update docs

docosaurus/blog/2023-08-21-r0-4-2/index.md

@@ -0,0 +1,27 @@
+---
+slug: release-0-4-2
+title: Gingerbread | v0.4.2
+authors: [martin]
+tags: [release notes, gingerbread]
+---
+
+Changed all the components of Gingerbread into a single repo and made it into a pypi package.
+
+
+<!-- [Docusaurus blogging features](https://docusaurus.io/docs/blog) are powered by the [blog plugin](https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog).
+
+Simply add Markdown files (or folders) to the `blog` directory.
+
+Regular blog authors can be added to `authors.yml`.
+
+The blog post date can be extracted from filenames, such as:
+
+- `2019-05-30-welcome.md`
+- `2019-05-30-welcome/index.md`
+
+A blog post folder can be convenient to co-locate blog post images: -->
+
+
+<!-- The blog supports tags as well!
+
+**And if you don't want a blog**: just delete this directory, and use `blog: false` in your Docusaurus config. -->

docosaurus/blog/2021-08-26-welcome/index.md → docosaurus/blog/2023-08-21-welcome/index.md

@@ -6,10 +6,12 @@ tags: [welcome, gingerbread, neomedsys, neogate]
 ---
 
 
-![NomedsysLogo](./259079067-c1fb68e7-a618-452b-a40f-518e5fee577a.jpg)
+![NomedsysLogo](./A@1200x.png)
 
 Welcome to the **Gingerbread** blog!
 
+In this blog we will post updates about the projects concerning the researchers.
+
 
 <!-- [Docusaurus blogging features](https://docusaurus.io/docs/blog) are powered by the [blog plugin](https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog).
 

docosaurus/docs/gingerbread/APIreference.md

@@ -0,0 +1,7 @@
+---
+sidebar_position: 2
+---
+
+# API reference
+
+The api reference can be found here 👉 https://neomedsys.github.io/gingerbread_sc/modules.html

docosaurus/docs/gingerbread/_category_.json

@@ -0,0 +1,8 @@
+{
+  "label": "Gingerbread",
+  "position": 2,
+  "link": {
+    "type": "generated-index",
+    "description": "5 minutes to learn the most important Gingerbread concepts."
+  }
+}

docosaurus/docs/gingerbread/quickstart.md

@@ -0,0 +1,53 @@
+---
+sidebar_position: 1
+---
+
+# Quickstart
+
+We are hosting the package on private pypi-server so we need to add a small configuration to the pip command.
+
+## Installation ☕
+
+**Using pip**
+
+For pypi we need to add a small configuration to the pip command. This will prompt you for a username and password, these are given by the NeoMedSys team.
+
+```bash title="~bash"
+pip install --index-url https://pypi.neomodels.app/ gingerbread
+```
+
+**Using poetry**
+
+First we need to add the authentication to poetry, this is done by running the following command.
+
+```bash title="~bash"
+poetry config http-basic.neomedsys <username> <password>
+```
+
+Then we need to add the private pypi-server to the poetry configuration.
+
+```bash title="~bash"
+poetry source add --priority=default neomedsys https://pypi.neomodels.app
+```
+
+Now we can install the package.
+
+```bash title="~bash"
+poetry add gingerbread
+```
+
+## Usage ✌
+
+After installing you can initate a new project by using the command line interface.
+
+**pip**
+```bash title="~bash"
+gingerbread-bake
+```
+
+**poetry**
+```bash title="~bash"
+poetry run gingerbread-bake
+```
+
+This will generate a folder named "gingerbread". This folder will contain the central_processing.py file and a models folder containing example model setup. These files are altered according to the researchers need. The config file needs to be in the format generated.

docosaurus/docs/intro.md

@@ -2,6 +2,29 @@
 sidebar_position: 1
 ---
 
+# Introduction
+
+Hello, my name is Gingerbread, and I am a template enabling researchers to better engage with NeoMedSys. I’ll do my best to walk you through the steps involved in creating a new project and utilizing the template.
+
+When you are ready to begin, click the **Next** button below.
+
+![NomedsysLogo](./225026458-f80a82cc-f019-4b25-ac3e-7d465ebba073.png)
+
+
+# The philosophy
+The project’s guiding principle is to give researchers a straightforward framework that is simple to utilize.
+
+This framework includes built-in MedQuery certifications, eliminating the need to manually add them for every project.
+
+The framework also has the usual packages like poetry, CUDA etc. installed, so you can start working on your project right away.
+
+The framework is also designed to be easily extensible, so you can add your own packages and certifications as you see fit, which in turn will modulerize into the production pipeline.
+
+Another aspect of the framework is that it is easier to have a common understanding of how it all operates both for experiments and in production through regular documentation and code updates.
+
+The idea is also for researchers to add issues in the Github repository if there is any changes they would like to see in the framework, so that the framework can be improved over time and if there are any bugs or limitations.
+
+<!-- 
 # Tutorial Intro
 
 Let's discover **Docusaurus in less than 5 minutes**.
@@ -44,4 +67,4 @@ The `cd` command changes the directory you're working with. In order to work wit
 
 The `npm run start` command builds your website locally and serves it through a development server, ready for you to view at http://localhost:3000/.
 
