megadetector 5.0.10__py3-none-any.whl → 5.0.12__py3-none-any.whl

{api → megadetector/api}/batch_processing/api_core/batch_service/score.py

@@ -19,7 +19,7 @@ print('score.py, tf.test.is_gpu_available:', tf.test.is_gpu_available())
 PRINT_EVERY = 500
 
 
-#%% Helper functions *copied* from ct_utils.py and md_visualization/visualization_utils.py
+#%% Helper functions *copied* from ct_utils.py and visualization/visualization_utils.py
 
 IMAGE_ROTATIONS = {
     3: 180,
@@ -237,7 +237,7 @@ class TFDetector:
             image_id: a path to identify the image; will be in the "file" field of the output object
             detection_threshold: confidence above which to include the detection proposal
         Returns:
-        A dict with the following fields, see the 'images' key in https://github.com/agentmorris/MegaDetector/tree/master/api/batch_processing#batch-processing-api-output-format
+        A dict with the following fields, see the 'images' key in https://github.com/agentmorris/MegaDetector/tree/main/megadetector/api/batch_processing#batch-processing-api-output-format
             - 'file' (always present)
             - 'max_detection_conf'
             - 'detections', which is a list of detection objects containing keys 'category', 'conf' and 'bbox'

{api → megadetector/api}/synchronous/api_core/animal_detection_api/api_backend.py

@@ -18,7 +18,7 @@ from io import BytesIO
 
 from detection.run_detector import load_detector, convert_to_tf_coords
 import config
-import md_visualization.visualization_utils as vis_utils 
+import visualization.visualization_utils as vis_utils 
 
 #%% Initialization
 

{api → megadetector/api}/synchronous/api_core/animal_detection_api/api_frontend.py

@@ -21,7 +21,7 @@ from io import BytesIO
 from flask import Flask, Response, jsonify, make_response, request
 from requests_toolbelt.multipart.encoder import MultipartEncoder
 
-import md_visualization.visualization_utils as vis_utils
+import visualization.visualization_utils as vis_utils
 import config
 
 

{classification → megadetector/classification}/analyze_failed_images.py

@@ -18,9 +18,9 @@ from PIL import Image, ImageFile
 import requests
 from tqdm import tqdm
 
-from data_management.megadb.megadb_utils import MegadbUtils
-from md_utils import path_utils
-from md_utils import sas_blob_utils
+from megadetector.data_management.megadb.megadb_utils import MegadbUtils
+from megadetector.utils import path_utils
+from megadetector.utils import sas_blob_utils
 
 
 #%% Example usage

{classification → megadetector/classification}/cache_batchapi_outputs.py

@@ -46,7 +46,7 @@ Detections JSON format:
 
 Batch Detection API Output Format:
 
-github.com/agentmorris/MegaDetector/tree/master/api/batch_processing#api-outputs
+github.com/agentmorris/MegaDetector/tree/main/megadetector/api/batch_processing#api-outputs
 
 """
 

{classification → megadetector/classification}/create_classification_dataset.py

@@ -74,7 +74,7 @@ import numpy as np
 import pandas as pd
 from tqdm import tqdm
 
-from classification import detect_and_crop
+from megadetector.classification import detect_and_crop
 
 
 #%% Example usage

{classification → megadetector/classification}/crop_detections.py

@@ -9,7 +9,7 @@ This script takes as input a detections JSON file, usually the output of
 detection/run_tf_detector_batch.py or the output of the Batch API in the
 "Batch processing API output format".
 
-See https://github.com/agentmorris/MegaDetector/tree/master/api/batch_processing.
+See https://github.com/agentmorris/MegaDetector/tree/main/megadetector/api/batch_processing.
 
 The script can crop images that are either available locally or that need to be
 downloaded from an Azure Blob Storage container.

