megadetector 5.0.28__tar.gz → 10.0.1__tar.gz

{megadetector-5.0.28/megadetector.egg-info → megadetector-10.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: megadetector
-Version: 5.0.28
+Version: 10.0.1
 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>
@@ -47,10 +47,13 @@ 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
-Requires-Dist: python-dateutil
 Dynamic: license-file
 
 # MegaDetector

{megadetector-5.0.28 → megadetector-10.0.1}/README.md

@@ -1,4 +1,4 @@
-# MegaDetector
+<img src="images/md_logo_450px.png" width="450"/><br/>
 
 ...helping conservation biologists spend less time doing boring things with camera trap images.
 
@@ -74,6 +74,7 @@ Here are a few of the organizations that have used MegaDetector... we're only li
 * [Research Institute of Organic Agriculture](https://www.fibl.org/en/) (FiBL)
 * [A/Vian Ecological Consulting](https://avianeco.com/)
 * [Wildlife Insights](https://www.wildlifeinsights.org/)
+* [MammalWeb](https://www.mammalweb.org/)
 
 * [Applied Conservation Macro Ecology Lab](http://www.acmelab.ca/), University of Victoria
 * [Banff National Park Resource Conservation](https://www.pc.gc.ca/en/pn-np/ab/banff/nature/conservation), Parks Canada
@@ -85,9 +86,11 @@ Here are a few of the organizations that have used MegaDetector... we're only li
 * [Centre for Ecosystem Science](https://www.unsw.edu.au/research/), UNSW Sydney
 * [Cross-Cultural Ecology Lab](https://crossculturalecology.net/), Macquarie University
 * [DC Cat Count](https://hub.dccatcount.org/), led by the Humane Rescue Alliance
+* [Department of Anthropology and Archaeology](https://arts.ucalgary.ca/anthropology-archaeology), University of Calgary
 * [Department of Fish and Wildlife Sciences](https://www.uidaho.edu/cnr/departments/fish-and-wildlife-sciences), University of Idaho
 * [Department of Society & Conservation](https://www.umt.edu/environment/about/departments/socon/), W.A. Franke College of Forestry & Conservation, University of Montana
 * [Department of Wildlife Ecology and Conservation](https://wec.ifas.ufl.edu/), University of Florida
+* [Fodrie Lab](https://fodriefishecol.wixsite.com/unc-fish/), Institute of Marine Sciences, UNC Chapel Hill
 * [Gola Forest Programme](https://www.rspb.org.uk/our-work/conservation/projects/scientific-support-for-the-gola-forest-programme/), Royal Society for the Protection of Birds (RSPB)
 * [Graeme Shannon's Research Group](https://wildliferesearch.co.uk/group-1), Bangor University 
 * [Grizzly Bear Recovery Program](https://www.fws.gov/office/grizzly-bear-recovery-program), U.S. Fish & Wildlife Service
@@ -111,6 +114,7 @@ Here are a few of the organizations that have used MegaDetector... we're only li
 * [Wildlife Research](https://www.dfw.state.or.us/wildlife/research/index.asp), Oregon Department of Fish and Wildlife
 * [Wildlife Division](https://www.michigan.gov/dnr/about/contact/wildlife), Michigan Department of Natural Resources
 * [Kohl Wildlife Lab](https://kohlwildlifelab.com/), University of Georgia
+* [SPEC Lab](https://thespeclab.weebly.com/) and [Cherry Lab](https://www.ckwri.tamuk.edu/about/michael-j-cherry-phd), Caesar Kleberg Wildlife Research Institute, Texas A&M Kingsville
 * Ecology and Conservation of Amazonian Vertebrates Research Group, Federal University of Amapá
 * Department of Ecology, TU Berlin
 * Ghost Cat Analytics
@@ -135,7 +139,11 @@ Here are a few of the organizations that have used MegaDetector... we're only li
 * [Trapper](https://trapper-project.readthedocs.io/en/latest/overview.html) ([tutorial](https://trapper-project.readthedocs.io/en/latest/tutorial.html))
 * [BirdLife Malta](https://birdlifemalta.org/) ([tweet](https://x.com/BirdLife_Malta/status/1817456839862173783?t=S-KRiZ5R1-CoW8-tbYNjqQ&s=03)) ([LI post](https://www.linkedin.com/posts/birdlifemalta_worldnatureconservationday-shearwater-colony-activity-7223220656589463553-X2Mc/?utm_source=share&utm_medium=member_android))
 * [Endangered Landscapes and Seascapes Programme](https://www.endangeredlandscapes.org/), Cambridge Conservation Initiative ([blog post](https://www.endangeredlandscapes.org/news/ai-for-wildlife-monitoring-a-real-time-alert-system-for-bears-and-wild-boars-in-romanias-carpathian-mountains/))
-
+* [UK National Hedgehog Monitoring Programme](https://www.the-ies.org/analysis/lens-wild-innovations-wildlife-0) ([blog post](https://www.the-ies.org/analysis/lens-wild-innovations-wildlife-0))
+* [Fort Collins Science Center](https://www.usgs.gov/centers/fort-collins-science-center/), U.S. Geological Survey ([blog post](https://www.usgs.gov/centers/fort-collins-science-center/science/early-detection-and-rapid-response-tools-invasive-tegu))
+* [Ontario Ministry of Natural Resources](https://www.ontario.ca/page/ministry-natural-resources) ([post](https://www.facebook.com/ONresources/posts/artificial-intelligence-ai-to-the-rescueone-disadvantage-of-trail-cameras-and-ca/1012916944364710/))
+* [Loisaba Conservancy](https://www.loisaba.com/) ([blog post](https://www.loisaba.com/post/help-scientists-understand-how-an-invasive-cactus-affects-mammal-behaviour))
+* [Urban Rivers](https://urbanrivers.org/) ([blog post](https://www.morescode-analytics.com/2025/06/27/filtering-90-pct-blank-wildlife.html))
 * [Road Ecology Center](https://roadecology.ucdavis.edu/), University of California, Davis ([Wildlife Observer Network platform](https://roadecology.ucdavis.edu/research/projects/wildlife-observer-network))
 * [The Nature Conservancy in California](https://www.nature.org/en-us/about-us/where-we-work/united-states/california/) ([Animl platform](https://github.com/tnc-ca-geo/animl-frontend)) ([story](https://www.vision-systems.com/non-factory/environment-agriculture/article/14304433/the-nature-conservancy-brings-cameras-ai-to-invasive-species-prevention))
 * [San Diego Zoo Wildlife Alliance](https://science.sandiegozoo.org/)  ([Animl R package](https://github.com/conservationtechlab/animl))
@@ -143,7 +151,7 @@ Here are a few of the organizations that have used MegaDetector... we're only li
 
