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mkdocs.yml
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site_name: PlantCV
site_url: https://plantcv.readthedocs.io/
site_description: Plant phenotyping using computer vision
site_author: PlantCV Development Team
repo_url: https://github.com/danforthcenter/plantcv
copyright: Copyright 2020, Donald Danforth Plant Science Center
theme: readthedocs
nav:
- Home: index.md
- Documentation:
- 'Installation': installation.md
- 'Updating PlantCV': updating.md
- 'Frequently Asked Questions': faq.md
- 'Analysis Approaches': analysis_approach.md
- 'Using Jupyter Notebooks': jupyter.md
- 'Summary of Output Measurements': output_measurements.md
- 'Contributing':
- 'Contributing to PlantCV': CONTRIBUTING.md
- 'Code of Conduct': CODE_OF_CONDUCT.md
- 'Adding/Editing Documentation': documentation.md
- 'Pull Request Review Process' : pr_review_process.md
- "Tutorials": tutorials.md
- 'Workflow Parallelization': pipeline_parallel.md
- 'Exporting Data': db-exporter.md
- 'PlantCV Namespace':
- 'PlantCV':
- 'Inputs and Outputs':
- 'Print Image': print_image.md
- 'Plot Image': plot_image.md
- 'Read Image': read_image.md
- 'Read Bayer Raw Image': read_bayer.md
- 'Analysis Methods':
- 'Analyze Color': analyze_color2.md
- 'Analyze Pixel Distributions': analyze_distribution.md
- 'Analyze Grayscale': analyze_grayscale.md
- 'Analyze Size and Shape': analyze_size.md
- 'Horizontal Boundary Tool': analyze_bound_horizontal2.md
- 'Vertical Boundary Tool': analyze_bound_vertical2.md
- 'Analyze Thermal': analyze_thermal.md
- 'Analyze Spectral Reflectance': analyze_spectral_reflectance.md
- 'Analyze Spectral Index': analyze_spectral_index.md
- 'Analyze YII': analyze_yii.md
- 'Analyze NPQ': analyze_npq.md
- 'Annotation Tools':
- 'Points': Points.md
- 'Apply Mask': apply_mask.md
- 'Auto Crop': auto_crop.md
- 'Background Subtraction': background_subtraction.md
- 'Canny Edge Detection': canny_edge_detect.md
- 'Closing': closing.md
- 'Color Palette': color_palette.md
- 'Colorspace Conversion':
- 'RGB to Gray': rgb2gray.md
- 'RGB to CMYK': rgb2cmyk.md
- 'RGB to LAB': rgb2lab.md
- 'RGB to HSV': rgb2hsv.md
- 'Create Labels': create_labels.md
- 'Crop': crop.md
- 'Crop and Position Mask': crop_position_mask.md
- 'Dilation': dilate.md
- 'Distance Transform': distance_transform.md
- 'Erosion': erode.md
- 'Fill Objects': fill.md
- 'Fill Holes': fill_holes.md
- 'Flood Fill': floodfill.md
- 'Flip Image': flip.md
- 'Filters':
- 'Eccentricity Filter': filters_eccentricity.md
- 'Object Filter': filters_obj_props.md
- 'Laplace Filter': laplace_filter.md
- 'Sobel Filter': sobel_filter.md
- 'Scharr Filter': scharr_filter.md
- 'Gaussian Blur': gaussian_blur.md
- 'Get Kernel': get_kernel.md
- 'Histogram Normalization': HistEqualization.md
- 'Hyperspectral Data':
- 'Analyze Spectral Reflectance': analyze_spectral_reflectance.md
- 'Analyze Spectral Index': analyze_spectral_index.md
- 'Calibrate HSI': calibrate.md
- 'Crop HSI': crop.md
- 'Spectral Index': spectral_index.md
- 'Extract wavelength': extract_wavelength.md
- 'Rotate HSI': hyperspectral_rot90.md
- 'Spectral data objects': Spectral_data.md
