Code

Zarr Tile Sink#1446

Code

Merged

annehaley merged 42 commits intomastergirder/large_image:masterfrom zarr-sinkgirder/large_image:zarr-sinkCopy head branch name to clipboardMar 21, 2024

+463-190

Commits

Commits on Jan 26, 2024

• Initial method setup

  annehaley

  committed
  0f537bb

  Copy full SHA for 0f537bb

• Populate addTile method; tests successful up to 3-D

  annehaley

  committed
  5c6990b

  Copy full SHA for 5c6990b

• Use test source to copy 5D images to Zarr sink

  annehaley

  committed
  29d8b19

  Copy full SHA for 29d8b19

Commits on Jan 29, 2024

• Remove old TODOs

  annehaley

  committed
  599503f

  Copy full SHA for 599503f

• Refactor __init__ to simplify (split into multiple methods)

  annehaley

  committed
  10a1f7e

  Copy full SHA for 10a1f7e

• Update Exception class in __del__ method

  annehaley

  committed
  12946a0

  Copy full SHA for 12946a0

Commits on Jan 31, 2024

• Merge branch 'master' into zarr-sink

  annehaley

  authored
  f8fb42e

  Copy full SHA for f8fb42e

Commits on Feb 1, 2024

• Enable cropping during write; does not modify internal data

  annehaley

  committed
  d697920

  Copy full SHA for d697920

Commits on Feb 9, 2024

• Merge branch 'master' into zarr-sink

  annehaley

  authored
  b50ecd9

  Copy full SHA for b50ecd9

Commits on Mar 5, 2024

• Protect __del__ method and ensure both close operations are called

  annehaley

  committed
  f36f1a8

  Copy full SHA for f36f1a8

• Set _axes, _dtype, _bandCount, sizeX, sizeY, levels, and _framecount in addTile

  annehaley

  committed
  6b6a6a4

  Copy full SHA for 6b6a6a4

Commits on Mar 6, 2024

• Attempt to improve performance of addTile: remove np.pad and unnecessary usage of create_dataset

  annehaley

  committed
  d6dd5ad

  Copy full SHA for d6dd5ad

• Merge branch 'master' into zarr-sink

  annehaley

  authored
  b7ed234

  Copy full SHA for b7ed234

• Fix lint failure: remove trailing whitespace

  annehaley

  committed
  df8819f

  Copy full SHA for df8819f

Commits on Mar 7, 2024

• Set self._levels to None in addTile

  annehaley

  committed
  0a832fd

  Copy full SHA for 0a832fd

• Avoid creating full mask

  annehaley

  committed
  cd0c715

  Copy full SHA for cd0c715

Commits on Mar 8, 2024

• Use np.where instead of np.place

  annehaley

  committed
  41ea6b5

  Copy full SHA for 41ea6b5

• Merge branch 'master' into zarr-sink

  annehaley

  authored
  eaaf29e

  Copy full SHA for eaaf29e

• Rename mask_placement_slices -> placement_slices and avoid mask creation

  annehaley

  committed
  0414f71

  Copy full SHA for 0414f71

Commits on Mar 11, 2024

• Include statement to add samples axis to mask if necessary

  annehaley

  committed
  3da02f6

  Copy full SHA for 3da02f6

Commits on Mar 13, 2024

• Refactor checking of axes arg; ensure "s" axis exists

  annehaley

  committed
  d0d6129

  Copy full SHA for d0d6129

Commits on Mar 14, 2024

• Use samples axis length in chunking (instead of 32) and rechunk if length changes

  annehaley

  committed
  07e744f

  Copy full SHA for 07e744f

Commits on Mar 18, 2024

• Switch to using DirectoryStore internally (instead of SQLiteStore)

  annehaley

  committed
  5118fbc

  Copy full SHA for 5118fbc

• Refactor addTile: ensure placement from kwargs is used (including first iteration)

  annehaley

  committed
  e1e9831

  Copy full SHA for e1e9831

• Refactor addTile: move attribute changes within addLock context

  annehaley

  committed
  6706f69

  Copy full SHA for 6706f69

• style: whitespace changes to fix lint failure

  annehaley

  committed
  b58fcda

  Copy full SHA for b58fcda

• Refactor addTile: expand mask dimensions with tile dimensions

  annehaley

  committed
  756502b

  Copy full SHA for 756502b

• Merge branch 'master' into zarr-sink

  annehaley

  authored
  58897b3

  Copy full SHA for 58897b3

• fix: add NoneType protection to mask axis padding

  annehaley

  committed
  a0b3fbc

  Copy full SHA for a0b3fbc

Commits on Mar 19, 2024

• Merge branch 'master' into zarr-sink

  annehaley

  authored
  f0e7482

  Copy full SHA for f0e7482

• fix: Revert to using SQLiteStore when opening existing Zarr file

  annehaley

  committed
  5317daa

  Copy full SHA for 5317daa

• fix: move start of self._addLock context

  annehaley

  committed
  32c9c58

  Copy full SHA for 32c9c58

• fix: set dtype of np.empty when initializing root

  annehaley

  committed
  728faee

  Copy full SHA for 728faee

• fix: call validateZarr in beginning of getMetadata if necessary

  annehaley

  committed
  14bee28

  Copy full SHA for 14bee28

• fix: Set _bandCount from length of s axis if exists

  annehaley

  committed
  ce1b1b7

  Copy full SHA for ce1b1b7

• test: enable new algorithm progression tests

  annehaley

  committed
  5fac3a8

  Copy full SHA for 5fac3a8

• test: write basic use case tests for zarr sink in test_sink.py

  annehaley

  committed
  23b70f7

  Copy full SHA for 23b70f7

• style: fix line too long; use string append

  annehaley

  committed
  414ba67

  Copy full SHA for 414ba67

Commits on Mar 20, 2024

• style: avoid explicit string concatenation

  annehaley

  committed
  f35d06e

  Copy full SHA for f35d06e

• test: add testNew and initialize _levels

  annehaley

  committed
  157c731

  Copy full SHA for 157c731

• fix: unindent mask reshape clause

  annehaley

  committed
  62e6572

  Copy full SHA for 62e6572

• test: add testAddTileWithMask and fix caching to pass

  annehaley

  committed
  71d1068

  Copy full SHA for 71d1068