 Also see:
 
-* The [list of MD-related GUIs, platforms, and GitHub repos](https://github.com/agentmorris/MegaDetector/blob/main/megadetector.md#is-there-a-gui) within the MegaDetector User Guide
+* The [list of MD-related GUIs, platforms, and GitHub repos](https://github.com/agentmorris/MegaDetector/blob/main/megadetector.md#is-there-a-gui) within the MegaDetector User Guide... although you can never have too many lists, so here they are in a concise comma-separated list: [Wildlife Insights](https://wildlifeinsights.org/), [Animal Detect](https://www.animaldetect.com), [TrapTagger](https://wildeyeconservation.org/trap-tagger-about/), [WildTrax](https://www.wildtrax.ca/), [Agouti](https://agouti.eu/), [Trapper](https://trapper-project.readthedocs.io/en/latest/overview.html), [Camelot](https://camelotproject.org/), [WildePod](https://wildepod.org/), [wpsWatch](https://wildlabs.net/inventory/products/wpswatch), [TNC Animl](https://animl.camera/) ([code](https://github.com/tnc-ca-geo/animl-frontend)), [Wildlife Observer Network](https://roadecology.ucdavis.edu/research/projects/wildlife-observer-network), [Zooniverse ML Subject Assistant](https://subject-assistant.zooniverse.org/#/intro), [Dudek AI Image Toolkit](https://ait.dudek.com), [Zamba Cloud](https://github.com/drivendataorg/zamba), [OCAPI](https://www.terroiko.fr/ocapi/).
 
 * [Peter's map of AddaxAI (formerly EcoAssist) users](https://addaxdatascience.com/addaxai/) (who are also MegaDetector users!)
 