{classification → megadetector/classification}/detect_and_crop.py

@@ -113,11 +113,11 @@ from tqdm import tqdm
 
 from api.batch_processing.data_preparation.prepare_api_submission import (
     BatchAPIResponseError, Task, TaskStatus, divide_list_into_tasks)
-from classification.cache_batchapi_outputs import cache_detections
-from classification.crop_detections import load_and_crop
-from data_management.megadb import megadb_utils
-from md_utils import path_utils
-from md_utils import sas_blob_utils
+from megadetector.classification.cache_batchapi_outputs import cache_detections
+from megadetector.classification.crop_detections import load_and_crop
+from megadetector.data_management.megadb import megadb_utils
+from megadetector.utils import path_utils
+from megadetector.utils import sas_blob_utils
 
 
 #%% Example usage

{classification → megadetector/classification}/evaluate_model.py

@@ -51,7 +51,7 @@ import torch
 import torchvision
 import tqdm
 
-from classification import efficientnet, train_classifier
+from megadetector.classification import efficientnet, train_classifier
 
 
 #%% Example usage

{classification → megadetector/classification}/json_to_azcopy_list.py

@@ -16,8 +16,8 @@ import os
 
 from tqdm import tqdm
 
-from data_management.megadb import megadb_utils
-from md_utils import sas_blob_utils
+from megadetector.data_management.megadb import megadb_utils
+from megadetector.utils import sas_blob_utils
 
 images_dir = ''
 queried_images_json_path = 'run_idfg2/queried_images.json'

{classification → megadetector/classification}/json_validator.py

@@ -65,26 +65,30 @@ exist in Azure Blob Storage. In total, we output the following files:
 
 """
 
+#%% Imports
+
 from __future__ import annotations
 
 import argparse
-from collections import defaultdict
-from collections.abc import Container, Iterable, Mapping, MutableMapping
-from concurrent import futures
-from datetime import datetime
 import json
 import os
 import pprint
 import random
-from typing import Any
 
 import pandas as pd
-from md_utils import path_utils
-from md_utils import sas_blob_utils
+
 from tqdm import tqdm
+from collections import defaultdict
+from collections.abc import Container, Iterable, Mapping, MutableMapping
+from concurrent import futures
+from datetime import datetime
+from typing import Any
+
+from megadetector.utils import path_utils
+from megadetector.utils import sas_blob_utils
 
-from data_management.megadb import megadb_utils
-from taxonomy_mapping.taxonomy_graph import (
+from megadetector.data_management.megadb import megadb_utils
+from megadetector.taxonomy_mapping.taxonomy_graph import (
     build_taxonomy_graph, dag_to_tree, TaxonNode)
 
 

{classification → megadetector/classification}/map_classification_categories.py

@@ -52,7 +52,7 @@ import networkx as nx
 import pandas as pd
 from tqdm import tqdm
 
-from taxonomy_mapping.taxonomy_graph import (
+from megadetector.taxonomy_mapping.taxonomy_graph import (
     build_taxonomy_graph, dag_to_tree, TaxonNode)
 
 

{classification → megadetector/classification}/merge_classification_detection_output.py

@@ -70,7 +70,7 @@ from typing import Any
 import pandas as pd
 from tqdm import tqdm
 
-from md_utils.ct_utils import truncate_float
+from megadetector.utils.ct_utils import truncate_float
 
 
 #%% Example usage

{classification → megadetector/classification}/run_classifier.py

@@ -25,6 +25,7 @@ from __future__ import annotations
 import argparse
 import json
 import os
+
 from tqdm import tqdm
 from typing import Any
 from collections.abc import Callable, Sequence
@@ -36,7 +37,7 @@ import torch.utils
 import torchvision as tv
 from torchvision.datasets.folder import default_loader
 
-from classification import train_classifier
+from megadetector.classification import train_classifier
 
