trace-digitiser 2.1.0__tar.gz → 2.2.0__tar.gz

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/CHANGELOG.md

@@ -4,6 +4,63 @@ All notable changes to trace-digitiser are recorded here.
 The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/)
 and the project uses [semantic versioning](https://semver.org/).
 
+## [2.2.0] - 2026-11-15
+
+Tested on the figures of published papers whose underlying numbers are
+published too (Leypunskiy et al. 2017, eLife 6:e23539: markers with error
+bars, a line over shaded bands; Foley et al. 2019, eLife 8:e50063: bar charts;
+Pearl and Reed 1920, PNAS 6:275, a microfilm scan), 2.1.0 read what it found
+accurately but often found nothing. This release finds much more of it, there
+and on the figures of a paper held out until the changes were made (Andreani
+et al. 2022, eLife 11:e74327). Line plots digitise as before: the package's
+validation suite and the Hearn and Whitmore (2026) examples give the same
+results.
+
+### Added
+
+- **A test set of published figures**
+  ([`validation/published-figures`](https://github.com/comparativechrono/trace-digitiser/tree/main/validation/published-figures)):
+  seven figures from those four papers, the numbers behind them from their
+  authors' data, and a script that reads them with nothing given and with the
+  help a user can give, and compares. Its README has the results of 2.1.0 and
+  2.2.0, case by case, including the few that 2.2.0 reads worse. It is run
+  before each release and is not part of the package.
+
+### Fixed
+
+- **Bar charts in the style of GraphPad Prism**: black, grey, hatched and
+  outlined bars are found, on an axis that does not start at 0 (2.1.0 found 3
+  of the 35 bars of Foley et al.'s figure 2, and read those upside down; all
+  35 are now read, within 0.3 % of the axis). Bars are the columns filled from
+  the baseline, so an error bar or a significance bracket joined to a bar no
+  longer spoils it; a border of another colour (a black outline round a grey
+  bar) is part of the bar; a bar cut by the edge of the plot area is kept.
+- **Error bars drawn in the colour of their bar or marker** (the default in
+  Prism, MATLAB and matplotlib) are followed beyond the bar's end, or from the
+  marker, to their caps; one running across a fitted line goes on beyond it.
+  Where only the half beyond a bar's end shows, a note says so.
+- **Markers sitting on a line of their own colour** (a fitted line, their
+  error bars) are found: other sizes are tried where the lines' ridges
+  outnumber the markers, and such a colour counts as a colour of markers if
+  its markers are joined to its lines and much thicker than them. Round
+  letters of words written in the plot, and a legend's markers beside their
+  words, are left out; a marker found in two series of close colours is kept
+  in the nearer one.
+- **A plot area given by hand** (a box drawn in the workbench, or numbers read
+  off a picture) moves to the middle of the axis lines within a few pixels of
+  it, and their thickness is measured: with a thick axis line the tick labels
+  were looked for inside it, and the axis title was read instead.
+- Long tick marks of a small plot in a large picture are found, so that its
+  labels are anchored to them.
+- A colour that fills areas (a shaded band behind a plot) is not taken for a
+  trace of a line plot.
+- Tick labels that Tesseract misreads as a line of text (75 as 15, in large
+  Helvetica) are read once more as a single word when an axis is not settled.
+- Looking at a whole page of a scanned paper (`describe_figure`, the
+  workbench's first look at a page of a PDF) took a minute and a half, nearly
+  all of it in the search for polar axes; the circles are now proposed on a
+  smaller copy of the page (16 seconds in all).
+
 ## [2.1.0] - 2026-11-14
 
 Everything in 2.0.0 works as before. What is new is readers for other kinds of
@@ -165,6 +222,7 @@ First version tracked in this repository; identical to the 1.2.0 files on PyPI.
 Releases 0.1.0 to 1.0.0 (6-7 June 2026) were uploaded to PyPI directly and are
 not recorded here.
 
