v4.5

What's Changed

• update-to-jupyter-notebook-instructions by @annacasto in #1587
• Fixed bug: crash when ROI was empty by @rayn-alex in #1589
• Add geospatial metadata attribute to spectral_data class by @k034b363 in #1595

Full Changelog: v4.4...v4.5

PlantCV v4.4

What's Changed

• Pin NumPy to v1.x by @nfahlgren in #1560
• Using generators instead of list comprehension by @natejly in #1544
• Adding missing docstrings by @natejly in #1547
• Deepsource f string fix by @natejly in #1542
• Style fixes by @natejly in #1543
• replacing implicit enumerate by @natejly in #1539
• added-buttons-to-public by @ghernandez-57 in #1524
• added google colab and github buttons to thermal tutorial by @ghernandez-57 in #1527
• add buttons to hyperspectral_smf_tutorial by @ghernandez-57 in #1530
• add google colab and github buttons to machine_learning_tutorial.md by @ghernandez-57 in #1531
• Moved self's "n" attribute initialization to init by @natejly in #1528
• Unnecessary lambda removal by @natejly in #1540
• 1553-combined-object-filter by @k034b363 in #1555
• Constella reworks by @natejly in #1541
• Suppress divide by zero and invalid number warnings by @nfahlgren in #1563
• Turn plotting off after use in tests to avoid warnings by @nfahlgren in #1565
• Fix casting issues that trigger NumPy deprecation warnings by @nfahlgren in #1564
• auto_grid error handling by @nfahlgren in #1562
• Add geospatial attributes to spectral_data class by @k034b363 in #1580
• Add quality control for image color by @kmurphy61 in #1574
• Add kmeans cli by @k034b363 in #1571
• Add "Quick Cutto" ROI function by @HaleySchuhl in #1576
• 1575 image tiling by @k034b363 in #1578

Full Changelog: v4.3.1...v4.4

PlantCV v4.3.1

What's Changed

• Prune test and doc files from sdist by @nfahlgren in #1551

Full Changelog: v4.3...v4.3.1

PlantCV v4.3

What's Changed

• fix-PY-W0069 by @k034b363 in #1433
• docs: add k034b363 as a contributor for code by @allcontributors in #1437
• fix-PYL-R1705 by @k034b363 in #1432
• fix-PTC-W0010 by @k034b363 in #1435
• fix part of PYL-R1710 by @k034b363 in #1438
• Randomize color order default for pcv.watershed() by @tj-schultz in #1441
• docs: add tj-schultz as a contributor for code by @allcontributors in #1445
• Change None values to none strings by @nfahlgren in #1442
• fix-PYL-C0209 by @k034b363 in #1439
• Add min_size to detect_color_card kwargs by @HaleySchuhl in #1449
• visualize.colorspaces.py bugfix by @HaleySchuhl in #1451
• Deepsource fix remove extra line return in init file by @HaleySchuhl in #1447
• 1436 merging function by @k034b363 in #1446
• Update codecov action by @nfahlgren in #1462
• Add pcv.filters.eccentricity by @HaleySchuhl in #1430
• Add DEEPSOURCE_DSN to environment by @nfahlgren in #1464
• Correct camera distortions using checkerboard calibration by @annacasto in #1422
• Improved handling of empty submasks in analyze.spectral_reflectance by @rayn-alex in #1463
• Changed label from segment_sort output obs access to params value by @tj-schultz in #1458
• docs: add tj-schultz as a contributor for code, and bug by @allcontributors in #1465
• docs: add rayn-alex as a contributor for code, bug, and question by @allcontributors in #1466
• Run pytest on the whole project directory by @nfahlgren in #1469
• casted dict keys into list to avoid type error by @natejly in #1468
• docs: add natejly as a contributor for code by @allcontributors in #1470
• Exclude configs from coverage analysis by @nfahlgren in #1471
• fixing assigning result of a function call with no return value by @natejly in #1467
• Exclude more files from coverage analysis by @nfahlgren in #1472
• Add method to quickly filter binary images by @nfahlgren in #1477
• New function analyze.distribution by @kmurphy61 in #1473
• Fixed uninformative assert statements in tests for transform.merge_images() by @k034b363 in #1480
• Bump supported versions of Python to 3.9-3.11 by @nfahlgren in #1491
• Add kmeans classifier function by @k034b363 in #1478
• update _make_pseudo_rgb with more accurate target wavelength for red by @HaleySchuhl in #1492
• Fix bug in plotting debug mode by @nfahlgren in #1496
• fix-PYL-W0612 by @k034b363 in #1497
• Added fatal_error for incorrect block_size value in detect_color_card by @tj-schultz in #1457
• Added tuple check to compare variables by @natejly in #1495
• Removing list comprehension to allow for short circuit evaluation by @natejly in #1494
• Removed generator in threshold_methods.py by @kaitlynrying in #1448
• docs: add kaitlynrying as a contributor for code by @allcontributors in #1501
• Remove deprecated files by @nfahlgren in #1499
• Rois debug numbering by @HaleySchuhl in #1488
• Fixed error in documentation for camera calibration by @annacasto in #1505
• Clean up pytest errors by @nfahlgren in #1517
• draw_roi bugfix by @HaleySchuhl in #1511
• parallel docs for windows Update by @HaleySchuhl in #1519
• Update watershed.py to make the function return labels by @HaleySchuhl in #1482
• Add kmeans tutorial by @k034b363 in #1512
• bugfix for roi_type="largest" in roi.filter by @HaleySchuhl in #1518
• Adding simple rgb tutorial to the tutorial gallergy by @annacasto in #1502
• Adding camera calibration tutorial by @annacasto in #1506
• add buttons to vis tutorial by @ghernandez-57 in #1521
• docs: add ghernandez-57 as a contributor for code, and doc by @allcontributors in #1525
• Added buttons to vis-nir tutorial by @ghernandez-57 in #1522
• google colab button to grayscale tutorial by @ghernandez-57 in #1523
• affine_color_correct docs - code example calling wrong function by @HaleySchuhl in #1533
• Read images over HTTP by @nfahlgren in #1532

New Contributors

• @k034b363 made their first contribution in #1433
• @tj-schultz made their first contribution in #1441
• @rayn-alex made their first contribution in #1463
• @natejly made their first contribution in #1468
• @kaitlynrying made their first contribution in #1448
• @ghernandez-57 made their first contribution in #1521

Full Changelog: v4.2.1...v4.3

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