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 #1135
• Changed print to plot in segment_sort.md by @JoeDuenwald in #1136
• Changed print to plot in segment_tangent_angle.md by @JoeDuenwald in #1137
• Changed print to plot in shift.md by @JoeDuenwald in #1138
• Update 4x with updates in main by @nfahlgren in #1139
• Simplify histogram code and fix bug in minimum value calculation by @nfahlgren in #1141
• Update 4.x by @nfahlgren in #1142
• Update release 4.0 by @nfahlgren in #1143
• Fix threshold dual channels returning bad dtype by @JorgeGtz in #1144
• Release 4.0 bugfix by @HaleySchuhl in #1146
• Make helper roi_filter function by @JorgeGtz in #1147
• Add pcv.create_labels function by @HaleySchuhl in #1149
• Add iteration helper function by @nfahlgren in #1148
• Add composition helper function by @nfahlgren in #1152
• Add grayscale to rgb helper by @nfahlgren in #1153
• Add affine color correction function by @JorgeGtz in #1150
• Update release 4 by @nfahlgren in #1157
• Add analysis submodule and shape analysis function by @nfahlgren in #1154
• Added-warn-function-replace-print by @zeeuqsze in #1159
• Add warn cluster contour splitimg by @zeeuqsze in #1160
• Add-warn-replace-print-obj-comp by @zeeuqsze in #1163
• add-warn-replace-print-roi_objects by @zeeuqsze in #1164
• add-warn-replace-print-analyze_index by @zeeuqsze in #1165
• add-warn-replace-print-roi_methods by @zeeuqsze in #1166
• add-warn-replace-print-threshold_methods by @zeeuqsze in #1167
• add-warn-replace-print-helpers by @zeeuqsze in #1168
• Add analyze color function to analyze submodule by @nfahlgren in #1170
• start function bound horizontal by @JorgeGtz in #1161
• Define type for markers in watershed by @nfahlgren in #1175
• Update release4 by @nfahlgren in #1176
• Iterate analyze grayscale by @nfahlgren in #1172
• Add updated analysis function for thermal images that utilizes iteration by @nfahlgren in #1177
• Add type to markers by @nfahlgren in #1181
• Update codecov action to v3 by @nfahlgren in #1180
• Update release 4.0 by @nfahlgren in #1183
• Add analyze.spectral_reflectance function by @nfahlgren in #1178
• Add analyze.spectral_index function by @nfahlgren in #1179
• Remove obj from homology.acute by @nfahlgren in #1186
• Update x axis pseudolandmarks, remove obj input parameter by @HaleySchuhl in #1169
• Update y axis pseudolandmarks by @HaleySchuhl in #1185
• Updates to stored "tips" and "branch_pts" getting stored to observations during Morphology workflows by @HaleySchuhl in #995
• Skip CSV output for x-y points by @nfahlgren in #1198
• Update pseudocolor remove obj and obj_padding by @nfahlgren in #1184
• auto_crop replace objects param with mask by @HaleySchuhl in #1192
• Move landmark_reference_pt_dist to the homology submodule by @nfahlgren in #1199
• Refactor scale_features by @nfahlgren in #1200
• Deprecate cluster_contours by @HaleySchuhl in #1195
• Deprecate cluster contours splitimg by @HaleySchuhl in #1196
• Deprecate cluster contours mask by @HaleySchuhl in #1197
• Generalize photosynthesis filenaming by @wurDevTim in #984
• Deprecate acute_vertex by @nfahlgren in #1187
• Deprecate analyze bound horizontal by @nfahlgren in #1188
• Deprecate analyze bound vertical by @nfahlgren in #1189
• Deprecate analyze color by @nfahlgren in #1190
• find_color_card typo fix, move "label" param into correct function by @HaleySchuhl in #1202
• Minor docs fixes by @nfahlgren in #1204
• Deprecate analyze_nir_intensity by @nfahlgren in #1205
• Deprecate analyze_object by @nfahlgren in #1206
• Deprecate analyze_thermal_values by @nfahlgren in #1207
• Remove hyperspectral.analyze_index by @nfahlgren in #1208
• Deprecate rectangle mask by @nfahlgren in #1209
• Iterate psii analysis by @nfahlgren in #1201
• remove max_val param from threshold.binary() by @afinit in #1210
