megadetector 5.0.28__py3-none-any.whl → 5.0.29__py3-none-any.whl

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  1. megadetector/api/batch_processing/api_core/batch_service/score.py +4 -5
  2. megadetector/api/batch_processing/api_core_support/aggregate_results_manually.py +1 -1
  3. megadetector/api/batch_processing/api_support/summarize_daily_activity.py +1 -1
  4. megadetector/api/batch_processing/integration/digiKam/xmp_integration.py +2 -2
  5. megadetector/api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py +1 -1
  6. megadetector/api/batch_processing/integration/eMammal/test_scripts/select_images_for_testing.py +1 -1
  7. megadetector/api/synchronous/api_core/tests/load_test.py +2 -3
  8. megadetector/classification/aggregate_classifier_probs.py +3 -3
  9. megadetector/classification/analyze_failed_images.py +5 -5
  10. megadetector/classification/cache_batchapi_outputs.py +5 -5
  11. megadetector/classification/create_classification_dataset.py +11 -12
  12. megadetector/classification/crop_detections.py +10 -10
  13. megadetector/classification/csv_to_json.py +8 -8
  14. megadetector/classification/detect_and_crop.py +13 -15
  15. megadetector/classification/evaluate_model.py +7 -7
  16. megadetector/classification/identify_mislabeled_candidates.py +6 -6
  17. megadetector/classification/json_to_azcopy_list.py +1 -1
  18. megadetector/classification/json_validator.py +29 -32
  19. megadetector/classification/map_classification_categories.py +9 -9
  20. megadetector/classification/merge_classification_detection_output.py +12 -9
  21. megadetector/classification/prepare_classification_script.py +19 -19
  22. megadetector/classification/prepare_classification_script_mc.py +23 -23
  23. megadetector/classification/run_classifier.py +4 -4
  24. megadetector/classification/save_mislabeled.py +6 -6
  25. megadetector/classification/train_classifier.py +1 -1
  26. megadetector/classification/train_classifier_tf.py +9 -9
  27. megadetector/classification/train_utils.py +10 -10
  28. megadetector/data_management/annotations/annotation_constants.py +1 -1
  29. megadetector/data_management/camtrap_dp_to_coco.py +45 -45
  30. megadetector/data_management/cct_json_utils.py +101 -101
  31. megadetector/data_management/cct_to_md.py +49 -49
  32. megadetector/data_management/cct_to_wi.py +33 -33
  33. megadetector/data_management/coco_to_labelme.py +75 -75
  34. megadetector/data_management/coco_to_yolo.py +189 -189
  35. megadetector/data_management/databases/add_width_and_height_to_db.py +3 -2
  36. megadetector/data_management/databases/combine_coco_camera_traps_files.py +38 -38
  37. megadetector/data_management/databases/integrity_check_json_db.py +202 -188
  38. megadetector/data_management/databases/subset_json_db.py +33 -33
  39. megadetector/data_management/generate_crops_from_cct.py +38 -38
  40. megadetector/data_management/get_image_sizes.py +54 -49
  41. megadetector/data_management/labelme_to_coco.py +130 -124
  42. megadetector/data_management/labelme_to_yolo.py +78 -72
  43. megadetector/data_management/lila/create_lila_blank_set.py +81 -83
  44. megadetector/data_management/lila/create_lila_test_set.py +32 -31
  45. megadetector/data_management/lila/create_links_to_md_results_files.py +18 -18
  46. megadetector/data_management/lila/download_lila_subset.py +21 -24
  47. megadetector/data_management/lila/generate_lila_per_image_labels.py +91 -91
  48. megadetector/data_management/lila/get_lila_annotation_counts.py +30 -30
  49. megadetector/data_management/lila/get_lila_image_counts.py +22 -22
  50. megadetector/data_management/lila/lila_common.py +70 -70
  51. megadetector/data_management/lila/test_lila_metadata_urls.py +13 -14
  52. megadetector/data_management/mewc_to_md.py +339 -340
  53. megadetector/data_management/ocr_tools.py +258 -252
  54. megadetector/data_management/read_exif.py +231 -224
  55. megadetector/data_management/remap_coco_categories.py +26 -26
  56. megadetector/data_management/remove_exif.py +31 -20
  57. megadetector/data_management/rename_images.py +187 -187
  58. megadetector/data_management/resize_coco_dataset.py +41 -41
  59. megadetector/data_management/speciesnet_to_md.py +41 -41
  60. megadetector/data_management/wi_download_csv_to_coco.py +55 -55
  61. megadetector/data_management/yolo_output_to_md_output.py +117 -120
  62. megadetector/data_management/yolo_to_coco.py +195 -188
  63. megadetector/detection/change_detection.py +831 -0
