megadetector 5.0.7__py3-none-any.whl → 5.0.9__py3-none-any.whl

data_management/labelme_to_yolo.py

@@ -1,16 +1,19 @@
-########
-#
-# labelme_to_yolo.py
-#
-# Create YOLO .txt files in a folder containing labelme .json files.
-#
-########
+"""
+
+labelme_to_yolo.py
+
+Create YOLO .txt files in a folder containing labelme .json files.
+
+"""
 
 #%% Imports
 
 import os
 import json
 
+from multiprocessing.pool import Pool, ThreadPool
+from functools import partial
+
 from md_utils.path_utils import recursive_file_list
 from tqdm import tqdm
 
@@ -21,22 +24,21 @@ def labelme_file_to_yolo_file(labelme_file,
                               category_name_to_category_id,
                               yolo_file=None,
                               required_token=None,
-                              right_edge_quantization_threshold=None,
                               overwrite_behavior='overwrite'):
     """
     Convert the single .json file labelme_file to yolo format, writing the results to the text
     file yolo_file (defaults to s/json/txt).
     
-    If required_token is not None and the labelme_file does not contain the key [required_token],
-    no-ops.
+    If required_token is not None and the dict in labelme_file does not contain the key [required_token],
+    this function no-ops (i.e., does not generate a YOLO file).    
     
-    right_edge_quantization_threshold is an off-by-default hack to handle cases where 
-    boxes that really should be running off the right side of the image only extend like 99%
-    of the way there, due to what appears to be a slight bias inherent to MD.  If a box extends
-    within [right_edge_quantization_threshold] (a small number, from 0 to 1, but probably around 
-    0.02) of the right edge of the image, it will be extended to the far right edge.    
+    overwrite_behavior should be 'skip' or 'overwrite' (default).
     """
     
+    result = {}
+    result['labelme_file'] = labelme_file
+    result['status'] = 'unknown'
+    
     assert os.path.isfile(labelme_file), 'Could not find labelme .json file {}'.format(labelme_file)
     assert labelme_file.endswith('.json'), 'Illegal labelme .json file {}'.format(labelme_file)
     
@@ -45,7 +47,8 @@ def labelme_file_to_yolo_file(labelme_file,
     
     if os.path.isfile(yolo_file):
         if overwrite_behavior == 'skip':
-            return
+            result['status'] = 'skip-exists'
+            return result
         else:
             assert overwrite_behavior == 'overwrite', \
                 'Unrecognized overwrite behavior {}'.format(overwrite_behavior)
@@ -54,7 +57,8 @@ def labelme_file_to_yolo_file(labelme_file,
         labelme_data = json.load(f)
         
     if required_token is not None and required_token not in labelme_data:
-        return
+        result['status'] = 'skip-no-required-token'
+        return result
     
     im_height = labelme_data['imageHeight']
     im_width = labelme_data['imageWidth']
@@ -73,7 +77,7 @@ def labelme_file_to_yolo_file(labelme_file,
         p0 = shape['points'][0]
         p1 = shape['points'][1]
         
-        # LabelMe: [[x0,y0],[x1,y1]] (arbitrarily sorted) (absolute coordinates)
+        # Labelme: [[x0,y0],[x1,y1]] (arbitrarily sorted) (absolute coordinates)
         #
         # YOLO: [class, x_center, y_center, width, height] (normalized coordinates)
         minx_abs = min(p0[0],p1[0])
@@ -83,10 +87,12 @@ def labelme_file_to_yolo_file(labelme_file,
         
         if (minx_abs >= (im_width-1)) or (maxx_abs <= 0) or \
             (miny_abs >= (im_height-1)) or (maxy_abs <= 0):
-                print('Skipping invalid shape in {}'.format(labelme_file))
+                print('Skipping invalid shape in {}'.format(labelme_file))                
                 continue
             
-        # Clip to [0,1]
+        # Clip to [0,1]... it's not obvious that the YOLO format doesn't allow bounding
+        # boxes to extend outside the image, but YOLOv5 and YOLOv8 get sad about boxes
+        # that extend outside the image.
         maxx_abs = min(maxx_abs,im_width-1)
         maxy_abs = min(maxy_abs,im_height-1)
         minx_abs = max(minx_abs,0.0)
@@ -97,11 +103,6 @@ def labelme_file_to_yolo_file(labelme_file,
         miny_rel = miny_abs / (im_height-1)
         maxy_rel = maxy_abs / (im_height-1)
         