-Open `docs/intro.md` (this page) and edit some lines: the site **reloads automatically** and displays your changes.
+Open `docs/intro.md` (this page) and edit some lines: the site **reloads automatically** and displays your changes. -->

docosaurus/docs/tutorial-extras/_category_.json → docosaurus/docs/medquery/_category_.json

@@ -1,5 +1,5 @@
 {
-  "label": "Tutorial - Extras",
+  "label": "Medquery",
   "position": 3,
   "link": {
     "type": "generated-index"

docosaurus/docs/medquery/quickstart.md

@@ -0,0 +1,32 @@
+---
+sidebar_position: 1
+---
+
+# Quickstart ✌
+
+:::danger Not ready
+This feature is in alpha and not ready for use.
+:::
+
+Gingerbread comes with medquery and the certificates to access the database already installed.
+
+Here is an example code for downloading data.
+
+```python title="python"
+import data_download as dd
+
+mqd = dd.MedqueryDataDownloader()
+mqd.download_data(
+                project_id="booby",
+                get_affines=True,
+                get_all=True,
+                include_mask=False,
+                batch_size=20
+                )
+```
+
+This will download the data into ./data and add it to a hdf5 file. hdf5 files are storage files that simulates a harddrive. This makes it easier to store and lazy load during training. Check out the documentation here: https://docs.h5py.org/en/stable/
+
+We have also included two functions to convert the hdf5 files to nifti. This is useful if you want to use the data in other software. The functions are hdf5_to_nifti_all and hdf5_to_nifti_single. The first one will convert all the data in the hdf5 file to nifti. The second one will convert a single image.
+
+For more information check out the reference api in the documentation.

docosaurus/docs/neogate/_category_.json

@@ -0,0 +1,7 @@
+{
+  "label": "NeoGate",
+  "position": 2,
+  "link": {
+    "type": "generated-index"
+  }
+}

docosaurus/docs/neogate/info.md

@@ -0,0 +1,8 @@
+---
+sidebar_position: 2
+---
+
+# Overview
+
+
+![NomedsysLogo](./design1.svg)

docosaurus/docs/neogate/quickstart.md

@@ -0,0 +1,53 @@
+---
+sidebar_position: 1
+---
+
+# Quickstart ✌
+
+We are hosting the package on private pypi-server so we need to add a small configuration to the pip command.
+
+# Installation ☕
+
+**Using pip**
+
+For pypi we need to add a small configuration to the pip command. This will prompt you for a username and password, these are given by the NeoMedSys team.
+
+```jsx title="~bash"
+pip install --index-url https://pypi.neomedsys.app/ gingerbread
+```
+
+**Using poetry**
+
+First we need to add the authentication to poetry, this is done by running the following command.
+
+```jsx title="~bash"
+poetry config http-basic.neomedsys <username> <password>
+```
+
+Then we need to add the private pypi-server to the poetry configuration.
+
+```jsx title="~bash"
+poetry source add --priority=default neomedsys https://pypi.neomodels.app
+```
+
+Now we can install the package.
+
+```jsx title="~bash"
+poetry add gingerbread
+```
+
+### Usage
+
+After installing you can initate a new project by using the command line interface.
+
+**pip**
+```jsx title="~bash"
+gingerbread-bake
+```
+
+**poetry**
+```jsx title="~bash"
+poetry run gingerbread-bake
+```
+
+This will generate a folder named "gingerbread". This folder will contain the central_processing.py file and a models folder containing example model setup. These files are altered according to the researchers need. The config file needs to be in the format generated.

docosaurus/docusaurus.config.js

@@ -8,18 +8,18 @@ const darkCodeTheme = require('prism-react-renderer/themes/dracula');
 const config = {
   title: 'NeoMedSys',
   tagline: 'NeoMedSys is cool',
-  favicon: 'img/favicon.png',
+  favicon: 'img/favicon2.png',
 
   // Set the production url of your site here
-  url: 'https://your-docusaurus-test-site.com',
+  url: 'http://gingerbread-sc.vercel.app',
   // Set the /<baseUrl>/ pathname under which your site is served
   // For GitHub pages deployment, it is often '/<projectName>/'
   baseUrl: '/',
 
   // GitHub pages deployment config.
   // If you aren't using GitHub pages, you don't need these.
   organizationName: 'facebook', // Usually your GitHub org/user name.
-  projectName: 'docusaurus', // Usually your repo name.
+  projectName: 'gingerbread', // Usually your repo name.
 
   onBrokenLinks: 'throw',
   onBrokenMarkdownLinks: 'warn',
@@ -70,7 +70,7 @@ const config = {
           src: 'img/favicon.png',
         },
         items: [
-          {to: '/reference', label: 'Reference', position: 'left'},
+          // {to: '/reference', label: 'Reference', position: 'left'},
           {
             type: 'docSidebar',
             sidebarId: 'tutorialSidebar',
@@ -128,7 +128,7 @@ const config = {
             ],
           },
         ],
-        copyright: `Copyright © ${new Date().getFullYear()} My Project, Inc. Built with Docusaurus.`,
+        copyright: `Copyright © ${new Date().getFullYear()} Neomedsys, Gingerbread.`,
       },
       prism: {
         theme: lightCodeTheme,