  64. megadetector/detection/process_video.py +340 -337
  65. megadetector/detection/pytorch_detector.py +304 -262
  66. megadetector/detection/run_detector.py +177 -164
  67. megadetector/detection/run_detector_batch.py +364 -363
  68. megadetector/detection/run_inference_with_yolov5_val.py +328 -325
  69. megadetector/detection/run_tiled_inference.py +256 -249
  70. megadetector/detection/tf_detector.py +24 -24
  71. megadetector/detection/video_utils.py +290 -282
  72. megadetector/postprocessing/add_max_conf.py +15 -11
  73. megadetector/postprocessing/categorize_detections_by_size.py +44 -44
  74. megadetector/postprocessing/classification_postprocessing.py +415 -415
  75. megadetector/postprocessing/combine_batch_outputs.py +20 -21
  76. megadetector/postprocessing/compare_batch_results.py +528 -517
  77. megadetector/postprocessing/convert_output_format.py +97 -97
  78. megadetector/postprocessing/create_crop_folder.py +219 -146
  79. megadetector/postprocessing/detector_calibration.py +173 -168
  80. megadetector/postprocessing/generate_csv_report.py +508 -499
  81. megadetector/postprocessing/load_api_results.py +23 -20
  82. megadetector/postprocessing/md_to_coco.py +129 -98
  83. megadetector/postprocessing/md_to_labelme.py +89 -83
  84. megadetector/postprocessing/md_to_wi.py +40 -40
  85. megadetector/postprocessing/merge_detections.py +87 -114
  86. megadetector/postprocessing/postprocess_batch_results.py +313 -298
  87. megadetector/postprocessing/remap_detection_categories.py +36 -36
  88. megadetector/postprocessing/render_detection_confusion_matrix.py +205 -199
  89. megadetector/postprocessing/repeat_detection_elimination/find_repeat_detections.py +57 -57
  90. megadetector/postprocessing/repeat_detection_elimination/remove_repeat_detections.py +27 -28
  91. megadetector/postprocessing/repeat_detection_elimination/repeat_detections_core.py +702 -677
  92. megadetector/postprocessing/separate_detections_into_folders.py +226 -211
  93. megadetector/postprocessing/subset_json_detector_output.py +265 -262
  94. megadetector/postprocessing/top_folders_to_bottom.py +45 -45
  95. megadetector/postprocessing/validate_batch_results.py +70 -70
  96. megadetector/taxonomy_mapping/map_lila_taxonomy_to_wi_taxonomy.py +52 -52
  97. megadetector/taxonomy_mapping/map_new_lila_datasets.py +15 -15
  98. megadetector/taxonomy_mapping/prepare_lila_taxonomy_release.py +14 -14
  99. megadetector/taxonomy_mapping/preview_lila_taxonomy.py +66 -66
  100. megadetector/taxonomy_mapping/retrieve_sample_image.py +16 -16
  101. megadetector/taxonomy_mapping/simple_image_download.py +8 -8
  102. megadetector/taxonomy_mapping/species_lookup.py +33 -33
  103. megadetector/taxonomy_mapping/taxonomy_csv_checker.py +14 -14
  104. megadetector/taxonomy_mapping/taxonomy_graph.py +10 -10
  105. megadetector/taxonomy_mapping/validate_lila_category_mappings.py +13 -13
  106. megadetector/utils/azure_utils.py +22 -22
  107. megadetector/utils/ct_utils.py +1018 -200
  108. megadetector/utils/directory_listing.py +21 -77
  109. megadetector/utils/gpu_test.py +22 -22
  110. megadetector/utils/md_tests.py +541 -518
  111. megadetector/utils/path_utils.py +1457 -398
  112. megadetector/utils/process_utils.py +41 -41
  113. megadetector/utils/sas_blob_utils.py +53 -49
  114. megadetector/utils/split_locations_into_train_val.py +61 -61
  115. megadetector/utils/string_utils.py +147 -26
  116. megadetector/utils/url_utils.py +463 -173
  117. megadetector/utils/wi_utils.py +2629 -2526
  118. megadetector/utils/write_html_image_list.py +137 -137
  119. megadetector/visualization/plot_utils.py +21 -21
  120. megadetector/visualization/render_images_with_thumbnails.py +37 -73
  121. megadetector/visualization/visualization_utils.py +401 -397
  122. megadetector/visualization/visualize_db.py +197 -190
  123. megadetector/visualization/visualize_detector_output.py +79 -73
  124. {megadetector-5.0.28.dist-info → megadetector-5.0.29.dist-info}/METADATA +135 -132
  125. megadetector-5.0.29.dist-info/RECORD +163 -0
  126. {megadetector-5.0.28.dist-info → megadetector-5.0.29.dist-info}/WHEEL +1 -1
  127. {megadetector-5.0.28.dist-info → megadetector-5.0.29.dist-info}/licenses/LICENSE +0 -0
  128. {megadetector-5.0.28.dist-info → megadetector-5.0.29.dist-info}/top_level.txt +0 -0
  129. megadetector/data_management/importers/add_nacti_sizes.py +0 -52
  130. megadetector/data_management/importers/add_timestamps_to_icct.py +0 -79
  131. megadetector/data_management/importers/animl_results_to_md_results.py +0 -158
