Merge pull request #44 from oanegros/mask-loading

v1.0.0

.github/workflows/tests.yml

@@ -15,16 +15,16 @@ jobs:
       max-parallel: 4
       fail-fast: false
       matrix:
-        blender-version: ["4.0.0"]
+        blender-version: ["4.1.1"]
         os: [ubuntu-latest, windows-latest, macos-13]
         # os: [ubuntu-latest]
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11.6'
           cache: 'pip'
-      - run: pip install bpy==${{ matrix.blender-version }}
+      # - run: pip install bpy==${{ matrix.blender-version }}
 
       - name: Install poetry
         run: pip install poetry

Makefile

@@ -1,12 +1,14 @@
 test:
-	poetry install --with test
-	poetry pytest -v
+	python -m pip install .
+	pytest -v
+
 
 version := $(shell grep version pyproject.toml | grep -o -E "\b[0-9]+\.[0-9]+\.[0-9]+\b")
 
 template:
 	cd tif2blender/assets/template && zip -r tif2blender.zip ../../../tif2blender
 
+# git clean -dfX
 release:
 	git clean -dfX
 	make template

README.md

@@ -1,54 +1,54 @@
 # tif to blender 
-This is a project building bioimage support for the open source software blender. This currently exists as the Blender add-on `tif loader` which is able to easily load tif files as volumetric objects in Blender. 
-
-This originally started as a script for the [Blender for Biologists workshop](https://github.com/oanegros/Blender_for_Biologists_2023) Because the scope seems to have outgrown this workshop, the development has split off.
+This is a project building bioimage support for the open source software blender. This currently exists as the Blender add-on `tif2blender` which is able to easily load tif files as volumetric objects in Blender. 
 
 Please make some pretty figures with this add-on! 
 If you post using this addon on social media please either tag me (@GrosOane on twitter) or use hashtag `#tif2blender`.
 
+## Video introduction
+
+See the [video introduction](https://youtu.be/TCQojYEYxVo) to the tif2blender add-on on youtube.
+
 <img src="./figures/newprettyside.png" width="600"/>
 
 ## Current Features
-The `tif loader` Blender addon is still under active development, but some notable features are already supported:
+The `tif2blender` Blender addon is still under active development, but some notable features are already supported:
 
-- 3D to 5D (zyx to tzcyx in any axis order) tifs are supported. 
+- up to 5D (up to tzcyx in any axis order) tifs are supported. 
 - Axes order and pixel size will be attempted to be read out automatically
 - Otsu initial volumetric emission material is applied
 - Scale bars are added to the `Geometry Nodes` container of your volumetric data
 
-## Video introduction
 
-See the [video introduction](https://youtu.be/TCQojYEYxVo) to the tif2blender add-on on youtube.
 
 
-## Installing `tif loader`
+## Installing `tif2blender`
 
 Download:
 
-- Download blender from https://www.blender.org/download/. Download Blender 4.0.x for the newest version of tif2blender. Blender 3.5 and 3.6 are also supported in different releases, so please check on the releases page!
+- Download blender from https://www.blender.org/download/. Check the supported blender version next to the release!
 
-- Download the tif loader zip file from the [releases page](https://github.com/oanegros/tif2blender/releases). 
+- Download the tif2blender zip file from the [releases page](https://github.com/oanegros/tif2blender/releases). 
 
 Start blender.
 
-Install the `tif loader` Add-On:
+Install the `tif2blender` Add-On:
 - In Blender go to `Edit > Preferences`
 - Go to `Add-Ons` tab in `Preferences`
 - Press `Install` and give the `tif_loader.zip` file (as .zip)
-- In the added `tif loader` add-on window in `Preferences`: press the tick box to enable, and the arrow to unfold the details
+- In the added `tif2blender` add-on window in `Preferences`: press the tick box to enable, and the arrow to unfold the details
 - in the details press `install tifffile`
 - (if this fails please try restarting blender and seeing if it can then find `tifffile`)
 
-This should create the `tif loader` panel in `Scene Properties`.
+This should create the `tif2blender` panel in `Scene Properties`.
 
-## Using `tif loader`
+## Using `tif2blender`
 Load in tif-files in the file explorer from the panel in `Scene Properties`. 
 
 Loading with preset environment recently had a small bug, fixed on 7th nov 18:45. So either uncheck this or update your tif_loader(see below), if you have this issue. For any other problems, please open an [issue](https://github.com/oanegros/tif2blender/issues).
 
-- The `tif loader` panel should be able to automatically read out your axis order and pixel size, but these can otherwise also manually be entered
+- The `tif2blender` panel should be able to automatically read out your axis order and pixel size, but these can otherwise also manually be entered
 - Any tif stack from zyx to tzcyx (in any axis order) is supported
-- The `tif loader` resaves your tif as a `.vdb` file (in a `blender_volumes` subfolder) and loads this as a volume object in your blender scene, connected to a `Container` object.
+- The `tif2blender` resaves your tif as a `.vdb` file (in a `blender_volumes` subfolder) and loads this as a volume object in your blender scene, connected to a `Container` object.
 - With large files (over 2048 px in an axis), the volumes will be split to avoid blender crashes.
 - With the `Import option: Force Remake` you will force remaking the vdb files, if this is unchecked and the vdb files exist, these will be loaded.
 - With the `Import option: Preset Environment` some default environment variables will be set. These overwrite current other environment settings, but are useful for quickly looking at data:
@@ -57,22 +57,13 @@ Loading with preset environment recently had a small bug, fixed on 7th nov 18:45
   - Sets `Cycles` `Samples` to manageable numbers for volumetric data
   - Sets `View Transform` to `Standard` (the default `Filmic` crunches dynamic range post-render)
 
-Upon load, multiple defaults are applied, but all of these can be changed as granularly as you want:
-- A default `Emission Material` is applied. You can find and edit this in the `Shading` tab when selecting a volume (not the container of the volume):
-  - This takes each channel from an Otsu threshold up. This threshold is set and can be changed in the `Map Range`
-  - This is piped to the `Emission Strength` of the `Volume shader`.
-- A default `Scale bar` is applied. This is implemented as a `Geometry Nodes Modifier` of the `Container` of the volumes. You can find and edit this in the `Geometry Nodes` tab if you have the `Container` selected:
-  - By default this starts at 10 `µm per tick` but this can be changed.
-  - This has many visualization options, default is a thin `grid` with `crosshatch ticks` on the major axes
-  - By default this has `Frontface culling` on, so that this only renders the back axes from the view angle, however, you can also specifically select which axes to draw.
-  - The `crosshatch` ticks can be replaced with any geometry.
+Upon load, multiple defaults are applied, but all of these can be changed as granularly as you want.
 
-More tutorial-like description can be found at [Blender for Biologists](https://github.com/oanegros/Blender_for_Biologists_2023). However, this asssumes a less capable version of `tif loader` that does not apply an initial material, for didactic purposes.
 
-## Updating `tif loader`
-To update the `tif loader` add-on (future versions may have bugfixes, new features) a few steps need to be taken:
+## Updating `tif2blender`
+To update the `tif2blender` add-on (future versions may have bugfixes, new features) a few steps need to be taken:
 - In Blender go to `Edit > Preferences`
-- Go to `Add-Ons` tab in `Preferences` and find the `tif loader` add-on
+- Go to `Add-Ons` tab in `Preferences` and find the `tif2blender` add-on
 - Press `Remove` 
 - Restart Blender
 - Install the new version.