v4.2.1

What's Changed

• Update PyPi deploy workflow to use OIDC authentication by @nfahlgren in #1424

Full Changelog: v4.2...v4.2.1

v4.2

What's Changed

• Enable multi label input by @nfahlgren in #1361
• 1363 floodfill function by @maliagehan in #1364
• Documentation minor bug fixes by @HaleySchuhl in #1372
• Update spectral wavelengths for CropReporter datasets by @nfahlgren in #1374
• Update README.md with Deepsource badge by @HaleySchuhl in #1386
• add new function called detect_color_card by @HaleySchuhl in #1362
  • added flexibility to handle rotation in color cards, consistent chip labeling regardless of orientation, and reduced number of input parameters. Pre-existing pcv.transform.find_color_card still exists but will be deprecated in the future.
• Bugfix/data wrangling update: Roi coord dtype cast by @HaleySchuhl in #1376
• too many leading '#' for block comment by @dhiraj-ms in #1402
• Removed whitespace surrounding docstring text by @zeeuqsze in #1392
• Whitespace after "," by @dhiraj-ms in #1399
• PTC-W0019 - Consider using literal syntax by @zeeuqsze in #1408
• changing doc string conventions for deepsource best practices by @joshqsumner in #1391
• FLK-D200 by @kmurphy61 in #1393
• grouping imports per deepsource by @joshqsumner in #1396
• changing max linewidth in file by @joshqsumner in #1398
• changes for deepsource expecting 2 blank lines by @joshqsumner in #1401
• Deleted variable mask=mask by @zeeuqsze in #1404
• removing redundant object specification by @joshqsumner in #1403
• Py w0069 by @joshqsumner in #1406
• docs: add mtwatso2-eng as a contributor for code by @allcontributors in #1409
• changed comparison order per deepsource standards by @joshqsumner in #1394
• added line after docstring by @AFis-245 in #1397
• docs: add AFis-245 as a contributor for code by @allcontributors in #1410
• Replaced obs with _ by @zeeuqsze in #1405
• Removing unused libraries by @dhiraj-ms in #1407
• Update colorspaces.py add CMYK by @HaleySchuhl in #1390
• PYL-W0612 deepsource replace unused vars by @HaleySchuhl in #1395
• Remove old utility scripts by @nfahlgren in #1411
• Add metadata method by @HaleySchuhl in #1375
• Updated color correction tutorial by @HaleySchuhl in #1415

New Contributors

• @AFis-245 made their first contribution in #1397

Full Changelog: v4.0.1...v4.2

PlantCV v4.0.1

What's Changed

• Bug fix: collapse hierarchical headers for CSV files by @nfahlgren in #1350
• docs: add maldil as a contributor for code by @allcontributors in #1351
• Update Points.md by @JoeDuenwald in #1352
• Bump upper version of NumPy by @nfahlgren in #1347
• Update matplotlib supported versions by @nfahlgren in #1353
• Update pandas supported versions by @nfahlgren in #1354

Full Changelog: v4.0...v4.0.1

PlantCV v4.0

Many thanks to all the contributors for all that hard work that has gone into this release!

