template for pathology atlas repositories
see [make-html-WSI](https://github.com/pathologyatlas/make-html-WSI) for more information and [TODO](https://github.com/pathologyatlas/TODO) to add cases
In this README file replace the following:
TemplateEN with description of file in English
TemplateTR with description of file in Turkish
template with repository name
update html file <head>
<title>TemplateEN templateTR</title>
<meta name="keywords" content="TemplateEN, templateTR, patoloji, atlas, pathology, whole slide image">
<meta name="description" content="TemplateEN templateTR">
vips dzsave HE.svs HE
update html file to match .dzi file
add to begining of qmd page
---
description: |
TemplateEN
TemplateTR
date: last-modified
categories: [template]
page-layout: full
bibliography: references.bib
---
consider using git_push.sh script to upload files to github, since the number of generated files is huge
after upload complete, do not forget to activate github pages for the new repository
source("./R/language.R")
output_type <- knitr::opts_knit$get("rmarkdown.pandoc.to")
## TemplateTR {#sec-template}
## TemplateEN {#sec-template}
if (!file.exists("./screenshots/template_screenshot.png")) {
webshot2::webshot(
url = "https://images.patolojiatlasi.com/template/HE.html",
file = "./screenshots/template_screenshot.png"
)
}
knitr::include_url(url = "https://images.patolojiatlasi.com/template/HE.html")
#| label: template_screenshot
#| fig-cap: "TemplateTR"
knitr::include_graphics("./screenshots/template_screenshot.png")
::: {.content-hidden when-format="html"} TemplateTR :::
::: {.content-visible when-format="pdf"} TemplateTR :::
**templateTR**
[{width="25%"}](https://images.patolojiatlasi.com/template/HE.html) [Tam Ekran Görmek İçin Resmi Tıklayın](https://images.patolojiatlasi.com/template/HE.html)
Mikroskopik görüntüleri inceleyin:
<iframe src="https://images.patolojiatlasi.com/template/HE.html" style="height:600px;width:100%;" data-external="1"></iframe>
asis, echo = (language == "TR")
**templateTR**
[{width="25%"}](https://images.patolojiatlasi.com/template/HE_annotated.html) [İşaretlenmiş mikroskopik görüntüleri Tam Ekran Görmek İçin Resmi Tıklayın](https://images.patolojiatlasi.com/template/HE_annotated.html)
İşaretlenmiş mikroskopik görüntüleri inceleyin:
<iframe src="https://images.patolojiatlasi.com/template/HE_annotated.html" style="height:600px;width:100%;" data-external="1"></iframe>
asis, echo = (language == "TR")
<button id="tani-case-template-btn">Tanıyı Göster</button>
<div id="answer-template" style="display: none;">templateTR</div>
<script>
const showAnswer-templateBtn = document.getElementById('tani-case-template-btn');
const answer-template = document.getElementById('answer-template');
showAnswer-templateBtn.addEventListener('click', () => {
if (answer-template.style.display === 'none') {
answer-template.style.display = 'block';
showAnswer-templateBtn.textContent = 'Tanıyı Gizle';
} else {
answer-template.style.display = 'none';
showAnswer-templateBtn.textContent = 'Tanıyı Göster';
}
});
</script>
asis, echo = ((language=="TR") & (output_type=="html"))
{{< video https://www.youtube.com/embed/ >}}
asis, echo = ((language=="TR") & (output_type!="html"))
[https://www.youtube.com/watch?v=](https://www.youtube.com/watch?v=)
**templateEN**
[{width="25%"}](https://images.patolojiatlasi.com/template/HE.html) [Click for Full Screen WSI](https://images.patolojiatlasi.com/template/HE.html)
See Microscopy with viewer:
<iframe src="https://images.patolojiatlasi.com/template/HE.html" style="height:600px;width:100%;" data-external="1"></iframe>
asis, echo = (language == "EN")
**templateEN**
[{width="25%"}](https://images.patolojiatlasi.com/template/HE_annotated.html) [Click for Full Screen Annotated WSI](https://images.patolojiatlasi.com/template/HE_annotated.html)
See Annotated Microscopy with viewer:
<iframe src="https://images.patolojiatlasi.com/template/HE_annotated.html" style="height:600px;width:100%;" data-external="1"></iframe>
asis, echo = (language == "EN")
<button id="dx-case-template-btn">Show the Diagnosis</button>
<div id="answer-template" style="display: none;">templateEN</div>
<script>
const showAnswer-templateBtn = document.getElementById('dx-case-template-btn');
const answer-template = document.getElementById('answer-template');
showAnswer-templateBtn.addEventListener('click', () => {
if (answer-template.style.display === 'none') {
answer-template.style.display = 'block';
showAnswer-templateBtn.textContent = 'Hide the Diagnosis';
} else {
answer-template.style.display = 'none';
showAnswer-templateBtn.textContent = 'Show the Diagnosis';
}
});
</script>
r, eval=TRUE, echo=FALSE, include=FALSE, error=TRUE
if (!file.exists("./screenshots/template_screenshot.png")) {
url <- "https://img.youtube.com/vi/U9glkfQLTm4/maxresdefault.jpg"
download.file(url, destfile = "./screenshots/template_screenshot.png", mode = "wb")
}
**TemplateTR**
[{width="25%"}](https://www.youtube.com/watch?v=) [Video İçin Tıklayın](https://www.youtube.com/watch?v=)
asis, echo = ((language=="EN") & (output_type=="html"))
{{< video https://www.youtube.com/embed/ >}}
asis, echo = ((language=="EN") & (output_type!="html"))
[https://www.youtube.com/watch?v=](https://www.youtube.com/watch?v=)
=html
<iframe src="https://images.patolojiatlasi.com/template/HE.html" style="height:600px;width:100%;" data-external="1"></iframe>