megadetector 10.0.15__py3-none-any.whl

megadetector/classification/prepare_classification_script.py

@@ -0,0 +1,194 @@
+"""
+
+prepare_classification_script.py
+
+Notebook-y script used to prepare a series of shell commands to run a classifier
+(other than MegaClassifier) on a MegaDetector result set.
+
+Differs from prepare_classification_script_mc.py only in the final class mapping step.
+
+"""
+
+#%% Job options
+
+import os
+
+def main(): # noqa
+    organization_name = 'idfg'
+    job_name = 'idfg-2022-01-27-EOE2021S_Group6'
+    input_filename = 'idfg-2022-01-27-EOE2021S_Group6_detections.filtered_rde_0.60_0.85_30_0.20.json'
+    image_base = '/datadrive/idfg/EOE2021S_Group6'
+    crop_path = os.path.join(os.path.expanduser('~/crops'),job_name + '_crops')
+    device_id = 1
+
+    working_dir_base = os.path.join(os.path.expanduser('~/postprocessing'),
+                                                    organization_name,
+                                                    job_name)
+
+    output_base = os.path.join(working_dir_base,'combined_api_outputs')
+
+    assert os.path.isdir(working_dir_base)
+    assert os.path.isdir(output_base)
+
+    output_file = os.path.join(working_dir_base,'run_idfgclassifier_' + job_name +  '.sh')
+
+    input_files = [
+        os.path.join(
+            os.path.expanduser('~/postprocessing'),
+                            organization_name,
+                            job_name,
+                            'combined_api_outputs',
+                            input_filename
+            )
+        ]
+
+    for fn in input_files:
+        assert os.path.isfile(fn)
+
+
+    #%% Constants
+
+    include_cropping = False
+
+    classifier_base = os.path.expanduser('~/models/camera_traps/idfg_classifier/idfg_classifier_20200905_042558')
+    assert os.path.isdir(classifier_base)
+
+    checkpoint_path = os.path.join(classifier_base,'idfg_classifier_ckpt_14_compiled.pt')
+    assert os.path.isfile(checkpoint_path)
+
+    classifier_categories_path = os.path.join(classifier_base,'label_index.json')
+    assert os.path.isfile(classifier_categories_path)
+
+    classifier_output_suffix = '_idfg_classifier_output.csv.gz'
+    final_output_suffix = '_idfgclassifier.json'
+
+    threshold_str = '0.65'
+    n_threads_str = '50'
+    image_size_str = '300'
+    batch_size_str = '64'
+    num_workers_str = '8'
+    logdir = working_dir_base
+
+    classification_threshold_str = '0.05'
+
+    # This is just passed along to the metadata in the output file, it has no impact
+    # on how the classification scripts run.
+    typical_classification_threshold_str = '0.75'
+
+    classifier_name = 'idfg4'
+
+
+    #%% Set up environment
+
+    commands = []
+    # commands.append('cd MegaDetector/classification\n')
+    # commands.append('conda activate cameratraps-classifier\n')
+
+
+    #%% Crop images
+
+    if include_cropping:
+
+        commands.append('\n### Cropping ###\n')
+
+        # fn = input_files[0]
+        for fn in input_files:
+
+            input_file_path = fn
+            crop_cmd = ''
+
+            crop_comment = '\n# Cropping {}\n'.format(fn)
+            crop_cmd += crop_comment
+
+            crop_cmd += "python crop_detections.py \\\n" + \
+                input_file_path + ' \\\n' + \
+                crop_path + ' \\\n' + \
+                '--images-dir "' + image_base + '"' + ' \\\n' + \
+                '--threshold "' + threshold_str + '"' + ' \\\n' + \
+                '--square-crops ' + ' \\\n' + \
