mzarowka / hsitools Goto Github PK

Stack plots in a row, using patchwork

• Create a list of plots.
• Plot RGB and selected maps.
• Plot profiles.

Add a page or section where the user can input human-readable metadata, like the one below. Then, dump it into the rds and Quarto document and render it to HTML/PDF at the end.

• Site name
• Country
• Core name
• Project name or other identifiers
• Coordinates if needed
• Scan date
• Person scanning
• Person processing
• Other info and comments

Automatically write/store output of run_core() to .rds and script?

Get rois recorded in GIS software, read into session and overwrite shiny app output, or use in functions.

Save profile data to file

• Pixel depth.
• Calibrated pixel depth.
• Translated depth, metric.
• Proxies.
• Options: csv, parquet.

The last terra version fully compatible with Shiny was 1.7-46, later versions throw an error when displaying plots in shiny.

Vignette on calculation of hyperspectral indices from the processed data.

Hunt down and remove rgdal dependencies - archived on cran as 1.6-7

Temporary bypass to install

remotes::install_version("rgdal", version = "1.6-7", repos = "http://cran.us.r-project.org")

What if files come from either a) an older version of the Specim scanner, b) an entirely different manufacturer, or c) strange magic made it a non-typical, chaotic structure? Can we let users choose DARK/WHITE/CAPTURE files at the first step in Shiny?

Prepare vignette for data normalization.

If files are listed and subset by position, some filenames (e.g. starting with W) mess up the workflow. Work on names, rather than position.

run_core() allows proceeding without any layers selected, throwing an error later in prepare_core(), default to all?

Add λREMP index calculation from Ghanbari et al., 2023.

From calibrated pixels, use true top and true bottom to assign actual depths.

Using internal HSItools:::rois_to_vect() coerce "analysisRegions" to terra SpatVectors before shiny session ends.

Add option to process only ROIs, either roi selection screen of first screen.

Read metadata from header files and provide a nice output for user.

• Spatial imputation in masked regions based on the neighborhoods?
• possibly with Random Forests, GANs or...?

Calibrate pixel depth from tape measurement.

Example data won't load if the package is installed and called from a non-dev environment.

Plot image of the core and or ROIs

• Read SpatRaster and RGB layers.
• #26
• Optional - write to file.

Write options to the same directory as processed core is

Generalize prepare_core() so it accepts path to normalize full capture.

Add calculation of derivatives and amplitudes.

The second shiny dashboard is where reflectance can be loaded and displayed, and plots and spectral maps are displayed as the user changes the brush.

Add an option to remove recorded rois in shiny?

Save processing details to reprocess and modify the settings later.

• Save shiny output.

Provide three modes for RABD calculations:

• RABD max - if the range is provided, find the wavelength where a minimum of reflectance is found, flexible.
• RABD mid - if the range is provided, find the wavelength closest to the mid-point.
• RABD strict - calculate RABD directly at the selected wavelength.

Add ROI overlays to plots

Following the napari-sediment (python workflow) create standalone documentation.
Future release on CRAN makes it hard to create rich documentation with numerous figures such as screenshots etc.

Documentation developed with Quarto is available here: https://mzarowka.quarto.pub/hsitools/ with GitHub repo https://github.com/mzarowka/HSItools-documentation

Get mean values of selected proxies from selection.

Gather and expand the list of spectral indices with references:

• R850/R900; minerogenic inputs: Saunders, K.M., Roberts, S.J., Perren, B., Butz, C., Sime, L., Davies, S., Van Nieuwenhuyze, W., Grosjean, M., Hodgson, D.A., 2018. Holocene dynamics of the Southern Hemisphere westerly winds and possible links to CO2 outgassing. Nature Geosci 11, 650–655. https://doi.org/10.1038/s41561-018-0186-5
• R570/R630; minerogenic inputs, microclastics: Rein, B., Sirocko, F., 2002. In-situ reflectance spectroscopy – analysing techniques for high-resolution pigment logging in sediment cores. Int J Earth Sci (Geol Rundsch) 91, 950–954. https://doi.org/10.1007/s00531-002-0264-0
• R570/R630 and R590/R690, minerogenic inputs, microclastics: Trachsel, M., Grosjean, M., Schnyder, D., Kamenik, C., Rein, B., 2010. Scanning reflectance spectroscopy (380–730 nm): a novel method for quantitative high-resolution climate reconstructions from minerogenic lake sediments. J Paleolimnol 44, 979–994. https://doi.org/10.1007/s10933-010-9468-7

Function to plot SpatRaster with spectral maps

• Read data with layer selection and one of the suggested palettes.
• #25
• Overlay on RGB.
• Optional - write to file.

Add RABA calculation function.

Prepare alternative workflow for large SpatRasters from the newer hyperspectral cameras to avoid memory allocation errors.

General vignette on data plotting.

• HSI maps.
• RGB plots.
• Profiles.
• Compositing.

When adding many ROIs, the lower portion of the table becomes cutoof from view

The path stored in .rds is an absolute path, leading to reprocessing issues when the directory structure is changed.

Vignette on filtering, spectral smoothing etc.