93 (10), 1550–1557. https://doi.org/10.2138/am.2008.2834.
+
   - Iron_AmMin_paper contains the supplementary material for the article:
 
   Le Losq C., Berry A. J., Kendrick M. A., Neuville D. R. and O'Neill H. St. C. (2019) *Determination of the oxidation state of iron in Mid-Ocean Ridge basalt glasses by Raman spectroscopy.* American Mineralogist 104, doi.org/10.2138/am-2019-6887
diff --git a/examples/rameau_example/Figure1.pdf b/examples/rameau_example/Figure1.pdf
diff --git a/examples/rameau_example/Figure2.pdf b/examples/rameau_example/Figure2.pdf
diff --git a/examples/rameau_example/Figure3.pdf b/examples/rameau_example/Figure3.pdf
diff --git a/examples/rameau_example/Figure_ext.pdf b/examples/rameau_example/Figure_ext.pdf
diff --git a/examples/rameau_example/Python_treatment.ipynb b/examples/rameau_example/Python_treatment.ipynb
diff --git a/examples/rameau_example/Python_treatment_ext.ipynb b/examples/rameau_example/Python_treatment_ext.ipynb
diff --git a/examples/rameau_example/README.md b/examples/rameau_example/README.md
@@ -2,7 +2,7 @@
 
 Rameau is a set of functions and a class from the rampy library that provides a way to calculate the water content of a glass from its Raman spectrum.
 
-At this stage, it provides access to external Raman calibrations, from the Le Losq et al. (2012) and Di Genova et al. (2017) articles.
+At this stage, it provides access to external Raman calibrations, from the Le Losq et al. (2012), Di Genova et al. (2017) and Thomas et al. (2008) articles.
 
 # INSTALLATION
 
@@ -50,13 +50,13 @@ The virtual machine will see everything in the working directory, so after you j
 
 ## Jupyter notebook or rameau.py script ?
 
-- the Python_treatment.ipynb Jupyter notebook provides some interactive example with figures showcasing the different calibrations.
+- the Python_treatment.ipynb and Python_treatment_ext.ipynb Jupyter notebooks provide some interactive examples with figures showcasing the different calibrations.
 
 - however, the easiest usage is to work with the rameau.py script provided in this folder. This allows calling rameau directly from the terminal, providing a simple set of arguments.
 
 ## Folder prepration
 
-- Put rameau.py or the notebook in your working directory (e.g. you can download this example directory and work in it)
+- Put rameau.py or the notebooks in your working directory (e.g. you can download this example directory and work in it)
 
 - Spectra should be in a subfolder called "raw".
 
@@ -135,3 +135,5 @@ $ python rameau.py -i dataset.xlsx -s 2018_RSES -o results.csv -l 532.0 -m predi
 C. Le Losq, D. R. Neuville, R. Moretti, J. Roux, Determination of water content in silicate glasses using Raman spectrometry: Implications for the study of explosive volcanism. American Mineralogist. 97, 779–790 (2012).
 
 D. Di Genova et al., Effect of iron and nanolites on Raman spectra of volcanic glasses: A reassessment of existing strategies to estimate the water content. Chemical Geology. 475, 76–86 (2017).
+
+S.-M. Thomas, R. Thomas, P. Davidson, P. Reichart, M. Koch-Muller, G. Dollinger, Application of Raman Spectroscopy to Quantify Trace Water Concentrations in Glasses and Garnets. American Mineralogist 2008, 93 (10), 1550–1557. https://doi.org/10.2138/am.2008.2834.
diff --git a/examples/rameau_example/dataset.xlsx b/examples/rameau_example/dataset.xlsx