Merge brainreg-napari into brainreg

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+ignore = E203, E231, W503, E722
+max-line-length = 79
+exclude = __init__.py,build,.eggs

.github/workflows/test_and_deploy.yml

@@ -35,18 +35,22 @@ jobs:
           python-version: "3.10"
         - os: windows-latest
           python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.8"
 
     steps:
       - name: Cache atlases
         uses: actions/cache@v3
         with:
             path: ~/.brainglobe
             key: atlases
-      - uses: neuroinformatics-unit/actions/test@v2
+
+      - name: Setup QT libraries
+        uses: tlambert03/setup-qt-libs@v1
+
+      - name: Run tests
+        uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          use-xvfb: true
 
   test-with-conda:
     needs: [linting, manifest]

.gitignore

@@ -2,7 +2,7 @@
 *.conf.custom
 
 # Byte-compiled / optimized / DLL files
-__pycache__/
+**/__pycache__/
 *.py[cod]
 *$py.class
 
@@ -122,3 +122,4 @@ tests/data/test_output
 
 
 *.DS_Store
+pip-wheel-metadata/

.napari/config.yml

@@ -0,0 +1,7 @@
+labels:
+  ontology: EDAM-BIOIMAGING:alpha06
+  terms:
+  - Image registration
+  - Affine registration
+  - Multi-channel
+summary: Multi-atlas whole-brain microscopy registration

BR-CORE-README.md

@@ -0,0 +1,177 @@
+[![Python Version](https://img.shields.io/pypi/pyversions/brainreg.svg)](https://pypi.org/project/brainreg)
+[![PyPI](https://img.shields.io/pypi/v/brainreg.svg)](https://pypi.org/project/brainreg)
+[![Wheel](https://img.shields.io/pypi/wheel/brainreg.svg)](https://pypi.org/project/brainreg)
+[![Development Status](https://img.shields.io/pypi/status/brainreg.svg)](https://github.com/brainglobe/brainreg)
+[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainreg/tests)](
+    https://github.com/brainglobe/brainreg/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainreg/branch/master/graph/badge.svg?token=FbPgwBIGnd)](https://codecov.io/gh/brainglobe/brainreg)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+
+# brainreg
+
+brainreg is an update to
+[amap](https://github.com/SainsburyWellcomeCentre/amap_python) (itself a port
+of the [original Java software](https://www.nature.com/articles/ncomms11879))
+to include multiple registration backends, and to support the many atlases
+provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).
+
+Documentation can be found [here](https://brainglobe.info/documentation/brainreg/index.html).
+
+For segmentation of bulk structures in 3D space
+(e.g. injection sites, Neuropixels probes), please see
+[brainreg-segment](https://github.com/brainglobe/brainreg-segment).
+
+**N.B. There is also a [napari plugin](https://github.com/brainglobe/brainreg-napari) if you'd rather use brainreg with a graphical user interface. Currently this interface is slightly limited compared to the command line tool**
+
+This software is at a very early stage, and was written with our data in mind.
+Over time we hope to support other data types/formats. If you have any issues, please get in touch [on the forum](https://forum.image.sc/tag/brainglobe) or by
+[raising an issue](https://github.com/brainglobe/brainreg/issues).
+
+## Details
+
+The aim of brainreg is to register the template brain
+ (e.g. from the [Allen Reference Atlas](https://mouse.brain-map.org/static/atlas))
+  to the sample image. Once this is complete, any other image in the template
+  space can be aligned with the sample (such as region annotations, for
+  segmentation of the sample image). The template to sample transformation
+  can also be inverted, allowing sample images to be aligned in a common
+  coordinate space.
+
+To do this, the template and sample images are filtered, and then registered in
+a three step process (reorientation, affine registration, and freeform
+registration.) The resulting transform from template to standard space is then
+applied to the atlas.
+
+Full details of the process are in the
+[original aMAP paper](https://www.nature.com/articles/ncomms11879).
+![reg_process](https://user-images.githubusercontent.com/13147259/143553945-a046e918-7614-4211-814c-fc840bb0159d.png)
+
+**Overview of the registration process**
+
+## Installation
+
+```bash
+pip install brainreg[napari]
+```
+
+To only install the command line tool with no GUI (e.g. to run brainreg on an HPC cluster), just run:
+
+```bash
+pip install brainreg
+```
+
+**N.B. If you are using macOS, please run `conda install -c conda-forge niftyreg` to ensure all dependencies are installed.**
+
+## Usage
+
+### Basic usage
+
+```bash
+brainreg /path/to/raw/data /path/to/output/directory -v 5 2 2 --orientation psl
+```
+
+## Arguments
+
+### Mandatory
+
+* Path to the directory of the images. (Can also be a text file pointing to the files\)
+* Output directory for all intermediate and final results
+
+**You must also specify the voxel sizes, see [Specifying voxel size](https://brainglobe.info/documentation/general/image-definition.html#voxel-sizes)**
+
+### Additional options
+
+* `-a` or `--additional` Paths to N additional channels to downsample to the same coordinate space.
+* `--sort-input-file` If set to true, the input text file will be sorted using natural sorting. This means that the file paths will be sorted as would be expected by a human and not purely alphabetically.
+* `--brain_geometry` Can be one of `full` (default) for full brain registration, `hemisphere_l` for left hemisphere data-set and `hemisphere_r` for right hemisphere data-set.
+
+#### Misc options
+
+* `--n-free-cpus` The number of CPU cores on the machine to leave unused by the program to spare resources.
+* `--debug` Debug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues.
+* `--save-original-orientation` Option to save the registered atlas with the same orientation as the input data.
+
+### Atlas
+
+By default, brainreg will use the 25um version of the [Allen Mouse Brain Atlas](https://mouse.brain-map.org/). To use another atlas \(e.g. for another species, or another resolution\), you must use the `--atlas` flag, followed by the string describing the atlas, e.g.:
+
+```bash
+--atlas allen_mouse_50um
+```
+
+_To find out which atlases are available, once brainreg is installed, please run `brainglobe list`. The name of the resulting atlases is the string to pass with the `--atlas` flag._
+
+### Registration backend
+
+To change the registration algorithm used, use the `--backend` flag. The default is `niftyreg` as that is currently the only option.
+
+### Input data orientation
+
+If your data does not match the [brainglobe](https://github.com/brainglobe) default orientation \(the origin voxel is the most anterior, superior, left-most voxel, then you must specify the orientation by using the `--orientation` flag. What follows must be a string in the [bg-space](https://github.com/brainglobe/bg-space) "initials" form, to describe the origin voxel.
+
+If the origin of your data \(first, top left voxel\) is the most anterior, superior, left part of the brain, then the orientation string would be "asl" \(anterior, superior, left\), and you would use:
+
+```bash
+--orientation asl
+```
+
+### Registration options
+
+To change how the actual registration performs, see [Registration parameters](https://brainglobe.info/documentation/brainreg/user-guide/parameters.html)
+
+Full command-line arguments are available with `brainreg -h`, but please
+[get in touch](mailto:[email protected]?subject=brainreg) if you have any questions.
+
+### Visualisation
+
+brainreg comes with a plugin ([brainglobe-napari-io](https://github.com/brainglobe/brainglobe-napari-io)) for [napari](https://github.com/napari/napari) to view your data
+
+##### Sample space
+
+Open napari and drag your brainreg output directory (the one with the log file) onto the napari window.
+
+Various images should then open, including:
+
+* `Registered image` - the image used for registration, downsampled to atlas resolution
+* `atlas_name` - e.g. `allen_mouse_25um` the atlas labels, warped to your sample brain
+* `Boundaries` - the boundaries of the atlas regions
+
+If you downsampled additional channels, these will also be loaded.
+
+Most of these images will not be visible by default. Click the little eye icon to toggle visibility.
+
+_N.B. If you use a high resolution atlas (such as `allen_mouse_10um`), then the files can take a little while to load._
+
+![sample_space](https://raw.githubusercontent.com/brainglobe/napari-brainreg/master/resources/sample_space.gif)
+
+##### Atlas space
+
+`napari-brainreg` also comes with an additional plugin, for visualising your data
+in atlas space.
+
+This is typically only used in other software, but you can enable it yourself:
+
+* Open napari
+* Navigate to `Plugins` -> `Plugin Call Order`
+* In the `Plugin Sorter` window, select `napari_get_reader` from the `select hook...` dropdown box
+* Drag `brainreg_standard` (the atlas space viewer plugin) above `brainreg` (the normal plugin) to ensure that the atlas space plugin is used preferentially.
+
+### Contributing
+
+Contributions to brainreg are more than welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).
+
+### Citing brainreg
+
+If you find brainreg useful, and use it in your research, please let us know and also cite the paper:
+
+> Tyson, A. L., Vélez-Fort, M.,  Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T.,  Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)
+
+Please also cite aMAP (the original pipeline from which this software is based):
+
+>Niedworok, C.J., Brown, A.P.Y., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M. and Margrie, T.W., (2016). AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications. 7, 1–9. <https://doi.org/10.1038/ncomms11879>
+
+Lastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:
+
+>Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, <https://doi.org/10.21105/joss.02668>
+
+**Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!**

