fix: Implemented vds initialization without writing chunks

README.md

@@ -42,7 +42,7 @@ import numpy as np
 
 from ovds_utils.metadata import MetadataTypes, MetadataValue
 from ovds_utils.ovds.enums import BrickSizes, Formats
-from ovds_utils.vds import VDS, Channel, Components, Formats
+from ovds_utils.vds import VDS, Channel, Components, Formats, AccessModes
 
 metadata = {
     "example": MetadataValue(value="value", category="category#1", type=MetadataTypes.String)
@@ -57,6 +57,7 @@ vds = VDS(
     data=zeros,
     metadata_dict=metadata,
     databrick_size=BrickSizes.BrickSize_64,
+    access_mode=AccessModes.Create,
     channels=[
         Channel(
             name="Channel0",

setup.py

@@ -17,7 +17,7 @@ def get_dependencies():
 
 setup(
     name='ovds_utils',
-    version='0.2.12',
+    version='0.3.0',
     author="Michal Murawski",
     author_email="[email protected]",
     description="Utilities package for Open VDS.",

src/ovds_utils/logging.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 import os
 import sys
@@ -6,7 +8,7 @@
 FORMAT = "%(asctime)s::%(name)s::%(levelname)s::%(message)s"
 
 
-def get_logger(name):
+def get_logger(name) -> logging.Logger:
     logger = logging.getLogger(name)
     console_handler = logging.StreamHandler(sys.stdout)
     logger.setLevel(LOG_LEVEL)

src/ovds_utils/metadata.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import Any, AnyStr, Dict, Union
 
 import openvds

src/ovds_utils/ovds/copy.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from subprocess import PIPE, Popen
 
 from ovds_utils.logging import get_logger

src/ovds_utils/ovds/enums.py

@@ -34,11 +34,17 @@ class BrickSizes(Enum):
     _2048 = openvds.core.VolumeDataLayoutDescriptor.BrickSize.BrickSize_2048
     _4096 = openvds.core.VolumeDataLayoutDescriptor.BrickSize.BrickSize_4096
 
+    @classmethod
+    def get_from_info(cls, vds_info: dict):
+        return getattr(cls, "_"+vds_info["layoutDescriptor"]["brickSize"].rsplit("_")[-1])
+
 
 class AccessModes(Enum):
     Create = openvds.IVolumeDataAccessManager.AccessMode.AccessMode_Create
     ReadOnly = openvds.IVolumeDataAccessManager.AccessMode.AccessMode_ReadOnly
     ReadWrite = openvds.IVolumeDataAccessManager.AccessMode.AccessMode_ReadWrite
+    CreateWithoutLODGeneration = openvds.IVolumeDataAccessManager.AccessMode.AccessMode_CreateWithoutLODGeneration
+    ReadWriteWithoutLODGeneration = openvds.IVolumeDataAccessManager.AccessMode.AccessMode_ReadWriteWithoutLODGeneration
 
 
 class Dimensions(Enum):

src/ovds_utils/ovds/utils.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 from pathlib import Path
 from subprocess import PIPE, Popen

src/ovds_utils/ovds/writing.py

@@ -1,13 +1,14 @@
+from __future__ import annotations
+
 from logging import getLogger
 from typing import Any, AnyStr, Dict, List
 
 import numpy as np
 import openvds
 
-from .enums import InitValue
+from .enums import AccessModes, InitValue
 from .utils import copy_ovds_metadata
 
-
 logger = getLogger(__name__)
 
 FORMAT2NPTYPE = {
@@ -137,7 +138,6 @@ def create_vds(
     default_max_pages: int = 8,
     channels_data=None,
     init_value: InitValue = InitValue.zero,
-    # close: bool = True
 ):
     (
         layout_descriptor,
@@ -157,23 +157,6 @@ def create_vds(
         full_resolution_dimension=full_resolution_dimension,
     )
 
