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GitHub / danforthcenter/plantcv issues and pull requests

#1731 - Regional filter for color card detection

Pull Request - State: open - Opened by joshqsumner 18 days ago

#1730 - Quiet print statements from `pcv.homology.acute`

Pull Request - State: open - Opened by HaleySchuhl 19 days ago - 1 comment
Labels: ready to review, cleanup

#1729 - Quiet print statements in `pcv.homology.acute`

Issue - State: open - Opened by HaleySchuhl 19 days ago
Labels: update, cleanup

#1728 - `Rotate` transformation is not applied about the center of an image

Pull Request - State: closed - Opened by NMiklave 25 days ago - 1 comment
Labels: bugfix, ready to review

#1727 - add "thermal" mode to readimage()

Pull Request - State: open - Opened by AFis-245 about 1 month ago - 1 comment
Labels: new feature, work in progress

#1726 - Add support for automatic size scaling using color cards

Pull Request - State: open - Opened by HaleySchuhl about 1 month ago - 1 comment
Labels: enhancement, new feature, ready to review, update

#1725 - Pin scipy to <1.16

Pull Request - State: closed - Opened by nfahlgren about 1 month ago - 1 comment
Labels: bugfix, ready to review

#1724 - Add the option to read thermal images

Issue - State: open - Opened by AFis-245 about 1 month ago - 6 comments
Labels: new feature

#1723 - Reduce cyclomatic complexity readbayer

Pull Request - State: closed - Opened by nfahlgren about 1 month ago - 1 comment
Labels: ready to review, cleanup

#1722 - Add the option to use real world units in some functions

Issue - State: open - Opened by HaleySchuhl about 1 month ago
Labels: enhancement

#1721 - Can we simplify calculation of the longest path?

Issue - State: open - Opened by HaleySchuhl about 1 month ago
Labels: update, cleanup

#1720 - `morphology.segment_skeleton` returned segment_objects to list

Pull Request - State: closed - Opened by HaleySchuhl about 2 months ago - 1 comment
Labels: bugfix, ready to review, update

#1719 - fill segments --> fill_segments.py --> line 38

Issue - State: closed - Opened by hkmanching about 2 months ago - 1 comment
Labels: help wanted

#1718 - Readimage circ import

Pull Request - State: open - Opened by NMiklave about 2 months ago - 1 comment
Labels: cleanup

#1717 - Size scaling implementation in analysis functions

Pull Request - State: closed - Opened by HaleySchuhl about 2 months ago - 1 comment
Labels: enhancement, ready to review, update

#1716 - docs: add NMiklave as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] about 2 months ago
Labels: contributor

#1715 - Create a logical operation helper function

Pull Request - State: closed - Opened by nfahlgren about 2 months ago - 1 comment
Labels: ready to review, cleanup

#1714 - Add NDCI to spectral indices supported

Pull Request - State: closed - Opened by HaleySchuhl about 2 months ago - 1 comment
Labels: new feature, ready to review

#1713 - Add NDCI to spectral indices

Issue - State: closed - Opened by HaleySchuhl about 2 months ago
Labels: new feature

#1712 - Add global size parameters to `Params` class

Pull Request - State: closed - Opened by HaleySchuhl 2 months ago - 1 comment
Labels: new feature, ready to review

#1711 - Contact PlantCV v4 contributors

Issue - State: open - Opened by k034b363 2 months ago

#1710 - Apply commit b5d1502

Pull Request - State: closed - Opened by steve5636 2 months ago - 1 comment

#1709 - Migrate tutorials to the website

Pull Request - State: closed - Opened by HaleySchuhl 2 months ago - 3 comments
Labels: documentation, ready to review, update

#1708 - Create helpers for color conversion

Pull Request - State: closed - Opened by nfahlgren 2 months ago - 1 comment
Labels: ready to review, cleanup

