Remove pims-nd2 dependency

nd2_dask/__init__.py

@@ -4,7 +4,7 @@
     __version__ = "unknown"
 
 # replace the asterisk with named imports
-from .nd2_reader import napari_get_pims_reader
+from .nd2_reader import napari_get_nd2_reader
 
 
 __all__ = ["napari_get_reader"]

nd2_dask/nd2_reader.py

@@ -11,7 +11,6 @@
 """
 import numpy as np
 from nd2reader import ND2Reader
-from pims import ND2_Reader
 from dask import delayed
 import dask.array as da
 import toolz as tz
@@ -32,14 +31,6 @@
     ]
 
 
-def get_pims_nd2_vol(nd2_data, c, frame):
-    nd2_data.default_coords['c']=c
-    nd2_data.bundle_axes = 'zyx'
-    v = nd2_data[frame]
-    v = np.array(v)
-    return v
-
-
 def get_nd2reader_nd2_vol(path, c, frame):
     with ND2Reader(path) as nd2_data:
         nd2_data.default_coords['c']=c
@@ -48,29 +39,6 @@ def get_nd2reader_nd2_vol(path, c, frame):
         v = np.array(v)
     return v    
 
-# @napari_hook_implementation(specname="napari_get_reader")
-def napari_get_pims_reader(path):
-    """Returns reader if path is valid .nd2 file, otherwise None
-
-    Parameters
-    ----------
-    path : str or list of str
-        Path to file, or list of paths.
-
-    Returns
-    -------
-    function or None
-        If the path is a recognized nd2 file, return a function that accepts the
-        same path or list of paths, and returns a list of layer data tuples.
-    """
-
-    # can only read nd2 files
-    if not path.endswith(".nd2"):
-        return None
-
-    # otherwise we return the *function* that can read ``path``.
-    return pims_reader
-
 
 @napari_hook_implementation(specname="napari_get_reader")
 def napari_get_nd2_reader(path):
@@ -96,52 +64,6 @@ def napari_get_nd2_reader(path):
     return nd2_reader
 
 
-def pims_reader(path, max_retries=30):
-    """Take a path or list of paths and return a list of LayerData tuples.
-
-    Readers are expected to return data as a list of tuples, where each tuple
-    is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
-    both optional.
-
-    Parameters
-    ----------
-    path : str or list of str
-        Path to file, or list of paths.
-
-    Returns
-    -------
-    layer_data : list of tuples
-        A list of LayerData tuples where each tuple in the list contains
-        (data, metadata, layer_type), where data is a numpy array, metadata is
-        a dict of keyword arguments for the corresponding viewer.add_* method
-        in napari, and layer_type is a lower-case string naming the type of layer.
-        Both "meta", and "layer_type" are optional. napari will default to
-        layer_type=="image" if not provided
-    """
-
-    tries = 0
-    while tries < max_retries:
-        try:
-            nd2_data = ND2_Reader(path)
-            channels = [nd2_data.metadata[f"plane_{i}"]["name"] for i in range(0, nd2_data.sizes['c'])]
-            n_timepoints = nd2_data.sizes['t']
-            frame_shape = nd2_data.frame_shape
-            frame_dtype = nd2_data.pixel_type
-            nd2vol = tz.curry(get_pims_nd2_vol)
-            channel_dict = dict(zip(channels, [[] for _ in range(len(channels))]))
-            layer_list = get_layer_list(channels, nd2vol, nd2_data, frame_shape, frame_dtype, n_timepoints)
-
-            for (data, _, _) in layer_list:
-                shape = np.asarray(data[0]).shape
-            break
-        except Exception as e:
-            tries += 1
-            if tries > max_retries:
-                raise e
-
-    return layer_list
-
-
 def nd2_reader(path):
     """Take a path or list of paths and return a list of LayerData tuples.
 

requirements.txt

@@ -1,7 +1,6 @@
 napari-plugin-engine>=0.1.4
 numpy
 nd2reader
-pims-nd2
 dask
 toolz
 vispy

setup.py

@@ -26,7 +26,7 @@ def read(fname):
 
 setup(
     name='nd2_dask',
-    version='0.0.2',
+    version='0.0.3',
     author='Draga Doncila Pop',
     author_email='[email protected]',
     license='BSD-3',