-        if (right_edge_quantization_threshold is not None):
-            right_edge_distance = 1.0 - maxx_rel
-            if right_edge_distance < right_edge_quantization_threshold:
-                maxx_rel = 1.0
-        
         assert maxx_rel >= minx_rel
         assert maxy_rel >= miny_rel
         
@@ -119,32 +120,45 @@ def labelme_file_to_yolo_file(labelme_file,
     with open(yolo_file,'w') as f:
         for s in yolo_lines:
             f.write(s + '\n')
-        
+    
+    result['status'] = 'converted'
+    return result
+
 
 def labelme_folder_to_yolo(labelme_folder,
                            category_name_to_category_id=None,
                            required_token=None,
-                           right_edge_quantization_threshold=None,
-                           overwrite_behavior='overwrite'):
+                           overwrite_behavior='overwrite',
+                           relative_filenames_to_convert=None,
+                           n_workers=1,
+                           use_threads=True):
     """
     Given a folder with images and labelme .json files, convert the .json files
     to YOLO .txt format.  If category_name_to_category_id is None, first reads
     all the labels in the folder to build a zero-indexed name --> ID mapping.
     
     If required_token is not None and a labelme_file does not contain the key [required_token],
-    it won't be converted.
+    it won't be converted.  Typically used to specify a field that indicates which files have
+    been reviewed.
     
-    right_edge_quantization_threshold is an off-by-default hack to handle cases where 
-    boxes that really should be running off the right side of the image only extend like 99%
-    of the way there, due to what appears to be a slight bias inherent to MD.  If a box extends
-    within [right_edge_quantization_threshold] (a small number, from 0 to 1, but probably around 
-    0.02) of the right edge of the image, it will be extended to the far right edge.    
+    If relative_filenames_to_convert is not None, this should be a list of .json (not image)
+    files that should get converted, relative to the base folder.
     
-    returns category_name_to_category_id, whether it was passed in or constructed.
+    overwrite_behavior should be 'skip' or 'overwrite' (default).
+    
+    returns a dict with:
+        'category_name_to_category_id', whether it was passed in or constructed
+        'image_results': a list of results for each image (converted, skipped, error)
+        
     """
     
-    labelme_files_relative = recursive_file_list(labelme_folder,return_relative_paths=True)
-    labelme_files_relative = [fn for fn in labelme_files_relative if fn.endswith('.json')]
+    if relative_filenames_to_convert is not None:
+        labelme_files_relative = relative_filenames_to_convert
+        assert all([fn.endswith('.json') for fn in labelme_files_relative]), \
+            'relative_filenames_to_convert contains non-json files'
+    else:
+        labelme_files_relative = recursive_file_list(labelme_folder,return_relative_paths=True)
+        labelme_files_relative = [fn for fn in labelme_files_relative if fn.endswith('.json')]
     
     if required_token is None:
         valid_labelme_files_relative = labelme_files_relative
@@ -163,9 +177,9 @@ def labelme_folder_to_yolo(labelme_folder,
                 
             valid_labelme_files_relative.append(fn_relative)
     
-    print('{} of {} files are valid'.format(len(valid_labelme_files_relative),
-                                           len(labelme_files_relative)))
-    
+        print('{} of {} files are valid'.format(len(valid_labelme_files_relative),
+                                                len(labelme_files_relative)))
+        
     del labelme_files_relative
         
     if category_name_to_category_id is None:
@@ -184,26 +198,54 @@ def labelme_folder_to_yolo(labelme_folder,
         # ...for each file
         
     # ...if we need to build a category mapping
-            
-    for fn_relative in tqdm(valid_labelme_files_relative):
-        
-        fn_abs = os.path.join(labelme_folder,fn_relative)
-        labelme_file_to_yolo_file(fn_abs,
-                                  category_name_to_category_id,
-                                  yolo_file=None,
-                                  required_token=required_token,
-                                  right_edge_quantization_threshold=\
-                                      right_edge_quantization_threshold,
-                                  overwrite_behavior=overwrite_behavior)
     
