megadetector 5.0.28__tar.gz → 5.0.29__tar.gz

{megadetector-5.0.28/megadetector.egg-info → megadetector-5.0.29}/PKG-INFO

@@ -1,132 +1,135 @@
-Metadata-Version: 2.4
-Name: megadetector
-Version: 5.0.28
-Summary: MegaDetector is an AI model that helps conservation folks spend less time doing boring things with camera trap images.
-Author-email: Your friendly neighborhood MegaDetector team <cameratraps@lila.science>
-Maintainer-email: Your friendly neighborhood MegaDetector team <cameratraps@lila.science>
-License:     MIT License
-        
-            Permission is hereby granted, free of charge, to any person obtaining a copy
-            of this software and associated documentation files (the "Software"), to deal
-            in the Software without restriction, including without limitation the rights
-            to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-            copies of the Software, and to permit persons to whom the Software is
-            furnished to do so, subject to the following conditions:
-        
-            The above copyright notice and this permission notice shall be included in all
-            copies or substantial portions of the Software.
-        
-            THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-            IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-            FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-            AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-            LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-            OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-            SOFTWARE.
-        
-Project-URL: Homepage, https://github.com/agentmorris/MegaDetector
-Project-URL: Documentation, https://megadetector.readthedocs.io
-Project-URL: Bug Reports, https://github.com/agentmorris/MegaDetector/issues
-Project-URL: Source, https://github.com/agentmorris/MegaDetector
-Keywords: camera traps,conservation,wildlife,ai,megadetector
-Classifier: Programming Language :: Python :: 3
-Requires-Python: <3.14,>=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: mkl==2024.0; sys_platform != "darwin"
-Requires-Dist: numpy>=1.26.4
-Requires-Dist: Pillow>=9.5
-Requires-Dist: tqdm>=4.64.0
-Requires-Dist: jsonpickle>=3.0.2
-Requires-Dist: humanfriendly>=10.0
-Requires-Dist: matplotlib>=3.8.0
-Requires-Dist: opencv-python>=4.8.0
-Requires-Dist: requests>=2.31.0
-Requires-Dist: pyqtree>=1.0.0
-Requires-Dist: scikit-learn>=1.3.1
-Requires-Dist: pandas>=2.1.1
-Requires-Dist: python-dateutil
-Requires-Dist: send2trash
-Requires-Dist: dill
-Requires-Dist: ultralytics-yolov5==0.1.1
-Requires-Dist: yolov9pip==0.0.4
-Requires-Dist: python-dateutil
-Dynamic: license-file
-
-# MegaDetector
-
-This package is a pip-installable version of the support/inference code for [MegaDetector](https://github.com/agentmorris/MegaDetector/?tab=readme-ov-file#megadetector), an object detection model that helps conservation biologists spend less time doing boring things with camera trap images.  Complete documentation for this Python package is available at [megadetector.readthedocs.io](https://megadetector.readthedocs.io).
-
-If you aren't looking for the Python package specifically, and you just want to learn more about what MegaDetector is all about, head over to the [MegaDetector repo](https://github.com/agentmorris/MegaDetector/?tab=readme-ov-file#megadetector).
-
-If you don't want to run MegaDetector, and you just want to use the utilities in this package - postprocessing, manipulating large volumes of camera trap images, etc. - you may want to check out the [megadetector-utils](https://pypi.org/project/megadetector-utils/) package, which is identical to this one, but excludes all of the PyTorch/YOLO dependencies, and is thus approximately one zillion times smaller.
-
-## Installation
-
-Install with:
-
-`pip install megadetector`
-
-MegaDetector model weights aren't downloaded at the time you install the package, but they will be (optionally) automatically downloaded the first time you run the model.
-
-## Package reference
-
-See [megadetector.readthedocs.io](https://megadetector.readthedocs.io).
-
-
-## Examples of things you can do with this package
-
