megadetector 10.0.2__tar.gz → 10.0.4__tar.gz

{megadetector-10.0.2/megadetector.egg-info → megadetector-10.0.4}/PKG-INFO

@@ -1,135 +1,134 @@
-Metadata-Version: 2.4
-Name: megadetector
-Version: 10.0.2
-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.
+Metadata-Version: 2.4
+Name: megadetector
+Version: 10.0.4
+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: 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-10.0.2 → megadetector-10.0.4}/README.md

@@ -274,7 +274,7 @@ Code written on or before April 28, 2023 is [copyright Microsoft](https://github
 
 ## Contributing
 
-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!
+This project welcomes contributions, as pull requests, issues, or suggestions by [email](mailto:cameratraps@lila.science).  We have a [list](https://dmorris.net/task-viewer/?file=https://raw.githubusercontent.com/agentmorris/MegaDetector/refs/heads/main/TODO.md) 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!
 

megadetector-10.0.4/megadetector/data_management/animl_to_md.py

@@ -0,0 +1,158 @@
+"""
+
+animl_to_md.py
+
+Convert a .csv file produced by the Animl package:
+
+https://github.com/conservationtechlab/animl-py
+
+...to a MD results file suitable for import into Timelapse.
+
+Columns are expected to be:
+
+file
+category (MD category identifies: 1==animal, 2==person, 3==vehicle)
+detection_conf
+bbox1,bbox2,bbox3,bbox4
+class
+classification_conf
+
+"""
+
+#%% Imports and constants
+
+import sys
+import argparse
+
+import pandas as pd
+
+from megadetector.utils.ct_utils import write_json
+from megadetector.detection.run_detector import DEFAULT_DETECTOR_LABEL_MAP
+detection_category_id_to_name = DEFAULT_DETECTOR_LABEL_MAP
+
+
+#%% Main function
+
+def animl_results_to_md_results(input_file,output_file=None):
+    """
+    Converts the .csv file [input_file] to the MD-formatted .json file [output_file].
+
+    If [output_file] is None, '.json' will be appended to the input file.
+    """
+
+    if output_file is None:
+        output_file = input_file + '.json'
+
+    df = pd.read_csv(input_file)
+
+    expected_columns = ('file','category','detection_conf',
+                        'bbox1','bbox2','bbox3','bbox4','class','classification_conf')
+
+    for s in expected_columns:
+        assert s in df.columns,\
+            'Expected column {} not found'.format(s)
+
+    classification_category_name_to_id = {}
+    filename_to_results = {}
+
+    # i_row = 0; row = df.iloc[i_row]
+    for i_row,row in df.iterrows():
+
+        # Is this the first detection we've seen for this file?
+        if row['file'] in filename_to_results:
+            im = filename_to_results[row['file']]
+        else:
+            im = {}
+            im['detections'] = []
+            im['file'] = row['file']
+            filename_to_results[im['file']] = im
+
+        assert isinstance(row['category'],int),'Invalid category identifier in row {}'.format(im['file'])
+        detection_category_id = str(row['category'])
+        assert detection_category_id in detection_category_id_to_name,\
+            'Unrecognized detection category ID {}'.format(detection_category_id)
+
+        detection = {}
+        detection['category'] = detection_category_id
+        detection['conf'] = row['detection_conf']
+        bbox = [row['bbox1'],row['bbox2'],row['bbox3'],row['bbox4']]
+        detection['bbox'] = bbox
+        classification_category_name = row['class']
+
+        # Have we seen this classification category before?
+        if classification_category_name in classification_category_name_to_id:
+            classification_category_id = \
+                classification_category_name_to_id[classification_category_name]
+        else:
+            classification_category_id = str(len(classification_category_name_to_id))
+            classification_category_name_to_id[classification_category_name] = \
+                classification_category_id
+
+        classifications = [[classification_category_id,row['classification_conf']]]
+        detection['classifications'] = classifications
+
+        im['detections'].append(detection)
+
+    # ...for each row
+
+    info = {}
+    info['format_version'] = '1.3'
+    info['detector'] = 'Animl'
+    info['classifier'] = 'Animl'
+
+    results = {}
+    results['info'] = info
+    results['detection_categories'] = detection_category_id_to_name
+    results['classification_categories'] = \
+        {v: k for k, v in classification_category_name_to_id.items()}
+    results['images'] = list(filename_to_results.values())
+
+    write_json(output_file,results)
+
+# ...animl_results_to_md_results(...)
+
+
+#%% Interactive driver
+
+if False:
+
+    pass
+
+    #%%
+
+    input_file = r"G:\temp\animl-runs\animl-runs\Coati_v2\manifest.csv"
+    output_file = None
+    animl_results_to_md_results(input_file,output_file)
+
+
+#%% Command-line driver
+
+def main():
+    """
+    Command-line driver for animl_to_md
+    """
+
+    parser = argparse.ArgumentParser(
+        description='Convert an Animl-formatted .csv results file to MD-formatted .json results file')
+
+    parser.add_argument(
+        'input_file',
+        type=str,
+        help='input .csv file')
+
+    parser.add_argument(
+        '--output_file',
+        type=str,
+        default=None,
+        help='output .json file (defaults to input file appended with ".json")')
+
+    if len(sys.argv[1:]) == 0:
+        parser.print_help()
+        parser.exit()
+
+    args = parser.parse_args()
+
+    animl_results_to_md_results(args.input_file,args.output_file)
+
+if __name__ == '__main__':
+    main()