Merge pull request #36 from sebi06/work_in_progress

Work in progress

README.md

@@ -87,4 +87,4 @@ napari.run()
 
 ## Remarks
 
-The code to read multi-dimensional with delayed reading using Dask array was heavily inspired by input from: [Pradeep Rajasekhar](https://github.com/pr4deepr).
+The code to read multi-dimensional with delayed reading using Dask array was heavily inspired by input from: [Pradeep Rajasekhar](https://github.com/pr4deepr).

demo/notebooks/omezarr_from_czi_5d.ipynb

@@ -280,7 +280,7 @@
         }
       ],
       "source": [
-        "# this is how we can open the file we just wrote in napari\n",
+        "# this is how we can open the file we just write in napari\n",
         "viewer = napari.Viewer()\n",
         "viewer.open(zarr_path)"
       ]

demo/scripts/use_read_tools.py

@@ -29,7 +29,7 @@
 # return a array with dimension order STZCYX(A)
 array6d, mdata, dim_string6d = read_tools.read_6darray(filepath,
                                                        output_order="STCZYX",
-                                                       use_dask=False,
+                                                       use_dask=True,
                                                        chunk_zyx=False,
                                                        # T=0,
                                                        # Z=0

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = czitools
-version = 0.4.0
+version = 0.4.1
 author = Sebastian Rhode
 author_email = sebrhode@gmail.com
 url = https://github.com/sebi06/czitools

src/czitools/__init__.py

@@ -1,3 +1,3 @@
 # __init__.py
 # version of the czitools package
-__version__ = "0.4.0"
+__version__ = "0.4.1"

src/czitools/read_tools.py

@@ -18,7 +18,7 @@
 import dask
 import dask.array as da
 import os
-from tqdm import trange
+from tqdm import trange, tqdm
 from tqdm.contrib.itertools import product
 
 
@@ -142,11 +142,11 @@ def read_6darray(filepath: Union[str, os.PathLike[str]],
 
             for s in trange(size_s):
                 time_stack = []
-                for time in range(size_t):
+                for time in trange(size_t):
                     ch_stack = []
                     for ch in trange(size_c):
                         z_stack = []
-                        for z in range(size_z):
+                        for z in trange(size_z):
                             if mdata.image.SizeS is not None:
 
                                 z_slice = da.from_delayed(