- change to MIT license

- thread local image reader instances
- add keywords and categories
- add python dependencies
- README

README.md

@@ -1,4 +1,115 @@
 # ndbioimage
+[![Pytest](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
+
 ## Work in progress
 Rust rewrite of python version. Read bio image formats using the bio-formats java package.
-[https://www.openmicroscopy.org/bio-formats/](https://www.openmicroscopy.org/bio-formats/)
+[https://www.openmicroscopy.org/bio-formats/](https://www.openmicroscopy.org/bio-formats/)
+
+Exposes (bio) images as a numpy ndarray-like object, but without loading the whole
+image into memory, reading from the file only when needed. Some metadata is read
+and stored in an [ome](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47) structure.
+Additionally, it can automatically calculate an affine transform that corrects for chromatic aberrations etc. and apply
+it on the fly to the image.
+
+Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything
+[bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
+
+## Installation
+
+```
+pip install ndbioimage
+```
+
+### Installation with option to write mp4 or mkv:
+Work in progress! Make sure ffmpeg is installed.
+
+```
+pip install ndbioimage[write]
+```
+
+## Usage
+### Python
+
+- Reading an image file and plotting the frame at channel=2, time=1
+
+```
+import matplotlib.pyplot as plt
+from ndbioimage import Imread
+with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
+    plt.imshow(im[2, 1])
+```        
+
+- Showing some image metadata
+
+```
+from ndbioimage import Imread
+from pprint import pprint
+with Imread('image_file.tif') as im:
+    pprint(im)
+```
+
+- Slicing the image without loading the image into memory
+
+```
+from ndbioimage import Imread
+with Imread('image_file.tif', axes='cztyx') as im:
+    sliced_im = im[1, :, :, 100:200, 100:200]
+```
+
+sliced_im is an instance of Imread which will load any image data from file only when needed
+
+
+- Converting (part) of the image to a numpy ndarray
+
+```
+from ndbioimage import Imread
+import numpy as np
+with Imread('image_file.tif', axes='cztyx') as im:
+    array = np.asarray(im[0, 0])
+```
+
+### Rust
+```
+use ndarray::Array2;
+use ndbioimage::Reader;
+
+let path = "/path/to/file";
+let reader = Reader::new(&path, 0).unwrap();
+println!("size: {}, {}", reader.size_y, reader.size_y);
+let frame = reader.get_frame(0, 0, 0).unwrap();
+if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
+    println!("{:?}", arr);
+} else {
+    println!("could not convert Frame to Array<i8>");
+}
+let xml = reader.get_ome_xml().unwrap();
+println!("{}", xml);
+```
+
+### Command line
+```ndbioimage --help```: show help  
+```ndbioimage image```: show metadata about image  
+```ndbioimage image -w {name}.tif -r```: copy image into image.tif (replacing {name} with image), while registering channels  
+```ndbioimage image -w image.mp4 -C cyan lime red``` copy image into image.mp4 (z will be max projected), make channel colors cyan lime and red
+
+## Adding more formats
+Readers for image formats subclass AbstractReader. When an image reader is imported, Imread will
+automatically recognize it and use it to open the appropriate file format. Image readers
+are required to implement the following methods:
+
+- staticmethod _can_open(path): return True if path can be opened by this reader
+- \_\_frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file
+
+Optional methods:
+- get_ome: reads metadata from file and adds them to an OME object imported
+  from the ome-types library
+- open(self): maybe open some file handle
+- close(self): close any file handles
+
+Optional fields:
+- priority (int): Imread will try readers with a lower number first, default: 99
+- do_not_pickle (strings): any attributes that should not be included when the object is pickled,
+  for example: any file handles
+
+# TODO
+- more image formats