---
title: "TIVITA workflows"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{TIVITA workflows}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
resource_files:
  - figures/logo.svg
  - figures/logo-dark.svg
---

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<style>
.cttir-vignette-logo { float: right; width: 120px; max-width: 30%; margin: 0 0 1rem 1.5rem; }
.cttir-vignette-logo img { width: 100%; height: auto; border: 0; background: transparent; box-shadow: none; }
.cttir-vignette-logo .cttir-vignette-logo-light { display: block; }
.cttir-vignette-logo .cttir-vignette-logo-dark { display: none; }
@media (prefers-color-scheme: dark) {
  .cttir-vignette-logo .cttir-vignette-logo-light { display: none; }
  .cttir-vignette-logo .cttir-vignette-logo-dark { display: block; }
}
[data-bs-theme="light"] .cttir-vignette-logo .cttir-vignette-logo-light { display: block; }
[data-bs-theme="light"] .cttir-vignette-logo .cttir-vignette-logo-dark { display: none; }
[data-bs-theme="dark"] .cttir-vignette-logo .cttir-vignette-logo-light { display: none; }
[data-bs-theme="dark"] .cttir-vignette-logo .cttir-vignette-logo-dark { display: block; }
</style>
<div class="cttir-vignette-logo">
  <img class="cttir-vignette-logo-light" src="figures/logo.svg" alt="hypermodR logo" width="120" height="139" />
  <img class="cttir-vignette-logo-dark" src="figures/logo-dark.svg" alt="hypermodR logo" width="120" height="139" />
</div>
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```{r setup, include=FALSE}
library(hypermodR)
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", error = FALSE)
```
This example checks source orientation, not a camera. The only admitted profile
here is a synthetic y,x,band declaration. Tissue, Mini and Surgery device/export
profiles require independent calibration and reference-output evidence.

```{r tivita}
measurement <- list(
  cube = array(seq_len(24), c(2, 3, 4)),
  wavelengths = c(500, 600, 700, 800), metadata = list(synthetic = TRUE),
  references = list(), timestamp = "2026-01-01", path = "synthetic"
)
x <- hm_from_tivis(
  measurement,
  hm_tivita_profile(wavelengths = measurement$wavelengths)
)
b <- hm_read_block(x)
if (!isTRUE(all(
  identical(as.numeric(b$values), as.numeric(measurement$cube)),
  identical(dim(b$values), c(2L, 3L, 4L, 1L))
))) {
  cli::cli_abort("Example assertion failed.", class = "hm_example_error")
}
hm_instrument_profiles()
```

`hm_from_tivis()` requires an explicit source profile. It does not infer a grid
from the camera name or the measurement's band count. Radiometric calibration
remains unknown unless established separately. Masks retain unknown/invalid
pixels; registered SpecCube, RGB, DICOM and parameter-display assets retain
distinct roles. A vendor display does not establish quantitative export parity.