- various fixes

README.md

@@ -1,12 +1,14 @@
 # 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, but without loading the whole
-image into memory, reading from the file only when needed. Some metadata is read
+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.
@@ -23,6 +25,7 @@ pip install ndbioimage
 ```
 
 ### Installation with option to write mp4 or mkv:
+
 Work in progress! Make sure ffmpeg is installed.
 
 ```
@@ -30,6 +33,7 @@ pip install ndbioimage[write]
 ```
 
 ## Usage
+
 ### Python
 
 - Reading an image file and plotting the frame at channel=2, time=1
@@ -60,7 +64,6 @@ with Imread('image_file.tif', axes='cztyx') as im:
 
 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
 
 ```
@@ -71,36 +74,45 @@ with Imread('image_file.tif', axes='cztyx') as im:
 ```
 
 ### Rust
-```
-use ndarray::Array2;
-use ndbioimage::Reader;
 
-let path = "/path/to/file";
-let reader = Reader::new(&path, 0)?;
-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>");
+```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(())
 }
-let xml = reader.get_ome_xml().unwrap();
-println!("{}", xml);
 ```
 
-``` 
-use ndarray::Array2;
-use ndbioimage::Reader;
+```rust
+use ndbioimage::{DynReader, Reader};
 
-let path = "/path/to/file";
-let reader = Reader::new(&path, 0)?;
-let view = reader.view();
-let view = view.max_proj(3)?;
-let array = view.as_array::<u16>()?
+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 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
+```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