0.4.1

🚀 Features

Change raw rescaling to happen on frontend + export original raw unscaled @ykevu (#383)

PR Addressing #373, #379, #381

• Non-png raw inputs are no longer rescaled at all on the backend in loaders.py (.png files are still rescaled to uint8)
• Instead, the frontend performs the rescaling on the raw array, and creates a second array "rawOriginal" which is passed to the arrayMachine.
  • This is a "TypedArray" which can support Uint8, Int8, Uint16, Int16, Uint32, Int32, Float32, and Float64. This will require further testing (by @steveyu323?) for a variety of dtypes since I only had access to uint8 and float64 files
• On export, rawOriginal is zipped instead of the rescaled raw array, so download or submission will give the user the original raw unscaled tiff.

Testing

• So far, I have tested uploading a file from Changhua that is float64, and the rendering on the site was fine. Upon downloading, the X.ome.tiff file inside retained float64 and the unscaled values. After reuploading this downloaded file to DCL, it looked fine as well. Functionality of all the editing and such still worked throughout all of this.

Potential Issues / Enhancements

• The loading times do not seem to have suffered very significantly, but will look into using gpu.js to speed up the reshaping operation (which currently has 4 nested for loops).

Small changes

• REPLACE tool was renamed to COMBINE on its button, tooltip, and instructions. The hotkey and code referencing the tool is unchanged.

🐛 Bug Fixes

BUG: fix bug when no cells on canvas. @ykevu (#397)

What

• Fixes a bug where an error is thrown when trying to load in an image/frame with 0 cells, as a relevant function assumed a non-empty list of cells.

Fix GPU rendering bugs, cell 0 bugs, and bug in saving raw array @ykevu (#384)

PR Addressing #380, #382, and more

• Fixed GPU rendering bugs for the COMBINE and FLOOD tools (#380).
  • These tools also rendered outlines when used and ran into the same issues as those fixed in #376, so similar fixes were applied.
• Fixed bugs related to "Cell 0" edits (#382).
  • If no cell was selected, it was possible to create cells with label 0 on the canvas. Possible from:
    1. Hitting esc while using the BRUSH tool. Fixed by switching to SELECT when esc is hit.
    2. Hitting esc to select nothing and then switching to the THRESHOLD tool. Fixed by selecting a new cell when hitting the THRESHOLD tool if current cell is 0.
    3. Hitting esc to select nothing and then pressing the autofit tool. Fixed by not using the autofit tool if current cell is 0.
• Fixed bug in how raw array was saved in the reshaping.
  • Threshold and watershed tools were broken because these tools pass the raw array to the backend. Originally the unscaled raw array was simply being scaled and the scaling function was called with "as Uint8Array[][][]" but this doesn't work due to how the array buffers work, so a new array is made when the reshaping is done to fix this.

Fix bugs breaking brush tool and unintended undo behavior @ykevu (#378)

Significant Changes (Fix #377)

• Fix bug where brush tool broke when switching to another tab and back.
  • EditMachine.js now sends ENTER_TAB to EditSegmentMachine.js when the SEGMENT tab is selected. EditSegmentMachine will
    accordingly send SET_PAN_ON_DRAG depending on the state it is in so as not to potentially break the state.
• Fix bug where undoing from a pan tool to a non-pan tool (brush) would break the brush.
  • panOnDrag state is now stored in the undo history for CanvasMachine.js, and upon restoring, a CHECK_DRAG event is sent to restore the appropriate state.

Small changes

• Fix bug where using CTRL+Z to undo would always switch to the DISPLAY tab.
  • An event listener was listening for Z presses to switch to DISPLAY tab, so Z was removed from this and a mousetrap binding was instead created to not trigger on combination hotkeys
• Drop uploading now actually uses the user-selected axes
• .zip added to list of acceptable file formats (application/zip was not working on my Windows machine)
• Added hotkey tooltip on select (V)

Fix canvas rendering bugs caused by issues with gpu rendering kernel @ykevu (#376)

What

Fixes canvas rendering bugs, namely #366 and #367, which were both caused by issues in the gpu rendering kernel. Specifically, a check is now called to ensure that a value is contained within the bounds of expected values before trying to render the label associated with that value (out of bounds indexing was resulting not in errors but the cells reappearing upon deletion). Additionally, the max number of cells displayed has been increased to 5000.