-    (
-        layout_descriptor,
-        axis_descriptors,
-        channel_descriptors,
-        metadata_container
-    ) = create_vds_attributes(
-        databrick_size=databrick_size,
-        metadata_dict=metadata_dict,
-        channles=channels,
-        axes=axes,
-        lod_levels=lod,
-        negative_margin=negative_margin,
-        positive_margin=positive_margin,
-        options=options,
-        brick_size_2d_multiplier=brick_size_2d_multiplier,
-        full_resolution_dimension=full_resolution_dimension,
-    )
     vds = openvds.create(
         url=path,
         connectionString=connection_string,
@@ -183,18 +166,20 @@ def create_vds(
         metadata=metadata_container,
     )
     access_manager = openvds.getAccessManager(vds)
+
     if channels_data:
         for i, data in enumerate(channels_data):
             channel = channels[i]
             accessor = access_manager.createVolumeDataPageAccessor(
                 dimensionsND=channel.dimensions_nd.value,
-                accessMode=access_mode,
+                accessMode=AccessModes.Create.value,
                 lod=lod,
                 channel=i,
                 maxPages=default_max_pages,
             )
             write_pages(accessor, data, channel.format.value)
-    else:
+
+    if init_value != InitValue.omit_init:
         for i in range(len(channels)):
             channel = channels[i]
             accessor = access_manager.createVolumeDataPageAccessor(
@@ -204,12 +189,6 @@ def create_vds(
                 channel=i,
                 maxPages=default_max_pages,
             )
-            if init_value != InitValue.omit_init:
-                INITVALUE[init_value](accessor, channel.format.value)
-            else:
-                logger.warning(
-                    "Values initialization was omitted. Remember to do it and close vds resource properly."
-                )
-                return vds
+            INITVALUE[init_value](accessor, channel.format.value)
 
     return vds

src/ovds_utils/vds.py

@@ -1,6 +1,7 @@
+from __future__ import annotations
+
 from copy import deepcopy
-from typing import AnyStr, List, Sequence, Tuple, Union
-from enum import Enum
+from typing import List, Sequence, Tuple, Union
 
 import numpy as np
 import openvds
@@ -102,10 +103,10 @@ class Axis:
     def __init__(
         self,
         samples: int,
-        name: AnyStr,
+        name: str,
         coordinate_min: float,
         coordinate_max: float,
-        unit: AnyStr = "unitless",
+        unit: str = "unitless",
     ) -> None:
         self.samples = samples
         self.name = name
@@ -120,9 +121,9 @@ def __repr__(self) -> str:
 class Channel:
     def __init__(
             self,
-            name: AnyStr,
+            name: str,
             format: Formats,
-            unit: AnyStr,
+            unit: str,
             value_range_min: float,
             value_range_max: float,
             components: Components,
@@ -228,17 +229,11 @@ def commit(self):
         self.accessor.commit()
 
 
-class Mode(str, Enum):
-    READ = "READ"
-    READ_WRITE = "READ_WRITE"
-    WRITE = "WRITE"
-
-
 class VDS:
     def __init__(
         self,
-        path: AnyStr,
-        connection_string: AnyStr = "",
+        path: str,
+        connection_string: str = "",
         databrick_size: BrickSizes = BrickSizes._128,
         metadata_dict: MetadataContainer = {},
         channels_data: List[np.array] = None,
@@ -250,18 +245,18 @@ def __init__(
         options: Options = Options._None,
         full_resolution_dimension: int = 0,
         brick_size_2d_multiplier: int = 4,
-        init_value: InitValue = InitValue.zero,
-        mode: Mode = Mode.READ
+        init_value: InitValue = InitValue.omit_init,
+        access_mode: AccessModes = AccessModes.ReadOnly
     ) -> None:
         super().__init__()
 
