Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
CMAS 3D, developed in MATLAB (R), is a program to support visualization of major element chemical data in three dimensions. Such projections are used to discuss correlations, metamorphic reactions and the chemical evolution of rocks, melts or minerals. It can also project data into 2D plots. The CMAS 3D interface makes it easy to use, and does not require any knowledge of Matlab (R) programming. CMAS 3D uses data compiled in a Microsoft Excel (TM) spreadsheet. Although useful for scientific research, the program is also a powerful tool for teaching.
ISSN: 0098-3004

hal-00413570
https://hal.archives-ouvertes.fr/hal-00413570
DOI : 10.1016/j.cageo.2008.07.002

Éditeur(s) : HAL CCSD
Résumé : International audience
MOTIVATION: Imaging mass spectrometry (IMS) is a maturating technique of molecular imaging. Confidence in the reproducible quality of IMS data is essential for its integration into routine use. However, the predominant method for assessing quality is visual examination, a time consuming, unstandardized and non-scalable approach. So far, the problem of assessing the quality has only been marginally addressed and existing measures do not account for the spatial information of IMS data. Importantly, no approach exists for unbiased evaluation of potential quality measures. RESULTS: We propose a novel approach for evaluating potential measures by creating a gold-standard set using collective expert judgements upon which we evaluated image-based measures. To produce a gold standard, we engaged 80 IMS experts, each to rate the relative quality between 52 pairs of ion images from MALDI-TOF IMS datasets of rat brain coronal sections. Experts' optional feedback on their expertise, the task and the survey showed that (i) they had diverse backgrounds and sufficient expertise, (ii) the task was properly understood, and (iii) the survey was comprehensible. A moderate inter-rater agreement was achieved with Krippendorff's alpha of 0.5. A gold-standard set of 634 pairs of images with accompanying ratings was constructed and showed a high agreement of 0.85. Eight families of potential measures with a range of parameters and statistical descriptors, giving 143 in total, were evaluated. Both signal-to-noise and spatial chaos-based measures performed highly with a correlation of 0.7 to 0.9 with the gold standard ratings. Moreover, we showed that a composite measure with the linear coefficients (trained on the gold standard with regularized least squares optimization and lasso) showed a strong linear correlation of 0.94 and an accuracy of 0.98 in predicting which image in a pair was of higher quality. AVAILABILITY AND IMPLEMENTATION: The anonymized data collected from the survey and the Matlab source code for data processing can be found at: https://github.com/alexandrovteam/IMS_quality. CONTACT: theodore.alexandrov@embl.de
Bioinformatics (Oxford, England)

hal-01163754
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01163754
DOI : 10.1093/bioinformatics/btv266
PUBMED : 26072506

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : International audience
This paper presents the background for the calculation of various numbers that can be used to characterize crystal-preferred orientation (CPO), also known as texture in materials science, for large datasets using the combined scripting possibilities of MTEX and MatLab®. The paper is focused on three aspects in particular: the strength of CPO represented by orientation and misorientation distribution functions (ODFs, MDFs) or pole figures (PFs); symmetry of PFs and components of ODFs; and elastic tensors. The traditional measurements of texture strength of ODFs, MDFs and PFs are integral measurements of the distribution squared. The M-index is a partial measure of the MDF as the difference between uniform and measured misorientation angles. In addition there other parameters based on eigen analysis, but there are restrictions on their use. Eigen analysis does provide some shape factors for the distributions. The maxima of an ODF provides information on the modes. MTEX provides an estimate of the lower bound uniform fraction of an ODF. Finally, we illustrate the decomposition of arbitrary elastic tensor into symmetry components as an example of components in anisotropic physical properties. Ten examples scripts and their output are provided in the appendix.
Geological Society Special Publication