+                '--threads "' + n_threads_str + '"' + ' \\\n' + \
+                '--logdir "' + logdir + '"' + ' \\\n' + \
+                '\n'
+            crop_cmd = '{}'.format(crop_cmd)
+            commands.append(crop_cmd)
+
+
+    #%% Run classifier
+
+    commands.append('\n### Classifying ###\n')
+
+    # fn = input_files[0]
+    for fn in input_files:
+
+        input_file_path = fn
+        classifier_output_path = crop_path + classifier_output_suffix
+
+        classify_cmd = ''
+
+        classify_comment = '\n# Classifying {}\n'.format(fn)
+        classify_cmd += classify_comment
+
+        classify_cmd += "python run_classifier.py \\\n" + \
+            checkpoint_path + ' \\\n' + \
+            crop_path + ' \\\n' + \
+            classifier_output_path + ' \\\n' + \
+            '--detections-json "' + input_file_path + '"' + ' \\\n' + \
+            '--classifier-categories "' + classifier_categories_path + '"' + ' \\\n' + \
+            '--image-size "' + image_size_str + '"' + ' \\\n' + \
+            '--batch-size "' + batch_size_str + '"' + ' \\\n' + \
+            '--num-workers "' + num_workers_str + '"' + ' \\\n'
+
+        if device_id is not None:
+            classify_cmd += '--device {}'.format(device_id)
+
+        classify_cmd += '\n\n'
+        classify_cmd = '{}'.format(classify_cmd)
+        commands.append(classify_cmd)
+
+
+    #%% Merge classification and detection outputs
+
+    commands.append('\n### Merging ###\n')
+
+    # fn = input_files[0]
+    for fn in input_files:
+
+        input_file_path = fn
+        classifier_output_path = crop_path + classifier_output_suffix
+        final_output_path = os.path.join(output_base,
+                                        os.path.basename(classifier_output_path)).\
+                                        replace(classifier_output_suffix,
+                                        final_output_suffix)
+        final_output_path = final_output_path.replace('_detections','')
+        final_output_path = final_output_path.replace('_crops','')
+
+        merge_cmd = ''
+
+        merge_comment = '\n# Merging {}\n'.format(fn)
+        merge_cmd += merge_comment
+
+        merge_cmd += "python merge_classification_detection_output.py \\\n" + \
+            classifier_output_path + ' \\\n' + \
+            classifier_categories_path + ' \\\n' + \
+            '--output-json "' + final_output_path + '"' + ' \\\n' + \
+            '--detection-json "' + input_file_path + '"' + ' \\\n' + \
+            '--classifier-name "' + classifier_name + '"' + ' \\\n' + \
+            '--threshold "' + classification_threshold_str + '"' + ' \\\n' + \
+            '--typical-confidence-threshold "' + typical_classification_threshold_str + '"' + ' \\\n' + \
+            '\n'
+        merge_cmd = '{}'.format(merge_cmd)
+        commands.append(merge_cmd)
+
+
+    #%% Write everything out
+
+    with open(output_file,'w') as f:
+        for s in commands:
+            f.write('{}'.format(s))
+
+    import stat
+    st = os.stat(output_file)
+    os.chmod(output_file, st.st_mode | stat.S_IEXEC)
+
+if __name__ == '__main__':
+    main()

megadetector/classification/prepare_classification_script_mc.py

@@ -0,0 +1,228 @@
+"""
+
+prepare_classification_script_mc.py
+
+Notebook-y script used to prepare a series of shell commands to run MegaClassifier
+on a MegaDetector result set.
+
+Differs from prepare_classification_script.py only in the final class mapping step.