#1707 - Add `pcv.transform.mask_color_card` function

Pull Request - State: closed - Opened by HaleySchuhl 2 months ago - 1 comment
Labels: new feature, ready to review, update

#1705 - 1704 cmyk plotting and threshold

Pull Request - State: closed - Opened by NMiklave 3 months ago - 3 comments
Labels: enhancement, bugfix, ready to review, update

#1703 - Update array stacking for color standard processing

Pull Request - State: closed - Opened by emmanuel-ferdman 3 months ago - 3 comments
Labels: ready to review, update

#1702 - Fix colors in `visualize.colorize_masks`

Pull Request - State: closed - Opened by k034b363 3 months ago - 1 comment
Labels: bugfix, ready to review

#1701 - Some color values are incorrect for visualize.colorize_masks

Issue - State: closed - Opened by k034b363 3 months ago
Labels: bug

#1700 - update calculation of longest path in `analyze.size`

Pull Request - State: closed - Opened by HaleySchuhl 3 months ago - 1 comment
Labels: bugfix, ready to review, update

#1699 - longest_path values unrealistically large?

Issue - State: closed - Opened by jksshack 3 months ago - 3 comments
Labels: help wanted

#1698 - docs: add abrown-37 as a contributor for ideas

Pull Request - State: closed - Opened by allcontributors[bot] 3 months ago
Labels: contributor

#1697 - Add contributor - Autumn Brown

Issue - State: closed - Opened by k034b363 3 months ago - 2 comments
Labels: contributor

#1696 - Morphology angle Outputs dtype bugfix

Pull Request - State: closed - Opened by HaleySchuhl 3 months ago - 1 comment
Labels: bugfix, ready to review, update

#1695 - adding nd2 as a image read mode

Pull Request - State: closed - Opened by annacasto 3 months ago - 3 comments
Labels: new feature, ready to review

#1694 - Docs update : mvapp link updated and add link to pcvr

Pull Request - State: closed - Opened by HaleySchuhl 3 months ago - 1 comment
Labels: documentation, ready to review

#1693 - New geospatial tutorial

Issue - State: closed - Opened by nfahlgren 3 months ago
Labels: new feature

#1692 - Update tutorials.md

Pull Request - State: closed - Opened by eseigel 3 months ago - 1 comment

#1691 - Create geospatial-plant-height.md

Pull Request - State: closed - Opened by eseigel 3 months ago - 1 comment

#1690 - Create geospatial-plant-height.md

Pull Request - State: closed - Opened by eseigel 3 months ago - 1 comment

#1689 - Retrieve debugging image

Issue - State: open - Opened by MoritzBlumer 3 months ago - 3 comments
Labels: new feature

#1688 - 1676 kmeans spectral

Pull Request - State: open - Opened by k034b363 4 months ago - 1 comment
Labels: enhancement, work in progress

#1687 - Update pinnings to NumPy v2

Pull Request - State: closed - Opened by nfahlgren 4 months ago - 4 comments
Labels: enhancement, bugfix, ready to review

#1686 - Trouble with install/import in colab

Issue - State: closed - Opened by chanelrichardson 4 months ago - 1 comment
Labels: bug, help wanted

#1685 - add capability to read in .czi image files

Issue - State: open - Opened by annacasto 4 months ago
Labels: new feature

#1684 - add capability to read in .nd2 image files.

Issue - State: open - Opened by annacasto 4 months ago
Labels: new feature

#1683 - Add check to train kmeans that inputs must be np arrays

Pull Request - State: closed - Opened by k034b363 5 months ago - 1 comment
Labels: bugfix, ready to review

#1682 - Kmeans training step should check for numpy arrays

Issue - State: closed - Opened by k034b363 5 months ago
Labels: bugfix, update

#1681 - Update PlantCV installation instructions and conda environment file to use only the conda-forge channel

Pull Request - State: closed - Opened by nfahlgren 5 months ago - 1 comment
Labels: documentation, ready to review

