Improved docs content and updated configuration

.pre-commit-config.yaml

@@ -1,11 +1,12 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: check-yaml # checks for correct yaml syntax for github actions ex.
+        args: ['--unsafe']
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: v0.0.290
     hooks:

docs/code_example.md

@@ -1,9 +1,11 @@
 # Code example
 
 These code snippets walk you through a small stitching workflow consisting of
-1) Preparing the input image data and metadata (tile positions, spacing, channels)
-2) Registering the tiles
-3) Stitching / fusing the tiles
+
+  1. Preparing the input image data and metadata (tile positions, spacing, channels)
+  2. Registering the tiles
+  3. Stitching / fusing the tiles
+
 
 ### 1) Prepare data for stitching
 

docs/data_formats.md

@@ -1,21 +1,63 @@
 # Data formats
 
-For use with `multiview-stitcher`, data needs to be transformed into a [modified `multiscaleimage.MultiscaleImage`](./objects/#image).
+!!! note
+    `multiview-stitcher` works with any numpy-like input arrays. Therefore, as long as the data can be read into a numpy array, it can be used with `multiview-stitcher`.
 
-## TIFF
+For attaching metadata to arrays, multiview-stitcher works with [SpatialImage](https://github.com/spatial-image/spatial-image) objects (with additional transform matrices attached). They can be constructed from Numpy, Dask or CuPy arrays as such:
 
-Manual reading of tif files is supported with a convenience function.
+```python
+from multiview_stitcher import spatial_image_utils as si_utils
+sim = si_utils.get_sim_from_array(
+    tile_array,
+    dims=["c", "y", "x"],
+    scale={'y': 0.5, 'x': 0.5},
+    translation={"y": 30, "x": 50},
+    transform_key="stage_metadata",
+    c_coords=['DAPI', 'GFP'],
+)
+```
 
-## CZI
+A multiscale version of this object is represented by instances of [MultiscaleSpatialImage](https://github.com/spatial-image/multiscale-spatial-image), which can be created as such:
 
-Mosaic czi file support thanks to [aicsimageio].
+```python
+from multiview_stitcher import msi_utils
+msim = msi_utils.get_msim_from_sim(sim, scale_factors=[2, 4])
+```
 
-## LIF
+The following code can be used to extract a given scale from a multiscale image:
 
-Mosaic lif file support thanks to [aicsimageio].
+```python
+sim = msi_utils.get_sim_from_msim(msim, scale="scale0")
+```
 
-## NGFF
 
-Support provided by `multiscaleimage.MultiscaleImage`.
+## OME-Zarr
 
-The latest NGFF spec does not fully support the transformations required for stitching applications (yet). Therefore, `multiview-stitcher` currently defines its own data format, see [here](features/Coordinate systems).
+!!! note
+    NGFF 0.4 (the latest OME-Zarr standard) currently only supports translation transformations. Therefore, affine transformations cannot yet be stored in OME-Zarr files.
+
+Some support for reading and writing OME-Zarrs is provided by [multiscaleimage.MultiscaleImage](https://github.com/spatial-image/multiscale-spatial-image).
+
+Further, `multiview_stitcher.ngff_utils` provides some convenience functions for reading and writing OME-Zarrs using [`ngff-zarr`](https://github.com/thewtex/ngff-zarr).
+
+
+## Further file formats
+
+[`bioio`](https://github.com/bioio-devs/bioio) is a very convenient library for reading a large variety of image files and it includes support for lazy loading. Here's example code of how to use `bioio` to load an image file into a tile compatible with `multiview-stitcher`:
+
+```python
+import bioio
+from multiview_stitcher import spatial_image_utils as si_utils
+
+# use bioio to load the image as a xarray.DataArray
+bioio_xr = BioImage("my_file.tiff").get_xarray_dask_stack().squeeze()
+
+sim = si_utils.get_sim_from_array(
+    bioio_xr.data,
+    dims=bioio_xr.dims,
+    scale=si_utils.get_spatial_dims_from_sim(bioio_xr),
+    translation=si_utils.get_origin_from_sim(bioio_xr),
+    c_coords=bioio_xr.coords["c"].values,
+    transform_key="stage_metadata",
+)
+```

