Merge pull request #164 from henrypinkard/main

Fix bug when querying unknown axis

python/ndstorage/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 1, 6)
+version_info = (0, 1, 7)
 __version__ = ".".join(map(str, version_info))

python/ndstorage/ndstorage_base.py

@@ -9,6 +9,7 @@
 - image_keys: a list of image_keys, e.g. [frozenset({'channel': 0, 'z': 1, 'time': 2}), frozenset({'channel': 0, 'z': 1, 'time': 3})]
 """
 from abc import ABC, abstractmethod
+from collections.abc import Mapping
 from typing import Any, Dict, List, Union, Tuple
 import numpy as np
 import dask
@@ -329,7 +330,7 @@ def has_image(self, channel: Union[int, str] = None, z: int = None, time: int =
     @abstractmethod
     def read_image(self, channel: Union[int, str] = None, z: int = None, time: int = None,
                    position: int = None, row: int = None, column: int = None,
-                   **kwargs: Union[int, str]) -> Union[np.ndarray, Tuple[np.ndarray, Dict[str, Any]]]:
+                   **kwargs: Union[int, str]) -> np.ndarray:
         """
         Read image data as numpy array.
 
@@ -622,7 +623,7 @@ def _parse_string_axes_values(self, image_coordinates):
                 self._string_axes_values[string_axis_name] = []
 
         # if its called on just one image, make it a list of one image
-        if isinstance(image_coordinates, dict):
+        if isinstance(image_coordinates, Mapping):
             image_coordinates = [image_coordinates.items()]
 
         for single_image_coordinates in image_coordinates:
@@ -651,18 +652,16 @@ def _consolidate_axes(self, channel: int or str, z: int, position: int,
         Combine all the axes with standard names and custom names into a single dictionary, eliminating
         any None values. Also, convert any string-valued axes passed as ints into strings
         """
-        if ('channel_name' in kwargs):
-            warnings.warn('channel_name is deprecated, use "channel" instead')
-            channel = kwargs['channel_name']
-            del kwargs['channel_name']
-
         axis_positions = {'channel': channel, 'z': z, 'position': position,
                     'time': time, 'row': row, 'column': column, **kwargs}
         # ignore ones that are None
         axis_positions = {n: axis_positions[n] for n in axis_positions.keys() if axis_positions[n] is not None}
         for axis_name in axis_positions.keys():
             # convert any string-valued axes passed as ints into strings
-            if self.axes_types[axis_name] == str and type(axis_positions[axis_name]) == int:
+            if axis_name not in self.axes_types.keys():
+                # can't convert to string if the axis is not known
+                pass
+            elif self.axes_types[axis_name] == str and type(axis_positions[axis_name]) == int:
                 axis_positions[axis_name] = self._string_axes_values[axis_name][axis_positions[axis_name]]
 
         return axis_positions

python/ndstorage/ndtiff_dataset.py

@@ -33,7 +33,8 @@ def __init__(self, dataset_path=None, file_io: NDTiffFileIO = BUILTIN_FILE_IO, s
         file_io: ndtiff.file_io.NDTiffFileIO
             A container containing various methods for interacting with files.
         summary_metadata : dict
-            Summary metadata for a dataset that is currently being written by another process
+            Summary metadata for a dataset that is currently being written by another process. If writable is True,
+            this should instead be provided by the initialize() method.
         name : str
             Name of the dataset if writing a new dataset
         writable : bool

python/ndstorage/ndtiff_file.py

@@ -162,6 +162,8 @@ def write_image(self, index_key, pixels, metadata, bit_depth='auto'):
         ied = self._write_ifd(index_key, pixels, metadata, rgb, image_height, image_width, bit_depth)
         while self.buffers:
             self.file.write(self.buffers.popleft())
+        # make sure the file is flushed to disk
+        self.file.flush()
         self.index_map[index_key] = ied
         return ied