-    # ...for each file
+    image_results = []
+    
+    n_workers = min(n_workers,len(valid_labelme_files_relative))
+    
+    if n_workers <= 1:
+        for fn_relative in tqdm(valid_labelme_files_relative):
+            
+            fn_abs = os.path.join(labelme_folder,fn_relative)
+            image_result = labelme_file_to_yolo_file(fn_abs,
+                                      category_name_to_category_id,
+                                      yolo_file=None,
+                                      required_token=required_token,
+                                      overwrite_behavior=overwrite_behavior)
+            image_results.append(image_result)
+        # ...for each file
+    else:
+        if use_threads:
+            pool = ThreadPool(n_workers)
+        else:
+            pool = Pool(n_workers)
+
+        valid_labelme_files_abs = [os.path.join(labelme_folder,fn_relative) for \
+                                   fn_relative in valid_labelme_files_relative]
+            
+        image_results = list(tqdm(pool.imap(
+            partial(labelme_file_to_yolo_file,
+                    category_name_to_category_id=category_name_to_category_id,
+                    yolo_file=None,
+                    required_token=required_token,
+                    overwrite_behavior=overwrite_behavior),
+                    valid_labelme_files_abs), 
+                    total=len(valid_labelme_files_abs)))
+
+    assert len(valid_labelme_files_relative) == len(image_results)
     
     print('Converted {} labelme .json files to YOLO'.format(
         len(valid_labelme_files_relative)))
     
-    return category_name_to_category_id
+    labelme_to_yolo_results = {}
+    labelme_to_yolo_results['category_name_to_category_id'] = category_name_to_category_id
+    labelme_to_yolo_results['image_results'] = image_results
     
-        
+    return labelme_to_yolo_results
+    
+# ...def labelme_folder_to_yolo(...)        
+
+
 #%% Interactive driver
 
 if False:
@@ -212,18 +254,19 @@ if False:
 
     #%%
 
-    import os
     labelme_file = os.path.expanduser('~/tmp/labels/x.json')
-    yolo_file = None
     required_token = 'saved_by_labelme'
-    right_edge_quantization_threshold = 0.015
     category_name_to_category_id = {'animal':0}
+    labelme_folder = os.path.expanduser('~/tmp/labels')
 
     #%%
     
-    labelme_folder = os.path.expanduser('~/tmp/labels')
-
-
+    category_name_to_category_id = \
+        labelme_folder_to_yolo(labelme_folder,
+                               category_name_to_category_id=category_name_to_category_id,
+                               required_token=required_token,
+                               overwrite_behavior='overwrite')
+    
 #%% Command-line driver
 
 # TODO

data_management/lila/add_locations_to_island_camera_traps.py

@@ -1,12 +1,12 @@
-########
-#
-# add_locations_to_island_camera_traps.py
-#
-# The Island Conservation Camera Traps dataset had unique camera identifiers embedded
-# in filenames, but not in the proper metadata fields.  This script copies that information
-# to metadata.
-#
-########
+"""
+
+add_locations_to_island_camera_traps.py
+
+The Island Conservation Camera Traps dataset had unique camera identifiers embedded
+in filenames, but not in the proper metadata fields.  This script copies that information
+to metadata.
+
+"""
 