+
+"""
+
+#%% Job options
+
+import os
+
+organization_name = 'idfg'
+job_name = 'idfg-2022-01-27-EOE2021S_Group6'
+input_filename = 'idfg-2022-01-27-EOE2021S_Group6_detections.filtered_rde_0.60_0.85_30_0.20.json'
+image_base = '/datadrive/idfg/EOE2021S_Group6'
+crop_path = os.path.join(os.path.expanduser('~/crops'),job_name + '_crops')
+device_id = 0
+
+working_dir_base = os.path.join(os.path.expanduser('~/postprocessing'),
+                                                   organization_name,
+                                                   job_name)
+
+output_base = os.path.join(working_dir_base,'combined_api_outputs')
+
+assert os.path.isdir(working_dir_base)
+assert os.path.isdir(output_base)
+
+output_file = os.path.join(working_dir_base,'run_megaclassifier_' + job_name +  '.sh')
+
+input_files = [
+    os.path.join(
+        os.path.expanduser('~/postprocessing'),
+                           organization_name,
+                           job_name,
+                           'combined_api_outputs',
+                           input_filename
+        )
+    ]
+
+for fn in input_files:
+    assert os.path.isfile(fn)
+
+
+#%% Constants
+
+classifier_base = os.path.expanduser('~/models/camera_traps/megaclassifier/v0.1/')
+assert os.path.isdir(classifier_base)
+
+checkpoint_path = os.path.join(classifier_base,'v0.1_efficientnet-b3_compiled.pt')
+assert os.path.isfile(checkpoint_path)
+
+classifier_categories_path = os.path.join(classifier_base,'v0.1_index_to_name.json')
+assert os.path.isfile(classifier_categories_path)
+
+target_mapping_path = os.path.join(classifier_base,'idfg_to_megaclassifier_labels.json')
+assert os.path.isfile(target_mapping_path)
+
+classifier_output_suffix = '_megaclassifier_output.csv.gz'
+final_output_suffix = '_megaclassifier.json'
+
+threshold_str = '0.65'
+n_threads_str = '50'
+image_size_str = '300'
+batch_size_str = '64'
+num_workers_str = '8'
+logdir = working_dir_base
+
+classification_threshold_str = '0.05'
+
+# This is just passed along to the metadata in the output file, it has no impact
+# on how the classification scripts run.
+typical_classification_threshold_str = '0.75'
+
+classifier_name = 'megaclassifier_v0.1_efficientnet-b3'
+
+
+#%% Set up environment
+
+commands = []
+# commands.append('cd MegaDetector/classification\n')
+# commands.append('conda activate cameratraps-classifier\n')
+
+
+#%% Crop images
+
+commands.append('\n### Cropping ###\n')
+
+# fn = input_files[0]
+for fn in input_files:
+
+    input_file_path = fn
+    crop_cmd = ''
+
+    crop_comment = '\n# Cropping {}\n'.format(fn)
+    crop_cmd += crop_comment
+
+    crop_cmd += "python crop_detections.py \\\n" + \
+         input_file_path + ' \\\n' + \
+         crop_path + ' \\\n' + \
+         '--images-dir "' + image_base + '"' + ' \\\n' + \
+         '--threshold "' + threshold_str + '"' + ' \\\n' + \
+         '--square-crops ' + ' \\\n' + \
+         '--threads "' + n_threads_str + '"' + ' \\\n' + \
+         '--logdir "' + logdir + '"' + ' \\\n' + \
+         '\n'
+    crop_cmd = '{}'.format(crop_cmd)
+    commands.append(crop_cmd)
+
+
+#%% Run classifier
+
+commands.append('\n### Classifying ###\n')
+
+# fn = input_files[0]
+for fn in input_files:
+
+    input_file_path = fn
+    classifier_output_path = crop_path + classifier_output_suffix
+
+    classify_cmd = ''
+
+    classify_comment = '\n# Classifying {}\n'.format(fn)
+    classify_cmd += classify_comment
+
+    classify_cmd += "python run_classifier.py \\\n" + \
+         checkpoint_path + ' \\\n' + \
+         crop_path + ' \\\n' + \
+         classifier_output_path + ' \\\n' + \
+         '--detections-json "' + input_file_path + '"' + ' \\\n' + \
+         '--classifier-categories "' + classifier_categories_path + '"' + ' \\\n' + \
+         '--image-size "' + image_size_str + '"' + ' \\\n' + \
+         '--batch-size "' + batch_size_str + '"' + ' \\\n' + \