#1680 - Added background image input to visualize.pseudocolor

Pull Request - State: closed - Opened by rayn-alex 5 months ago - 10 comments
Labels: enhancement, ready to review, update

#1677 - Use opencv headless

Pull Request - State: open - Opened by nfahlgren 5 months ago - 1 comment
Labels: enhancement, work in progress, breaking

#1676 - Allow kmeans to use hyper spectral images

Issue - State: open - Opened by k034b363 5 months ago
Labels: new feature

#1675 - Add help for challenging color card detection

Issue - State: open - Opened by HaleySchuhl 5 months ago
Labels: enhancement, documentation, update

#1674 - Regional filtering

Issue - State: open - Opened by HaleySchuhl 5 months ago
Labels: new feature, update

#1673 - add `metadata` to `_package_index` in spectral_index.py

Pull Request - State: closed - Opened by HaleySchuhl 6 months ago - 1 comment
Labels: bugfix, ready to review, update

#1672 - `metadata` attribute is missing in calculated spectral indices

Issue - State: closed - Opened by HaleySchuhl 6 months ago
Labels: bug, enhancement, update

#1671 - Reduce complexity and add helpers to `morphology.segment_insertion_angle`

Pull Request - State: closed - Opened by HaleySchuhl 6 months ago - 1 comment
Labels: work in progress, update, cleanup

#1670 - Update crop_position_mask.py

Pull Request - State: closed - Opened by eseigel 6 months ago - 1 comment
Labels: bug, enhancement, ready to review

#1669 - Update closing.py

Pull Request - State: closed - Opened by eseigel 6 months ago - 1 comment
Labels: enhancement, ready to review

#1668 - Update d type in fill_holes.py check

Pull Request - State: closed - Opened by eseigeldanf 6 months ago - 1 comment
Labels: ready to review

#1667 - Bug in outputs in `pcv.morphology.fill_segments` function

Issue - State: closed - Opened by HaleySchuhl 6 months ago - 1 comment
Labels: bug, bugfix, update

#1666 - update tuple outputs so they will be treated as single-value traits

Issue - State: open - Opened by HaleySchuhl 6 months ago
Labels: new feature, update

#1665 - docs: add clhendrikse as a contributor for tutorial, and doc

Pull Request - State: closed - Opened by allcontributors[bot] 6 months ago - 1 comment
Labels: contributor

#1664 - Add deprecation warning about `label` from the detect color card function

Pull Request - State: closed - Opened by HaleySchuhl 6 months ago - 1 comment
Labels: bugfix, ready to review, update, cleanup

#1663 - docs: add Sunitalama2 as a contributor for tutorial, and doc

Pull Request - State: closed - Opened by allcontributors[bot] 6 months ago - 1 comment
Labels: ready to review, contributor

#1662 - docs: add trogers623 as a contributor for tutorial, and doc

Pull Request - State: closed - Opened by allcontributors[bot] 6 months ago - 1 comment
Labels: ready to review, contributor

#1661 - docs: add eseigeldanf as a contributor for bug, tutorial, and doc

Pull Request - State: closed - Opened by allcontributors[bot] 6 months ago - 1 comment
Labels: ready to review, contributor

#1660 - Remove `label` parameter from `pcv.transform.detect_color_card` and `auto_correct_color` in v5.0

Issue - State: open - Opened by HaleySchuhl 6 months ago - 10 comments
Labels: update, cleanup

#1659 - updating the getting started page

Pull Request - State: closed - Opened by annacasto 6 months ago - 3 comments
Labels: documentation, ready to review

#1658 - adding json2csv to run-workflow

Pull Request - State: closed - Opened by joshqsumner 6 months ago - 1 comment
Labels: enhancement

#1657 - Linking to scribe tutorial for parallelization

Pull Request - State: closed - Opened by joshqsumner 6 months ago - 1 comment
Labels: documentation, ready to review

