Welcome to mineralML’s documentation!

Contents

• Introduction and Citation
• Collaborators
• Minerals
• Chemistry
• Units
• Installation & Updating
  • Installation
  • Updating
• Importing Package
• Importing Data
• Data Import Complete
• Submitting data
• FAQs and Troubleshooting
• Change Log
  • Version 0.0.3.18
  • Version 0.0.3.17
  • Version 0.0.3.16
  • Version 0.0.3.15
  • Version 0.0.3.14
  • Version 0.0.3.13
  • Version 0.0.3.12
  • Version 0.0.3.12
  • Version 0.0.3.11
  • Version 0.0.3.10
  • Version 0.0.3.9
  • Version 0.0.3.8
  • Version 0.0.3.6 and 0.0.3.7
  • Version 0.0.3.5
  • Version 0.0.3.4
  • Version 0.0.3.3
  • Version 0.0.3.2
  • Version 0.0.3.1
  • Version 0.0.3.0
  • Version 0.0.2.6
  • Version 0.0.2.5
  • Version 0.0.2.4
  • Version 0.0.2.3
  • Version 0.0.2.2
  • Version 0.0.2.1
  • Version 0.0.2.0
  • Version 0.0.1.9
  • Version 0.0.1.8
  • Version 0.0.1.7
  • Version 0.0.1.6
  • Version 0.0.1.5
  • Version 0.0.1.4
  • Version 0.0.1.3
  • Version 0.0.1.2
  • Version 0.0.1.1
  • Version 0.0.1
  • Version 0.0.0.7
  • Version 0.0.0.6
  • Version 0.0.0.5
  • Version 0.0.0.4
  • Version 0.0.0.3
  • Version 0.0.0.2
  • Version 0.0.0.1
  • Version 0.0.0.0

Prepare and Clean Data

• Helper Functions Quickstart
  • 1. Load and prepare data for analysis
  • 2. Clean and align columns of dataframe
  • 3. Convert between oxide and elemental wt%

Tabular Data

• mineralML Quickstart for Tabular Data
  • 1. Load and prepare data for analysis
  • 2. Apply the trained neural network (mm.predict_class_prob)
  • 3. Export prediction results
  • 4. Examine prediction results
  • 5. Plot in latent space

Microanalytical Tabular Data

• mineralML Quickstart for Tabular Microanalytical Data
  • 1. Load and prepare data for analysis
  • 2. Apply the trained neural network (mm.predict_class_prob)
  • 3. Export prediction results
  • 4. Calculate mineral components, plot minerals in empirical classification space
  • 5. Perform Thermobarometry

Mapped EDS Data

• mineralML Quickstart for Mapped EDS Data
  • 1. Load and prepare data for analysis
  • 2. Apply the trained neural network with mm.run_map
  • 3. Plot oxide concentration maps and prediction score maps
  • 4. Plot compositions of mapped minerals in various classification diagrams (ternary, quadrilateral).
  • 5. Plot chemical variation maps
• Interactive Tools for Mapped EDS Data
  • 1. Load and run a map
  • 2. Interactive pixel composition picker
  • 3. Plot pick locations
  • 4. Interactive line profiles
  • 5. Plot transect locations
  • 6. Batch extract profiles from saved transects
  • 7. Composite component map

Mapped EBSD Data

• mineralML Quickstart for Mapped EBSD and/or EDS Data
  • 1. Load and plot a phase map from an EBSD CTF file
  • 2. Load and prepare EDS data for analysis
  • 3. Apply the trained neural network with mm.run_map
  • 4. Plot EBSD and mineralML-generated EDS phase maps side-by-side
  • 5. Plot oxide concentration maps and prediction score maps
  • 6. Plot compositions of mapped minerals in various classification diagrams (ternary, quadrilateral).
  • 7. Plot chemical variation maps

Stoichiometry Calculators

• mineralML Stoichiometry Calculations
• BaseMineralCalculator
  • 1. Load and prepare data for analysis
  • AmphiboleCalculator and AmphiboleClassifier
  • ApatiteCalculator
  • BiotiteCalculator
  • CalciteCalculator
  • ChloriteCalculator
  • ClinopyroxeneCalculator, OrthopyroxeneCalculator, PyroxeneClassifier
  • EpidoteCalculator
  • FeldsparCalculator, FeldsparClassifier
  • GarnetCalculator
  • GlassCalculator, GlassClassifier
  • KalsiliteCalculator
  • LeuciteCalculator
  • MeliliteCalculator
  • MuscoviteCalculator
  • NephelineCalculator
  • OlivineCalculator
  • RhombohedralOxideCalculator, SpinelCalculator, OxideClassifier
  • QuartzCalculator
  • RutileCalculator
  • SerpentineCalculator
  • TitaniteCalculator
  • TourmalineCalculator
  • ZirconCalculator

Synthetic Data Generator

• Synthetic Mineral Generator
  • Load and prepare data for groundtruthing
• Olivine
• Feldspar
• Kalsilite

Detailed Code Documentation

• Building-block functions
  • mineralML Documentation
  • Core Functions
  • Sequential, Transfer-Learning Machine Learning Functions
  • Mapping Functions
  • Stoichiometric Functions
  • Synthetic Mineral Generator
  • Confusion Matrix Functions
  • Constants

References

• References