AFM-SPM/TopoStats issues and pull requests

#489 - Fix Mermaid diagrams on website...

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: documentation

#488 - Molecule trace x, y, z coordinates

Issue - State: closed - Opened by SylviaWhittle almost 2 years ago - 2 comments
Labels: enhancement

#487 - Add upper threshold option for grain height

Issue - State: open - Opened by SylviaWhittle almost 2 years ago - 4 comments
Labels: enhancement

#486 - Unit tests for area thresholding

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: enhancement, testing

#485 - versioneer.py > setuptools_scm; setup.cfg > pyproject.toml

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 3 comments

#484 - Switch to setuptools_scm and pyproject.toml

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: admin, CI/CD

#482 - Group binary I/O into io submodule

Issue - State: open - Opened by SylviaWhittle almost 2 years ago - 1 comment
Labels: enhancement

#481 - Notebooks

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 7 comments
Labels: Plotting, notebooks

#480 - Fixing plotting in light of feedback

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: bug, Plotting

#479 - Consistent bindwidth in histograms from plotting.py

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: bug, Plotting

#478 - Add grain density statistic

Issue - State: closed - Opened by SylviaWhittle almost 2 years ago
Labels: enhancement

#477 - Add output data for whole image

Issue - State: closed - Opened by SylviaWhittle almost 2 years ago
Labels: enhancement

#473 - Adding FAQ and Glossary; tidying configuration

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: documentation

#472 - 329 | notes that smallest_grain_size_nm2 > 0.0

Pull Request - State: closed - Opened by ns-rse about 2 years ago - 1 comment
Labels: documentation

#470 - Flag or skip images that are too small

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 2 comments
Labels: enhancement, Low Priority

#466 - Documentation versions

Issue - State: closed - Opened by ns-rse about 2 years ago - 1 comment
Labels: enhancement, documentation

#465 - Bespokre Matplotlib rc_params file

Issue - State: closed - Opened by ns-rse about 2 years ago - 1 comment
Labels: enhancement, Plotting

#464 - Fix interpolation issue

Pull Request - State: closed - Opened by SylviaWhittle about 2 years ago - 3 comments

#462 - Improvements to Plotting Jupyter Notebook

Issue - State: closed - Opened by ns-rse about 2 years ago - 1 comment
Labels: enhancement, notebooks

#461 - Add more zeroing steps

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 1 comment
Labels: enhancement

#460 - Add Height Sensor channel to validation.py

Pull Request - State: closed - Opened by SylviaWhittle about 2 years ago - 5 comments

#457 - MPL interpolation causes lines in MPL Images

Issue - State: closed - Opened by MaxGamill-Sheffield about 2 years ago - 9 comments
Labels: bug

#450 - Update use of yaml in io.py to address Deprecation Warning

Issue - State: closed - Opened by ns-rse about 2 years ago - 3 comments
Labels: IO

#448 - Change the plots in 'grains' into binary

Issue - State: closed - Opened by Jean-Du about 2 years ago - 1 comment
Labels: enhancement, Plotting

#446 - Introduce linting with Ruff

Issue - State: closed - Opened by ns-rse about 2 years ago
Labels: CI/CD, linting

#444 - Allow non-members to add labels to blank issues

Issue - State: closed - Opened by ns-rse about 2 years ago - 1 comment
Labels: admin

#436 - Sylvia whittle/268 si smallest grain size

Pull Request - State: closed - Opened by SylviaWhittle about 2 years ago

#435 - Improve logging verbosity configuration

Pull Request - State: closed - Opened by ns-rse about 2 years ago - 6 comments

#432 - Problems flattening mixed height images

Issue - State: closed - Opened by bdiggines about 2 years ago - 2 comments
Labels: bug

#431 - Remove grains based on height

Issue - State: open - Opened by Jean-Du about 2 years ago - 7 comments
Labels: enhancement

#422 - Identify possible channels for target file formats

Issue - State: closed - Opened by ns-rse about 2 years ago - 2 comments
Labels: bug, IO