-### Run MegaDetector on one image and count the number of detections
-
-```
-from megadetector.utils import url_utils
-from megadetector.visualization import visualization_utils as vis_utils
-from megadetector.detection import run_detector
-
-# This is the image at the bottom of this page, it has one animal in it
-image_url = 'https://github.com/agentmorris/MegaDetector/raw/main/images/orinoquia-thumb-web.jpg'
-temporary_filename = url_utils.download_url(image_url)
-
-image = vis_utils.load_image(temporary_filename)
-
-# This will automatically download MDv5a; you can also specify a filename.
-model = run_detector.load_detector('MDV5A')
-
-result = model.generate_detections_one_image(image)
-
-detections_above_threshold = [d for d in result['detections'] if d['conf'] > 0.2]
-print('Found {} detections above threshold'.format(len(detections_above_threshold)))
-```
-
-### Run MegaDetector on a folder of images
-
-```
-from megadetector.detection.run_detector_batch import \
-    load_and_run_detector_batch, write_results_to_file
-from megadetector.utils import path_utils
-import os
-
-# Pick a folder to run MD on recursively, and an output file
-image_folder = os.path.expanduser('~/megadetector_test_images')
-output_file = os.path.expanduser('~/megadetector_output_test.json')
-
-# Recursively find images
-image_file_names = path_utils.find_images(image_folder,recursive=True)
-
-# This will automatically download MDv5a; you can also specify a filename.
-results = load_and_run_detector_batch('MDV5A', image_file_names)
-
-# Write results to a format that Timelapse and other downstream tools like.
-write_results_to_file(results,
-                      output_file,
-                      relative_path_base=image_folder,
-                      detector_file=detector_filename)
-```
-
-## Contact
-
-Contact <a href="cameratraps@lila.science">cameratraps@lila.science</a> with questions.
-
-## Gratuitous animal picture
-
-<img src="https://github.com/agentmorris/MegaDetector/raw/main/images/orinoquia-thumb-web_detections.jpg"><br/>Image credit University of Minnesota, from the [Orinoquía Camera Traps](http://lila.science/datasets/orinoquia-camera-traps/) data set.
+Metadata-Version: 2.4
+Name: megadetector
+Version: 5.0.29
+Summary: MegaDetector is an AI model that helps conservation folks spend less time doing boring things with camera trap images.
+Author-email: Your friendly neighborhood MegaDetector team <cameratraps@lila.science>
+Maintainer-email: Your friendly neighborhood MegaDetector team <cameratraps@lila.science>
+License:     MIT License
+        
+            Permission is hereby granted, free of charge, to any person obtaining a copy
+            of this software and associated documentation files (the "Software"), to deal
+            in the Software without restriction, including without limitation the rights
+            to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+            copies of the Software, and to permit persons to whom the Software is
+            furnished to do so, subject to the following conditions:
+        
+            The above copyright notice and this permission notice shall be included in all
+            copies or substantial portions of the Software.
+        
+            THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+            IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+            FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+            AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+            LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+            OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+            SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/agentmorris/MegaDetector
+Project-URL: Documentation, https://megadetector.readthedocs.io
+Project-URL: Bug Reports, https://github.com/agentmorris/MegaDetector/issues
+Project-URL: Source, https://github.com/agentmorris/MegaDetector
+Keywords: camera traps,conservation,wildlife,ai,megadetector
+Classifier: Programming Language :: Python :: 3
+Requires-Python: <3.14,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mkl==2024.0; sys_platform != "darwin"
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: Pillow>=9.5
+Requires-Dist: tqdm>=4.64.0