 
 #%% Example usage

{classification → megadetector/classification}/train_classifier.py

@@ -16,28 +16,30 @@ During training, start tensorboard from within the classification/ directory:
 
 from __future__ import annotations
 
+import json
+import os
 import argparse
+
 from collections import defaultdict
 from collections.abc import Callable, Mapping, MutableMapping, Sequence
 from datetime import datetime
-import json
-import os
 from typing import Any
 
 import numpy as np
 import PIL.Image
 import sklearn.metrics
+import tqdm
+
 import torch
 from torch.utils import tensorboard
 import torchvision as tv
 from torchvision.datasets.folder import default_loader
-import tqdm
 
-from classification import efficientnet, evaluate_model
-from classification.train_utils import (
+from megadetector.classification import efficientnet, evaluate_model
+from megadetector.classification.train_utils import (
     HeapItem, recall_from_confusion_matrix, add_to_heap, fig_to_img,
     imgs_with_confidences, load_dataset_csv, prefix_all_keys)
-from md_visualization import plot_utils
+from megadetector.visualization import plot_utils
 
 
 #%% Example usage

{classification → megadetector/classification}/train_classifier_tf.py

@@ -16,25 +16,26 @@ During training, start tensorboard from within the classification/ directory:
 
 from __future__ import annotations
 
-import argparse
-from collections import defaultdict
-from collections.abc import Callable, Mapping, MutableMapping, Sequence
-from datetime import datetime
-import json
 import os
-from typing import Any, Optional
+import json
 import uuid
+import argparse
 
+import tqdm
 import numpy as np
 import sklearn.metrics
 import tensorflow as tf
+
+from collections import defaultdict
+from collections.abc import Callable, Mapping, MutableMapping, Sequence
+from datetime import datetime
+from typing import Any, Optional
 from tensorboard.plugins.hparams import api as hp
-import tqdm
 
-from classification.train_utils import (
+from megadetector.classification.train_utils import (
     HeapItem, recall_from_confusion_matrix, add_to_heap, fig_to_img,
     imgs_with_confidences, load_dataset_csv, prefix_all_keys)
-from md_visualization import plot_utils
+from megadetector.visualization import plot_utils
 
 AUTOTUNE = tf.data.experimental.AUTOTUNE
 

{classification → megadetector/classification}/train_utils.py

@@ -13,12 +13,10 @@ especially be agnostic to PyTorch vs. TensorFlow.
 
 from __future__ import annotations
 
-from collections.abc import Mapping, Sequence
 import dataclasses
 import heapq
 import io
 import json
-from typing import Any, Optional
 
 import matplotlib.figure
 import numpy as np
@@ -26,6 +24,9 @@ import pandas as pd
 import PIL.Image
 import scipy.interpolate
 
+from collections.abc import Mapping, Sequence
+from typing import Any, Optional
+
 
 #%% Classes
 

{data_management → megadetector/data_management}/camtrap_dp_to_coco.py

@@ -200,7 +200,8 @@ if False:
     
     #%% Validate
     
-    from data_management.databases.integrity_check_json_db import integrity_check_json_db, IntegrityCheckOptions
+    from megadetector.data_management.databases.integrity_check_json_db import \
+        integrity_check_json_db, IntegrityCheckOptions
     
     options = IntegrityCheckOptions()
     
@@ -217,7 +218,7 @@ if False:
 
     #%% Preview
     
-    from md_visualization.visualize_db import DbVizOptions, visualize_db
+    from megadetector.visualization.visualize_db import DbVizOptions, visualize_db
     
     options = DbVizOptions()
     options.parallelize_rendering = True
@@ -227,7 +228,7 @@ if False:
     preview_dir = r'c:\temp\camtrapdp-preview'
     htmlOutputFile,image_db = visualize_db(coco_file, preview_dir, camtrap_dp_folder, options=options)
     
-    from md_utils.path_utils import open_file
+    from megadetector.utils.path_utils import open_file
     open_file(htmlOutputFile)
     
     

{data_management → megadetector/data_management}/cct_json_utils.py

@@ -2,9 +2,9 @@
 
 cct_json_utils.py
 
-Utilities for working with COCO Camera Traps .json databases
+Utilities for working with COCO Camera Traps .json databases:
 