  132. megadetector/data_management/importers/auckland_doc_test_to_json.py +0 -373
  133. megadetector/data_management/importers/auckland_doc_to_json.py +0 -201
  134. megadetector/data_management/importers/awc_to_json.py +0 -191
  135. megadetector/data_management/importers/bellevue_to_json.py +0 -272
  136. megadetector/data_management/importers/cacophony-thermal-importer.py +0 -793
  137. megadetector/data_management/importers/carrizo_shrubfree_2018.py +0 -269
  138. megadetector/data_management/importers/carrizo_trail_cam_2017.py +0 -289
  139. megadetector/data_management/importers/cct_field_adjustments.py +0 -58
  140. megadetector/data_management/importers/channel_islands_to_cct.py +0 -913
  141. megadetector/data_management/importers/eMammal/copy_and_unzip_emammal.py +0 -180
  142. megadetector/data_management/importers/eMammal/eMammal_helpers.py +0 -249
  143. megadetector/data_management/importers/eMammal/make_eMammal_json.py +0 -223
  144. megadetector/data_management/importers/ena24_to_json.py +0 -276
  145. megadetector/data_management/importers/filenames_to_json.py +0 -386
  146. megadetector/data_management/importers/helena_to_cct.py +0 -283
  147. megadetector/data_management/importers/idaho-camera-traps.py +0 -1407
  148. megadetector/data_management/importers/idfg_iwildcam_lila_prep.py +0 -294
  149. megadetector/data_management/importers/import_desert_lion_conservation_camera_traps.py +0 -387
  150. megadetector/data_management/importers/jb_csv_to_json.py +0 -150
  151. megadetector/data_management/importers/mcgill_to_json.py +0 -250
  152. megadetector/data_management/importers/missouri_to_json.py +0 -490
  153. megadetector/data_management/importers/nacti_fieldname_adjustments.py +0 -79
  154. megadetector/data_management/importers/noaa_seals_2019.py +0 -181
  155. megadetector/data_management/importers/osu-small-animals-to-json.py +0 -364
  156. megadetector/data_management/importers/pc_to_json.py +0 -365
  157. megadetector/data_management/importers/plot_wni_giraffes.py +0 -123
  158. megadetector/data_management/importers/prepare_zsl_imerit.py +0 -131
  159. megadetector/data_management/importers/raic_csv_to_md_results.py +0 -416
  160. megadetector/data_management/importers/rspb_to_json.py +0 -356
  161. megadetector/data_management/importers/save_the_elephants_survey_A.py +0 -320
  162. megadetector/data_management/importers/save_the_elephants_survey_B.py +0 -329
  163. megadetector/data_management/importers/snapshot_safari_importer.py +0 -758
  164. megadetector/data_management/importers/snapshot_serengeti_lila.py +0 -1067
  165. megadetector/data_management/importers/snapshotserengeti/make_full_SS_json.py +0 -150
  166. megadetector/data_management/importers/snapshotserengeti/make_per_season_SS_json.py +0 -153
  167. megadetector/data_management/importers/sulross_get_exif.py +0 -65
  168. megadetector/data_management/importers/timelapse_csv_set_to_json.py +0 -490
  169. megadetector/data_management/importers/ubc_to_json.py +0 -399
  170. megadetector/data_management/importers/umn_to_json.py +0 -507
  171. megadetector/data_management/importers/wellington_to_json.py +0 -263
  172. megadetector/data_management/importers/wi_to_json.py +0 -442
  173. megadetector/data_management/importers/zamba_results_to_md_results.py +0 -180
  174. megadetector/data_management/lila/add_locations_to_island_camera_traps.py +0 -101
  175. megadetector/data_management/lila/add_locations_to_nacti.py +0 -151
  176. megadetector-5.0.28.dist-info/RECORD +0 -209
@@ -30,11 +30,11 @@ def crop_image_with_normalized_coordinates(
30
30
  bounding_box (tuple): tuple formatted as (x,y,w,h), where (0,0) is the
31
31
  upper-left of the image, and coordinates are normalized
32
32
  (so (0,0,1,1) is a box containing the entire image).
33
-
33
+
34
34
  Returns:
35
35
  PIL.Image: cropped image
36
36
  """
37
-
37
+
38
38
  im_width, im_height = image.size
39
39
  (x_norm, y_norm, w_norm, h_norm) = bounding_box
40
40
  (x, y, w, h) = (x_norm * im_width,
@@ -57,7 +57,7 @@ def render_images_with_thumbnails(
57
57
  """
58
58
  Given a primary image filename and a list of secondary images, writes to
59
59
  the provided output_image_filename an image where the one
60
- side is the primary image, and the other side is a grid of the
60
+ side is the primary image, and the other side is a grid of the
61
61
  secondary images, cropped according to the provided list of bounding
62
62
  boxes.
63
63
 
