hyperlyse

Hyperspectral Image Analysis tool

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See directory doc for documentation and dist_archive for Windows builds.

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Running with python

for required python packages, see src/requirements.txt

run:

cd [repo-root]/src
python main.py

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Using the Windows buids

1. Download the latest .zip archive from dist_archive
2. unpack
3. run hyperlyse.exe

Known issue: some overly ambitions anti-virus softwares might put some of the necessary files in quarantine when unpacking... then the applications does not start properly.

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Making new Windows builds

for required python packages, see requirements.txt

building with pyinstaller currently only works up to python 3.9

for building with pyinstaller on Windows, cd to /hyperlyse/src/ and run build.bat

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Changelog

v1.3.3

• Data loading: if a "scale factor" is found in ENVI .hdr file, the values of the data cube are scaled accordingly. No other transformations/scalings are applied.
• PCA visualizations: only the wavelengths selected sith the wavelength comparison slider are used (this is useful, if noisy upper and lower ends of the spectrum lead to "pure noise" components)

v1.3.2

• bugfix: crash on save similarity image

v1.3.1 (patch)

• default filename for spetrum export now only contains the object name once

v1.3

• R009 brightness adjustment slider for visualization image
• R010 UI element for y-range
• configuration in config.json
• semitransparent markers
• R011 define custom spectral range (x-axis) used for all comparison operations (with UI element)
• R012 select spectrum by rectangle (average)
• R013 new database architecture
  • DETAILED REQUIREMENTS
    • load and save, portable db format
    • select, display and compare specific DB spectrum
    • extended fields/metadata for database spectra
    • image of source material
  • SOLUTION
    • based on file system
    • for each spectrum, store:
      • jcamp-dx file with spectrum data and metadata
      • png image with visualization of source
    • load database -> recursivly parse arbitryry folder, or load single file
    • save to database -> just save anywhere
    • delete from database -> delete from filesystem
    • portable -> just copy filesystem
    • new fields and where they are stored in jcamp-dx:
      • name/id ==> ##TITLE
      • origin (e.g. name of color poster or manuscript) ==> ##TITLE
      • original HSI file ==> ##SOURCE REFERENCE
      • rectangle of measurement ==> ##SOURCE REFERENCE
      • measurement device ==> ##SPECTROMETER/DATASYSTEM
      • pigment intensity (light, medium, dark) ==> ##SAMPLE DESCRIPTION
• in the process: lots of internal refactoring

v1.2

• Migration to Qt6 (also updated the other python packages)
• Zooming: Slider instead of combo box - smaller increments
• R005 higher zoom level by default (--> make windows larger upon startup, make image fill whole area
• R006 no automatic scaling of y-axis (graph)
• R008 support for general envi files (not only from Specim IQ)
• R008.A comparison of spectra with different bands
• R007 PCA - without much user control. might be added on request.

v1.1

• R001 export image with marked samplepoint together with spectrum
• R002 zoom (for precise point selection)
• R003 export to JCAMP format
• R004 make spectra exports perfectly compatible with exports from SpecimIQ Studio
• spectral databases and spectra comparison features (experimental)
• advanced image view modes

open feature requests

(none)