- 'Write HSI data': write_data.md
- 'Image Add': image_add.md
- 'Image Subtract': image_subtract.md
- 'Image Fusion': image_fusion.md
- 'Invert': invert.md
- 'I/O Functions':
- 'Open Image from URL': io_open_url.md
- 'Random Subset': io_random_subset.md
- 'Read Dataset': io_read_dataset.md
- 'Kmeans Clustering Classifier': kmeans_classifier.md
- 'Landmark Analysis':
- 'Acute': homology_acute.md
- 'Space': homology_space.md
- 'StarScape': homology_starscape.md
- 'Constella': homology_constella.md
- 'ConstellaQC': homology_constellaqc.md
- 'x-Axis Pseudolandmarks': homology_x_axis_pseudolandmarks.md
- 'y-Axis Pseudolandmarks': homology_y_axis_pseudolandmarks.md
- 'Scale Features': homology_scale_features.md
- 'Landmark Reference Point Distribution': homology_landmark_reference_pt_dist.md
- 'Logical Operations':
- 'Logical Operations-And': logical_and.md
- 'Logical Operations-Or': logical_or.md
- 'Logical Operations-XOr': logical_xor.md
- 'Median Blur': median_blur.md
- 'Morphology Functions':
- 'Analyze_stem': analyze_stem.md
- 'Check Cycles': check_cycles.md
- 'Fill Segments': fill_segments.md
- 'Find Branches': find_branch_pts.md
- 'Find Tips': find_tips.md
- 'Prune': prune.md
- 'Segment Angles': segment_angle.md
- 'Combine Segments': segment_combine.md
- 'Segment Curvature': segment_curvature.md
- 'Segment Euclidean Length': segment_euclidean_length.md
- 'Segment ID': segment_id.md
- 'Segment Insertion Angle': segment_insertion_angle.md
- 'Segment Path Length': segment_pathlength.md
- 'Segment Skeleton': segment_skeleton.md
- 'Segment Sort': segment_sort.md
- 'Segment Tangent Angle': segment_tangent_angle.md
- 'Skeletonize': skeletonize.md
- 'Naive Bayes Classifier': naive_bayes_classifier.md
- 'Objects Class': objects.md
- 'Opening': opening.md
- 'Output Mask': output_mask.md
- 'Outputs Class': outputs.md
- 'Photosynthesis Functions':
- 'Read CropReporter Data': photosynthesis_read_cropreporter.md
- 'Reassign Frame Labels': photosynthesis_reassign_frame_labels.md
- 'Analyze YII': analyze_yii.md
- 'Analyze NPQ': analyze_npq.md
- 'Visualize chlorophyll Fluorescence': visualize_chlorophyll_fluorescence.md
- 'Params (Debugging)': params.md
- 'Print Image': print_image.md
- 'Plot Image': plot_image.md
- "Quality Control Tools":
- "Exposure": qc_exposure.md
- 'Read Image': read_image.md
- 'Read Bayer Raw Image': read_bayer.md
- 'Report Size Marker': report_size_marker.md
- 'Region of Interest Tools':
- 'Create a Circular ROI': roi_circle.md
- 'Create an Elliptical ROI': roi_ellipse.md
- 'Create a Rectangular ROI': roi_rectangle.md
- 'Create a Custom ROI': roi_custom.md
- 'Create ROI from Binary Image': roi_from_binary_image.md
- 'Create Multi ROIs': 'roi_multi.md'
- 'Create Grid of ROIs Automatically': roi_auto_grid.md
- 'Create Grid of Circular ROIs Automatically': roi_auto_wells.md
- 'Filter a mask by ROI': roi_filter.md
- 'Filter a mask by ROI (quickly)': roi_quick_filter.md
- 'Convert ROI to Mask': roi2mask.md
- 'Segment Image Series': segment_image_series.md
- 'Shift Image': shift.md
- 'Spatial Clustering': spatial_clustering.md
- 'Spectral Index': spectral_index.md
- 'Standard Deviation Filter': stdev_filter.md