• remove max_val param from threshold.mean() by @afinit in #1212
• remove max_val param from threshold.otsu() by @afinit in #1213
• remove max_val param from threshold.gaussian() by @afinit in #1214
• remove max_val param from threshold.triangle() by @afinit in #1218
• remove max_val param from threshold.texture() by @afinit in #1219
• remove max_val param from threshold._call_threshold() by @afinit in #1220
• remove max_val param from threshold._call_adaptive_threshold() by @afinit in #1221
• Remove deprecated plantcv.rotate function by @afinit in #1222
• remove max_val param from threshold.dual_channels() by @afinit in #1224
• Add all-contributors table and badge by @nfahlgren in #1215
• Deprecate object composition by @nfahlgren in #1216
• optimizing naive_bayes_classifier by @afinit in #1223
• Add config file for Read the Docs by @nfahlgren in #1226
• Update release-4.0 from main by @nfahlgren in #1230
• Deprecate visualize cluster contours by @HaleySchuhl in #1229
• Deprecate roi objects by @HaleySchuhl in #1228
• docs: add maliagehan as a contributor for projectManagement, code, and 3 more by @allcontributors in #1234
• docs: add HaleySchuhl as a contributor for code, doc, and 6 more by @allcontributors in #1236
• docs: add DannieSheng as a contributor for code, doc, and 2 more by @allcontributors in #1240
• docs: add dschneiderch as a contributor for code, doc, and 2 more by @allcontributors in #1242
• docs: add GrantKonkel as a contributor for code, and doc by @allcontributors in #1245
• docs: add bganglia as a contributor for code, doc, and test by @allcontributors in #1246
• docs: add JoeDuenwald as a contributor for doc by @allcontributors in #1248
• docs: add JorgeGtz as a contributor for code, doc, and 4 more by @allcontributors in #1251
• docs: add sdkenney42 as a contributor for doc by @allcontributors in #1253
• docs: add maxjfeldman as a contributor for code, doc, and ideas by @allcontributors in #1254
• docs: add jshoyer as a contributor for code, doc, and ideas by @allcontributors in #1255
• docs: add jdavidpeery as a contributor for code, doc, and 2 more by @allcontributors in #1256
• docs: add leowlima as a contributor for doc by @allcontributors in #1257
• docs: add jberry47 as a contributor for code, doc, and 2 more by @allcontributors in #1258
• docs: add calizarr as a contributor for code, doc, and test by @allcontributors in #1259
• docs: add aapokor as a contributor for code, doc, and test by @allcontributors in #1260
• docs: add scallen81 as a contributor for code by @allcontributors in #1261
• docs: add lacostag as a contributor for doc by @allcontributors in #1262
• docs: add Stylopidae1793 as a contributor for doc by @allcontributors in #1263
• docs: add jwheeler5 as a contributor for code, doc, and test by @allcontributors in #1264
• docs: add AdamDimech as a contributor for code, doc, and 2 more by @allcontributors in #1265
• docs: add annacasto as a contributor for code, doc, and 4 more by @allcontributors in #1266
• docs: add ic as a contributor for code, doc, and test by @allcontributors in #1267
• docs: add lchavez037 as a contributor for doc by @allcontributors in #1268
• docs: add adrianethompson as a contributor for code, doc, and tutorial by @allcontributors in #1269
• docs: add SethPolydore as a contributor for code, doc, and test by @allcontributors in #1270
• docs: add Jake-Jasper as a contributor for code, and doc by @allcontributors in #1271
• docs: add joshqsumner as a contributor for code, doc, and 3 more by @allcontributors in #1272
• docs: add vektorious as a contributor for code, doc, and test by @allcontributors in #1273
• docs: add cluebbert as a contributor for code by @allcontributors in #1274
• docs: add AzlinII as a contributor for code by @allcontributors in #1275
