-
Notifications
You must be signed in to change notification settings - Fork 265
/
mkdocs.yml
233 lines (232 loc) · 10.7 KB
/
mkdocs.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
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
- '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
- '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