@@ -65,11 +65,11 @@ def render_images_with_thumbnails(
65
65
  wide.
66
66
 
67
67
  The height of the output image will be determined by the original aspect
68
- ratio of the primary image.
69
-
68
+ ratio of the primary image.
69
+
70
70
  Args:
71
71
  primary_image_filename (str): filename of the primary image to load as str
72
- primary_image_width (int): width at which to render the primary image; if this is
72
+ primary_image_width (int): width at which to render the primary image; if this is
73
73
  None, will render at the original image width
74
74
  secondary_image_filename_list (list): list of filenames of the secondary images
75
75
  secondary_image_bounding_box_list (list): list of tuples, one per secondary
@@ -78,7 +78,7 @@ def render_images_with_thumbnails(
78
78
  and coordinates are normalized (so (0,0,1,1) is a box containing
79
79
  the entire image.
80
80
  cropped_grid_width (int): width of the cropped-image area
81
- output_image_filename (str): filename to write the output image
81
+ output_image_filename (str): filename to write the output image
82
82
  primary_image_location (str, optional): 'right' or left'; reserving 'top', 'bottom', etc.
83
83
  for future use
84
84
  """
@@ -89,11 +89,11 @@ def render_images_with_thumbnails(
89
89
  'Length of secondary image list and bounding box list should be equal'
90
90
 