BR-NAPARI-README.md

@@ -0,0 +1,75 @@
+[![Python Version](https://img.shields.io/pypi/pyversions/brainreg-napari.svg)](https://pypi.org/project/brainreg-napari)
+[![PyPI](https://img.shields.io/pypi/v/brainreg-napari.svg)](https://pypi.org/project/brainreg-napari)
+[![Wheel](https://img.shields.io/pypi/wheel/brainreg-napari.svg)](https://pypi.org/project/brainreg-napari)
+[![Development Status](https://img.shields.io/pypi/status/brainreg-napari.svg)](https://github.com/brainglobe/brainreg-napari)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+[![codecov](https://codecov.io/gh/brainglobe/brainreg-napari/branch/master/graph/badge.svg?token=HEBXJPLD2S)](https://codecov.io/gh/brainglobe/brainreg-napari)
+
+# brainreg-napari
+
+Napari plugin to run [brainreg](https://github.com/brainglobe/brainreg),
+developed by [Stephen Lenzi](https://github.com/stephenlenzi).
+
+## Installation
+
+```bash
+pip install brainreg-napari
+```
+
+## Usage
+
+Documentation and tutorials for the plugin can be found [here](https://brainglobe.info/documentation/brainreg/index.html).
+
+For segmentation of bulk structures in 3D space
+(e.g. injection sites, Neuropixels probes), please see
+[brainreg-segment](https://github.com/brainglobe/brainreg-segment).
+
+This software is at a very early stage, and was written with our data in mind.
+Over time we hope to support other data types/formats. If you have any issues, please get in touch [on the forum](https://forum.image.sc/tag/brainglobe) or by
+[raising an issue](https://github.com/brainglobe/brainreg/issues).
+
+## Details
+
+brainreg is an update to
+[amap](https://github.com/SainsburyWellcomeCentre/amap-python) (itself a port
+of the [original Java software](https://www.nature.com/articles/ncomms11879))
+to include multiple registration backends, and to support the many atlases
+provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).
+
+The aim of brainreg is to register the template brain
+ (e.g. from the [Allen Reference Atlas](https://mouse.brain-map.org/static/atlas))
+  to the sample image. Once this is complete, any other image in the template
+  space can be aligned with the sample (such as region annotations, for
+  segmentation of the sample image). The template to sample transformation
+  can also be inverted, allowing sample images to be aligned in a common
+  coordinate space.
+
+To do this, the template and sample images are filtered, and then registered in
+a three step process (reorientation, affine registration, and freeform
+registration.) The resulting transform from template to standard space is then
+applied to the atlas.
+
+Full details of the process are in the
+[original aMAP paper](https://www.nature.com/articles/ncomms11879).
+![reg_process](https://user-images.githubusercontent.com/13147259/143553945-a046e918-7614-4211-814c-fc840bb0159d.png)
+**Overview of the registration process**
+
+## Contributing
+
+Contributions to brainreg-napari are more than welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).
+
+### Citing brainreg
+
+If you find brainreg useful, and use it in your research, please let us know and also cite the paper:
+
+> Tyson, A. L., Vélez-Fort, M.,  Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T.,  Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867 [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)
+
+Please also cite aMAP (the original pipeline from which this software is based):
+
+>Niedworok, C.J., Brown, A.P.Y., Jorge Cardoso, M., Osten, P., Ourselin, S., Modat, M. and Margrie, T.W., (2016). AMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data. Nature Communications. 7, 1–9. <https://doi.org/10.1038/ncomms11879>
+
+Lastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:
+
+>Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, <https://doi.org/10.21105/joss.02668>
+
+**Don't forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!**