updates

examples.py

@@ -1,12 +1,12 @@
-from src.OMEZarr import OMEZarr
-from src.core import utils
+from OME_Zarr.src.OMEZarr import OMEZarr
+from OME_Zarr.src.core import utils
 import numpy as np
 import dask.array as da
 import os
 import numcodecs
-import zarr
+import zarr, napari
 
-basepath = 'data/filament.zarr'
+basepath = 'OME_Zarr/data/filament.zarr'
 
 oz = OMEZarr(basepath)
 
@@ -18,15 +18,28 @@
 oz.labelobj.image_labels['original'].typeobj
 oz.labelobj.image_labels['original'].dtype('0')
 
-newdir = 'data/filament_ex.zarr'
+newdir = 'OME_Zarr/data/filament_ex.zarr'
 oz.baseobj.extract(newdir = newdir, paths = ['0', '1'])
 
 noz = OMEZarr(newdir)
 noz.baseobj.typeobj
 noz.baseobj.path_order
-noz.baseobj.chunks('0')
+
+noz.baseobj.chunks()
 noz.baseobj.rechunk((10, 70, 70))
-noz.baseobj.chunks('0')
+noz.baseobj.chunks()
 
 noz.baseobj.get_scale('0')
 noz.baseobj.get_scale('1')
+
+noz.baseobj.asflat()
+noz.baseobj.asnested()
+
+noz.baseobj.dtype('0')
+noz.baseobj.astype(np.float32)
+noz.baseobj.dtype('0')
+
+napari.view_path(noz.baseobj.basepath)
+
+
+

src/OMEZarr.py

@@ -5,7 +5,7 @@
 
 class BaseReader(Collection, ZarrayManipulations): # TODO: Add s3fs stuff here.
     def __init__(self,
-                 basepath
+                 basepath: str
                  ):
         Collection.__init__(self, basepath)
         if self.is_multiscales:
@@ -33,8 +33,9 @@ def __init__(self):
 
 class OMEZarrObject(BaseReader, _MultiSeries, _Labels):
     def __init__(self,
-                 basepath
+                 basepath: str
                  ):
+        """ The main reader class """
         BaseReader.__init__(self, basepath)
         if self.is_labels:
             _Labels.__init__(self)
@@ -55,11 +56,14 @@ def __getitem__(self, item):
             raise Exception('Data is neither multiseries nor labels.')
 
 class OMEZarr:
-    def __init__(self, directory):
+    def __init__(self,
+                 directory: str
+                 ):
+        """ A class that classifies OME-Zarr data as image and label objects. """
         self.baseobj = None
         self.labelobj = None
         self.unstructured_collections = {}
-        self.collection_paths, self.array_paths = utils.get_collection_paths(directory, return_arraypaths = True)
+        self.collection_paths, self.multiscales_paths, self.array_paths = utils.get_collection_paths(directory, return_all = True)
         for fpath in self.collection_paths:
             obj = OMEZarrObject(fpath)
             if fpath == directory: