- python: remove deprecated shape argument

- rust: make frame argument to save more generic

README.md

@@ -14,36 +14,35 @@ makes that very hard anyway.
 - Colormaps
 - Extra tags, globally or frame dependent.
 
+# Python
 ## Installation
-    pip install tiffwrite
+```pip install tiffwrite```
+
 or
 
-- install [rust](https://rustup.rs/)     
+- install [rust](https://rustup.rs/)
+- ``` pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite ```
 
-    
-    pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite
-
-# Usage
-## Write an image stack
+## Usage
+### Write an image stack
     tiffwrite(file, data, axes='TZCXY', dtype=None, bar=False, *args, **kwargs)
 
 - file:         string; filename of the new tiff file.
 - data:         2 to 5D numpy array in one of these datatypes: (u)int8, (u)int16, float32.
 - axes:         string; order of dimensions in data, default: TZCXY for 5D, ZCXY for 4D, CXY for 3D, XY for 2D data.
 - dtype:        string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.
-- bar:          bool; whether or not to show a progress bar.
+- bar:          bool; whether to show a progress bar.
 - args, kwargs: arguments to be passed to IJTiffFile, see below.
 
 
-## Write one frame at a time
-    with IJTiffFile(file, shape, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
+### Write one frame at a time
+    with IJTiffFile(file, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
                     timeinterval=None, **extratags) as tif:
     some loop:
         tif.save(frame, c, z, t)
 
-- file:         string; filename of the new tiff file.
-- shape:        iterable; shape (C, Z, T) of data to be written in file.
-- dtype:        string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.
+- path:         string; path to the new tiff file.
+- dtype:        string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported by Fiji.
 - colors:       iterable of strings; one color per channel, valid colors (also html) are defined in matplotlib.colors.
                     Without colormap BioFormats will set the colors in this order: rgbwcmy.
                     Note that the color green is dark, the usual green is named 'lime' here.
@@ -51,22 +50,24 @@ or
 - pxsize:       float; pixel size im um.
 - deltaz:       float; z slice interval in um.
 - timeinterval: float; time between frames in seconds.
-- extratags:    other tags to be saved, example: Artist='John Doe', Tag4567=[400, 500] or
-                    Copyright=Tag('ascii', 'Made by me'). See tiff_tag_registry.items().
+- compression:  int; zstd compression level: -7 to 22.
+- comment:      str; comment to be saved in tif
+- extratags:    Sequence\[Tag\]; other tags to be saved, example: Tag.ascii(315, 'John Doe') or Tag.ascii(33432, 'Made by me').
+
 
 - frame:        2D numpy array with data.
 - c, z, t:      int; channel, z, time coordinates of the frame.
 
     
-# Examples
-## Write an image stack
+## Examples
+### Write an image stack
     from tiffwrite import tiffwrite
     import numpy as np
 
     image = np.random.randint(0, 255, (5, 3, 64, 64), 'uint16')
     tiffwrite('file.tif', image, 'TCXY')
 
-## Write one frame at a time
+### Write one frame at a time
     from tiffwrite import IJTiffFile
     import numpy as np
 
@@ -76,20 +77,34 @@ or
                 for t in range(10):
                     tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)
 
-## Saving multiple tiffs simultaneously
+### Saving multiple tiffs simultaneously
     from tiffwrite import IJTiffFile
     import numpy as np
-    
-    shape = (3, 5, 10)  # channels, z, time
+
     with IJTiffFile('fileA.tif') as tif_a, IJTiffFile('fileB.tif') as tif_b:
-        for c in range(shape[0]):
-            for z in range(shape[1]):
-                for t in range(shape[2]):
+        for c in range(3):
+            for z in range(5):
+                for t in range(10):
                     tif_a.save(np.random.randint(0, 10, (32, 32)), c, z, t)
                     tif_b.save(np.random.randint(0, 10, (32, 32)), c, z, t)
 
-## Tricks & tips
-- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the ifd's such that the file will
-be opened as a correctly ordered hyperstack.
-- Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very
-useful.
+
+# Rust
+    use ndarray::Array2;
+    use tiffwrite::IJTiffFile;
+
+    {  // f will be closed when f goes out of scope
+        let mut f = IJTiffFile::new("file.tif")?;
+        for c in 0..3 {
+            for z in 0..5 {
+                for t in 0..10 {
+                    let arr = Array2::<u16>::zeros((100, 100));
+                    f.save(&arr, c, z, t)?;
+                }
+            }
+        }
+    }
+
+# Tricks & tips
+- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the ifd's such that the file will be opened as a correctly ordered hyperstack.
+- Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very useful.