Creating herbarium labels with typst
For a recent description of a novel lichen species I had to create herbarium labels for the specimens which I had collected. I have always wanted to automate this so that I would not have to create all the labels manually in LibreOffice.
I have experimented with the type setting system typst for a preprint and I thought that this could be a great opportunity to apply this to my problem.
Current state of my herbarium database
My herbarium database is a simple spreadsheet. Newly entered specimens receive a unique number and additional information such as, genus and species, coordinates, habitat descriptions, etc.
This is a section of my current database:
When I wanted to create herbarium labels in the past, I just transferred the content of the cells into a word processor and arranged everyting around until it looked (reasonably) ok:
However I could also export the database as CSV and then parse it using some script to generate labels automatically. This is how it looks once exported:
Typst to the rescue
Fortunately typst offers a great scripting capabilities including a way to load CSV files and programatically analyze and typset its content. I was not quite sure how to start though. So I searched for similar examples online and took inspiration from a typst script on how to create conference name tags automatically. My data was a little bit more complex then this example but it was a nice basis for what I wanted to do.
Here is the typst script I came up with:
// order of columns is supposed to be: 1:herb number, 2:year, 3:month, 4:day, 5:country, 6:area, 7:collection spot, 8:GPS-Waypoint, 9:lat, 10:long, 11:altitude, 12:description, 13:genus, 14:species, 15:substrate, 16:collectors, 17:n capsules, 18:notes
#let label(number, year, month, day, country, area, spot, waypoint, lat, long, altitude, description,genus, species,substrate, collectors, ncapsules, notes) = {
let main-color = luma(255) //white
let secondary-color = luma(0) //black
let header = [
#align(center)[#v(3mm)#text(size: 12pt, tracking: 0.6pt, weight: "bold")[Herbarium Philipp Resl Nr.#number]]
]
let spname = align(center, box(inset: 1mm)[
#set align(center)
#set par(leading: 0.25em)
#text(size:17pt, style:"italic", [#genus #species])
])
let desc = align(left, box(inset: 1mm)[
#set par(leading: 0.25em)
#set align(left)
#text(size:12pt, [*#country*: #area, #spot, #lat #long, #altitude m a.s.l., #description. \ Substrate: #substrate])
//#v(-5mm)
])
let notess = align(left, box(inset: 1mm)[
#set par(leading: 0.25em)
#text(size:12pt, [*Notes*: #notes])
])
let colldate = align(left, box(inset: 1mm)[
#set align(left)
#text(size:12pt, [#h(2mm) #day.#month.#year #h(1fr) leg. #collectors #h(2mm)])
])
// A single herbarium label consists of the different parts(header, spname, desc, notess, colldate) created above with different formating, texsizes, etc.. These parts are then combined here.
let content = [
// arrange content
#header
#v(1fr)
#spname
#v(1fr)
#desc
#notess
#v(1fr)
#colldate
#v(1fr)
]
box(
height: 80mm,
width: 130mm,
clip: true,
inset: 3mm,
stroke: .1mm,
content
)
}
// set page dimensions and landscape format
#set page(paper: "a4", margin: 10mm, flipped: true)
// load database file
#let specimens = csv("database.csv", delimiter: ";")
// only actually print labels for the last N entries
// this is to avoid creating a PDF from the whole database all the time.
#let N = 6
#let totallen = specimens.len()
#let subsamples = specimens.slice(totallen - N, totallen)
// create variable to store the individual labels
#let labels = []
#for p in subsamples {
// order of columns is supposed to be: 1:herb number, 2:year, 3:month, 4:day, 5:country, 6:area, 7:collection spot, 8:GPS-Waypoint, 9:lat, 10:long, 11:altitude, 12:description, 13:genus, 14:species, 15:substrate, 16:collectors, 17:n capsules, 18:notes
lebels = labels + label(p.at(0), p.at(1), p.at(2), p.at(3), p.at(4), p.at(5), p.at(6) , p.at(7), p.at(8), p.at(9), p.at(10), p.at(11), p.at(12), p.at(13), p.at(14), p.at(15), p.at(16), p.at(17)) + box(height: 80mm, width: 1mm,clip: true)
}
#set par(leading: 1mm, spacing: 1mm)
#align(center, labels)
Creating typst labels
I use typst in a docker container. I compile the above script (which is called label.typ) using the following command:
docker run -v $(pwd):/data --rm --user $(id -u):$(id -g) -it reslp/typst:0.13.1 typst compile label.typ
This creates a PDF with the labels:
Much better I think!
I still want to find a better way to select which labels I would like to create from the database but since I usually only create labels from specimens entered last, the current approach works.