- readme

README.md

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+# ndbioimage
+
+[![Pytest](https://github.com/pomppervova/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/pomppervova/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/)
+
+Exposes (bio) images as a numpy ndarray-like object (Python) or a struct that can be sliced like an ndarray Array
+(Rust), 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.
+
+To transition to semver, versions before 0.1.0 were yanked from crates.io.
+
+## Installation
+
+```sh
+pip install ndbioimage
+```
+
+### Installation with option to write mp4 or mkv:
+
+Work in progress! Make sure ffmpeg is installed.
+
+```sh
+pip install ndbioimage[write]
+```
+
+## Usage
+
+### Python
+
+- Reading an image file and plotting the frame at channel=2, time=1
+
+```python
+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
+
+```python
+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
+
+```python
+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
+
+```python
+from ndbioimage import Imread
+import numpy as np
+with Imread('image_file.tif', axes='cztyx') as im:
+    array = np.asarray(im[0, 0])
+```
+
+### Rust
+
+```rust
+use ndarray::Array2;
+use ndbioimage::{DynReader, Frame, Reader};
+
+fn main() -> Result<(), ndbioimage::error::Error> {
+    let path = "/path/to/file";
+    let reader = DynReader::new(&path, 0, 0)?;
+    println!("shape: {}", reader.shape());
+    let frame = reader.get_frame(0, 0, 0)?;
+    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.metadata()?.to_xml()?;
+    println!("{}", xml);
+    Ok(())
+}
+```
+
+```rust
+use ndbioimage::{DynReader, Reader};
+
+fn main() -> Result<(), ndbioimage::error::Error> {
+    let path = "/path/to/file";
+    let reader = DynReader::new(&path, 0, 0)?;
+    let view = reader.view();
+    let view = view.max_proj(3)?;
+    let array = view.as_array::<u16>()?;
+    println!("{:?}", array.shape());
+    Ok(())
+}
+```
+
+### Command line
+
+```ndbioimage --help```: show help  
+```ndbioimage info image```: show metadata about image  
+```ndbioimage tiff image image.tif -r```: copy image into image.tif, while registering channels  
+```ndbioimage movie image image.mp4 -C cyan lime red``` copy image into image.mp4 (z will be max projected), make channel
+colors cyan lime and red