What's Changed

• Update 4.x branch by @DannieSheng in #785
• Update the 4.x branch from the main branch by @nfahlgren in #803
• update photosynthesis package to use xarray and analyze entire induction curve protocols by @dschneiderch in #790
• Update 4x from main by @nfahlgren in #806
• Update 4x by @nfahlgren in #812
• Synchronize the main branch with the 4x branch by @nfahlgren in #824
• Addition of constellation homologies workflow with tutorials by @jgerardhodge in #690
• Update YII and NPQ measurements and options by @nfahlgren in #826
• Update 4x by @HaleySchuhl in #835
• Update 4x by @nfahlgren in #847
• Annotation sub-package and point annotation tool (a.k.a. interactive CustomROI) by @HaleySchuhl in #816
• Rebase from master by @HaleySchuhl in #854
• Two io functions by @JorgeGtz in #823
• Update with master by @JorgeGtz in #857
• Update 4x by @nfahlgren in #860
• Pixel scatter visualization by @JorgeGtz in #810
• 2D threshold by @JorgeGtz in #840
• Merges docs fix into the 4x branch by @nfahlgren in #862
• Rebase 4.x branch on the main branch by @nfahlgren in #878
• Create time lapse video (visualize sub package) by @DannieSheng in #762
• Update 4x by @nfahlgren in #884
• Watershed segmentation by @JorgeGtz in #767
• Update 4x by @HaleySchuhl in #897
• Hyperspectral rotation by @HaleySchuhl in #888
• Update 4x by @nfahlgren in #908
• Write hyperspectral data by @JorgeGtz in #889
• Update 4x by @nfahlgren in #919
• Refactor parallel subpackage to use dataframes and grouping by @nfahlgren in #887
• Added automatic grid detection to multi by @jdavidpeery in #911
• Update sample_images to handle phenodata datasets by @nfahlgren in #925
• replace list expression with explicit for loop in segment_image_series by @JorgeGtz in #929
• Apply bugfix to v4 by @nfahlgren in #936
• Update 4x by @nfahlgren in #943
• Add helper function to centralize usage of OpenCV findContours by @nfahlgren in #939
• Update 4.0 by @nfahlgren in #944
• Update roi rectangle objects class by @HaleySchuhl in #946
• Update roi.ellipse to use objects class by @HaleySchuhl in #951
• Update roi custom objects class by @HaleySchuhl in #953
• Update find objects objects class by @HaleySchuhl in #947
• standard color correction matrix function by @JorgeGtz in #931
• Fix test cache dir by @nfahlgren in #957
• Pin matplotlib version by @nfahlgren in #960
• use objects class in roi2mask by @JorgeGtz in #952
• Reconfigure dask futures and client management by @nfahlgren in #958
• Update release 4.0 by @HaleySchuhl in #969
• Update 4.x by @nfahlgren in #970
• Add parameters to mean adaptive thresh by @JorgeGtz in #937
• Update release 4.0 by @HaleySchuhl in #1004
• Update 4.x by @HaleySchuhl in #1005
• Utilize Objects class in pcv.roi.from_binary_image by @HaleySchuhl in #980
• Update report size marker objects class by @HaleySchuhl in #955
• Update roi circle objects class by @HaleySchuhl in #993
• Update visualize_ovelay_two_imgs.md by @jmgordon1223 in #1016
• make Objects class return Objects instance while iterating by @JorgeGtz in #1068
• Pull down updates into 4.x branch by @HaleySchuhl in #1091
• Update release 4.0 by @HaleySchuhl in #1093
• Hsi read data flexible hdr format by @HaleySchuhl in #956
• Changed print to plot in otsu_thresholds.md by @JoeDuenwald in #1101
• Changed print to plot in output_mask.md by @JoeDuenwald in #1102
• Changed print to plot in photosynthesis_analyze_fvfm.md by @JoeDuenwald in #1103
• Limit upper pandas version by @nfahlgren in #1107
• Update 4x by @nfahlgren in #1104
• Update release-4.0 by @nfahlgren in #1108
• Replace command-line scripts with console scripts by @nfahlgren in #1099
• Changed print to plot in rgb2lab.md by @JoeDuenwald in #1117
• Changed print to plot in rgb2hsv.md by @JoeDuenwald in #1116
• Changed print to plot in rgb2gray.md by @JoeDuenwald in #1115
• Changed print to plot in rgb2cmyk.md by @JoeDuenwald in #1114
• Changed print to plot in report_size_marker.md by @JoeDuenwald in #1113
• Changed print to plot in rectangle_mask.md by @JoeDuenwald in #1112
• Changed print to plot in read_image.md by @JoeDuenwald in #1111
• Changed print to plot in photosynthesis_read_cropreporter.md by @JoeDuenwald in #1109
• Changed print to plot in read_bayer.md by @JoeDuenwald in #1110
• Changed print to plot in roi_objects.md by @JoeDuenwald in #1118
• Changed print to plot in scharr_filter.md by @JoeDuenwald in #1124
• Changed print to plot in scale_features.md by @JoeDuenwald in #1123
• Changed print to plot in saturation_threshold.md by @JoeDuenwald in #1122
• Changed both prints to plot in rotate2.md by @JoeDuenwald in #1121
• Changed print to plot in roi2mask.md by @JoeDuenwald in #1120
• Changed print to plot in roi_rectangle.md by @JoeDuenwald in #1119
• Rename objects parameter in pcv.auto_crop by @HaleySchuhl in #954
• update roi_objects with Objects class by @JorgeGtz in #1037
• Changed second print to plot in roi_objects.md by @JoeDuenwald in #1126
• Changed print to plot in segment_angle.md by @JoeDuenwald in #1127
• Changed print to plot in segment_curvature.md by @JoeDuenwald in #1128
• Changed print to plot in segment_euclidean_length.md by @JoeDuenwald in #1129
• Changed print to plot in segment_id.md by @JoeDuenwald in #1130
• Changed both prints to plot in opening.md by @JoeDuenwald in #1131
• Changed print to plot in segment_insertion_angle.md by @JoeDuenwald in #1133
• Changed print to plot in segment_pathlength.md by @JoeDuenwald in #1134
• Changed print to plot in segment_skeleton.md by @JoeDuenwald in https://github.com/...