These changes were tested by Changhua and me and appear to be working properly.

Why

Users can now render up to 5000 cells at once on a canvas and will not experience bugs when deleting the highest valued cells in a given frame.

Fix bug causing segmentations to be lost upon reload @ykevu (#372)

What

My guess is that after Tom fixed the bug related to adding c to cells, the "feature" field was renamed to "c", so the idbWebWorker was unable to find what segmentation feature was being edited, and segmentations were thus not being tracked.

Why

Users can now reload without losing their segmentation changes (eg. brush adds/removes).

Fix bugs related to cells not properly deleting @ykevu (#368)

What

Addressed the bug from Issue #365, in which after deleting a cell, one cannot write over the deleted cell's area when using exclusion mode.

Additionally, added some snippets of code required for the tests and source code to run on Windows.

Fix

The bug arose because the deleted cell was only removed from the cells matrix but its label persisted in the labels matrix. Added a new function to the Edit class called clean_labels() which deletes any labels that do not correspond to existing cells that is called every time an action is performed that adds masks (eg. brush, flood, etc.). Additionally, a more esoteric bug was found involving overlapped cells reappearing after deletion, which should be addressed by this change as well.

Why

Users can now properly edit areas previously occupied by deleted cells, rendering the delete tool usable in exclusion mode.

🧰 Maintenance

Bump json5 from 1.0.1 to 1.0.2 in /frontend @dependabot (#391)

Bumps json5 from 1.0.1 to 1.0.2.

Release notes

Sourced from json5's releases.

v1.0.2

• Fix: Properties with the name __proto__ are added to objects and arrays. (#199) This also fixes a prototype pollution vulnerability reported by Jonathan Gregson! (#295). This has been backported to v1. (#298)

Changelog

Sourced from json5's changelog.

Unreleased [code, diff]

v2.2.3 [code, diff]

• Fix: json5@2.2.3 is now the 'latest' release according to npm instead of v1.0.2. (#299)

v2.2.2 [code, diff]

• Fix: Properties with the name __proto__ are added to objects and arrays. (#199) This also fixes a prototype pollution vulnerability reported by Jonathan Gregson! (#295).

v2.2.1 [code, diff]

• Fix: Removed dependence on minimist to patch CVE-2021-44906. (#266)

v2.2.0 [code, diff]

• New: Accurate and documented TypeScript declarations are now included. There is no need to install @types/json5. (#236, #244)

v2.1.3 [code, diff]

• Fix: An out of memory bug when parsing numbers has been fixed. (#228, #229)

v2.1.2 [code, diff]

... (truncated)

Commits

• a62db1e 1.0.2
• e0c23fe docs: update CHANGELOG for v1.0.2
• 62a6540 fix: add proto to objects and arrays
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Bump decode-uri-component from 0.2.0 to 0.2.2 in /frontend @dependabot (#390)

Bumps decode-uri-component from 0.2.0 to 0.2.2.

Release notes

Sourced from decode-uri-component's releases.

v0.2.2

• Prevent overwriting previously decoded tokens 980e0bf

SamVerschueren/decode-uri-component@v0.2.1...v0.2.2

v0.2.1

• Switch to GitHub workflows 76abc93
• Fix issue where decode throws - fixes #6 746ca5d
• Update license (#1) 486d7e2
• Tidelift tasks a650457
• Meta tweaks 66e1c28

SamVerschueren/decode-uri-component@v0.2.0...v0.2.1

Commits

• a0eea46 0.2.2
• 980e0bf Prevent overwriting previously decoded tokens
• 3c8a373 0.2.1
• 76abc93 Switch to GitHub workflows
• 746ca5d Fix issue where decode throws - fixes #6
• 486d7e2 Update license (#1)
• a650457 Tidelift tasks
• 66e1c28 Meta tweaks
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Bump loader-utils from 1.4.0 to 1.4.2 in /frontend @dependabot (#389)

Bumps loader-utils from 1.4.0 to 1.4.2.