+[2.2.0]: https://github.com/comparativechrono/trace-digitiser/compare/v2.1.0...v2.2.0
 [2.1.0]: https://github.com/comparativechrono/trace-digitiser/compare/v2.0.0...v2.1.0
 [2.0.0]: https://github.com/comparativechrono/trace-digitiser/compare/1d34f75...v2.0.0
 [1.2.0]: https://pypi.org/project/trace-digitiser/1.2.0/

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/MANIFEST.in

@@ -5,3 +5,5 @@ recursive-include tests *.py *.csv
 recursive-include examples *.py *.md *.jpg *.ipynb
 prune examples/output
 include CHANGELOG.md RELEASING.md
+# The published-figure test set (validation/published-figures) is run from the repository, not shipped.
+prune validation

{trace_digitiser-2.1.0/src/trace_digitiser.egg-info → trace_digitiser-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trace-digitiser
-Version: 2.1.0
+Version: 2.2.0
 Summary: Recover the data from figure images - lines, points, bars, actograms, heat maps - on your own computer: no uploads, no AI model.
 Author: Trace Digitiser Contributors
 License-Expression: MIT
@@ -267,6 +267,18 @@ Labels under 8 pixels high are never given high confidence, however well they ag
 that small is misread in consistent ways — the decimal point dropped from every label, say. If
 your figure has such labels, enlarging the image does not help; typing in two numbers does.
 
+**Published figures.** The tests above draw their own figures.
+[`validation/published-figures`](https://github.com/comparativechrono/trace-digitiser/tree/main/validation/published-figures)
+holds seven figures from four papers whose authors published the numbers behind them — markers with error bars, a
+line over shaded bands, ten bar charts, dot plots, and a scanned page from 1920 — and reads them with nothing given
+and with the help a user can give. With nothing given, 2.2.0 reads all 35 bars of the bar charts to within 0.3 % of
+the axis, and the 29 points of a scatter plot of four series to within 0.5 % (2.1.0 read none of either); with two
+ticks clicked on each axis and the dots' colour, the census dots of the 1920 figure to within 0.9 %. On the figures
+of a paper held out until the changes were made, with the plot area drawn, it reads 24 bars to within 0.4 % once
+two ticks are clicked, and 33 of 37 points once the ticks of a slanted axis and the colours are. Stacked plots with no gap between them, dot
+plots whose dots overlap, and tick labels that are slanted or hand-lettered still need help or remain hard; that
+folder's README has the details.
+
 ### Test it on data you know
 
 The best test of a digitisation is one on data like yours. `round_trip` draws a known series as a
@@ -312,6 +324,7 @@ cd trace-digitiser
 pip install -e ".[dev]"
 pytest                      # the tests that need Tesseract are skipped without it
 ruff check src tests
+python validation/published-figures/run.py   # figures from papers against their authors' data (minutes)
 ```
 
 `src/trace_digitiser/` in the order the work is done:

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/README.md

@@ -227,6 +227,18 @@ Labels under 8 pixels high are never given high confidence, however well they ag
 that small is misread in consistent ways — the decimal point dropped from every label, say. If
 your figure has such labels, enlarging the image does not help; typing in two numbers does.
 
+**Published figures.** The tests above draw their own figures.
+[`validation/published-figures`](https://github.com/comparativechrono/trace-digitiser/tree/main/validation/published-figures)
+holds seven figures from four papers whose authors published the numbers behind them — markers with error bars, a
+line over shaded bands, ten bar charts, dot plots, and a scanned page from 1920 — and reads them with nothing given
+and with the help a user can give. With nothing given, 2.2.0 reads all 35 bars of the bar charts to within 0.3 % of
+the axis, and the 29 points of a scatter plot of four series to within 0.5 % (2.1.0 read none of either); with two
+ticks clicked on each axis and the dots' colour, the census dots of the 1920 figure to within 0.9 %. On the figures
+of a paper held out until the changes were made, with the plot area drawn, it reads 24 bars to within 0.4 % once
+two ticks are clicked, and 33 of 37 points once the ticks of a slanted axis and the colours are. Stacked plots with no gap between them, dot
+plots whose dots overlap, and tick labels that are slanted or hand-lettered still need help or remain hard; that
+folder's README has the details.
+
 ### Test it on data you know
 
 The best test of a digitisation is one on data like yours. `round_trip` draws a known series as a
@@ -272,6 +284,7 @@ cd trace-digitiser
 pip install -e ".[dev]"
 pytest                      # the tests that need Tesseract are skipped without it
 ruff check src tests
+python validation/published-figures/run.py   # figures from papers against their authors' data (minutes)
 ```
 