docs/docs_requirements.txt

@@ -1,39 +1,84 @@
-astor==0.8.1
-Babel==2.13.0
-certifi==2023.7.22
-charset-normalizer==3.3.0
+appnope==0.1.4
+asttokens==2.4.1
+attrs==24.2.0
+babel==2.16.0
+backcall==0.2.0
+beautifulsoup4==4.12.3
+bleach==6.1.0
+certifi==2024.8.30
+charset-normalizer==3.4.0
 click==8.1.7
 colorama==0.4.6
+decorator==5.1.1
+defusedxml==0.7.1
+docopt==0.6.2
+EditorConfig==0.12.4
+executing==2.1.0
+fastjsonschema==2.20.0
 ghp-import==2.1.0
-griffe==0.36.5
-idna==3.4
-Jinja2==3.1.3
-Mako==1.2.4
-Markdown==3.5
-MarkupSafe==2.1.3
+griffe==1.4.1
+idna==3.10
+importlib_metadata==8.5.0
+importlib_resources==6.4.5
+ipython==8.12.3
+jedi==0.19.1
+Jinja2==3.1.4
+jsbeautifier==1.15.1
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter_client==8.6.3
+jupyter_core==5.7.2
+jupyterlab_pygments==0.3.0
+Markdown==3.7
+MarkupSafe==3.0.1
+matplotlib-inline==0.1.7
 mergedeep==1.3.4
-mike==1.1.2
-mkdocs==1.5.3
-mkdocs-autorefs==0.5.0
-mkdocs-material==9.4.5
-mkdocs-material-extensions==1.2
-mkdocstrings==0.23.0
-mkdocstrings-python==1.7.3
-mkgendocs==0.9.2
-packaging==23.2
-paginate==0.5.6
-pathspec==0.11.2
-pip==23.3
-platformdirs==3.11.0
-Pygments==2.16.1
-pymdown-extensions==10.3
-python-dateutil==2.8.2
-PyYAML==6.0.1
+mike==2.1.3
+mistune==3.0.2
+mkdocs==1.6.1
+mkdocs-autorefs==1.2.0
+mkdocs-get-deps==0.2.0
+mkdocs-material==9.5.41
+mkdocs-material-extensions==1.3.1
+mkdocs-mermaid2-plugin==1.1.1
+mkdocstrings==0.26.2
+mkdocstrings-python==1.12.1
+nbclient==0.10.0
+nbconvert==7.16.4
+nbformat==5.10.4
+packaging==24.1
+paginate==0.5.7
+pandocfilters==1.5.1
+parso==0.8.4
+pathspec==0.12.1
+pexpect==4.9.0
+pickleshare==0.7.5
+pipreqs==0.5.0
+platformdirs==4.3.6
+prompt_toolkit==3.0.48
+ptyprocess==0.7.0
+pure_eval==0.2.3
+Pygments==2.18.0
+pymdown-extensions==10.11.2
+pyparsing==3.2.0
+python-dateutil==2.9.0.post0
+PyYAML==6.0.2
 pyyaml_env_tag==0.1
-regex==2023.10.3
-requests==2.31.0
-setuptools==65.5.1
+pyzmq==26.2.0
+referencing==0.35.1
+regex==2024.9.11
+requests==2.32.3
+rpds-py==0.20.0
 six==1.16.0
-urllib3==2.0.7
+soupsieve==2.6
+stack-data==0.6.3
+tinycss2==1.3.0
+tornado==6.4.1
+traitlets==5.14.3
+urllib3==2.2.3
 verspec==0.1.0
-watchdog==3.0.0
+watchdog==5.0.3
+wcwidth==0.2.13
+webencodings==0.5.1
+yarg==0.1.9
+zipp==3.20.2

docs/features.md

@@ -2,66 +2,74 @@
 
 Below is a list of features which are either already implemented or are on the roadmap.
 
+## Dimensionality
+- [x] 2D
+- [x] 3D
+
 ## Registration
 
-### Pairwise registration
-- [x] phase correlation
+### Pairwise registration methods
+- [x] Phase correlation
 - [x] ANTsPy
-- [ ] elastix (`itk-elastix`) will be used for up to affine transformations
-- [ ] bead alignment
-- [ ] phase correlation for rotation + translation
+- [ ] Elastix (`itk-elastix`)
+- [ ] Bead alignment
+- [ ] Phase correlation for rotation + translation
 
-### Group registration
+### Global paramater resolution
 
-- [x] registration graph construction
-- [x] automatic determination of suitable reference view
-- [x] parameter concatenation along graph connectivity paths
-- [ ] global optimization of registration parameters from (potentially overdetermined) pairwise transforms
-- [ ] drift correction / temporal alignment
+- [x] Graph construction
+- [x] Automatic determination of reference view
+- [x] Parameter concatenation along graph connectivity paths
+- [x] Global optimization of registration parameters from (potentially overdetermined) pairwise transforms
 