+Requires-Dist: jsonpickle>=3.0.2
+Requires-Dist: humanfriendly>=10.0
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: opencv-python>=4.8.0
+Requires-Dist: requests>=2.31.0
+Requires-Dist: pyqtree>=1.0.0
+Requires-Dist: scikit-learn>=1.3.1
+Requires-Dist: pandas>=2.1.1
+Requires-Dist: python-dateutil
+Requires-Dist: send2trash
+Requires-Dist: python-dateutil
+Requires-Dist: clipboard
+Requires-Dist: dill
+Requires-Dist: ruff
+Requires-Dist: pytest
+Requires-Dist: ultralytics-yolov5==0.1.1
+Requires-Dist: yolov9pip==0.0.4
+Dynamic: license-file
+
+# MegaDetector
+
+This package is a pip-installable version of the support/inference code for [MegaDetector](https://github.com/agentmorris/MegaDetector/?tab=readme-ov-file#megadetector), an object detection model that helps conservation biologists spend less time doing boring things with camera trap images.  Complete documentation for this Python package is available at [megadetector.readthedocs.io](https://megadetector.readthedocs.io).
+
+If you aren't looking for the Python package specifically, and you just want to learn more about what MegaDetector is all about, head over to the [MegaDetector repo](https://github.com/agentmorris/MegaDetector/?tab=readme-ov-file#megadetector).
+
+If you don't want to run MegaDetector, and you just want to use the utilities in this package - postprocessing, manipulating large volumes of camera trap images, etc. - you may want to check out the [megadetector-utils](https://pypi.org/project/megadetector-utils/) package, which is identical to this one, but excludes all of the PyTorch/YOLO dependencies, and is thus approximately one zillion times smaller.
+
+## Installation
+
+Install with:
+
+`pip install megadetector`
+
+MegaDetector model weights aren't downloaded at the time you install the package, but they will be (optionally) automatically downloaded the first time you run the model.
+
+## Package reference
+
+See [megadetector.readthedocs.io](https://megadetector.readthedocs.io).
+
+
+## Examples of things you can do with this package
+
+### Run MegaDetector on one image and count the number of detections
+
+```
+from megadetector.utils import url_utils
+from megadetector.visualization import visualization_utils as vis_utils
+from megadetector.detection import run_detector
+
+# This is the image at the bottom of this page, it has one animal in it
+image_url = 'https://github.com/agentmorris/MegaDetector/raw/main/images/orinoquia-thumb-web.jpg'
+temporary_filename = url_utils.download_url(image_url)
+
+image = vis_utils.load_image(temporary_filename)
+
+# This will automatically download MDv5a; you can also specify a filename.
+model = run_detector.load_detector('MDV5A')
+
+result = model.generate_detections_one_image(image)
+
+detections_above_threshold = [d for d in result['detections'] if d['conf'] > 0.2]
+print('Found {} detections above threshold'.format(len(detections_above_threshold)))
+```
+
+### Run MegaDetector on a folder of images
+
+```
+from megadetector.detection.run_detector_batch import \
+    load_and_run_detector_batch, write_results_to_file
+from megadetector.utils import path_utils
+import os
+
+# Pick a folder to run MD on recursively, and an output file
+image_folder = os.path.expanduser('~/megadetector_test_images')
+output_file = os.path.expanduser('~/megadetector_output_test.json')
+
+# Recursively find images
+image_file_names = path_utils.find_images(image_folder,recursive=True)
+
+# This will automatically download MDv5a; you can also specify a filename.
+results = load_and_run_detector_batch('MDV5A', image_file_names)
+
+# Write results to a format that Timelapse and other downstream tools like.
+write_results_to_file(results,
+                      output_file,
+                      relative_path_base=image_folder,
+                      detector_file=detector_filename)
+```
+
+## Contact
+
+Contact <a href="cameratraps@lila.science">cameratraps@lila.science</a> with questions.
+
+## Gratuitous animal picture
+
+<img src="https://github.com/agentmorris/MegaDetector/raw/main/images/orinoquia-thumb-web_detections.jpg"><br/>Image credit University of Minnesota, from the [Orinoquía Camera Traps](http://lila.science/datasets/orinoquia-camera-traps/) data set.