hal-01277689
https://hal.archives-ouvertes.fr/hal-01277689
DOI : 10.1144/SP409.8

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We present GravProcess, a set of MATLAB routines to process gravity data from complex campaign surveys and calculate the associated gravity field. Data reduction, analysis, and representation are done using the MATLAB Graphical User Interface Tool, which can be installed on most systems and platforms. Data processing is divided into several steps: (1) Integration of gravity data, station location, and gravity line connection input files; (2) Gravity data reduction applying solid-Earth tide and instrumental drift corrections and, depending on the required processing level, air pressure and oceanic tidal corrections; (3) Automatic network adjustment and alignment to absolute base stations; (4) Free air and terrain corrections to calculate gravity values and anomalies, and to estimate the associated errors. The final step is dedicated to post-processing and includes graphical representations of data and an output text file, which can be used by Geographic Information System software. An example of this processing chain applied to a recent survey in northern Morocco is given and compared with previous available results.
ISSN: 0098-3004

hal-01217120
https://hal.archives-ouvertes.fr/hal-01217120
DOI : 10.1016/j.cageo.2015.04.005

Éditeur(s) : Amer Meteorological Soc
Résumé : The Lagrangian Transport Experiment (LATEX) was developed to study the influence of coupled physical and biogeochemical dynamics at the meso- and submesoscales on the transfers of matter and heat between the coastal zone and the open ocean. One of the goals of the Latex10 field experiment, conducted during September 2010 in the Gulf of Lion (northwest Mediterranean), was to mark a dynamical mesoscale feature by releasing a passive tracer [sulfur hexafluoride (SF6)] together with an array of Lagrangian buoys. The goal was to release the tracer in an initial patch as homogeneous as possible in the horizontal, and to study its turbulent mixing and dispersion while minimizing the contribution due to advection. For that, it was necessary to continuously adjust the vessel route in order to remain as closely as possible in the Lagrangian reference frame moving with the investigated mesoscale structure. To accomplish this task, a methodology and software were developed, which are presented here. The software is equipped with a series of graphical and user-friendly accessories and the entire package for MATLAB can be freely downloaded ().
Journal Of Atmospheric And Oceanic Technology (0739-0572) (Amer Meteorological Soc), 2013-08 , Vol. 30 , N. 8 , P. 1940-1950

Droits : 2013 American Meteorological Society
http://archimer.ifremer.fr/doc/00155/26590/24719.pdf
DOI:10.1175/JTECH-D-12-00183.1
http://archimer.ifremer.fr/doc/00155/26590/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We present a graphical user interface to facilitate the processing of teleseismic shear-wave splitting observations. In contrast to a fully automated technique, we present a manual, per-event approach that maintains user control during the sequence of processing. The SplitLab environment is intended to undertake the repetitive processing steps while enabling the user to focus on quality control and eventually the interpretation of the results. Pre-processing modules of SplitLab create a database of events and link the corresponding seismogram files. The seismogram viewer tool uses this database to perform the measurement interactively. Post-processing of the combined results of such a project includes a viewer and export option. Our emphasis lies in the application to teleseismic shear-wave splitting analysis, but our code can be extended easily for other purposes. SplitLab can be downloaded at http://www.gm.univ-montp2.fr/splitting/.
ISSN: 0098-3004

hal-00412372
https://hal.archives-ouvertes.fr/hal-00412372
https://hal.archives-ouvertes.fr/hal-00412372/document
https://hal.archives-ouvertes.fr/hal-00412372/file/Wuestefeld_Splitlab_CompGeosc2008_hal.pdf
DOI : 10.1016/j.cageo.2007.08.002

Éditeur(s) : HAL CCSD Geological Society of London
Résumé : This paper presents the background for the calculation of physical properties of an aggregate from constituent crystal properties and the texture of the aggregate in a coherent manner. Emphasis is placed on the important tensor properties of 2nd and 4th rank with applications in rock deformation, structural geology, geodynamics and geophysics. We cover texture information that comes from pole figure diffraction and single orientation measurements (electron backscattered diffraction or EBSD, electron channelling pattern, Laue pattern, optical microscope universal-stage). In particular, we provide explicit formulae for the calculation of the averaged tensor from individual orientations or from an orientation distribution function (ODF). For the latter we consider numerical integration and an approach based on the expansion into spherical harmonics. This paper also serves as a reference paper for the mathematical tensor capabilities of the texture analysis software MTEX, which is a comprehensive, freely available MatLab toolbox that covers a wide range of problems in quantitative texture analysis, for example, ODF modelling, pole figure to ODF inversion, EBSD data analysis and grain detection. MTEX offers a programming interface which allows the processing of involved research problems as well as highly customizable visualization capabilities; MTEX is therefore ideal for presentations, publications and teaching demonstrations.
Deformation Mechanisms, Rheology and Tectonics: Microstructures, Mechanics and Anisotropy