 #%% Imports and constants
 

data_management/lila/add_locations_to_nacti.py

@@ -1,147 +1,147 @@
-########
-#
-# add_locations_to_nacti.py
-#
-# As of 10.2023, NACTI metadata only has very coarse location information (e.g. "Florida"),
-# but camera IDs are embedded in filenames.  This script pulls that information from filenames
-# and adds it to metadata.
-#
-########
-
-#%% Imports and constants
-
-import os
-import json
-import shutil
-
-from tqdm import tqdm
-from collections import defaultdict
-
-input_file = r'd:\lila\nacti\nacti_metadata.json.1.13\nacti_metadata.json'
-output_file = r'g:\temp\nacti_metadata.1.14.json'
-
-
-#%% Read metadata
-
-with open(input_file,'r') as f:
-    d = json.load(f)
-    
-assert d['info']['version'] == 1.13
-
-
-#%% Map images to locations (according to the metadata)
-
-file_name_to_original_location = {}
-
-# im = dataset_labels['images'][0]
-for im in tqdm(d['images']):
-    file_name_to_original_location[im['file_name']] = im['location']
-
-original_locations = set(file_name_to_original_location.values())
-
-print('Found {} locations in the original metadata:'.format(len(original_locations)))
-for loc in original_locations:
-    print('[{}]'.format(loc))
-
-
-#%% Map images to new locations
-
-def path_to_location(relative_path):
-    
-    relative_path = relative_path.replace('\\','/')
-    if relative_path in file_name_to_original_location:
-        location_name = file_name_to_original_location[relative_path]
-        if location_name == 'San Juan Mntns, Colorado':
-            # "part0/sub000/2010_Unit150_Ivan097_img0003.jpg"
-            tokens = relative_path.split('/')[-1].split('_')
-            assert tokens[1].startswith('Unit')
-            location_name = 'sanjuan_{}_{}_{}'.format(tokens[0],tokens[1],tokens[2])
-        elif location_name == 'Lebec, California':
-            # "part0/sub035/CA-03_08_13_2015_CA-03_0009738.jpg"
-            tokens = relative_path.split('/')[-1].split('_')
-            assert tokens[0].startswith('CA-') or tokens[0].startswith('TAG-')
-            location_name = 'lebec_{}'.format(tokens[0])   
-        elif location_name == 'Archbold, FL':
-            # "part1/sub110/FL-01_01_25_2016_FL-01_0040421.jpg"
-            tokens = relative_path.split('/')[-1].split('_')
-            assert tokens[0].startswith('FL-')
-            location_name = 'archbold_{}'.format(tokens[0])   
-        else:
-            assert location_name == ''
-            tokens = relative_path.split('/')[-1].split('_')
-            if tokens[0].startswith('CA-') or tokens[0].startswith('TAG-') or tokens[0].startswith('FL-'):
-                location_name = '{}'.format(tokens[0])
-            
-    else:
-        
-        location_name = 'unknown'    
-    
-    # print('Returning location {} for file {}'.format(location_name,relative_path))          
-
-    return location_name
-
-file_name_to_updated_location = {}
-updated_location_to_count = defaultdict(int)
-for im in tqdm(d['images']):
-    
-    updated_location = path_to_location(im['file_name'])
-    file_name_to_updated_location[im['file_name']] = updated_location
-    updated_location_to_count[updated_location] += 1
-
-updated_location_to_count = {k: v for k, v in sorted(updated_location_to_count.items(), 
-                         key=lambda item: item[1],
-                         reverse=True)}
-
-updated_locations = set(file_name_to_updated_location.values())
-
-print('Found {} updated locations in the original metadata:'.format(len(updated_locations)))
-for loc in updated_location_to_count:
-    print('{}: {}'.format(loc,updated_location_to_count[loc]))
-
-
-#%% Re-write metadata
-
-for im in d['images']:
-    im['location'] = file_name_to_updated_location[im['file_name']]
-d['info']['version'] = 1.14
-
-with open(output_file,'w') as f:
-    json.dump(d,f,indent=1)
-    
-
-#%% For each location, sample some random images to make sure they look consistent
-
-input_base = r'd:\lila\nacti-unzipped'
-assert os.path.isdir(input_base)
-
-location_to_images = defaultdict(list)
-
-for im in d['images']:
-    location_to_images[im['location']].append(im)
-    
-n_to_sample = 10
-import random
-random.seed(0)
-sampling_folder_base = r'g:\temp\nacti_samples'
-
-for location in tqdm(location_to_images):
-    
-    images_this_location = location_to_images[location]
-    if len(images_this_location) > n_to_sample:
-        images_this_location = random.sample(images_this_location,n_to_sample)
-        
-    for i_image,im in enumerate(images_this_location):
-        
-        fn_relative = im['file_name']
-        source_fn_abs = os.path.join(input_base,fn_relative)
-        assert os.path.isfile(source_fn_abs)
-        ext = os.path.splitext(fn_relative)[1]            
-        target_fn_abs = os.path.join(sampling_folder_base,'{}/{}'.format(
-            location,'image_{}{}'.format(str(i_image).zfill(2),ext)))
-        os.makedirs(os.path.dirname(target_fn_abs),exist_ok=True)
-        shutil.copyfile(source_fn_abs,target_fn_abs)
-        
