ToolsRTM

RTM-SUITE · TOOLSRTM

Leaf, canopy, soil & atmosphere,
in R and Python.

ToolsRTM covers leaf optics (PROSPECT-D, PROSPECT-PRO, Fluspect-B, Fluspect-B-Cx, LIBERTY), canopy models (fourSAIL, foursail2, INFORM), soil optics (BSM, MARMIT) and the full soil–canopy–atmosphere chain (SPART) — plus LUT/parameter sampling, sensor convolution, vegetation indices, and trait inversion (classical ML and deep learning), in R and Python, kept numerically in sync and verified against each other.

PROSPECT · Fluspect · LIBERTY fourSAIL · fourSAIL2 · INFORM · SPART MARMIT LUTs & sensor convolution ML & deep-learning inversion R & Python

Explore R Tutorials Explore Python Tutorials Interactive Function Explorer →

Nineteen R tutorials, one shared 20-chapter Python path

The R side is nineteen standalone ToolsRTM pkgdown articles (t01–t19), grouped below by theme: models themselves, then trait inversion (ML and deep learning), sensitivity analysis, and satellite/spatial applications. The Python side is organised differently — toolsrtm and scopeinpython share one continuous 20-chapter learning path, so almost every chapter is ToolsRTM material (only Chapter 06 is SCOPE-specific); this page links the ToolsRTM-relevant chapters and the package-tagged code examples directly, and points to the full path for the complete narrative.

Two ways in

R

R Tutorials

19 rendered pkgdown articles: models, LUTs, sensor convolution, indices, inversion, spatial mapping.

19 tutorials

Py

Python Tutorials

The ToolsRTM-relevant chapters of the shared 20-chapter Python path, plus package-tagged code examples.

18 chapters + examples

API

Function Explorer

Interactive map of every real ToolsRTM/toolsrtm function — workflow, network graph, code examples.

40 functions

Leaf, canopy, soil & atmosphere models · t01–t09, t16

Five leaf models × three canopy models × two soil models × SPART for the full chain to top-of-atmosphere.

01

Getting Started with ToolsRTM

A first simulation, start to finish.

02

From Leaf to Canopy Reflectance

Chaining a leaf model into a canopy model.

03

SPART: Soil-Plant-Atmosphere RT

Top-of-canopy vs. top-of-atmosphere reflectance.

04

Comparing Radiative Transfer Models

All 15 leaf×canopy combinations, side by side.

05

Building Look-Up Tables

Parameter sampling for a simulation LUT.

06

Large-Scale and Parallel RTM Simulation

Running a LUT across many cores.

07

Sensor Convolution

Native spectrum → real sensor bands.

08

Hyperspectral and VNIR Sensor Convolution

PRISMA and other hyperspectral sensors.

09

Vegetation Indices and Spectral Features

NDVI, red-edge and friends, from simulated bands.

16

MARMIT + fourSAIL + SPART

Realistic, moisture-dependent soil reflectance inside a full canopy run.

Trait inversion & machine learning · t11, t12, t13, t14

Going backwards: from a reflectance spectrum to the vegetation trait that produced it.

11

From Physics to Vegetation Traits: Hybrid Inversion

LUT-trained models applied to real and synthetic spectra.

12

Comparing ML Algorithms for RTM Inversion

Random Forest, SVM, PLSR and ensembles, head-to-head.

13

Deep Learning for RTM Inversion

Dense networks and a 1D-CNN on hyperspectral bands, vs. Random Forest.

14

End-to-End RTM Inversion Pipeline

Simulate → convolve → invert, as one pipeline.

Sensitivity analysis · t10

Which trait actually moves the signal, and where in the spectrum.

10

Understanding RTM Sensitivity

One-at-a-time sweeps, Sobol indices, and Johnson relative weights.

Satellite & spatial applications · t15, t17, t18, t19

Real pixels: actual Sentinel-2 scenes via STAC, pixel-by-pixel inversion, and FLEX sub-pixel heterogeneity.

15

From Satellite Reflectance to Traits: Real EO Application

Inverting a real, not simulated, scene.

17

Monitoring a Forest Site Through Time

A real forest site, tracked across a time series.

18

Data-Driven Spatial Index Mapping

Trait maps from real Sentinel-2 imagery.

19

FLEX Cal/Val: ESU Heterogeneity Mapping

Scaling up to FLEX's coarser footprint with sub-pixel heterogeneity.

Source code, on GitHub

Real, runnable code — the packages themselves and the standalone scripts each tutorial theme grew from.

R

ToolsRTM (R package)

Source of the R package itself.

Py

toolsrtm (Python package)

Source of the Python port.

R

Scripts/R/ForPROSAIL

Standalone leaf-model scripts.

R

Scripts/R/ForFoursail2

Standalone canopy-model scripts.

R

Scripts/R/ForINFORM

Standalone forest-canopy scripts.

R

Scripts/R/ForMARMIT

Standalone soil-optics scripts.

R

Scripts/R/ForSPART

Standalone soil-plant-atmosphere scripts.

R

Scripts/R/Pipeline

Simulate → convolve → invert, end to end.

R

Scripts/R/Sensibility

Standalone sensitivity-analysis scripts.

Py

Scripts/Python

The same script themes, in Python.