Release notes

Sourced from loader-utils's releases.

v1.4.2

1.4.2 (2022-11-11)

Bug Fixes

• ReDoS problem (#226) (17cbf8f)

v1.4.1

1.4.1 (2022-11-07)

Bug Fixes

• security problem (#220) (4504e34)

Changelog

Sourced from loader-utils's changelog.

1.4.2 (2022-11-11)

Bug Fixes

• ReDoS problem (#226) (17cbf8f)

1.4.1 (2022-11-07)

Bug Fixes

• security problem (#220) (4504e34)

Commits

• 331ad50 chore(release): 1.4.2
• 17cbf8f fix: ReDoS problem (#226)
• 8f082b3 chore(release): 1.4.1
• 4504e34 fix: security problem (#220)
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Bump moment-timezone from 0.5.34 to 0.5.37 in /frontend @dependabot (#374)

Bumps moment-timezone from 0.5.34 to 0.5.37.

Changelog

Sourced from moment-timezone's changelog.

0.5.37 2022.08-25

• Re-publish npm package, because of extra folder present in 0.5.36, check moment/moment-timezone#999

0.5.36 2022.08-25

• IANA TZDB 2022c
• improvements/fixes to data pipeline

0.5.35 2022-08-23

• Fix command injection in data pipeline GHSA-56x4-j7p9-fcf9
• Fix cleartext transmission of sensitive information GHSA-v78c-4p63-2j6c

Thanks to the OpenSSF Alpha-Omega project for reporting these!

Commits

• ffe6f34 Add changelog for 0.5.37
• 450ca63 Bump version to 0.5.37
• 95f1a9b Build moment-timezone 0.5.36
• abba28c Add changelog for 0.5.36
• ac6de03 Bump version to 0.5.36
• 7a5cadf tests: Fix country tests for 2022c
• 6754c75 data: generate 2022c data+tests
• f74a364 bugfix: Wipe tests/zones before generation
• e850f9f grunt: do not bundle zone and contry tests
• f13e22b data: automatically create data/*/VERSION.json for latest
• Additional commits viewable in compare view

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Bump terser from 5.11.0 to 5.14.2 in /frontend @dependabot (#361)

Bumps terser from 5.11.0 to 5.14.2.

Changelog

Sourced from terser's changelog.

v5.14.2

• Security fix for RegExps that should not be evaluated (regexp DDOS)
• Source maps improvements (#1211)
• Performance improvements in long property access evaluation (#1213)

v5.14.1

• keep_numbers option added to TypeScript defs (#1208)
• Fixed parsing of nested template strings (#1204)

v5.14.0

• Switched to @​jridgewell/source-map for sourcemap generation (#1190, #1181)
• Fixed source maps with non-terminated segments (#1106)
• Enabled typescript types to be imported from the package (#1194)
• Extra DOM props have been added (#1191)
• Delete the AST while generating code, as a means to save RAM

v5.13.1

• Removed self-assignments (varname=varname) (closes #1081)
• Separated inlining code (for inlining things into references, or removing IIFEs)
• Allow multiple identifiers with the same name in var destructuring (eg var { a, a } = x) (#1176)

v5.13.0

• All calls to eval() were removed (#1171, #1184)
• source-map was updated to 0.8.0-beta.0 (#1164)
• NavigatorUAData was added to domprops to avoid property mangling (#1166)

v5.12.1

• Fixed an issue with function definitions inside blocks (#1155)
• Fixed parens of new in some situations (closes #1159)

v5.12.0

• TERSER_DEBUG_DIR environment variable
• @​copyright comments are now preserved with the comments="some" option (#1153)

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Update URL to flake8 to fix precommit job. @rossbar (#398)

In principle this could use a bigger makeover; specifically reviewing the versions of all the hooks. In practice most of them should be replaced with ruff.

General maintenance to try to get the CI back into a fully operational state.

Move code of conduct and contributing to top level @tddough98 (#360)

The GitHub Community Standards tab doesn't recognize these files if they are not at the top level. This moves them out of the documentation folder.

Run tests when pushing to main @tddough98 (#359)

When merging into main for the 0.4 release, the tests didn't run. This gets the tests GitHub Action to run when pushing to main. Coverage for coveralls is based on tests on main, so this will keep the coverage badge up to date.