HyperBlend is a new type of hyperspectral image simulator based on Blender.

Overview

HyperBlend version 0.1.0

This is the HyperBlend leaf spectra simulator developed in Spectral Laboratory of University of Jyväskylä. You can use and modify this software under MIT licence.

Currently, HyperBlend can only simulate point-spectrometer-like spectral data. It needs actual measured reflectance and transmittance data which it tries to replicate.

Installing

Clone the repository to some location on your machine. Create a python environment by running conda env create -n hb --file hb_env.yml in yor anaconda command prompt when in project root directory. Use your favourite IDE for editing and running the code (developed using PyCharm). Command line build and run is untested, but it should work as well.

You will also need open-source 3D-modeling and rendering software Blender, which you can download and install from (blender.org). At least versions 2.8x and 2.9x should work (developed on version 2.93.5). Change your Blender executable path to constants.py.

Working principle

The measured reflectances and transmittances look like this:

wavelength [nm] reflectance transmittance
400 0.21435 0.26547
401 0.21431 0.26540
... ... ...

We call this the target. Reflectance and transmittance values represent the fraction of reflected and transmitted light so both values are separately bound to closed interval [0,1] and their sum cannot exceed 1.

We use a Blender scene with a rectangular box that represents a leaf. The material of the leaf has four adjustable parameters: absorption particle density, scattering particle density, scattering anisotropy, and mix factor. These control how the light is scattered and absorbed in the leaf material.

For each wavelength in the target, we adjust the leaf material parameters until the modeled reflectance and transmittance match the target values.

Usage

The entry point of the software is __main__.py file. For testing the software without actual data, run

from src import presets

presets.optimize_default_target()

that uses hard-coded test spectrum of a leaf.

The base element of the software is a measurement set identified by set_name, which consists of one or more samples identified by sample_id. To initialize a new set, initialize an Optimization object which will create a directory structure for given set_name under optimization directory.

To use real measured data, you should use

data.toml_handling.write_target(set_name:str, data, sample_id=0)

where data is a list of wavelength, reflectance, transmittance 3-tuples (or lists). This will write the data to disk in human-readable toml-formatted form that the rest of the code can understand.

Now you can start the optimization process. To summarize a simple use case in one snippet:

from src.optimization import Optimization
from data import toml_handlling as TH

data = [[400, 0.21435, 0.26547], [401, 0.21431, 0.26540]]
set_name = 'test_set'

o = Optimization(set_name)
TH.write_target(set_name, data, sample_id=0)
o.run_optimization()

The results are written onto disk in the set's directory as toml files and plotted to .png images.

Project structure, i.e., where to find stuff

Descriptions of the most important files.

  • optimization Optimization results and targets are stored here in set-wise sub-directories.
  • src Top level source code package.
    • __main__.py Entrypoint of the software.
    • constants.py Mainly names of things that should not be changed unless you are sure what you are doing. With the exception of path to Blender executable that you have to change to match your installation.
    • optimization.py Optimization work is done here.
    • plotter.py Responsible for plotting the results.
    • presets.py Default runnable example with hard-coded spectral values.
    • data Package responsible for data structure. Making changes in here will likely result in failure to read old optimization results.
      • file_handling.py Creation and removal of files and directories. Data structure reduction and expansion for more convenient file sharing.
      • file_names.py Knows all filenames in the project. Generator-parser pairs.
      • path_handling.py Knows the most important paths used in the project. Some paths may still need to be generated manually.
      • toml_handling.py Writing and reading of result data files.
    • rendering Package responsible for calling Blender.
    • utils Package containing miscellaneous utility modules.
  • bs_render_single.py Blender render script file.
  • scene_leaf_material.blend Bender scene file that is run by the bs_render_single.py.
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Comments
  • Usage of the program

    Usage of the program

    Hi!

    Thanks for this implementation, I have been looking to run it since a couple of days but I can't get it to be done. Is there any tutorial or instructions for somebody who is new to this type of software (and blender)? I tried running bs_render_single.py from IDE, from Conda Prompt, and from blender itself, but nothing seems to work.

    Also, I tried to run main.py from windows cmd, from my IDE, and from Conda prompt, but it throws errors in references. I tried changing all the references to match what is being called, but I end up with an error that some files (and the directory optimization) does not exist. Tried to run code from the readme, but still can't get to work.

    Would be very helpful if somebody can help me through some basic follow up on how to run this implementation.

    Best regards!

    opened by fieterovich 12
Releases(v0.2.0)
  • v0.2.0(Nov 28, 2022)

    This is the second released version of HyperBlend on our way towards a full canopy scale vegetation simulator. HyperBlend is developed in Spectral Laboratory of University of Jyväskylä by Kimmo Riihiaho (kimmo.a.riihiaho at jyu.fi).

    Version 0.2.0 will break many things in the previous version. Don't expect simulations created in 0.1.0 to work. Also the folder structure and some constants have been reorganized and renamed.

    Main improvements in this version:

    1. Simulation speed 200 times faster (simulation accuracy decreases 2-4 times)
      • You can still use the old simulation method if you need maximum accuracy
    2. Incorporation of the PROSPECT leaf model
      • You can now use PROSPECT parameters such as water thickness and chlorophyll content
      • It is fairly simple to plug in any other leaf model you would like. Just follow how our local prospect module does it, and you should be fine
    Source code(tar.gz)
    Source code(zip)
  • v0.1.0(Nov 11, 2021)

    This is the first release of HyperBlend. This release only demonstrates the usability of Blender in simulating hyperspectral reflectance and transmittance properties of plant leaves. Future releases will add more useful functionalities to the software.

    Created by @11kaks

    Source code(tar.gz)
    Source code(zip)
Owner
SILMAE
Spectral Imaging Laboratory for Multidisciplinary Analysis and Expertise
SILMAE
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