@@ -201,7 +209,7 @@ Code for:
 
 #### megadetector/api
 
-Code for hosting our models as an API, either for synchronous operation (i.e., for real-time inference) or as a batch process (for large biodiversity surveys).
+Code for hosting our models as an API, either for synchronous operation (i.e., for real-time inference) or as a batch process (for large biodiversity surveys).  This folder is largely deprecated, and primarily exists now only to hold documentation that is still relevant, to which there are permanent links.  Mostly everything in this folder has been moved to the "archive" folder.
 
 
 #### megadetector/classification
@@ -269,3 +277,7 @@ 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).
+
+Speaking of contributions... thanks to Erin Roche from Idaho Fish and Game for the MegaDetector logo at the top of this page!

{megadetector-5.0.28 → megadetector-10.0.1}/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-10.0.1}/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-10.0.1}/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-10.0.1}/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-10.0.1}/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-10.0.1}/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,

{megadetector-5.0.28 → megadetector-10.0.1}/megadetector/classification/create_classification_dataset.py

@@ -37,7 +37,7 @@ avoiding overlapping locations between the train/val/test splits.
 This script outputs 3 files to <output_dir>:
 
 1) classification_ds.csv, contains columns:
-   
+
     - 'path': str, path to cropped images
     - 'dataset': str, name of dataset
     - 'location': str, location that image was taken, as saved in MegaDB
@@ -75,6 +75,7 @@ import pandas as pd
 from tqdm import tqdm
 
 from megadetector.classification import detect_and_crop
+from megadetector.utils import ct_utils
 
 
 #%% Example usage
@@ -108,7 +109,7 @@ def main(output_dir: str,
          test_frac: Optional[float],
          splits_method: Optional[str],
          label_spec_json_path: Optional[str]) -> None:
-    
+
     # input validation
     assert set(mode) <= {'csv', 'splits'}
     if label_spec_json_path is not None:
@@ -160,9 +161,8 @@ def main(output_dir: str,
             labels = labels.map(lambda x: x.split(',')).explode()
             # look into sklearn.preprocessing.MultiLabelBinarizer
         label_names = sorted(labels.unique())
-        with open(os.path.join(output_dir, LABEL_INDEX_FILENAME), 'w') as f:
-            # Note: JSON always saves keys as strings!
-            json.dump(dict(enumerate(label_names)), f, indent=1)
+        # Note: JSON always saves keys as strings!
+        ct_utils.write_json(os.path.join(output_dir, LABEL_INDEX_FILENAME), dict(enumerate(label_names)))
 
     if 'splits' in mode:
         assert splits_method is not None
@@ -181,8 +181,7 @@ def main(output_dir: str,
             split_to_locs = create_splits_smallest_label_first(
                 df, val_frac, test_frac, test_split=test_set_locs,
                 label_spec_json_path=label_spec_json_path)
-        with open(os.path.join(output_dir, SPLITS_FILENAME), 'w') as f:
-            json.dump(split_to_locs, f, indent=1)
+        ct_utils.write_json(os.path.join(output_dir, SPLITS_FILENAME), split_to_locs)
 
 
 #%% Support functions
@@ -236,7 +235,7 @@ def create_classification_csv(
             'missing crops': list of tuple (img_path, i), where i is the
                 i-th crop index
     """
-    
+
     assert 0 <= confidence_threshold <= 1
 
     columns = [
@@ -359,7 +358,7 @@ def create_splits_random(df: pd.DataFrame, val_frac: float,
     Returns: dict, keys are ['train', 'val', 'test'], values are lists of locs,
         where each loc is a tuple (dataset, location)
     """
-    
+
     if test_split is not None:
         assert test_frac == 0
     train_frac = 1. - val_frac - test_frac
@@ -445,7 +444,7 @@ def create_splits_smallest_label_first(
     Returns: dict, keys are ['train', 'val', 'test'], values are lists of locs,
         where each loc is a tuple (dataset, location)
     """
-    
+
     # label => list of datasets to prioritize for test and validation sets
     prioritize = {}
     if label_spec_json_path is not None:
@@ -525,7 +524,7 @@ def sort_locs_by_size(loc_to_size: MutableMapping[tuple[str, str], int],
     Returns: list of (dataset, location) tuples, ordered from smallest size to
         largest. Locations from prioritized datasets come first.
     """
-    
+
     result = []
     if prioritize is not None:
         # modify loc_to_size in place, so copy its keys before iterating
@@ -610,7 +609,7 @@ def _parse_args() -> argparse.Namespace:
 
 
 if __name__ == '__main__':
-    
+
     args = _parse_args()
     main(output_dir=args.output_dir,
          mode=args.mode,

