AquaGrammar Help & tutorials

AquaGrammar Help

Getting started

Your first Aquagram®, in four steps. Nothing here needs configuring, and you do not need to supply a file: two datasets come bundled.

Before you begin

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  • Windows 10 or Windows 11.
  • No instrument required. Preview reads prepared files only; it never connects to a MicroNIR.

The four steps are always listed down the left side of the window, and the current one is highlighted. You can click back to an earlier step at any time without losing your work.

Step 1 · Open a file

You are offered three cards.

  • Open your own file — drag a MicroNIR file onto the dashed card, or select Choose file. Accepted: .sam, vendor CSV, vendor XLSX.
  • Demo 1 — Natural Systems — select Open Demo 1 for nine bundled groups of rock and mineral scans.
  • Demo 2 — Water — select Open Demo 2 for four bundled groups of water-source scans.

If you are here to learn the tool, start with Demo 1. AquaGrammar moves to step 2 by itself once the file is read.

Step 2 · Select sample groups

Your file is split into sample groups, each showing its name and how many repeat scans it contains — Stone1 (n=15) means fifteen repeats of Stone1.

  1. Tick the groups you want. Nothing is selected initially. Unticked groups are excluded completely — they contribute to nothing later. Select all and Clear selection are in the bottom-right corner.
  2. Check the counter above the list ("4 of 9 selected"). It always reflects your current choice.
  3. Choose an SNV range. Three options sit below the list:
  • 1st overtone 1300–1600 — the recommended choice. This is the region the twelve Classic-12 coordinates actually fall in, so each spectrum is normalized against the range being plotted.
  • Full range — normalizes across every wavelength in the file.
  • Combination 1100–1300 — normalizes on the combination band.
  1. Select Continue to row processing.

Sort and the Cards / List toggle only change how groups are displayed. They never change your selection.

What happens when you continue: SNV is applied to every selected scan over the range you chose, each wavelength is then standardized across every scan in the file as (value − mean) / SD, and finally repeats are averaged within each group. This is automatic and has no other settings.

Step 3 · Process rows

The left panel, Inputs for Aquagram®, lists one row per group you selected, under the heading *Original groups · SNV applied*. Each row has a coloured dot showing the colour its line will take.

You can go straight on — just tick the rows you want to plot and skip to step 4. Or combine them first, using the Operation panel on the right:

  • Average — the mean of two or more ticked groups.
  • Add — the sum of two or more ticked groups.
  • Subtract — adjusts any number of ticked groups against one baseline group you choose separately, producing one result per adjusted group.

Select Create average row (or sum/subtract) and the result appears under *Processed results* on the left. You can rename it with the pencil icon, remove it with the ×, or feed it back into another operation.

When the rows you want are ticked, select Generate Classic-12 Aquagram®.

Step 4 · Read and export

Every row you ticked becomes one coloured line, listed in the legend beneath the chart.

  • Select a legend entry to hide or show that line.
  • Zoom with − / + above the chart; above 100% you can drag to pan.
  • Hover a line to read its WAMACS label, wavelength, and value.
  • View overall mean table opens the fixed twelve-row table — the mean across the rows you plotted.
  • Export XLSX / CSV / PNG / JPG. XLSX and CSV give you one column per plotted line, enough to rebuild the chart elsewhere. PNG and JPG capture the chart together with its legend.

To begin again, click an earlier step in the left rail, or open a different file.

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