• docs: add jmgordon1223 as a contributor for doc by @allcontributors in #1276
• docs: add zeeuqsze as a contributor for doc, tutorial, and 2 more by @allcontributors in #1277
• docs: add fbarbe00 as a contributor for code by @allcontributors in #1278
• docs: add typelogic as a contributor for code by @allcontributors in #1279
• docs: add Sanazjd as a contributor for code, doc, and 2 more by @allcontributors in #1280
• docs: add fabid as a contributor for code by @allcontributors in #1281
• docs: add jgerardhodge as a contributor for code, doc, and test by @allcontributors in #1282
• docs: add kmurphy61 as a contributor for doc, tutorial, and 3 more by @allcontributors in #1283
• docs: add stiphyMT as a contributor for code by @allcontributors in #1284
• docs: add ygarrot as a contributor for doc by @allcontributors in #1285
• docs: add stevenhwu as a contributor for code by @allcontributors in #1286
• docs: add kbgilbert as a contributor for design by @allcontributors in #1287
• docs: add nfahlgren as a contributor for projectManagement, code, and 8 more by @allcontributors in #1288
• docs: add maliagehan as a contributor for talk, tutorial, and 3 more by @allcontributors in #1289
• docs: add wurDevTim as a contributor for code, doc, and test by @allcontributors in #1290
• docs: add afinit as a contributor for code, doc, and test by @allcontributors in #1291
• Update release-4.0 [skip ci] by @nfahlgren in #1292
• Deprecate get_nir by @HaleySchuhl in #1294
• Deprecate analyze spectral by @HaleySchuhl in #1295
• Update Watershed tutorial by @maliagehan in #1298
• Add grayscale tutorial and replace old NIR by @HaleySchuhl in #1300
• Limit jupyterlab [skip ci] by @nfahlgren in #1307
• Update PSII dataset names by @nfahlgren in #1309
• Tutorial update vis nir by @HaleySchuhl in #1301
• Tutorial Update thermal by @HaleySchuhl in #1302
• Update vis tutorial by @HaleySchuhl in #1303
• Update multi object tutorial by @HaleySchuhl in #1305
• Update ml / Naive Bayes tutorial by @HaleySchuhl in #1306
• Update morphology_tutorial by @HaleySchuhl in #1308
• Update tutorial input output by @HaleySchuhl in #1311
• Hyperspectral tutorial by @maliagehan in #1313
• Remove max value references by @HaleySchuhl in #1314
• Replace plotnine with altair by @nfahlgren in #1319
• Update seed tutorial URLs by @Stylopidae1793 in #1316
• Add hyperspectral crop by @maliagehan in #1323
• update contribution guide by @maliagehan in #1320
• Revise updating.md by @HaleySchuhl in #1324
• Only add tabulate naive bayes.md [skip ci] by @HaleySchuhl in #1318
• Rename to ksize in adaptive thresholding methods by @HaleySchuhl in #1325
• Cropreporter adding pam by @wurDevTim in #1217
• Add extra table of contents links by @nfahlgren in #1326
• Deprecate print results by @nfahlgren in #1327
• smf gallery wall by @maliagehan in #1329
• Rename job_extra to job_extra_directives by @nfahlgren in #1333
• Update installation guide by @nfahlgren in #1332
• Add sample label param by @nfahlgren in #1328
• Remove binder buttons from tutorial gallery by @HaleySchuhl in #1331
• Change license mpl2 by @nfahlgren in #1334
• Update PSII tutorial by @nfahlgren in #1336
• Update json2csv outputs by @nfahlgren in #1335
• Tutorial arabidopsis multi plant by @HaleySchuhl in #1338
• Set num_labels to num ROIs by @nfahlgren in #1340
• Remove find objects functions by @dhiraj-ms in #1341
• docs: add dhiraj-ms as a contributor for code, doc, and test by @allcontributors in #1342
• update docs by @HaleySchuhl in #1339
• Release 4.0 by @nfahlgren in #1346

New Contributors

• @wurDevTim made their first contribution in #984
• @afinit made their first contribution in #1210
• @allcontributors made their first contribution in #1234
• @dhiraj-ms made their first contribution in #1341

Full Changelog: v3.14.3...v4.0