{megadetector-5.0.28 → megadetector-10.0.1}/megadetector/classification/crop_detections.py

@@ -33,7 +33,7 @@ bounding box width or height. In the case that the square crop boundaries exceed
 the original image size, the crop is padded with 0s.
 
 This script outputs a log file to:
-   
+
    <output_dir>/crop_detections_log_{timestamp}.json
 
 ...which contains images that failed to download and crop properly.
@@ -107,7 +107,7 @@ def main(detections_json_path: str,
         threads: int, number of threads to use for downloading images
         logdir: str, path to directory to save log file
     """
-    
+
     # error checking
     assert 0 <= confidence_threshold <= 1, \
             'Invalid confidence threshold {}'.format(confidence_threshold)
@@ -149,7 +149,7 @@ def main(detections_json_path: str,
         for d in info_dict['detections']:
             if d['category'] not in detection_categories:
                 print('Warning: ignoring detection with category {} for image {}'.format(
-                    d['category'],img_path))                
+                    d['category'],img_path))
                 # This will be removed later when we filter for animals
                 d['category'] = 'unsupported'
             else:
@@ -235,7 +235,7 @@ def download_and_crop(
         total_downloads: int, number of images downloaded
         total_new_crops: int, number of new crops saved to cropped_images_dir
     """
-    
+
     # True for ground truth, False for MegaDetector
     # always save as .jpg for consistency
     crop_path_template = {
@@ -297,7 +297,7 @@ def load_local_image(img_path: str |  BinaryIO) -> Optional[Image.Image]:
     """
     Attempts to load an image from a local path.
     """
-    
+
     try:
         with Image.open(img_path) as img:
             img.load()
@@ -347,7 +347,7 @@ def load_and_crop(img_path: str,
         did_download: bool, whether image was downloaded from Azure Blob Storage
         num_new_crops: int, number of new crops successfully saved
     """
-    
+
     did_download = False
     num_new_crops = 0
 
@@ -393,7 +393,7 @@ def load_and_crop(img_path: str,
 
     assert img is not None, 'image "{}" failed to load or download properly'.format(
         debug_path)
-    
+
     if img.mode != 'RGB':
         img = img.convert(mode='RGB')  # always save as RGB for consistency
 
@@ -418,7 +418,7 @@ def save_crop(img: Image.Image, bbox_norm: Sequence[float], square_crop: bool,
 
     Returns: bool, True if a crop was saved, False otherwise
     """
-    
+
     img_w, img_h = img.size
     xmin = int(bbox_norm[0] * img_w)
     ymin = int(bbox_norm[1] * img_h)
@@ -456,7 +456,7 @@ def save_crop(img: Image.Image, bbox_norm: Sequence[float], square_crop: bool,
 #%% Command-line driver
 
 def _parse_args() -> argparse.Namespace:
-    
+
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description='Crop detections from MegaDetector.')
@@ -501,7 +501,7 @@ def _parse_args() -> argparse.Namespace:
 
 
 if __name__ == '__main__':
-    
+
     args = _parse_args()
     main(detections_json_path=args.detections_json,
          cropped_images_dir=args.cropped_images_dir,

{megadetector-5.0.28 → megadetector-10.0.1}/megadetector/classification/csv_to_json.py

@@ -40,7 +40,7 @@ Example CSV input:
 
 Example JSON output:
 
-"    
+"
   {
       "cervid": {
           "dataset_labels": {
@@ -107,17 +107,17 @@ import json
 from typing import Any
 
 import pandas as pd
+from megadetector.utils import ct_utils
 
 
 #%% Main function
 
-def main():
+def main(): # noqa
     args = _parse_args()
     js = csv_to_jsondict(args.input_csv_file)
     for label in js:
         js[label] = order_spec_dict(js[label])
-    with open(args.output_json_path, 'w') as f:
-        json.dump(js, f, indent=args.json_indent)
+    ct_utils.write_json(args.output_json_path, js, indent=args.json_indent)
 
