- read metadata into ome structure

- pytest
- use pathlib
- series as part of the path: path/PosN
- summary only shows some available metadata
- allow dict in Imread[dict(c=c, z=z, t=t)]
- bfread in different process so the user can start another jvm
- deal with multiple images (series/positions) in czi files
- use jpype instead of javabridge/bioformats
- poetry for install

README.md

@@ -1,10 +1,9 @@
-# ndbioimage
+# ndbioimage - Work in progress
 
-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 exposed as attributes to the Imread object (TODO: structure data in OME format).
-Additionally, it can automatically calculate an affine transform that corrects for
-chromatic abberrations etc. and apply it on the fly to the image.
+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
+and stored in an ome structure. Additionally, it can automatically calculate an affine
+transform that corrects for chromatic abberrations etc. and apply it on the fly to the image.
 
 Currently supports imagej tif files, czi files, micromanager tif sequences and anything
 bioformats can handle. 
@@ -13,13 +12,8 @@ bioformats can handle.
 
     pip install ndbioimage@git+https://github.com/wimpomp/ndbioimage.git
 
-### With bioformats (if java is properly installed)
-
-    pip install ndbioimage[bioformats]@git+https://github.com/wimpomp/ndbioimage.git
-
-### With affine transforms (only for python 3.8, 3.9 and 3.10)
-
-    pip install ndbioimage[transforms]@git+https://github.com/wimpomp/ndbioimage.git
+Optionally:
+https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/bioformats_package.jar
 
 ## Usage
 
@@ -27,34 +21,34 @@ bioformats can handle.
 
 
     import matplotlib.pyplot as plt
-    from ndbioimage import imread
-    with imread('image_file.tif', axes='ctxy', dtype=int) as im:
+    from ndbioimage import Imread
+    with Imread('image_file.tif', axes='ctxy', dtype=int) as im:
         plt.imshow(im[2, 1])
 
 - Showing some image metadata
 
 
-    from ndbioimage import imread
+    from ndbioimage import Imread
     from pprint import pprint
-    with imread('image_file.tif') as im:
+    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='cztxy') as im:
+    from ndbioimage import Imread
+    with Imread('image_file.tif', axes='cztxy') 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
+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
+    from ndbioimage import Imread
     import numpy as np
-    with imread('image_file.tif', axes='cztxy') as im:
+    with Imread('image_file.tif', axes='cztxy') as im:
         array = np.asarray(im[0, 0])
 
 ## Adding more formats
@@ -63,9 +57,8 @@ automatically recognize it and use it to open the appropriate file format. Image
 subclass Imread and are required to implement the following methods:
 
 - staticmethod _can_open(path): return True if path can be opened by this reader
-- \_\_metadata__(self): reads metadata from file and adds them to self as attributes,
-  - the shape of the data in the file needs to be set as self.shape = (X, Y, C, Z, T)
-  - other attributes like pxsize, acquisitiontime and title can be set here as well
+- property ome: reads metadata from file and adds them to an OME object imported
+from the ome-types library 
 - \_\_frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file
 
 Optional methods:
@@ -78,5 +71,5 @@ Optional fields:
 for example: any file handles
 
 # TODO
-- structure the metadata in OME format tree
+- more image formats
 - re-implement transforms