- 'Thresholding Methods':
- 'Binary Threshold': binary_threshold.md
- 'Custom Range Threshold': custom_range_threshold.md
- 'Gaussian Adaptive Threshold': gaussian_threshold.md
- 'Mask Bad Threshold': mask_bad_threshold.md
- 'Mean Adaptive Threshold': mean_threshold.md
- 'Otsu Auto Threshold': otsu_threshold.md
- 'Saturation Threshold': saturation_threshold.md
- 'Threshold Two Channels': threshold_dual_channels.md
- 'Triangle Auto Threshold': triangle_threshold.md
- 'Texture Threshold': texture_threshold.md
- 'Transformation Methods':
- 'Auto-Detect Color Card': transform_detect_color_card.md
- 'Auto-Detect Color Card (old)': find_color_card.md
- 'Auto Correct Color': transform_auto_correct_color.md
- 'Calibrate Camera': transform_calibrate_camera.md
- 'Checkerboard Calibration': transform_checkerboard_calibration.md
- 'Create Color Card Mask': create_color_card_mask.md
- 'Convert Color Card to Matrix': get_color_matrix.md
- 'Color Correction Workflow': transform_correct_color.md
- 'Quick Color Check': quick_color_check.md
- 'Affine Color Correction': transform_affine_color_correction.md
- 'Standard Color Matrix': std_color_matrix.md
- 'Gamma Correction': transform_gamma_correct.md
- 'Merge Images': transform_merge_images.md
- 'Nonuniform Illumination Correction': nonuniform_illumination.md
- 'Perspective warp': transform_warp.md
- 'Rescale Image Values': transform_rescale.md
- 'Resize Images': transform_resize.md
- 'Rotate': rotate2.md
- 'Transformation Helpers':
- 'Calculate Moore-Penrose Inverse Matrix': mp_inverse.md
- 'Create Color Correction Matrix': transformation_matrix.md
- 'Apply Color Correction Matrix': apply_transformation_matrix.md
- 'Load Matrix': load_matrix.md
- 'Save Matrix': save_matrix.md
- 'Visualization Methods':
- 'Auto Threshold Methods': visualize_auto_threshold_methods.md
- 'Chlorophyll Fluorescence': visualize_chlorophyll_fluorescence.md
- 'Colorize Label Image': visualize_colorize_label_img.md
- 'Colorize Masks': visualize_colorize_masks.md
- 'Colorspaces': visualize_colorspace.md
- 'Histogram': visualize_histogram.md
- 'Hyperspectral Histogram': visualize_hyper_histogram.md
- 'Overlay Images': visualize_ovelay_two_imgs.md
- 'Object Size ECDF': visualize_obj_size_ecdf.md
- 'Object Sizes': visualize_obj_sizes.md
- 'Pixel Scatter Plot': 'visualize_pixel_scatter_vis.md'
- 'Pseudocolor': visualize_pseudocolor.md
- 'Tile': visualize_tile.md
- 'Time Lapse Video': visualize_time_lapse_video.md
- 'Watershed Segmentation': watershed.md
- 'White balance': white_balance.md
- 'Within Frame': within_frame.md
- 'Machine Learning Training':
- 'Kmeans Clustering': train_kmeans.md
- 'Naive Bayes': naive_bayes.md
- 'Naive Bayes Multiclass': naive_bayes_multiclass.md
- 'Parallelization':
- 'Configure Parallelization': parallel_config.md
- 'Workflow Inputs Management': parallel_workflow_inputs.md
- 'Metadata Parser': parallel_metadata_parser.md
- 'Job Builder': parallel_job_builder.md
- 'Multiprocess': parallel_multiprocess.md
- 'Process Results': parallel_process_results.md
- 'Workflow Parallelization': pipeline_parallel.md
- 'Accessory tools': tools.md
markdown_extensions:
- toc:
permalink: True
- admonition