+         '--num-workers "' + num_workers_str + '"' + ' \\\n'
+
+    if device_id is not None:
+        classify_cmd += '--device {}'.format(device_id)
+
+    classify_cmd += '\n\n'
+    classify_cmd = '{}'.format(classify_cmd)
+    commands.append(classify_cmd)
+
+
+#%% Remap classifier outputs
+
+commands.append('\n### Remapping ###\n')
+
+# fn = input_files[0]
+for fn in input_files:
+
+    input_file_path = fn
+    classifier_output_path = crop_path + classifier_output_suffix
+    classifier_output_path_remapped = \
+        classifier_output_path.replace(".csv.gz","_remapped.csv.gz")
+    assert not (classifier_output_path == classifier_output_path_remapped)
+
+    output_label_index = classifier_output_path_remapped.replace(
+        "_remapped.csv.gz","_label_index_remapped.json")
+
+    remap_cmd = ''
+
+    remap_comment = '\n# Remapping {}\n'.format(fn)
+    remap_cmd += remap_comment
+
+    remap_cmd += "python aggregate_classifier_probs.py \\\n" + \
+        classifier_output_path + ' \\\n' + \
+        '--target-mapping "' + target_mapping_path + '"' + ' \\\n' + \
+        '--output-csv "' + classifier_output_path_remapped + '"' + ' \\\n' + \
+        '--output-label-index "' + output_label_index + '"' + ' \\\n' + \
+        '\n'
+
+    remap_cmd = '{}'.format(remap_cmd)
+    commands.append(remap_cmd)
+
+
+#%% Merge classification and detection outputs
+
+commands.append('\n### Merging ###\n')
+
+# fn = input_files[0]
+for fn in input_files:
+
+    input_file_path = fn
+    classifier_output_path = crop_path + classifier_output_suffix
+
+    classifier_output_path_remapped = \
+        classifier_output_path.replace(".csv.gz","_remapped.csv.gz")
+
+    output_label_index = classifier_output_path_remapped.replace(
+        "_remapped.csv.gz","_label_index_remapped.json")
+
+    final_output_path = os.path.join(output_base,
+                                     os.path.basename(classifier_output_path)).\
+        replace(classifier_output_suffix,
+        final_output_suffix)
+    final_output_path = final_output_path.replace('_detections','')
+    final_output_path = final_output_path.replace('_crops','')
+
+    merge_cmd = ''
+
+    merge_comment = '\n# Merging {}\n'.format(fn)
+    merge_cmd += merge_comment
+
+    merge_cmd += "python merge_classification_detection_output.py \\\n" + \
+         classifier_output_path_remapped + ' \\\n' + \
+         output_label_index + ' \\\n' + \
+         '--output-json "' + final_output_path + '"' + ' \\\n' + \
+         '--detection-json "' + input_file_path + '"' + ' \\\n' + \
+         '--classifier-name "' + classifier_name + '"' + ' \\\n' + \
+         '--threshold "' + classification_threshold_str + '"' + ' \\\n' + \
+         '--typical-confidence-threshold "' + typical_classification_threshold_str + '"' + ' \\\n' + \
+         '\n'
+    merge_cmd = '{}'.format(merge_cmd)
+    commands.append(merge_cmd)
+
+
+#%% Write everything out
+
+with open(output_file,'w') as f:
+    for s in commands:
+        f.write('{}'.format(s))
+
+import stat
+st = os.stat(output_file)
+os.chmod(output_file, st.st_mode | stat.S_IEXEC)

megadetector/classification/run_classifier.py

@@ -0,0 +1,287 @@
+"""
+
+run_classifier.py
+
+Run a species classifier.
+
+This script is the classifier counterpart to detection/run_tf_detector_batch.py.
+This script takes as input:
+1) a detections JSON file, usually the output of run_tf_detector_batch.py or the
+    output of the Batch API in the "Batch processing API output format"
+2) a path to a directory containing crops of bounding boxes from the detections
+    JSON file
+3) a path to a PyTorch TorchScript compiled model file
+4) (if the model is EfficientNet) an image size
+
+By default, this script overwrites the detections JSON file, adding in
+classification results. To output a new JSON file, use the --output argument.