91
91
  assert primary_image_location in ['left','right']
92
-
92
+
93
93
  # Load primary image and resize to desired width
94
94
  primary_image = vis_utils.load_image(primary_image_filename)
95
95
  if primary_image_width is not None:
96
- primary_image = vis_utils.resize_image(primary_image, primary_image_width,
96
+ primary_image = vis_utils.resize_image(primary_image, primary_image_width,
97
97
  target_height=-1)
98
98
 
99
99
  # Compute the number of grid elements for the secondary images
@@ -101,15 +101,15 @@ def render_images_with_thumbnails(
101
101
  grid_width = cropped_grid_width
102
102
  grid_height = primary_image.size[1]
103
103
  grid_aspect = grid_width / grid_height
104
-
104
+
105
105
  sample_crop_width = secondary_image_bounding_box_list[0][2]
106
106
  sample_crop_height = secondary_image_bounding_box_list[0][3]
107
-
107
+
108
108
  n_crops = len(secondary_image_filename_list)
109
-
109
+
110
110
  optimal_n_rows = None
111
111
  optimal_aspect_error = None
112
-
112
+
113
113
  for candidate_n_rows in range(1,n_crops+1):
114
114
  candidate_n_cols = math.ceil(n_crops / candidate_n_rows)
115
115
  candidate_grid_aspect = (candidate_n_cols*sample_crop_width) / \
@@ -118,39 +118,39 @@ def render_images_with_thumbnails(
118
118
  if optimal_n_rows is None or aspect_error < optimal_aspect_error:
119
119
  optimal_n_rows = candidate_n_rows
120
120
  optimal_aspect_error = aspect_error
121
-
121
+
122
122
  assert optimal_n_rows is not None
123
123
  grid_rows = optimal_n_rows
124
- grid_columns = math.ceil(n_crops/grid_rows)
125
-
124
+ grid_columns = math.ceil(n_crops/grid_rows)
125
+
126
126
  # Compute the width of each grid cell
127
127
  grid_cell_width = math.floor(grid_width / grid_columns)
128
128
  grid_cell_height = math.floor(grid_height / grid_rows)
129
-
129
+
130
130
  # Load secondary images and their associated bounding boxes. Iterate
131
131
  # through them, crop them, and save them to a list of cropped_images
132
132
  cropped_images = []
133
133
  for (name, box) in zip(secondary_image_filename_list,
134
134
  secondary_image_bounding_box_list):
135
-
135
+
136
136
  other_image = vis_utils.load_image(name)
137
137
  cropped_image = crop_image_with_normalized_coordinates(
138
138
  other_image, box)
139
-
139
+
140
140
  # Rescale this crop to fit within the desired grid cell size
141
141
  width_scale_factor = grid_cell_width / cropped_image.size[0]
142
142
  height_scale_factor = grid_cell_height / cropped_image.size[1]
143
143
  scale_factor = min(width_scale_factor,height_scale_factor)
144
-
144
+
145
145
  # Resize the cropped image, whether we're making it larger or smaller
146
146
  cropped_image = cropped_image.resize(
147
147
  ((int)(cropped_image.size[0] * scale_factor),
148
- (int)(cropped_image.size[1] * scale_factor)))
148
+ (int)(cropped_image.size[1] * scale_factor)))
149
149
 
150
- cropped_images.append(cropped_image)
150
+ cropped_images.append(cropped_image)
151
151
 
152
152
  # ...for each crop
153
-
153
+
154
154
  # Compute the final output image size. This will depend upon the aspect
155
155
  # ratio of the crops.
156
156
  output_image_width = primary_image.size[0] + grid_width
@@ -164,80 +164,45 @@ def render_images_with_thumbnails(
164
164
  primary_image_x = grid_width
165
165
  else:
166
166
  primary_image_x = 0
167
-
167
+
168
168
  output_image.paste(primary_image, (primary_image_x, 0))
169
169
 