-    # ...for each image
-    
-# ...for each location
-            
+"""
+
+add_locations_to_nacti.py
+
+As of 10.2023, NACTI metadata only has very coarse location information (e.g. "Florida"),
+but camera IDs are embedded in filenames.  This script pulls that information from filenames
+and adds it to metadata.
+
+"""
+
+#%% Imports and constants
+
+import os
+import json
+import shutil
+
+from tqdm import tqdm
+from collections import defaultdict
+
+input_file = r'd:\lila\nacti\nacti_metadata.json.1.13\nacti_metadata.json'
+output_file = r'g:\temp\nacti_metadata.1.14.json'
+
+
+#%% Read metadata
+
+with open(input_file,'r') as f:
+    d = json.load(f)
+    
+assert d['info']['version'] == 1.13
+
+
+#%% Map images to locations (according to the metadata)
+
+file_name_to_original_location = {}
+
+# im = dataset_labels['images'][0]
+for im in tqdm(d['images']):
+    file_name_to_original_location[im['file_name']] = im['location']
+
+original_locations = set(file_name_to_original_location.values())
+
+print('Found {} locations in the original metadata:'.format(len(original_locations)))
+for loc in original_locations:
+    print('[{}]'.format(loc))
+
+
+#%% Map images to new locations
+
+def path_to_location(relative_path):
+    
+    relative_path = relative_path.replace('\\','/')
+    if relative_path in file_name_to_original_location:
+        location_name = file_name_to_original_location[relative_path]
+        if location_name == 'San Juan Mntns, Colorado':
+            # "part0/sub000/2010_Unit150_Ivan097_img0003.jpg"
+            tokens = relative_path.split('/')[-1].split('_')
+            assert tokens[1].startswith('Unit')
+            location_name = 'sanjuan_{}_{}_{}'.format(tokens[0],tokens[1],tokens[2])
+        elif location_name == 'Lebec, California':
+            # "part0/sub035/CA-03_08_13_2015_CA-03_0009738.jpg"
+            tokens = relative_path.split('/')[-1].split('_')
+            assert tokens[0].startswith('CA-') or tokens[0].startswith('TAG-')
+            location_name = 'lebec_{}'.format(tokens[0])   
+        elif location_name == 'Archbold, FL':
+            # "part1/sub110/FL-01_01_25_2016_FL-01_0040421.jpg"
+            tokens = relative_path.split('/')[-1].split('_')
+            assert tokens[0].startswith('FL-')
+            location_name = 'archbold_{}'.format(tokens[0])   
+        else:
+            assert location_name == ''
+            tokens = relative_path.split('/')[-1].split('_')
+            if tokens[0].startswith('CA-') or tokens[0].startswith('TAG-') or tokens[0].startswith('FL-'):
+                location_name = '{}'.format(tokens[0])
+            
+    else:
+        
+        location_name = 'unknown'    
+    
+    # print('Returning location {} for file {}'.format(location_name,relative_path))          
+
+    return location_name
+
+file_name_to_updated_location = {}
+updated_location_to_count = defaultdict(int)
+for im in tqdm(d['images']):
+    
+    updated_location = path_to_location(im['file_name'])
+    file_name_to_updated_location[im['file_name']] = updated_location
+    updated_location_to_count[updated_location] += 1
+
+updated_location_to_count = {k: v for k, v in sorted(updated_location_to_count.items(), 
+                         key=lambda item: item[1],
+                         reverse=True)}
+
+updated_locations = set(file_name_to_updated_location.values())
+
+print('Found {} updated locations in the original metadata:'.format(len(updated_locations)))
+for loc in updated_location_to_count:
+    print('{}: {}'.format(loc,updated_location_to_count[loc]))
+
+
+#%% Re-write metadata
+
+for im in d['images']:
+    im['location'] = file_name_to_updated_location[im['file_name']]
+d['info']['version'] = 1.14
+
+with open(output_file,'w') as f:
+    json.dump(d,f,indent=1)
+    
+
+#%% For each location, sample some random images to make sure they look consistent
+
+input_base = r'd:\lila\nacti-unzipped'
+assert os.path.isdir(input_base)
+
+location_to_images = defaultdict(list)
+
+for im in d['images']:
+    location_to_images[im['location']].append(im)
+    
+n_to_sample = 10
+import random
+random.seed(0)
+sampling_folder_base = r'g:\temp\nacti_samples'
+
+for location in tqdm(location_to_images):
+    
+    images_this_location = location_to_images[location]
+    if len(images_this_location) > n_to_sample:
+        images_this_location = random.sample(images_this_location,n_to_sample)
+        
+    for i_image,im in enumerate(images_this_location):
+        
+        fn_relative = im['file_name']
+        source_fn_abs = os.path.join(input_base,fn_relative)
+        assert os.path.isfile(source_fn_abs)
+        ext = os.path.splitext(fn_relative)[1]            
+        target_fn_abs = os.path.join(sampling_folder_base,'{}/{}'.format(
+            location,'image_{}{}'.format(str(i_image).zfill(2),ext)))
+        os.makedirs(os.path.dirname(target_fn_abs),exist_ok=True)
+        shutil.copyfile(source_fn_abs,target_fn_abs)
+        
+    # ...for each image
+    
+# ...for each location
+