megadetector 10.0.2__py3-none-any.whl → 10.0.4__py3-none-any.whl

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()

megadetector/data_management/zamba_to_md.py

@@ -0,0 +1,188 @@
+"""
+
+zamba_to_md.py
+
+Convert a labels.csv file produced by Zamba Cloud to a MD results file suitable
+for import into Timelapse.
+
+Columns are expected to be:
+
+video_uuid (not used)
+original_filename (assumed to be a relative path name)
+top_k_label,top_k_probability, for k = 1..N
+[category name 1],[category name 2],...
+corrected_label
+
+Because the MD results file fundamentally stores detections, what we'll
+actually do is create bogus detections that fill the entire image.
+
+There is no special handling of empty/blank categories; because these results are
+based on a classifier, rather than a detector (where "blank" would be the absence of
+all other categories), "blank" can be queried in Timelapse just like any other class.
+
+"""
+
+#%% Imports and constants
+
+import sys
+import argparse
+
+import pandas as pd
+
+from megadetector.utils.ct_utils import write_json
+
+
+#%% Main function
+
+def zamba_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.
+
+    Args:
+        input_file (str): the .csv file to convert
+        output_file (str, optional): the output .json file (defaults to
+            [input_file].json)
+    """
+
+    if output_file is None:
+        output_file = input_file + '.json'
+
+    df = pd.read_csv(input_file)
+
+    expected_columns = ('video_uuid','corrected_label','original_filename')
+    for s in expected_columns:
+        assert s in df.columns,\
+            'Expected column {} not found, are you sure this is a Zamba results .csv file?'.format(
+                s)
+
+    # How many results are included per file?
+    assert 'top_1_probability' in df.columns and 'top_1_label' in df.columns
+    top_k = 2
+    while(True):
+        p_string = 'top_' + str(top_k) + '_probability'
+        label_string = 'top_' + str(top_k) + '_label'
+
+        if p_string in df.columns:
+            assert label_string in df.columns,\
+                'Oops, {} is a column but {} is not'.format(
+                    p_string,label_string)
+            top_k += 1
+            continue
+        else:
+            assert label_string not in df.columns,\
+                'Oops, {} is a column but {} is not'.format(
+                    label_string,p_string)
+            top_k -= 1
+            break
+
+    print('Found {} probability column pairs'.format(top_k))
+
+    # Category names start after the fixed columns and the probability columns
+    category_names = []
+    column_names = list(df.columns)
+    first_category_name_index = 0
+    while('top_' in column_names[first_category_name_index] or \
+          column_names[first_category_name_index] in expected_columns):
+        first_category_name_index += 1
+
+    i_column = first_category_name_index
+    while( (i_column < len(column_names)) and (column_names[i_column] != 'corrected_label') ):
+        category_names.append(column_names[i_column])
+        i_column += 1
+
+    print('Found {} categories:\n'.format(len(category_names)))
+
+    for s in category_names:
+        print(s)
+
+    info = {}
+    info['format_version'] = '1.3'
+    info['detector'] = 'Zamba Cloud'
+    info['classifier'] = 'Zamba Cloud'
+
+    detection_category_id_to_name = {}
+    for category_id,category_name in enumerate(category_names):
+        detection_category_id_to_name[str(category_id)] = category_name
+    detection_category_name_to_id = {v: k for k, v in detection_category_id_to_name.items()}
+
+    images = []
+
+    # i_row = 0; row = df.iloc[i_row]
+    for i_row,row in df.iterrows():
+
+        im = {}
+        images.append(im)
+        im['file'] = row['original_filename']
+
+        detections = []
+
+        # k = 1
+        for k in range(1,top_k+1):
+            label = row['top_{}_label'.format(k)]
+            confidence = row['top_{}_probability'.format(k)]
+            det = {}
+            det['category'] = detection_category_name_to_id[label]
+            det['conf'] = confidence
+            det['bbox'] = [0,0,1.0,1.0]
+            detections.append(det)
+
+        im['detections'] = detections
+
+    # ...for each row
+
+    results = {}
+    results['info'] = info
+    results['detection_categories'] = detection_category_id_to_name
+    results['images'] = images
+
+    write_json(output_file,results)
+
+# ...zamba_results_to_md_results(...)
+
+
+#%% Interactive driver
+
+if False:
+
+    pass
+
+    #%%
+
+    input_file = r"G:\temp\labels-job-b95a4b76-e332-4e17-ab40-03469392d36a-2023-11-04_16-28-50.060130.csv"
+    output_file = None
+    zamba_results_to_md_results(input_file,output_file)
+
+
+#%% Command-line driver
+
+def main():
+    """
+    Command-line driver for zamba_to_md
+    """
+
+    parser = argparse.ArgumentParser(
+        description='Convert a Zamba-formatted .csv results file to a 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()
+
+    zamba_results_to_md_results(args.input_file,args.output_file)
+
+if __name__ == '__main__':
+    main()