-https://github.com/agentmorris/MegaDetector/blob/master/data_management/README.md#coco-cameratraps-format
+https://github.com/agentmorris/MegaDetector/blob/main/megadetector/data_management/README.md#coco-cameratraps-format
 
 """
 

{data_management → megadetector/data_management}/cct_to_md.py

@@ -164,7 +164,7 @@ if False:
     
     #%%
     
-    from md_visualization import visualize_detector_output
+    from megadetector.visualization import visualize_detector_output
     
     visualize_detector_output.visualize_detector_output(
                               detector_output_path=output_filename,

{data_management → megadetector/data_management}/coco_to_labelme.py

@@ -17,7 +17,7 @@ import json
 from tqdm import tqdm
 from collections import defaultdict
 
-from md_visualization.visualization_utils import open_image
+from megadetector.visualization.visualization_utils import open_image
 
 
 #%% Functions

{data_management → megadetector/data_management}/coco_to_yolo.py

@@ -25,7 +25,7 @@ import shutil
 from collections import defaultdict
 from tqdm import tqdm
 
-from md_utils.path_utils import safe_create_link,find_images
+from megadetector.utils.path_utils import safe_create_link,find_images
 
 
 #%% Support functions

{data_management → megadetector/data_management}/databases/integrity_check_json_db.py

@@ -26,8 +26,8 @@ from multiprocessing.pool import ThreadPool
 from operator import itemgetter
 from tqdm import tqdm
 
-from md_visualization.visualization_utils import open_image
-from md_utils import ct_utils
+from megadetector.visualization.visualization_utils import open_image
+from megadetector.utils import ct_utils
 
 
 #%% Classes and environment

{data_management → megadetector/data_management}/get_image_sizes.py

@@ -12,15 +12,16 @@ every image, optionally writing the results to a new .json file.
 import argparse
 import json
 import os
-from PIL import Image
 import sys
 
+from PIL import Image
+
 from multiprocessing.pool import ThreadPool
 from multiprocessing.pool import Pool
 from functools import partial
 from tqdm import tqdm
 
-from md_utils.path_utils import find_images
+from megadetector.utils.path_utils import find_images
 
 image_base = ''
 default_n_threads = 1
@@ -137,7 +138,7 @@ if False:
     image_list_file = os.path.join(base_dir,'images.json')
     relative_image_list_file = os.path.join(base_dir,'images_relative.json')
     image_size_file = os.path.join(base_dir,'image_sizes.json')
-    from md_utils import path_utils
+    from megadetector.utils import path_utils
     image_names = path_utils.find_images(base_dir,recursive=True)
     
     with open(image_list_file,'w') as f:

{data_management → megadetector/data_management}/importers/auckland_doc_test_to_json.py

@@ -18,11 +18,12 @@ import datetime
 import ntpath
 import re
 import numpy as np
+
 from tqdm import tqdm
 
-from md_visualization import visualize_db
-from data_management.databases import integrity_check_json_db
-from md_utils.path_utils import find_images
+from megadetector.visualization import visualize_db
+from megadetector.data_management.databases import integrity_check_json_db
+from megadetector.utils.path_utils import find_images
 
 input_base_dir = r'e:\auckland-test\2_Testing'
 
@@ -342,8 +343,8 @@ os.startfile(html_output_file)
 
 #%% Precision-recall analysis
 
-from api.batch_processing.postprocessing.postprocess_batch_results import PostProcessingOptions
-from api.batch_processing.postprocessing.postprocess_batch_results import process_batch_results
+from megadetector.postprocessing.postprocess_batch_results import PostProcessingOptions
+from megadetector.postprocessing.postprocess_batch_results import process_batch_results
 
 api_output_file = r'g:\auckland-doc\auckland-doc_20200801\combined_api_outputs\auckland-doc_202008012020.08.01_reformatMaukahuka_Auckland_Island2_TestingSummer_Trial_2019_detections.filtered_rde_0.60_0.85_5_0.05.json'
 postprocessing_output_folder = r'G:\auckland-doc\auckland-doc_20200801\postprocessing'