#418 - Publish TopoStats 2.0 to Sheffield ORDA

Issue - State: closed - Opened by ns-rse about 2 years ago - 2 comments
Labels: admin

#412 - dnatracing refactor - skeletonisation tests required

Issue - State: open - Opened by MaxGamill-Sheffield about 2 years ago - 6 comments
Labels: testing

#410 - Histogram plotting crash

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 3 comments
Labels: bug

#404 - Grainstats crash

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 7 comments
Labels: bug

#403 - Add molecule number in the all_statistics.csv spreadsheet

Issue - State: closed - Opened by Jean-Du about 2 years ago - 5 comments
Labels: enhancement, good first issue

#402 - Dnatracing division by zero

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 2 comments
Labels: bug

#401 - TopoStats hangs while processing

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 4 comments
Labels: bug

#394 - Rename 'upper' and 'lower' in the config file into 'above' and 'below'

Issue - State: closed - Opened by Jean-Du about 2 years ago - 1 comment
Labels: documentation

#392 - Attach release builds to release notes automatically

Issue - State: closed - Opened by ns-rse about 2 years ago - 1 comment
Labels: Low Priority, CI/CD

#383 - Unrotate the image output from dnatracing.py

Issue - State: closed - Opened by Jean-Du about 2 years ago - 1 comment

#382 - Statistics and image output for single molecules

Issue - State: closed - Opened by Jean-Du about 2 years ago - 2 comments

#381 - Plane tilt removal crash

Issue - State: closed - Opened by SylviaWhittle about 2 years ago - 6 comments
Labels: bug

#366 - Failure of DNA tracing results in no grainstats produced

Issue - State: closed - Opened by MaxGamill-Sheffield over 2 years ago - 4 comments
Labels: bug, enhancement, Medium Priority, DNATracing

#361 - Rename '14-small_objects_removed' in the image output

Issue - State: closed - Opened by Jean-Du over 2 years ago - 1 comment
Labels: good first issue, Low Priority, Grains

#351 - Sylvia whittle/298 improve flattening

Pull Request - State: closed - Opened by SylviaWhittle over 2 years ago - 5 comments

#350 - Add Molecule Numbers to Plot Option

Issue - State: open - Opened by MaxGamill-Sheffield over 2 years ago - 2 comments

#349 - Rename 'plotting' in the config_file to 'image_output'

Issue - State: closed - Opened by Jean-Du over 2 years ago - 4 comments
Labels: wontfix, Low Priority

#340 - Add warning outputs for bad input images

Issue - State: closed - Opened by SylviaWhittle over 2 years ago - 2 comments
Labels: enhancement, Low Priority, user experience

#339 - #137 file types/asd

Pull Request - State: closed - Opened by MaxGamill-Sheffield over 2 years ago - 7 comments

#312 - Adai - Matching Trace Images

Issue - State: open - Opened by MaxGamill-Sheffield over 2 years ago - 2 comments

#304 - Support ASD file format

Issue - State: closed - Opened by ns-rse over 2 years ago - 2 comments
Labels: enhancement, IO

#302 - Improve validation of configuration

Issue - State: closed - Opened by ns-rse over 2 years ago - 4 comments
Labels: help wanted, Medium Priority, IO

#301 - Maxgamill sheffield/#243 si units

Pull Request - State: closed - Opened by MaxGamill-Sheffield over 2 years ago - 1 comment

#298 - Improve flattening

Issue - State: closed - Opened by SylviaWhittle over 2 years ago - 4 comments
Labels: bug

#295 - GrainStats refactor

Issue - State: closed - Opened by ns-rse over 2 years ago - 2 comments

#294 - dntracing to use bounded grains from GrainStats

Issue - State: closed - Opened by ns-rse over 2 years ago - 2 comments

#289 - Augment skeletonisation with scikit-image routines

Issue - State: closed - Opened by ns-rse over 2 years ago
Labels: enhancement, Medium Priority, DNATracing

#242 - Google Colab Notebooks for running analyses

Issue - State: closed - Opened by ns-rse over 2 years ago - 1 comment
Labels: documentation, blocked

#200 - Document config file options

Pull Request - State: closed - Opened by bobturneruk over 2 years ago - 5 comments

#183 - Refactoring and tests of dnatracing.py

Issue - State: open - Opened by ns-rse over 2 years ago - 7 comments
Labels: enhancement, Medium Priority

#181 - Require re-approval of Pull Requests after subsequent commits.