170
170
  # Compute the final locations of the secondary images in the output image
171
171
  i_row = 0; i_col = 0
172
172
  for image in cropped_images:
173
-
173
+
174
174
  x = i_col * grid_cell_width
175
175
  if primary_image_location == 'left':
176
176
  x += primary_image.size[0]
177
- y = i_row * grid_cell_height
177
+ y = i_row * grid_cell_height
178
178
  output_image.paste(image, (x,y))
179
179
  i_col += 1
180
180
  if i_col >= grid_columns:
181
181
  i_col = 0
182
182
  i_row += 1
183
-
183
+
184
184
  # ...for each crop
185
185
 
186
186
  # Write output image to disk
187
- output_image.save(output_image_filename)
187
+ output_image.save(output_image_filename)
188
188
 
189
189
  # ...def render_images_with_thumbnails(...)
190
190
 
191
191
 
192
- #%% Interactive driver
193
-
194
- if False:
195
-
196
- pass
197
-
198
- #%%
199
-
200
- primary_image_filename = '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0035.JPG'
201
-
202
- primary_image_width = 5152
203
-
204
- secondary_image_filename_list = ['/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0035.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0040.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0007.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0041.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0008.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0048.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0031.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0006.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0004.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0026.JPG', '/home/user/data/KRU/KRU_public/KRU_S1/13/13_R1/KRU_S1_13_R1_IMAG0005.JPG']
205
-
206
- secondary_image_bounding_box_list = [[0, 0, 0.1853, 0.6552], [0, 0, 0.1855, 0.6527], [0, 0.000252, 0.1991, 0.6925], [0, 0, 0.1855, 0.6527], [0, 0.001008, 0.1902, 0.6774], [0, 0, 0.1845, 0.658], [0, 0, 0.1824, 0.6711], [0, 0.00252, 0.2005, 0.6857], [0, 0.002268, 0.1983, 0.6852], [0, 0, 0.1752, 0.6897], [0, 0.001764, 0.1989, 0.6887]]
207
-
208
- # cropped_grid_width = 3091
209
- cropped_grid_width = 500
210
-
211
- primary_image_location = 'right'
212
-
213
- output_image_filename = os.path.expanduser('~/tmp/grid-test.jpg')
214
-
215
- render_images_with_thumbnails(
216
- primary_image_filename,
217
- primary_image_width,
218
- secondary_image_filename_list,
219
- secondary_image_bounding_box_list,
220
- cropped_grid_width,
221
- output_image_filename,
222
- primary_image_location='right')
223
-
224
- path_utils.open_file(output_image_filename)
225
-
226
-
227
192
  #%% Command-line driver
228
193
 
229
194
  # This is just a test driver, this module is not meant to be run from the command line.
230
195
 
231
- def main():
232
-
196
+ def main(): # noqa
197
+
233
198
  # Load images from a test directory.
234
199
  #
235
- # Make the first image in the directory the primary image,
236
- # the remaining ones the comparison images.
200
+ # Make the first image in the directory the primary image,
201
+ # the remaining ones the comparison images.
237
202
  test_input_folder = os.path.expanduser('~/data/KRU-test')
238
203
  output_image_filename = os.path.expanduser('~/tmp/thumbnail_test.jpg')
239
-
240
- files = path_utils.find_images(test_input_folder)
204
+
205
+ files = path_utils.find_images(test_input_folder)
241
206
 
242
207
  random.seed(0); random.shuffle(files)
243
208
  primary_image_filename = files[0]
@@ -256,7 +221,7 @@ def main():
256
221
  box[1] + random.uniform(-0.001, 0.001),
257
222
  0.2,
258
223
  0.2))
259
-
224
+
260
225
  primary_image_width = 1000
261
226
  cropped_grid_width = 1000
262
227
 
@@ -267,9 +232,8 @@ def main():
267
232
  secondary_image_bounding_box_list,
268
233
  cropped_grid_width,
269
234
  output_image_filename, 'right')
270
-
271
- from megadetector.utils import path_utils
235
+
272
236
  path_utils.open_file(output_image_filename)
273
-
237
+
274
238
  if __name__ == '__main__':
275
239
  main()