#1656 - updating install instructions

Pull Request - State: closed - Opened by annacasto 6 months ago - 1 comment
Labels: documentation, ready to review

#1655 - Updating install docs

Issue - State: open - Opened by annacasto 6 months ago

#1654 - changing parallelization defaults

Pull Request - State: closed - Opened by joshqsumner 6 months ago - 1 comment
Labels: enhancement, ready to review

#1653 - Parallelization docs linking

Pull Request - State: closed - Opened by joshqsumner 6 months ago - 1 comment
Labels: documentation, ready to review

#1652 - Json2csv update: handle lists of coordinates

Pull Request - State: open - Opened by HaleySchuhl 7 months ago - 2 comments
Labels: enhancement, bugfix, work in progress, update

#1651 - Exclude Objects touching/overlapping ROI border

Issue - State: open - Opened by jksshack 7 months ago - 2 comments
Labels: new feature

#1650 - Allow independent background image in plantcv.visualize.pseudocolor() and others.

Issue - State: closed - Opened by rayn-alex 7 months ago - 4 comments
Labels: new feature

#1649 - Add optional pixel to mm conversion in plantcv.analyze.size and others

Issue - State: open - Opened by rayn-alex 7 months ago - 10 comments
Labels: new feature, Epic

#1648 - Fix mask kmeans output type

Pull Request - State: closed - Opened by k034b363 7 months ago - 1 comment
Labels: bugfix, ready to review

#1647 - Add "prune by height" function to morphology subpackage

Pull Request - State: open - Opened by HaleySchuhl 7 months ago - 1 comment
Labels: new feature, work in progress, update, merge in order

#1646 - Add a radial option to analyze.distribution

Issue - State: open - Opened by k034b363 7 months ago
Labels: new feature

#1645 - JSONDecodeError using outputs.save_results

Issue - State: closed - Opened by jksshack 8 months ago - 3 comments
Labels: help wanted

#1644 - Add `segment_ends` and Update morphology tips outputs

Pull Request - State: closed - Opened by HaleySchuhl 8 months ago - 2 comments
Labels: new feature, bugfix, ready to review, update

#1643 - Skeleton tips easily overwritten within the `plantcv.morphology` sub-package

Issue - State: closed - Opened by HaleySchuhl 8 months ago
Labels: update, cleanup

#1642 - add tassel tutorial to gallery (merge updates to tutorial repo first)

Pull Request - State: closed - Opened by HaleySchuhl 8 months ago - 1 comment
Labels: documentation, ready to review

#1641 - Helper function for handling diverse input data types

Issue - State: open - Opened by k034b363 8 months ago - 1 comment
Labels: new feature

#1640 - update read_data to transform uint8 data

Pull Request - State: open - Opened by HaleySchuhl 8 months ago - 1 comment
Labels: enhancement, work in progress, update

#1639 - Update parallel configuration defaults: `append` and `tmp_dir`

Issue - State: closed - Opened by HaleySchuhl 8 months ago
Labels: enhancement, new feature, update

#1637 - All in one Dashboard

Issue - State: closed - Opened by danammeansbear 8 months ago - 1 comment

#1636 - docs: add jbraley1107 as a contributor for bug

Pull Request - State: closed - Opened by allcontributors[bot] 8 months ago
Labels: contributor

#1635 - Improve datatype checks

Issue - State: open - Opened by HaleySchuhl 9 months ago - 2 comments
Labels: enhancement, help wanted, update, good first issue/PR

#1634 - docs: add mlohbihler as a contributor for bug, and doc

Pull Request - State: closed - Opened by allcontributors[bot] 9 months ago - 1 comment
Labels: ready to review, contributor

#1633 - Update grayscale_tutorial.md

Pull Request - State: closed - Opened by zeeuqsze 9 months ago - 1 comment
Labels: documentation

#1632 - Update watershed_segmentation_tutorial.md

Pull Request - State: closed - Opened by zeeuqsze 9 months ago - 1 comment
Labels: documentation