PlantCV v3.14.3

What's Changed

• Fix ImportError in plantcv caused by change in skimage.feature function name by @fbarbe00 in #998
• Fixed check for binary image by @vektorious in #996
• Updated link and debug print to plot in texture_threshold.md by @kmurphy61 in #1008
• Changed print to plot in analyze_shape.md by @lacostag in #1012
• Update analyze_NIR_intensity.md by @Stylopidae1793 in #1009
• Change print to plot in analyze color by @sdkenney42 in #1017
• Changed print to plot in analyze_thermal_values.md by @JoeDuenwald in #1028
• Update save_matrix.md to remove quotations surrounding filename by @zeeuqsze in #1010
• Typo fix to mask in thermal_hist by @lchavez037 in #1011
• Updated plot to print in analyze_boundary (vertical and horizontal) by @leowlima in #1013
• Fixed typo in visualize_colorspace.md by @JoeDuenwald in #1014
• test PR, changed python versions listed for testing by @joshqsumner in #1015
• Changed print to plot in analyze_spectral.md by @JoeDuenwald in #1019
• changed print to plot in analyze_spectral by @lacostag in #1020
• Changed print to plot in analyze_stem.md by @JoeDuenwald in #1023
• Update apply_mask.md by @Stylopidae1793 in #1021
• Update PULL_REQUEST_TEMPLATE.md changed PR template link from stable branch to latest branch. by @zeeuqsze in #1022
• 1018 add install pytest cov to contribution guide by @maliagehan in #1024
• Scipy ndimage namespace fix by @joshqsumner in #1025
• Update print to plot gaussian_blur.md by @leowlima in #1026
• changed print to plot in apply_mask by @lacostag in #1027
• Changed print to plot in watershed.md by @JoeDuenwald in #1032
• change print to plot in acute_vertex.md.md by @lchavez037 in #1033
• changed white balance print to plot by @sdkenney42 in #1034
• Update_print to plot_gaussian_threshold.md by @leowlima in #1035
• removed an 'else: pass' from analyze_object by @joshqsumner in #1036
• Update HistEqualization by @leowlima in #1038
• update print to plot in watershed by @sdkenney42 in #1039
• Changed print to plot in erode.md by @JoeDuenwald in #1040
• Update canny_edge_detect.md by @jmgordon1223 in #1041
• changed print to plot in cluster_contours by @lacostag in #1042
• Change print to plot in skeletonize.md by @lchavez037 in #1043
• Update_image_add_print to plot by @leowlima in #1044
• update print to plot in triangle_threshold by @sdkenney42 in #1045
• changed print to plot in check_cycles by @lacostag in #1046
• change print to plot transform rescale by @sdkenney42 in #1047
• Update_image_subtract by @leowlima in #1048
• Changed print to plot in fill_segments.md by @JoeDuenwald in #1089
• Update_naive_bayes_classifier by @leowlima in #1088
• Updated print to plot in find_objects by @sdkenney42 in #1087
• updated print to plot in get_nir by @sdkenney42 in #1086
• Update_median_blur by @leowlima in #1085
• updated print to plot in image_add by @sdkenney42 in #1084
• Update_Mean_Threshold by @leowlima in #1083
• update print to plot in image_subtract by @sdkenney42 in #1082
• Changed print to plot in fill_holes.md by @JoeDuenwald in #1081
• Changed print to plot in canny_edge_detect.md by @JoeDuenwald in #1080
• Changed print to plot in check_cycles.md by @JoeDuenwald in #1079
• Changed print to plot in closing.md by @JoeDuenwald in #1078
• update print to plot in invert by @sdkenney42 in #1077
• Changed print to plot in cluster_contours_splitimg by @JoeDuenwald in #1076
• change print to plot stdev_filter.md by @lchavez037 in #1073
• Update_logical_or_print to plot by @leowlima in #1067
• Changed print to plot in crop_position_mask.md by @JoeDuenwald in #1066
• changed print to plot in roi_multi by @lacostag in #1065
• changed print to plot in roi_from_binary_image by @lacostag in #1064
• Update_logical_and_print to plot by @leowlima in #1062
• Changed print to plot in crop.md by @JoeDuenwald in #1061
• change print to plot in roi_ellipse by @lacostag in #1060
• changed print to plot in spectral_index by @sdkenney42 in #1059
• Update_laplace_filter_print to plot by @leowlima in #1058
• change print to plot in roi_circle by @lacostag in #1057
• Change print to plot spatial_clustering.md by @lchavez037 in #1056
• Changed print to plot in custom_range_threshold.md by @JoeDuenwald in #1055
• Changed print to plot in dilate.md by @JoeDuenwald in #1054
• Update_landmark_reference_pt_dist by @leowlima in #1053
• changed print to plot in stdev_filter by @sdkenney42 in #1052
• Change print to plot in distance_transform.md by @JoeDuenwald in #1051
• Change print to plot to sobel_filter by @lchavez037 in #1050
• Update closing.md by @jmgordon1223 in #1049
• Changed print to plot in extract_wavelength.md by @JoeDuenwald in #1094
• Changed print to plot in gaussian_threshold.md by @JoeDuenwald in #1095
• Changed print to plot in logical_xor.md by @JoeDuenwald in #1096
• Changed print to plot in nonuniform_illumination.md by @JoeDuenwald in #1097
• Changed print to plot in object_composition.md by @JoeDuenwald in #1098