hal-00688833
https://hal.archives-ouvertes.fr/hal-00688833

Éditeur(s) : HAL CCSD
Résumé : The method of shear-wave splitting provides a unique possibility to identify seismic anisotropy, which is a result of the preferred orientations of the anisotropic minerals by deformation. The novel software SplitLab, presented in this thesis, simplifies the data processing. The comparison of three independent techniques makes it possible to associate an objective quality to the results and also to define a criterion to automatically detect events without splitting (“Nulls”). This criterion is applied to shear-wave splitting measurements at 16 stations located on the East European Craton. The results indicate that the fast directions reflect the ancient blocks, which constitute the East European Craton. The fast directions in south-west are aligned with the margin of the craton and continue the general tendency of offcraton stations. The stations in the Ural foredeep show fast directions perpendicular to the general tendency of the mountain chain. Various indicators give reason to assume lithospheric origins of anisotropy
La mesure du déphasage des ondes de cisaillement offre la possibilité de caractériser l'anisotropie sismique présente dans les différentes couches de la Terre, qui résulte généralement des orientations préférentielles des minéraux anisotropes induites par la déformation. Le nouveau logiciel SplitLab présenté dans cette thèse, simplifie le traitement des données depuis la requête des données jusqu'à la masure de déphasage et l'interprétation des résultats. La comparaison de trois techniques indépendantes pour mesurer ce déphasage permet de quantifier la qualité des résultats et de détecter automatiquement les mesures sans déphasage apparent. Ce critère est appliqué aux mesures de déphasages des ondes SKS enregistrées en 16 stations situées sur le Craton Est Européen. Les résultats indiquent que les directions rapides reflètent les structures anciennes, qui constituent le Craton Est Européen. En outre, les directions rapides dans le Sud-ouest s'alignent avec la bordure du craton et sont en continuité avec la tendance générale définie par les stations éloignées du Craton. Les stations dans les unités externes de l'Oural montrent des directions rapides perpendiculaires à la tendance générale de la chaîne de montagne.
https://tel.archives-ouvertes.fr/tel-00539114

tel-00539114
https://tel.archives-ouvertes.fr/tel-00539114
https://tel.archives-ouvertes.fr/tel-00539114/document
https://tel.archives-ouvertes.fr/tel-00539114/file/thesewustefeld.pdf

Éditeur(s) : HAL CCSD Springer Verlag (Germany)
Résumé : We present a detailed rock-magnetic and archaeomagnetic study of two brick kilns, named OSA and OSB, discovered at the location of Osterietta, in northern Italy. The magnetic properties of representative samples have been investigated to identify the nature of the magnetic carriers, their domain state and thermal stability, and investigate their suitability for archaeomagnetic determinations. Thermally stable, mainly pseudosingle domain (PSD) magnetite is identified as the main magnetic carrier. The full geomagnetic field vector has been determined for the two kilns, including directional and intensity analysis. Archaeointensities have been recovered with both the classical Thellier and the multi-specimen protocols. The multi-specimen procedure was performed with a very fast-heating oven developed at Montpellier, France. A Matlab® code for anisotropy correction during the Thellier experiment is provided. The archaeointensity results obtained from both techniques for the OSA kiln are of high quality and in good mutual agreement. For the OSB kiln, Thellier results are characterized by large standard deviation and the multi-specimen (MSP) technique was not successful. The obtained full geomagnetic field vector (declination, inclination and intensity) has been used for the archaeomagnetic dating of the two structures suggesting that the OSA kiln was for the last time used between 1761?1841 A.D. and the OSB kiln between 1752?1831 A.D., at 95% probability. This study shows that intensity determinations do not restrict the dating results when referring to the last few centuries, as this period is characterized by very small intensity variations.
ISSN: 0039-3169

hal-01236052
https://hal.archives-ouvertes.fr/hal-01236052
DOI : 10.1007/s11200-015-0413-0