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

PlantCV v3.13.2

What's Changed

• Scale color correction matrices to 0-255 in quick color check by @JorgeGtz in #831
• Fix bug in channel order in color correction by @JorgeGtz in #832
• Trigger GitHub Actions deployment workflow when a release is published by @nfahlgren in #833

Full Changelog: v3.13.1...v3.13.2

PlantCV v3.13.1

What's Changed

• Fix line endings when switching between macOS/Linux and Windows by @nfahlgren in #811
• Increase flexibility for processing hyperspectral ENVI header files by @typelogic in #813
• Configure most functions to use the _debug module by @dschneiderch in #807
• Cast contour tuple as a list in find_objects by @JorgeGtz in #830
• Fix bug in color correction by @JorgeGtz in #829

New Contributors

• @typelogic made their first contribution in #813

Full Changelog: v3.13.0...v3.13.1

PlantCV v3.13.0

PlantCV Version 3.13 Updates

• Update imports to discontinue the deprecation warnings in pcv.watershed
• Update scikit-image requirement to scikit-image>=0.13
• Reorganizes our tutorials in several ways:
  • There is now a main tutorials page that is organized as a gallery of tutorial "cards" that can be filtered by keyword tags. Each card has a launch Binder button to access the interactive tutorial and a link to the static tutorial.
  • The tutorial card images and links to notebooks are remote and can be hosted from any GitHub (or other) repository.
  • The static tutorial pages are now grouped in a directory called "tutorials."
  • The static tutorial pages now only have a launch Binder button and render the complete Jupyter notebooks using nbviewer, rather than having a page that recreates the workflow and has a script version of the workflow.
• Added pcv.transform.gamma_correct which performs gamma correction on the input image (wrapper of the skimage gamma correction function).
• Updated the debug method in the backend within more miscellaneous functions.
• Expand the functionality of the metadata matcher portion of plantcv-workflow to support the matching of multiple metadata values.
  • Syntax at the command line (--match id:1,id:2,id:3)
  • Also supports lists in configuration file based parallelization
• Updates plantcv.hyperspectral.read_data to support Band Sequential (BSQ) in addition to Band Interleaved by Line (BIL) raw data formats for ENVI type multi/hyperspectral datasets.
• Adds pcv.visualize.obj_sizes function for annotating the sizes of separate objects onto a visualization.
• Add pcv.visualize. obj_size_ecdf for a new way to visualize: empirical cumulative distribution function (eCDF).
• Converted to base python classes int and bool since numpy is deprecating np.int and np.bool datatypes.
• Update the fill_segments function in the morphology sub-package
  • The added observations are corrected.
  • Also return the filled_mask (which is a label image as an output) along with the filled_image as outputs.
  • The filled_img is generate by calling the added colorize_label_img visualization function.

PlantCV v3.12.1

PlantCV Version 3.12.1 Updates

• Bugfix (from #770 ) for an update since OpenCV function pointPolygonTest was impacting 3 analysis functions from PCV.

• Numpy is deprecating np.int and np.bool; converted these to base python classes int and bool.