-        if mode in (Mode.READ_WRITE, Mode.READ):
+        if access_mode in {AccessModes.ReadOnly, AccessModes.ReadWrite, AccessModes.ReadWriteWithoutLODGeneration}:
             try:
                 self._vds_source = openvds.open(path, connection_string)
                 self.initialize(
                     path=path,
+                    access_mode=access_mode,
                     connection_string=connection_string,
-                    databrick_size=databrick_size,
                 )
             except RuntimeError as e:
                 if str(e) == "Open error: File::open ":
@@ -276,7 +271,7 @@ def __init__(
                 axes=axes,
                 metadata_dict=metadata_dict,
                 channels_data=channels_data,
-                access_mode=AccessModes.Create,
+                access_mode=access_mode,
                 lod=lod,
                 positive_margin=positive_margin,
                 negagitve_margin=negative_margin,
@@ -285,17 +280,18 @@ def __init__(
                 brick_size_2d_multiplier=brick_size_2d_multiplier,
                 init_value=init_value
             )
+
             self.initialize(
                 path=path,
-                connection_string=connection_string,
-                databrick_size=databrick_size,
+                access_mode=access_mode,
+                connection_string=connection_string
             )
 
     def initialize(
         self,
-        path: AnyStr,
-        connection_string: AnyStr = "",
-        databrick_size: BrickSizes = BrickSizes._128,
+        path: str,
+        access_mode: AccessModes,
+        connection_string: str = "",
     ):
         self.closed = False
         self.path = path
@@ -309,6 +305,7 @@ def initialize(
 
         vds_info = get_vds_info(path, connection_string)
         _info = vds_info['layoutInfo'] if 'layoutInfo' in vds_info else vds_info
+        databrick_size = BrickSizes.get_from_info(_info)
 
         for i, j in enumerate(_info['axisDescriptors']):
             self._axes[j['name']] = Axis(
@@ -320,6 +317,14 @@ def initialize(
             )
         self.chunks_count = self.count_number_of_chunks(self.shape, databrick_size)
         for i, j in enumerate(_info['channelDescriptors']):
+
+            if access_mode == AccessModes.Create:
+                _access_mode = AccessModes.ReadWrite
+            elif access_mode == AccessModes.CreateWithoutLODGeneration:
+                _access_mode = AccessModes.ReadWriteWithoutLODGeneration
+            else:
+                _access_mode = access_mode
+
             self._channels[j['name']] = Channel(
                 vds_source=self._vds_source,
                 shape=self.shape,
@@ -331,8 +336,8 @@ def initialize(
                 ),
                 value_range_max=j['valueRange'][1],
                 value_range_min=j['valueRange'][0],
-                accessor=self._create_accessor(channel=i),
-                chunks_count=self.count_number_of_chunks(self.shape, databrick_size)
+                accessor=self._create_accessor(channel=i, access_mode=_access_mode),
+                chunks_count=self.chunks_count
             )
 
     def channel(self, number: int) -> Channel:
@@ -346,7 +351,7 @@ def channels(self) -> List[Channel]:
     def axes(self) -> List[Axis]:
         return list(self._axes.values())[::-1]
 
-    def get_channel(self, name: AnyStr) -> Channel:
+    def get_channel(self, name: str) -> Channel:
         return self._channels[name]
 
     def close(self, flush: bool = True):
@@ -401,22 +406,22 @@ def lod(self) -> LOD:
     def __str__(self) -> str:
         return f"<{self.__class__.__qualname__}(path={self.path})>"
 
-    @ property
+    @property
     def axis_descriptors(self):
         return tuple((
             self._axes[k].name,
             self._axes[k].unit,
             self._axes[k].samples
         ) for k in self._axes)[::-1]
 
-    @ property
+    @property
     def shape(self):
         return tuple(self._axes[k].samples for k in self._axes)[::-1]
 
-    @ staticmethod
+    @staticmethod
     def create(
-        path: AnyStr,
-        connection_string: AnyStr,
+        path: str,
+        connection_string: str,
         databrick_size: BrickSizes,
         access_mode: AccessModes,
         channels: List[Channel],
@@ -447,7 +452,6 @@ def create(
             brick_size_2d_multiplier=brick_size_2d_multiplier,
             full_resolution_dimension=full_resolution_dimension,
             init_value=init_value,
-            # close=True
         )
 
     @property