{megadetector-5.0.28 → megadetector-5.0.29}/README.md

@@ -269,3 +269,5 @@ Code written on or before April 28, 2023 is [copyright Microsoft](https://github
 This project welcomes contributions, as pull requests, issues, or suggestions by [email](mailto:cameratraps@lila.science).  We have a [list](https://github.com/agentmorris/MegaDetector/issues/84) of issues that we're hoping to address, many of which would be good starting points for new contributors.  We also depend on other open-source tools that help users run MegaDetector (particularly [AddaxAI](https://github.com/PetervanLunteren/AddaxAI) (formerly EcoAssist), and open-source tools that help users work with MegaDetector results (particularly [Timelapse](https://github.com/saulgreenberg/Timelapse)).  If you are looking to get involved in GUI development, reach out to the developers of those tools as well!
 
 If you are interesting in getting involved in the conservation technology space, and MegaDetector just happens to be the first page you landed on, and none of our open issues are getting you fired up, don't fret!  Head over to the [WILDLABS discussion forums](https://wildlabs.net/discussions) and let the community know you're a developer looking to get involved.  Someone needs your help!
+
+Information about the coding conventions, linting, testing, and documentation tools used by this repo are available in [developers.md](developers.md).

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/batch_processing/api_core/batch_service/score.py

@@ -1,6 +1,7 @@
 import io
 import json
 import math
+from megadetector.utils import ct_utils
 import os
 import sys
 from datetime import datetime
@@ -353,7 +354,7 @@ class BatchScorer:
         return detections
 
 
-def main():
+def main(): # noqa
     print('score.py, main()')
 
     # information to determine input and output locations
@@ -387,8 +388,7 @@ def main():
     task_output_path = os.path.join(task_out_dir, f'job_{job_id}_task_{task_id}.json')
 
     # test that we can write to output path; also in case there is no image to process
-    with open(task_output_path, 'w') as f:
-        json.dump([], f)
+    ct_utils.write_json(task_output_path, [])
 
     # list images to process
     list_images_path = os.path.join(job_folder_mounted, f'{job_id}_images.json')
@@ -432,8 +432,7 @@ def main():
     except Exception as e:
         raise RuntimeError(f'score.py, main(), exception in score_images(): {e}')
 
-    with open(task_output_path, 'w', encoding='utf-8') as f:
-        json.dump(detections, f, ensure_ascii=False)
+    ct_utils.write_json(task_output_path, detections, ensure_ascii=False)
 
 if __name__ == '__main__':
     main()

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/batch_processing/api_core_support/aggregate_results_manually.py

@@ -22,7 +22,7 @@ import json
 from api.batch_processing.api_core.orchestrator_api.orchestrator import AMLMonitor
 
 
-def main():
+def main(): # noqa
     parser = argparse.ArgumentParser()
     parser.add_argument('shortened_request_id', type=str,
                         help='the request ID to restart monitoring')

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/batch_processing/api_support/summarize_daily_activity.py

@@ -124,7 +124,7 @@ def send_message():
     print('')
 
 
-def main():
+def main(): # noqa
     """
     Wake up at 5 minutes past midnight UTC to send a summary of yesterday's activities if there were any.
     Then goes in a loop to wake up and send a summary every 24 hours.

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/batch_processing/integration/digiKam/xmp_integration.py

@@ -17,7 +17,7 @@ import inspect
 import os
 import sys
 import json
-import pyexiv2
+import pyexiv2 # type: ignore
 import ntpath
 import threading
 import traceback
@@ -432,7 +432,7 @@ def args_to_object(args,obj):
             setattr(obj, n, v)
 
 
-def main():
+def main(): # noqa
     
     parser = argparse.ArgumentParser()
     parser.add_argument('--input_file', help = 'Path to the MegaDetector .json file', default=None)

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/batch_processing/integration/eMammal/test_scripts/push_annotations_to_emammal.py

@@ -51,7 +51,7 @@ def format_data_print_deployments(rows):
 
 #%% Command-line driver
 
-def main():
+def main(): # noqa
     
     parser = argparse.ArgumentParser()
     parser.add_argument('input_file', type=str, help='Input .json filename')

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/batch_processing/integration/eMammal/test_scripts/select_images_for_testing.py

@@ -10,7 +10,7 @@ from tqdm import tqdm
 
 #%% Main function
 
-def main():
+def main(): # noqa
     
     parser = argparse.ArgumentParser()
     parser.add_argument('input_file', type=str, help='Input .json filename')

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/api/synchronous/api_core/tests/load_test.py

@@ -1,4 +1,3 @@
-
 import os
 import json
 import io
@@ -47,7 +46,7 @@ def get_detections(response):
     print(text_result)
 
 
-def test_load(num_requests, params, max_images=1):
+def load_test(num_requests, params, max_images=1):
     requests = []
     