Issue - State: closed - Opened by ns-rse over 2 years ago - 4 comments
Labels: admin

#178 - scikit-image-0.19.3 breaks tests....

Issue - State: closed - Opened by ns-rse over 2 years ago - 1 comment
Labels: bug

#168 - Merge curvature calculations into dev

Issue - State: closed - Opened by ns-rse over 2 years ago - 1 comment

#160 - Dev: Minimum bounding box plot showing wrong bounding box

Issue - State: closed - Opened by MaxGamill-Sheffield over 2 years ago - 3 comments
Labels: Low Priority

#137 - Support loading and processing multiple file formats

Issue - State: closed - Opened by ns-rse almost 3 years ago - 9 comments
Labels: IO

#132 - dev-remove-gwyddion: Other Bruker formats not parsed

Issue - State: open - Opened by MaxGamill-Sheffield almost 3 years ago - 2 comments

#120 - Add version output logs for all used libraries

Issue - State: closed - Opened by SylviaWhittle almost 3 years ago
Labels: enhancement, Low Priority

#111 - Metadata file output

Issue - State: open - Opened by LunchBobs almost 3 years ago - 6 comments

#109 - Characterising complex box molecules with wiggling arms

Issue - State: closed - Opened by LunchBobs almost 3 years ago - 1 comment

#94 - 92 | Suggested nomenclature for branches

Pull Request - State: closed - Opened by ns-rse almost 3 years ago - 1 comment

#92 - Standardise nomenclature for branches in contributing guidelines

Issue - State: closed - Opened by ns-rse almost 3 years ago - 3 comments
Labels: documentation

#87 - Config file - what parameters should we capture?

Issue - State: closed - Opened by bobturneruk almost 3 years ago - 6 comments
Labels: blocked

#82 - Use pySPM to load files

Pull Request - State: closed - Opened by bobturneruk almost 3 years ago - 1 comment

#80 - Create example Jupyter Notebook (myBinder, Colab)

Issue - State: closed - Opened by bobturneruk almost 3 years ago - 1 comment
Labels: notebooks

#79 - User Guide / Instructions

Issue - State: closed - Opened by bobturneruk almost 3 years ago - 3 comments
Labels: documentation

#78 - tracingfuncs.reorderTrace.circularTrace causes certain points to be lost

Issue - State: closed - Opened by Jean-Du almost 3 years ago - 1 comment

#56 - Obtain plot x,y data from plotting.py plots

Issue - State: closed - Opened by SylviaWhittle about 3 years ago - 4 comments

#47 - Bacteria adaptation from @gdbenn

Pull Request - State: closed - Opened by bobturneruk over 3 years ago - 1 comment

#34 - Add documentation for splitstatsplotting.py, or remove from repo

Issue - State: closed - Opened by Jean-Du about 4 years ago - 1 comment
Labels: Low Priority

#32 - Add documentation for heightthresholding.py, or remove from repo

Issue - State: closed - Opened by Jean-Du about 4 years ago - 1 comment
Labels: Low Priority

#31 - Add documentation for tracingfuncs.py, or remove from repo

Issue - State: closed - Opened by Jean-Du about 4 years ago - 1 comment
Labels: documentation, Medium Priority

#30 - Add documentation for statsplotting.py, or remove from repo

Issue - State: closed - Opened by Jean-Du about 4 years ago - 1 comment
Labels: Low Priority

#29 - Reorganise functions in traceplotting.py

Issue - State: closed - Opened by Jean-Du about 4 years ago - 1 comment
Labels: Low Priority, Medium Priority, DNATracing

#28 - Add documentation for traceplotting.py, or remove from repo

Issue - State: closed - Opened by Jean-Du about 4 years ago - 1 comment
Labels: Low Priority

GitHub / AFM-SPM/TopoStats issues and pull requests