 
 #%% Support functions
@@ -126,7 +126,7 @@ def parse_csv_row(obj: dict[str, Any], rowtype: str, content: str) -> None:
     """
     Parses a row in the CSV.
     """
-    
+
     if rowtype == 'row':
         if 'dataset_labels' not in obj:
             obj['dataset_labels'] = defaultdict(list)
@@ -169,7 +169,7 @@ def csv_to_jsondict(csv_path: str) -> dict[str, dict[str, Any]]:
     """
     Converts CSV to json-style dictionary.
     """
-    
+
     df = pd.read_csv(csv_path, comment='#', skip_blank_lines=True)
     assert (df.columns == ['output_label', 'type', 'content']).all()
 
@@ -193,7 +193,7 @@ def order_spec_dict(spec_dict: dict[str, Any]) -> dict[str, Any]:
     """
     Returns spec_dict with keys in a specific order.
     """
-    
+
     if 'exclude' in spec_dict:
         spec_dict['exclude'] = order_spec_dict(spec_dict['exclude'])
     ordered_spec_dict: dict[str, Any] = {}
@@ -206,7 +206,7 @@ def order_spec_dict(spec_dict: dict[str, Any]) -> dict[str, Any]:
 #%% Command-line driver
 
 def _parse_args() -> argparse.Namespace:
-    
+
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description='Converts CSV to JSON format for label specification.')

{megadetector-5.0.28 → megadetector-10.0.1}/megadetector/classification/detect_and_crop.py

@@ -118,6 +118,7 @@ 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
+from megadetector.utils import ct_utils
 
 
 #%% Example usage
@@ -264,8 +265,7 @@ def main(queried_images_json_path: str,
     # save log of bad images
     date = datetime.now().strftime('%Y%m%d_%H%M%S')  # e.g., '20200722_110816'
     log_path = os.path.join(output_dir, f'detect_and_crop_log_{date}.json')
-    with open(log_path, 'w') as f:
-        json.dump(log, f, indent=1)
+    ct_utils.write_json(log_path, log)
 
 
 #%% Support functions
@@ -291,7 +291,7 @@ def load_detection_cache(detector_output_cache_dir: str,
             if no cached detections were found for the given dataset ds.
         detection_categories: dict, maps str category ID to str category name
     """
-    
+
     # cache of Detector outputs: dataset name => {img_path => detection_dict}
     detection_cache = {}
     detection_categories: dict[str, str] = {}
@@ -339,7 +339,7 @@ def filter_detected_images(
         detection_categories: dict, maps str category ID to str category name,
             empty dict if no cached detections are found
     """
-    
+
     datasets = set(img_path[:img_path.find('/')]
                    for img_path in potential_images_to_detect)
     detection_cache, detection_categories = load_detection_cache(
@@ -364,7 +364,7 @@ def split_images_list_by_dataset(images_to_detect: Iterable[str]
 
     Returns: dict, maps dataset name to a list of image paths
     """
-    
+
     images_by_dataset: dict[str, list[str]] = {}
     for img_path in images_to_detect:
         dataset = img_path[:img_path.find('/')]
@@ -402,7 +402,7 @@ def submit_batch_detection_api(images_to_detect: Iterable[str],
 
     Returns: dict, maps str dataset name to list of Task objects
     """
-    
+
     filtered_images_to_detect = [
         x for x in images_to_detect if path_utils.is_image_file(x)]
     not_images = set(images_to_detect) - set(filtered_images_to_detect)
@@ -450,8 +450,7 @@ def submit_batch_detection_api(images_to_detect: Iterable[str],
         for dataset in tasks_by_dataset
         for task in tasks_by_dataset[dataset]
     ]
-    with open(resume_file_path, 'w') as f:
-        json.dump(resume_json, f, indent=1)
+    ct_utils.write_json(resume_file_path, resume_json)
     return tasks_by_dataset
 
 
@@ -478,7 +477,7 @@ def submit_batch_detection_api_by_dataset(
 
     Returns: list of Task objects
     """
-    
+
     os.makedirs(task_lists_dir, exist_ok=True)
 
     date = datetime.now().strftime('%Y%m%d_%H%M%S')  # e.g., '20200722_110816'
@@ -522,7 +521,7 @@ def resume_tasks(resume_file_path: str, batch_detection_api_url: str
 