 `src/trace_digitiser/` in the order the work is done:

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/RELEASING.md

@@ -45,8 +45,21 @@ plans). Now that the repository is public, one can be added:
 2. In `CHANGELOG.md`, give the section for the version its date in place of
    "unreleased", and end its link at the new tag (`...vX.Y.Z` in place of
    `...HEAD`).
-3. Merge to `main` and wait for the *Tests* workflow to pass.
-4. On GitHub: *Releases -> Draft a new release*, create the tag `vX.Y.Z`
+3. Run the published-figure test set
+   ([`validation/published-figures`](validation/published-figures/README.md)),
+   which reads figures from papers whose data are published, and compare the
+   results with the last release's:
+
+   ```bash
+   python validation/published-figures/run.py \
+       --json validation/published-figures/results-X.Y.Z.json \
+       --compare validation/published-figures/results-<last release>.json
+   ```
+
+   Look into any case marked WORSE before going on. Commit the new results,
+   and update the table in that folder's README (`--markdown` prints it).
+4. Merge to `main` and wait for the *Tests* workflow to pass.
+5. On GitHub: *Releases -> Draft a new release*, create the tag `vX.Y.Z`
    (matching the version exactly, with a leading `v`) on `main`, and publish.
 
 Publishing the release starts the workflow. It checks that the tag matches the

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "trace-digitiser"
-version = "2.1.0"
+version = "2.2.0"
 description = "Recover the data from figure images - lines, points, bars, actograms, heat maps - on your own computer: no uploads, no AI model."
 readme = "README.md"
 license = "MIT"

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/src/trace_digitiser/__init__.py

@@ -231,6 +231,7 @@ def digitise(
     for p in panels:
         masks = detect_trace_masks(
             rgb, p, colours=trace_colours, exclude=exclude_boxes, achromatic=achromatic, darkness=dark,
+            lines_only=True,
         )
         if show_debug:
             print(f"Panel {p['panel_id']}: detected {len(masks)} trace(s)")

{trace_digitiser-2.1.0 → trace_digitiser-2.2.0}/src/trace_digitiser/axis_labels.py

@@ -176,13 +176,16 @@ class Preparation:
 # settled by the first (fast) attempt are therefore read again in other ways
 # and the readings pooled; the axis fit then keeps the readings that agree.
 # The settings and their order were chosen on labels 5 to 7 pixels high in
-# three typefaces: each one added reads labels that the ones before it miss.
+# three typefaces: each one added reads labels that the ones before it miss. The last was added for large print.
 PREPARATIONS = (
     Preparation(44, True, 2.0, True, True, 6),
     Preparation(64, False, 2.0, True, False, 7),
     Preparation(64, True, 0.0, False, False, 7, gamma=0.6),
     Preparation(32, False, 2.0, True, False, 7),
     Preparation(64, False, 0.0, False, False, 7, gamma=0.6),
+    # Large, clean print in some typefaces (MATLAB's Helvetica at 600 dpi) is misread as a line of text (75 as 15)
+    # and read right as a single word.
+    Preparation(64, False, 0.0, True, False, 8),
 )