Merge branch 'master' into parallel-uploads

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7]
+        python-version: [3.6, 3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -26,8 +26,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install brotli>=1.0.7
-        pip install cloud-volume>=3.4.0
+        pip install -e .[cloudvolume,meshing]
 #     - name: Lint with flake8
 #       run: |
 #         pip install flake8

CHANGELOG.md

@@ -8,6 +8,7 @@
 
 -   **Convenience API**
     -   Adds support for uint16 image channel creation with the convenience API (#71)
+    -   Now, the `array` class reports voxel size as a `float[3]` and `voxel_units` as a string (e.g. "nanometers") to match the input arguments to the `array` constructor (#83)
 -   **Parallelism**
     -   Fixes parallelism defaulting to n=1 (#70)
     -   This release adds support for parallel data uploads through `BossRemote#create_cutout`.

intern/convenience/array.py

@@ -303,6 +303,8 @@ def __init__(
                     )
                 )
             except:
+                # Default to nanometers if a voxel unit isn't provided
+                voxel_unit = voxel_unit or "nanometers"
                 # Create the coordframe:
                 coordframe = CoordinateFrameResource(
                     coordinate_frame_name or f"CF_{uri.collection}_{uri.experiment}",
@@ -486,7 +488,13 @@ def voxel_size(self):
                 self._coord_frame.y_voxel_size,
                 self._coord_frame.x_voxel_size,
             )
-        return (vox_size, self._coord_frame.voxel_unit)
+        return vox_size
+
+    @property
+    def voxel_unit(self):
+        if self._coord_frame is None:
+            self._populate_coord_frame()
+        return self._coord_frame.voxel_unit
 
     def _populate_exp(self):
         """
@@ -504,9 +512,33 @@ def _populate_coord_frame(self):
 
         Cache the results for later.
         """
+        if self._exp is None:
+            self._populate_exp()
         self._coord_frame = self.volume_provider.get_project(
             CoordinateFrameResource(self._exp.coord_frame)
         )
+
+    @property
+    def downsample_status(self):
+        """
+        Return the downsample status of the underlying channel.
+        """
+        return self._channel.downsample_status
+
+    @property
+    def available_resolutions(self):
+        """
+        Return a list of available resolutions for this channel.
+        
+        Arguments:
+            None
+           
+        Returns:
+            List[int]: A list of resolutions at which this dataset can be downloaded
+         
+        """
+        self._populate_exp()
+        return list(range(dataset._exp.num_hierarchy_levels))
 
     def __getitem__(self, key: Tuple) -> np.array:
         """

intern/resource/boss/resource.py

@@ -1,4 +1,4 @@
-# Copyright 2016 The Johns Hopkins University Applied Physics Laboratory
+# Copyright 2021 The Johns Hopkins University Applied Physics Laboratory
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -39,6 +39,11 @@ def __init__(self, name, description, creator='', raw={}):
         self.description = description
         self.creator = creator
         self.raw = raw
+        self._public = raw.get("public", None)
+
+    @property
+    def public(self):
+        return self._public
 
     def valid_volume(self):
         return False

intern/service/boss/v1/volume.py

@@ -285,15 +285,15 @@ def get_cutout(
                     parallel = int(parallel)
                 else:
                     raise ValueError("Parallel must be greater than 0.")
-                pool = multiprocessing.Pool(processes=parallel)
-                chunks = pool.starmap(self.get_cutout, [
-                    (
-                        resource, resolution, b[0], b[1], b[2],
-                        time_range, id_list, url_prefix, auth, session, send_opts,
-                        access_mode
-                        # TODO: kwargs
-                    )
-                 for b in blocks])
+                with multiprocessing.Pool(processes=parallel) as pool:
+                    chunks = pool.starmap(self.get_cutout, [
+                        (
+                            resource, resolution, b[0], b[1], b[2],
+                            time_range, id_list, url_prefix, auth, session, send_opts,
+                            access_mode
+                            # TODO: kwargs
+                        )
+                     for b in blocks])
 
                 for b, data in zip(blocks, chunks):
                     result[

requirements.txt

@@ -4,4 +4,3 @@ blosc>=1.4.4
 six
 mock
 nose2
-zmesh

setup.py

@@ -77,7 +77,7 @@ def get_version(rel_path):
     include_package_data=True,
     author="Johns Hopkins University Applied Physics Laboratory",
     install_requires=install_requires,
-    extras_require={"cloudvolume": ["cloud-volume>=3.4.0", "brotli>=1.0.7"]},
+    extras_require={'cloudvolume': ['cloud-volume>=3.4.0', 'brotli>=1.0.7'],'meshing': ['zmesh>=0.5.0']},
     dependency_links=dependency_links,
     author_email="[email protected]",
 )