New Contributors

• @fbarbe00 made their first contribution in #998
• @kmurphy61 made their first contribution in #1008
• @lacostag made their first contribution in #1012
• @Stylopidae1793 made their first contribution in #1009
• @sdkenney42 made their first contribution in #1017
• @JoeDuenwald made their first contribution in #1028
• @zeeuqsze made their first contribution in #1010
• @leowlima made their first contribution in #1013
• @joshqsumner made their first contribution in #1015

Full Changelog: v3.14.2...v3.14.3

v3.14.2

What's Changed

• Add gif to gitattributes to treat as binary by @nfahlgren in #935
• Rename main branch by @nfahlgren in #940
• Update code conduct by @nfahlgren in #941
• Enable actions release4 by @nfahlgren in #942
• Pin matplotlib to < 3.6 by @nfahlgren in #959
• Add wavelength means Observation to analyze_spectral function by @HaleySchuhl in #964
• Added compatibility for BIP data format of hsi images in read_image by @vektorious in #972
• Update installation.md by @HaleySchuhl in #977
• Morphology segment combine update by @HaleySchuhl in #933

New Contributors

• @vektorious made their first contribution in #972

Full Changelog: v3.14.1...v3.14.2

PlantCV v3.14.1

What's Changed

• Update segment_sort.py by @jdavidpeery in #892
• update documentation for visualize_colorspace by @jdavidpeery in #894
• fix bug in dtype_dict in hyperspectral read_data by @JorgeGtz in #890
• New docs page for pr review process by @jdavidpeery in #895
• Document default values by @jdavidpeery in #899
• Fix overindented docstrings by @nfahlgren in #901
• Remove unnecessary use of comprehension by @deepsource-autofix in #904
• Iterate dictionary directly by @deepsource-autofix in #905
• Remove blank lines after docstring by @deepsource-autofix in #900
• Group imports from same package by @deepsource-autofix in #903
• Doc updates by @HaleySchuhl in #910
• Hsi filename pattern matching by @HaleySchuhl in #916

Full Changelog: v3.14...v3.14.1

PlantCV v3.14

What's Changed

• Finish refactor debugging by @nfahlgren in #848
• add line return to Sample Images function by @HaleySchuhl in #856
• Add deepsource.io config file to repository by @nfahlgren in #858
• Reorganize tests into separate modules by @nfahlgren in #850
• Replace symlinks with image files by @nfahlgren in #861
• Remove unnecessary whitespace by @deepsource-autofix in #865
• Remove commented out code by @deepsource-autofix in #866
• Merge isinstance calls by @deepsource-autofix in #867
• Replace multiple == checks with in by @deepsource-autofix in #868
• Refactor unnecessary else / elif when if block has a return statement by @deepsource-autofix in #870
• Remove blank lines after docstring by @deepsource-autofix in #871
• Remove blank lines after docstring by @deepsource-autofix in #872
• Remove blank lines after docstring by @deepsource-autofix in #873
• Use literal syntax instead of function calls to create data structure by @deepsource-autofix in #874
• Update analysis_approach.md by @ygarrot in #876
• Update versioneer from 0.18 to 0.21 by @nfahlgren in #864
• Omit coverage for the file _version.py by @nfahlgren in #877
• Imported name is not used anywhere in the module PY-W2000 by @nfahlgren in #869
• added sample column to case without variables by @stiphyMT in #882
• support for other dtypes in color correction by @JorgeGtz in #885

New Contributors

• @deepsource-autofix made their first contribution in #865
• @ygarrot made their first contribution in #876
• @stiphyMT made their first contribution in #882

Full Changelog: v3.13.4...v3.14

PlantCV v3.13.4

What's Changed

• Update dependency OpenCV to v4 by @nfahlgren in #846

Full Changelog: v3.13.3...v3.13.4

PlantCV v3.13.3

What's Changed

• Use fewer contours in testing roi_objects by @JorgeGtz in #844
• Update hyperspectral calibration function by @nfahlgren and @JorgeGtz in #845. Thanks to @billygrahamram for bringing the issue to our attention and providing the sample data

Full Changelog: v3.13.2...v3.13.3