{data_management → megadetector/data_management}/importers/auckland_doc_to_json.py

@@ -13,11 +13,12 @@ import json
 import os
 import uuid
 import datetime
+
 from tqdm import tqdm
 
-from md_visualization import visualize_db
-from data_management.databases import integrity_check_json_db
-from md_utils.path_utils import find_images, split_path, insert_before_extension
+from megadetector.visualization import visualize_db
+from megadetector.data_management.databases import integrity_check_json_db
+from megadetector.utils.path_utils import find_images, split_path, insert_before_extension
 
 # Filenames will be stored in the output .json relative to this base dir
 input_base_dir = 'y:\\'

{data_management → megadetector/data_management}/importers/awc_to_json.py

@@ -12,12 +12,14 @@ import pandas as pd
 import uuid
 import json
 import time
-from tqdm import tqdm
 import humanfriendly
 import os
 import PIL
-from md_visualization import visualize_db
-from md_utils import path_utils
+
+from tqdm import tqdm
+
+from megadetector.visualization import visualize_db
+from megadetector.utils import path_utils
 
 input_metadata_file = r"D:\wildlife_data\awc\awc_imageinfo.csv"
 output_file = r"D:\wildlife_data\awc\awc_imageinfo.json"
@@ -170,7 +172,7 @@ print('Finished writing .json file with {} images, {} annotations, and {} catego
 
 #%% Validate the database's integrity
 
-from data_management.databases import integrity_check_json_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 options = integrity_check_json_db.IntegrityCheckOptions()
 sortedCategories,data = integrity_check_json_db.integrity_check_json_db(output_file, options)

{data_management → megadetector/data_management}/importers/bellevue_to_json.py

@@ -25,7 +25,7 @@ from PIL import Image
 from PIL.ExifTags import TAGS
 from tqdm import tqdm
 
-from md_utils.path_utils import find_images
+from megadetector.utils.path_utils import find_images
 
 # Filenames will be stored in the output .json relative to this base dir
 base_dir = r'C:\temp\camera_trap_images_no_people'
@@ -244,7 +244,7 @@ print('Finished writing json to {}'.format(output_filename))
 
 #%% Validate data
 
-from data_management.databases import integrity_check_json_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 options = integrity_check_json_db.IntegrityCheckOptions()
 options.baseDir = base_dir
@@ -257,7 +257,7 @@ sorted_categories  = integrity_check_json_db.integrity_check_json_db(output_file
 
 #%% Label previews
 
-from md_visualization import visualize_db
+from megadetector.visualization import visualize_db
 
 viz_options = visualize_db.DbVizOptions()
 viz_options.num_to_visualize = None

{data_management → megadetector/data_management}/importers/cacophony-thermal-importer.py

@@ -29,8 +29,8 @@ from zipfile import ZipFile
 
 import cv2
 
-from md_utils.ct_utils import truncate_float
-from md_utils import path_utils
+from megadetector.utils.ct_utils import truncate_float
+from megadetector.utils import path_utils
 
 base_dir = '/bigdata/home/sftp/cacophony-ferraro_/data/cacophony-thermal/'
 output_base = os.path.expanduser('~/tmp/new-zealand-wildlife-thermal-imaging')
@@ -686,7 +686,7 @@ if False:
     target_folder = os.path.expanduser('~/tmp/cacophony-thermal-out-individual-metadata')
     assert os.path.isdir(source_folder) and os.path.isdir(target_folder)
 
-    from md_utils import path_utils
+    from megadetector.utils import path_utils
     all_files = path_utils.recursive_file_list(source_folder)
     files_to_move = [fn for fn in all_files if '_metadata.json' in fn]
     print('Moving {} of {} files'.format(len(files_to_move),len(all_files)))
@@ -726,7 +726,7 @@ if False:
     filtered_video_filename = selected_clip['filtered_video_filename']
     video_filename = selected_clip['video_filename']
     
