From 0070d50fe95e41e92539ea022cbdd201bf8a65f1 Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Tue, 8 Oct 2024 08:45:46 +0200
Subject: [PATCH] start structuring documentation better

---
 docs/modules/image/multi_channel_image.md          | 14 ++++++++++++++
 docs/modules/persistence/.pages                    |  4 ++++
 .../general_overview.md}                           |  0
 docs/modules/persistence/image_data.md             |  4 ++++
 docs/modules/persistence/msi_data.md               |  1 +
 mkdocs.yml                                         |  1 +
 pyproject.toml                                     |  1 +
 7 files changed, 25 insertions(+)
 create mode 100644 docs/modules/image/multi_channel_image.md
 create mode 100644 docs/modules/persistence/.pages
 rename docs/modules/{persistence.md => persistence/general_overview.md} (100%)
 create mode 100644 docs/modules/persistence/image_data.md
 create mode 100644 docs/modules/persistence/msi_data.md

diff --git a/docs/modules/image/multi_channel_image.md b/docs/modules/image/multi_channel_image.md
new file mode 100644
index 0000000..7521a2e
--- /dev/null
+++ b/docs/modules/image/multi_channel_image.md
@@ -0,0 +1,14 @@
+## MultiChannelImage class
+This class makes our code a bit more standardized on how multi-channel images are handled internally.
+We use Xarray for the representation of the data and basically provide a wrapper around it providing reusable blocks of common functionality.
+
+The basic convention is to use the dimensions $(c, y, x)$ for the channel, $y$ and $x$ dimensions, respectively.
+The channels have coordinates in the DataArray, describing the channel names.
+
+### Flat representation
+
+TODO To be described, since it is a bit tricky with the whole multi-index support.
+
+### API Reference
+
+... depiction.image.
diff --git a/docs/modules/persistence/.pages b/docs/modules/persistence/.pages
new file mode 100644
index 0000000..7aaa7ae
--- /dev/null
+++ b/docs/modules/persistence/.pages
@@ -0,0 +1,4 @@
+nav:
+  - general_overview.md
+  - msi_data.md
+  - ...
diff --git a/docs/modules/persistence.md b/docs/modules/persistence/general_overview.md
similarity index 100%
rename from docs/modules/persistence.md
rename to docs/modules/persistence/general_overview.md
diff --git a/docs/modules/persistence/image_data.md b/docs/modules/persistence/image_data.md
new file mode 100644
index 0000000..b167178
--- /dev/null
+++ b/docs/modules/persistence/image_data.md
@@ -0,0 +1,4 @@
+# Image data
+## Format: OME-TIFF
+
+## Format: NetCDF4
diff --git a/docs/modules/persistence/msi_data.md b/docs/modules/persistence/msi_data.md
new file mode 100644
index 0000000..8e11526
--- /dev/null
+++ b/docs/modules/persistence/msi_data.md
@@ -0,0 +1 @@
+# MSI Data
diff --git a/mkdocs.yml b/mkdocs.yml
index 33b66df..5ca00a6 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -36,3 +36,4 @@ plugins:
             show_symbol_type_heading: yes
             show_source: no
             members_order: alphabetical
+  - awesome-pages
diff --git a/pyproject.toml b/pyproject.toml
index 4227605..e81c6d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,6 +84,7 @@ doc = [
     "mkdocs",
     "mkdocs-material",
     "mkdocstrings[python]",
+    "mkdocs-awesome-pages-plugin",
 ]
 apps = [
     "bfabric @ git+https://github.com/fgcz/bfabricPy.git@main"