- implement sliced views, including min, max, sum and mean operations
This commit is contained in:
32
README.md
32
README.md
@@ -74,7 +74,7 @@ use ndarray::Array2;
|
||||
use ndbioimage::Reader;
|
||||
|
||||
let path = "/path/to/file";
|
||||
let reader = Reader::new(&path, 0).unwrap();
|
||||
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) {
|
||||
@@ -86,30 +86,22 @@ let xml = reader.get_ome_xml().unwrap();
|
||||
println!("{}", xml);
|
||||
```
|
||||
|
||||
```
|
||||
use ndarray::Array2;
|
||||
use ndbioimage::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>()?
|
||||
```
|
||||
|
||||
### 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
|
||||
|
||||
Reference in New Issue
Block a user