-    from md_utils.path_utils import open_file
+    from megadetector.utils.path_utils import open_file
     # open_file(os.path.join(output_base,video_filename))
     open_file(os.path.join(output_base,filtered_video_filename))
     

{data_management → megadetector/data_management}/importers/carrizo_shrubfree_2018.py

@@ -18,9 +18,10 @@ import humanfriendly
 
 from tqdm import tqdm
 from PIL import Image
+
 import numpy as np
 
-from md_utils.path_utils import find_images
+from megadetector.utils.path_utils import find_images
 
 input_base = r'Z:\Shrub-free zone Carrizo 2018'
 input_metadata_file = os.path.join(input_base,'shrub-free 2018.csv')
@@ -237,7 +238,7 @@ print('Finished writing .json file with {} images, {} annotations, and {} catego
 
 #%% Validate output
 
-from data_management.databases import integrity_check_json_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 options = integrity_check_json_db.IntegrityCheckOptions()
 options.baseDir = image_directory
@@ -249,8 +250,8 @@ data = integrity_check_json_db.integrity_check_json_db(output_json_file,options)
 
 #%% Preview labels
 
-from md_visualization import visualize_db
-from data_management.databases import integrity_check_json_db
+from megadetector.visualization import visualize_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 viz_options = visualize_db.DbVizOptions()
 viz_options.num_to_visualize = None

{data_management → megadetector/data_management}/importers/carrizo_trail_cam_2017.py

@@ -9,17 +9,19 @@
 
 #%% Constants and environment
 
-import pandas as pd
 import os
 import json
 import uuid
 import time
 import humanfriendly
-from PIL import Image
+
+import pandas as pd
 import numpy as np
 
+from PIL import Image
 from tqdm import tqdm
-from md_utils.path_utils import find_images
+
+from megadetector.utils.path_utils import find_images
 
 input_base = r'Z:\Trail Cam Carrizo 2017'
 open_metadata_file = os.path.join(input_base, 'Carrizo open 2017.csv')
@@ -256,7 +258,7 @@ print('Finished writing .json file with {} images, {} annotations, and {} catego
 
 #%% Validate output
 
-from data_management.databases import integrity_check_json_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 options = integrity_check_json_db.IntegrityCheckOptions()
 options.baseDir = image_directory
@@ -268,8 +270,8 @@ data = integrity_check_json_db.integrity_check_json_db(output_json_file,options)
 
 #%% Preview labels
 
-from md_visualization import visualize_db
-from data_management.databases import integrity_check_json_db
+from megadetector.visualization import visualize_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 viz_options = visualize_db.DbVizOptions()
 viz_options.num_to_visualize = None

{data_management → megadetector/data_management}/importers/cct_field_adjustments.py

@@ -10,10 +10,11 @@
 
 #%% Constants and environment
 
-from data_management.databases import integrity_check_json_db
 import json
 import os
 
+from megadetector.data_management.databases import integrity_check_json_db
+
 inputJsonFile = r"D:\temp\CaltechCameraTraps_v2.0.json"
 outputJsonFile = r"D:\temp\CaltechCameraTraps_v2.1.json"
 

{data_management → megadetector/data_management}/importers/channel_islands_to_cct.py

@@ -882,7 +882,7 @@ print('Finished writing .json file with {} images, {} annotations, and {} catego
 
 #%% Validate output
 
-from data_management.databases import integrity_check_json_db
+from megadetector.data_management.databases import integrity_check_json_db
 
 fn = output_file
 options = integrity_check_json_db.IntegrityCheckOptions()
@@ -896,7 +896,7 @@ sortedCategories, data, error = integrity_check_json_db.integrity_check_json_db(
 
 #%% Preview labels
 
-from md_visualization import visualize_db
+from megadetector.visualization import visualize_db
 
 viz_options = visualize_db.DbVizOptions()
 viz_options.num_to_visualize = 159