+
+"""
+
+#%% Imports
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+
+from tqdm import tqdm
+from typing import Any
+from collections.abc import Callable, Sequence
+
+import pandas as pd
+import PIL
+import torch
+import torch.utils
+import torchvision as tv
+from torchvision.datasets.folder import default_loader
+
+from megadetector.classification import train_classifier
+
+
+#%% Example usage
+
+"""
+    python run_classifier.py \
+        detections.json \
+        /path/to/crops \
+        /path/to/model.pt \
+        --image-size 224
+"""
+
+
+#%% Classes
+
+class SimpleDataset(torch.utils.data.Dataset):
+    """
+    Very simple dataset.
+    """
+
+    def __init__(self, img_files: Sequence[str],
+                 images_dir: str | None = None,
+                 transform: Callable[[PIL.Image.Image], Any] | None = None):
+        """Creates a SimpleDataset."""
+        self.img_files = img_files
+        self.images_dir = images_dir
+        self.transform = transform
+
+    def __getitem__(self, index: int) -> tuple[Any, str]:
+        """
+        Returns: tuple, (img, img_file)
+        """
+        img_file = self.img_files[index]
+        if self.images_dir is not None:
+            img_path = os.path.join(self.images_dir, img_file)
+        else:
+            img_path = img_file
+        img = default_loader(img_path)
+        if self.transform is not None:
+            img = self.transform(img)
+        return img, img_file
+
+    def __len__(self) -> int:
+        return len(self.img_files)
+
+
+#%% Support functions
+
+def create_loader(cropped_images_dir: str,
+                  detections_json_path: str | None,
+                  img_size: int,
+                  batch_size: int,
+                  num_workers: int
+                  ) -> torch.utils.data.DataLoader:
+    """
+    Creates a DataLoader.
+
+    Args:
+        cropped_images_dir: str, path to image crops
+        detections_json_path: optional str, path to detections JSON
+        img_size: int, resizes smallest side of image to img_size,
+            then center-crops to (img_size, img_size)
+        batch_size: int, batch size in dataloader
+        num_workers: int, # of workers in dataloader
+    """
+
+    crop_files = []
+
+    if detections_json_path is None:
+        # recursively find all files in cropped_images_dir
+        for subdir, _, files in os.walk(cropped_images_dir):
+            for file_name in files:
+                rel_dir = os.path.relpath(subdir, cropped_images_dir)
+                rel_file = os.path.join(rel_dir, file_name)
+                crop_files.append(rel_file)
+
+    else:
+        # only find crops of images from detections JSON
+        print('Loading detections JSON')
+        with open(detections_json_path, 'r') as f:
+            js = json.load(f)
+        detections = {img['file']: img for img in js['images']}
+        detector_version = js['info']['detector']
+
+        for img_file, info_dict in tqdm(detections.items()):
+            if 'detections' not in info_dict or info_dict['detections'] is None:
+                continue
+            for i in range(len(info_dict['detections'])):
+                crop_filename = img_file + f'___crop{i:02d}_{detector_version}.jpg'
+                crop_path = os.path.join(cropped_images_dir, crop_filename)
+                if os.path.exists(crop_path):
+                    crop_files.append(crop_filename)
+
+    transform = tv.transforms.Compose([
+        # resizes smaller edge to img_size
+        tv.transforms.Resize(img_size, interpolation=PIL.Image.BICUBIC),
+        tv.transforms.CenterCrop(img_size),
+        tv.transforms.ToTensor(),
+        tv.transforms.Normalize(mean=train_classifier.MEANS,
+                                std=train_classifier.STDS, inplace=True)
+    ])
+
+    dataset = SimpleDataset(img_files=crop_files, images_dir=cropped_images_dir,
+                            transform=transform)
+    assert len(dataset) > 0
+    loader = torch.utils.data.DataLoader(
+        dataset, batch_size=batch_size, num_workers=num_workers,
+        pin_memory=True)
+    return loader
+
+
+#%% Main function
+
+def main(model_path: str,
+         cropped_images_dir: str,
+         output_csv_path: str,
+         detections_json_path: str | None,
+         classifier_categories_json_path: str | None,
+         img_size: int,
+         batch_size: int,
+         num_workers: int,
+         device_id: int | None = None) -> None:
+
+    # Evaluating with accimage is much faster than Pillow or Pillow-SIMD, but accimage
+    # is Linux-only.