 ## Transformations
 
-- [x] chunked `dask_image.ndinterp.affine_transform`
-- [ ] cupy-based transform
-- [ ] chaining transformations instead of working with static coordinate systems
+- [x] Chunked `dask_image.ndinterp.affine_transform`
+- [ ] Cupy-based transform
+- [ ] Chaining transformations instead of working with static coordinate systems
 
 ## Fusion
 
-- [x] chunkwise
-- [ ] modular API to plug in different fusion functions including:
-- Supported weights:
-  - [x] blending
-  - [x] content-based
-- Supported fusion methods:
-  - [x] weighted average
-  - [ ] multi-view deconvolution
-- [ ] fusion of overlapping label maps
-- [ ] GPU compatibility
-
-## Data formats
-- [x] zarr based intermediate file format for reading and writing, compatible with parallel dask workflows: [multiscale-spatial-data](https://github.com/spatial-image/multiscale-spatial-image)
-- [-] czi input
-  - [x] multi-positioning
-  - [ ] light-sheet
-- [x] tif input
-- [x] tif writing
+### General
+
+- [x] Modular API to plug in different fusion and weight functions
+- [ ] Support for fusion label maps
+- [ ] Cupy-based fusion
+
+### Supported fusion methods:
+
+  - [x] Weighted average
+  - [x] Maximum intensity projection
+  - [ ] Multi-view deconvolution
+
+### Supported weights:
+
+  - [x] Linear blending
+  - [x] Content-based
+
+## Supported data formats
+
+- [x] OME-Zarr
+- [x] Zarr based intermediate file format for reading and writing, compatible with parallel dask workflows: [multiscale-spatial-data](https://github.com/spatial-image/multiscale-spatial-image)
+- CZI input
+  - [x] Multi-positioning
+  - [ ] Light-sheet
+- [x] TIF input
+- [x] TIF writing
 
 ## Visualization
 
 ### Napari
-See [napari-stitcher](github.com/napari-stitcher).
+
+See [napari-stitcher](github.com/multiview-stitcher/napari-stitcher).
+
 - [x] 2D slice view: multiscale rendering
 - 3D rendered view:
-  - [x] lowest scale
-  - [ ] chunked rendering
-- [x] colormaps optimized for highlighting differences between overlapping views
-
-## Dimensionality
-- [x] 2d
-- [x] 3d
+  - [x] Lowest scale
+  - [ ] Chunked rendering
+- [x] Colormaps optimized for highlighting differences between overlapping views
 
 ## Supported usage modes
-- [x] as a library to build custom reconstruction workflows
-- [ ] predefined workflows/pipelines adapted to specific setups
-- [(x)] napari plugin
-- [ ] processing on HPC
+- [x] As a library to build custom reconstruction workflows
+- [x] Napari plugin
+- [ ] Convenience function for processing on HPC

docs/implementation_details.md

@@ -69,4 +69,4 @@ Further fusion weights can be obtained by the weight calculation function specif
 
 ### Content based fusion
 
-To improve multi-view fusion in the context of strongly scattering samples, [content-based fusion](https://preibischlab.mdc-berlin.de/assets/spim_congeal_2008.pdf) turns out to be helpful. This fusion method is available in `multiview-stitcher` by using `multiview_stitcher.fusion.fuse(..., fusion_func=fusion.weighted_average_fusion, weights_method=weights.content_based)` (see [above](###Fusion-framework)).
+To improve multi-view fusion in the context of strongly scattering samples, [content-based fusion](https://preibischlab.mdc-berlin.de/assets/spim_congeal_2008.pdf) turns out to be helpful. This fusion method is available in `multiview-stitcher` by using `multiview_stitcher.fusion.fuse(..., fusion_func=fusion.weighted_average_fusion, weights_method=weights.content_based)`.

docs/index.md

@@ -11,12 +11,14 @@ It leverages [`xarray`](https://github.com/xarray) in combination with [`spatial
 
 ### Napari plugin
 
-There's an associated napari plugin: [napari-stitcher](https://github.com/napari-stitcher).
+There's an associated napari plugin: [napari-stitcher](https://github.com/multiview-stitcher/napari-stitcher).
 
-### Work in progress
-
-WARNING: THIS IS WORK IN PROGRESS, THE API IS NOT YET STABLE.
 
 ### Previous work
 
-`multiview-stitcher` improves and replaces [MVRegFus](https://github.com/multiview-stitcher/MVRegFus).
+`multiview-stitcher` improves and replaces [MVRegFus](https://github.com/m-albert/MVRegFus).
+
+
+!!! note
+
+    `multiview-stitcher` is a work in progress. The API is not yet stable.