     # read the images anew for each request
@@ -104,7 +103,7 @@ if __name__ == "__main__":
     max_images = 1
 
     start = datetime.now()
-    responses = test_load(num_requests, params, max_images=max_images)
+    responses = load_test(num_requests, params, max_images=max_images)
     end = datetime.now()
     total_time = end - start
     print('Total time for {} requests: {}'.format(num_requests, total_time))

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/classification/aggregate_classifier_probs.py

@@ -44,7 +44,7 @@ def main(classifier_results_csv_path: str,
     Because the output CSV is often very large, we process it in chunks of 1000
     rows at a time.
     """
-    
+
     chunked_df_iterator = pd.read_csv(
         classifier_results_csv_path, chunksize=1000, float_precision='high',
         index_col='path')
@@ -80,7 +80,7 @@ def main(classifier_results_csv_path: str,
 #%% Command-line driver
 
 def _parse_args() -> argparse.Namespace:
-    
+
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description='Aggregate classifier probabilities to target classes.')
@@ -100,7 +100,7 @@ def _parse_args() -> argparse.Namespace:
 
 
 if __name__ == '__main__':
-    
+
     args = _parse_args()
     main(classifier_results_csv_path=args.classifier_results_csv,
          target_mapping_json_path=args.target_mapping,

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/classification/analyze_failed_images.py

@@ -62,7 +62,7 @@ def check_image_condition(img_path: str,
         'bad': image exists, but cannot be opened even when setting
             ImageFile.LOAD_TRUNCATED_IMAGES=True
     """
-    
+
     if (account is None) or (container is None) or (datasets_table is not None):
         assert account is None
         assert container is None
@@ -133,7 +133,7 @@ def analyze_images(url_or_path: str, json_keys: Optional[Sequence[str]] = None,
         sas_token: str, optional SAS token (without leading '?') if the
             container is not publicly accessible
     """
-    
+
     datasets_table = None
     if (account is None) or (container is None):
         assert account is None
@@ -190,8 +190,8 @@ def analyze_images(url_or_path: str, json_keys: Optional[Sequence[str]] = None,
 
 #%% Command-line driver
 
-def _parse_args() -> argparse.Namespace:    
-    
+def _parse_args() -> argparse.Namespace:
+
     parser = argparse.ArgumentParser(
         description='Analyze a list of images that failed to download or crop.')
     parser.add_argument(
@@ -220,7 +220,7 @@ def _parse_args() -> argparse.Namespace:
 
 
 if __name__ == '__main__':
-    
+
     args = _parse_args()
     analyze_images(url_or_path=args.failed_images, json_keys=args.json_keys,
                    account=args.account, container=args.container,

{megadetector-5.0.28 → megadetector-5.0.29}/megadetector/classification/cache_batchapi_outputs.py

@@ -66,6 +66,7 @@ from api.batch_processing.data_preparation.prepare_api_submission import (
     TaskStatus, Task)
 from api.batch_processing.postprocessing.combine_api_outputs import (
     combine_api_output_dictionaries)
+from megadetector.utils import ct_utils
 
 
 #%% Support functions
@@ -84,7 +85,7 @@ def cache_json(json_path: str,
         detector_output_cache_base_dir: str
         detector_version: str
     """
-    
+
     with open(json_path, 'r') as f:
         js = json.load(f)
 
@@ -138,7 +139,7 @@ def cache_detections(detections: Mapping[str, Any], dataset: str,
 
     Returns: str, message
     """
-    
+
     # combine detections with cache
     dataset_cache_path = os.path.join(
         detector_output_cache_dir, f'{dataset}.json')
@@ -155,8 +156,7 @@ def cache_detections(detections: Mapping[str, Any], dataset: str,
                f'{dataset_cache_path}')
 
     # write combined detections back out to cache
-    with open(dataset_cache_path, 'w') as f:
-        json.dump(merged_dataset_cache, f, indent=1)
+    ct_utils.write_json(dataset_cache_path, merged_dataset_cache)
     return msg
 
 
@@ -188,7 +188,7 @@ def _parse_args() -> argparse.Namespace:
 
 
 if __name__ == '__main__':
-    
+
     args = _parse_args()
     cache_json(
         json_path=args.json_file,