+    try:
+        import accimage # noqa
+        tv.set_image_backend('accimage')
+    except:
+        print('Warning: could not start accimage backend (ignore this if you\'re not using Linux)')
+
+    # create dataset
+    print('Creating data loader')
+    loader = create_loader(
+        cropped_images_dir, detections_json_path=detections_json_path,
+        img_size=img_size, batch_size=batch_size, num_workers=num_workers)
+
+    label_names = None
+    if classifier_categories_json_path is not None:
+        with open(classifier_categories_json_path, 'r') as f:
+            categories = json.load(f)
+        label_names = [categories[str(i)] for i in range(len(categories))]
+
+    # create model
+    print('Loading saved model')
+    model = torch.jit.load(model_path)
+    model, device = train_classifier.prep_device(model, device_id=device_id)
+
+    test_epoch(model, loader, device=device, label_names=label_names,
+               output_csv_path=output_csv_path)
+
+
+def test_epoch(model: torch.nn.Module,
+               loader: torch.utils.data.DataLoader,
+               device: torch.device,
+               label_names: Sequence[str] | None,
+               output_csv_path: str) -> None:
+    """
+    Runs for 1 epoch.
+
+    Writes results to the output CSV in batches.
+
+    Args:
+        model: torch.nn.Module
+        loader: torch.utils.data.DataLoader
+        device: torch.device
+        label_names: optional list of str, label names
+        output_csv_path: str
+    """
+
+    # set dropout and BN layers to eval mode
+    model.eval()
+
+    header = True
+    mode = 'w'  # new file on first write
+
+    with torch.no_grad():
+        for inputs, img_files in tqdm(loader):
+            inputs = inputs.to(device, non_blocking=True)
+            outputs = model(inputs)
+            probs = torch.nn.functional.softmax(outputs, dim=1).cpu().numpy()
+
+            if label_names is None:
+                label_names = [str(i) for i in range(probs.shape[1])]
+
+            df = pd.DataFrame(data=probs, columns=label_names,
+                              index=pd.Index(img_files, name='path'))
+            df.to_csv(output_csv_path, index=True, header=header, mode=mode)
+
+            if header:
+                header = False
+                mode = 'a'
+
+
+#%% Command-line driver
+
+def _parse_args() -> argparse.Namespace:
+
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description='Run classifier.')
+    parser.add_argument(
+        'model',
+        help='path to TorchScript compiled model')
+    parser.add_argument(
+        'crops_dir',
+        help='path to directory containing cropped images')
+    parser.add_argument(
+        'output',
+        help='path to save CSV file with classifier results (can use .csv.gz '
+             'extension for compression)')
+    parser.add_argument(
+        '-d', '--detections-json',
+        help='path to detections JSON file, used to filter paths within '
+             'crops_dir')
+    parser.add_argument(
+        '-c', '--classifier-categories',
+        help='path to JSON file for classifier categories. If not given, '
+             'classes are numbered "0", "1", "2", ...')
+    parser.add_argument(
+        '--image-size', type=int, default=224,
+        help='size of input image to model, usually 224px, but may be larger '
+             'especially for EfficientNet models')
+    parser.add_argument(
+        '--batch-size', type=int, default=1,
+        help='batch size for evaluating model')
+    parser.add_argument(
+        '--device', type=int, default=None,
+        help='preferred CUDA device')
+    parser.add_argument(
+        '--num-workers', type=int, default=8,
+        help='# of workers for data loading')
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+
+    args = _parse_args()
+    main(model_path=args.model,
+         cropped_images_dir=args.crops_dir,
+         output_csv_path=args.output,
+         detections_json_path=args.detections_json,
+         classifier_categories_json_path=args.classifier_categories,
+         img_size=args.image_size,
+         batch_size=args.batch_size,
+         num_workers=args.num_workers,
+         device_id=args.device)