N5VolumeService: Add blosc compression option

janelia-flyem · Sep 4, 2020 · 6fae4ac · 6fae4ac
1 parent 8984d77
commit 6fae4ac
Showing 1 changed file with 9 additions and 7 deletions.
diff --git a/flyemflows/volumes/n5_volume_service.py b/flyemflows/volumes/n5_volume_service.py
@@ -54,13 +54,13 @@
         },
         "compression": {
             "description": "The type of compression to use for all blocks.\n"
-                           'Choices: ["raw", "gzip", "bzip2", "xz", "lz4"]',
+                           'Choices: ["raw", "gzip", "bzip2", "xz", "lz4", "blosc"]',
             "type": "string",
-            "enum": ["raw", "gzip", "bzip2", "xz", "lz4"],
+            "enum": ["raw", "gzip", "bzip2", "xz", "lz4", "blosc"], # blosc means blosc-lz4, apparently.
             "default": "raw"
         },
         "compression-level": {
-            "description": "The compression setting (ignored when compression is 'raw').",
+            "description": "The compression setting (ignored for 'raw' and 'blosc').",
             "type": "integer",
             "default": 5
         }
@@ -258,7 +258,7 @@ def _ensure_datasets_exist(self, volume_config):
         writable = volume_config["n5"]["writable"]
         if writable is None:
             writable = create_if_necessary
-        
+
         mode = 'r'
         if writable:
             mode = 'a'
@@ -269,10 +269,12 @@ def _ensure_datasets_exist(self, volume_config):
         bounding_box_zyx = np.array(volume_config["geometry"]["bounding-box"])[:,::-1]
         creation_shape = np.array(volume_config["n5"]["creation-settings"]["shape"][::-1])
         replace_default_entries(creation_shape, bounding_box_zyx[1])
-        
+
         compression = volume_config["n5"]["creation-settings"]["compression"]
         compression_options = {}
-        if compression != "raw":
+        if compression == "blosc":
+            compression_options['clevel'] = volume_config["n5"]["creation-settings"]["compression-level"]
+        elif compression != "raw":
             compression_options['level'] = volume_config["n5"]["creation-settings"]["compression-level"]
 
         if create_if_necessary:
@@ -283,7 +285,7 @@ def _ensure_datasets_exist(self, volume_config):
                                        "(or extend) the data with, because you didn't specify a "
                                        "volume creation shape (or bounding box")
                 max_scale = choose_pyramid_depth(creation_shape, 512)
-            
+
             available_scales = [*range(1+max_scale)]
         else:
             available_scales = volume_config["geometry"]["available-scales"]