     Returns: dict, maps str dataset name to list of Task objects
     """
-    
+
     with open(resume_file_path, 'r') as f:
         resume_json = json.load(f)
 
@@ -559,7 +558,7 @@ def wait_for_tasks(tasks_by_dataset: Mapping[str, Iterable[Task]],
             saved to <output_dir>/batchapi_response/{task_id}.json
         poll_interval: int, # of seconds between pinging the task status API
     """
-    
+
     remaining_tasks: list[tuple[str, Task]] = [
         (dataset, task) for dataset, tasks in tasks_by_dataset.items()
         for task in tasks]
@@ -597,8 +596,7 @@ def wait_for_tasks(tasks_by_dataset: Mapping[str, Iterable[Task]],
                 if not os.path.exists(save_dir):
                     tqdm.write(f'Creating API output dir: {save_dir}')
                     os.makedirs(save_dir)
-                with open(os.path.join(save_dir, f'{task.id}.json'), 'w') as f:
-                    json.dump(task.response, f, indent=1)
+                ct_utils.write_json(os.path.join(save_dir, f'{task.id}.json'), task.response)
             message = task.response['Status']['message']
             num_failed_shards = message['num_failed_shards']
             if num_failed_shards != 0:
@@ -676,7 +674,7 @@ def download_and_crop(
     Returns: list of str, images with bounding boxes that failed to download or
         crop properly
     """
-    
+
     # error checking before we download and crop any images
     valid_img_paths = set(queried_images_json.keys())
     if images_missing_detections is not None:
@@ -838,7 +836,7 @@ def _parse_args() -> argparse.Namespace:
 
 
 if __name__ == '__main__':
-    
+
     args = _parse_args()
     main(queried_images_json_path=args.queried_images_json,
          output_dir=args.output_dir,

{megadetector-5.0.28 → megadetector-10.0.1}/megadetector/classification/efficientnet/model.py

@@ -93,7 +93,7 @@ class MBConvBlock(nn.Module):
 
         Args:
             inputs (tensor): Input tensor.
-            drop_connect_rate (bool): Drop connect rate (float, between 0 and 1).
+            drop_connect_rate (bool, optional): Drop connect rate (float, between 0 and 1).
 
         Returns:
             Output of this block after processing.
@@ -135,7 +135,7 @@ class MBConvBlock(nn.Module):
         """Sets swish function as memory efficient (for training) or standard (for export).
 
         Args:
-            memory_efficient (bool): Whether to use memory-efficient version of swish.
+            memory_efficient (bool, optional): Whether to use memory-efficient version of swish.
         """
         self._swish = MemoryEfficientSwish() if memory_efficient else Swish()
 
@@ -221,7 +221,7 @@ class EfficientNet(nn.Module):
         """Sets swish function as memory efficient (for training) or standard (for export).
 
         Args:
-            memory_efficient (bool): Whether to use memory-efficient version of swish.
+            memory_efficient (bool, optional): Whether to use memory-efficient version of swish.
 
         """
         self._swish = MemoryEfficientSwish() if memory_efficient else Swish()
@@ -323,7 +323,7 @@ class EfficientNet(nn.Module):
 
         Args:
             model_name (str): Name for efficientnet.
-            in_channels (int): Input data's channel number.
+            in_channels (int, optional): Input data's channel number.
             override_params (other key word params):
                 Params to override model's global_params.
                 Optional key:
@@ -349,14 +349,14 @@ class EfficientNet(nn.Module):
 
         Args:
             model_name (str): Name for efficientnet.
-            weights_path (None or str):
+            weights_path (None or str, optional):
                 str: path to pretrained weights file on the local disk.
                 None: use pretrained weights downloaded from the Internet.
-            advprop (bool):
+            advprop (bool, optional):
                 Whether to load pretrained weights
                 trained with advprop (valid when weights_path is None).
-            in_channels (int): Input data's channel number.
-            num_classes (int):
+            in_channels (int, optional): Input data's channel number.
+            num_classes (int, optional):
                 Number of categories for classification.
                 It controls the output size for final linear layer.
             override_params (other key word params):