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

megadetector/utils/path_utils.py

@@ -36,6 +36,7 @@ from tqdm import tqdm
 from megadetector.utils.ct_utils import is_iterable
 from megadetector.utils.ct_utils import make_test_folder
 from megadetector.utils.ct_utils import sort_dictionary_by_value
+from megadetector.utils.ct_utils import environment_is_wsl
 
 # Should all be lower-case
 IMG_EXTENSIONS = ('.jpg', '.jpeg', '.gif', '.png', '.tif', '.tiff', '.bmp')
@@ -622,21 +623,7 @@ def is_executable(filename):
     return which(filename) is not None
 
 
-#%% Platform-independent way to open files in their associated application
-
-def environment_is_wsl():
-    """
-    Determines whether we're running in WSL.
-
-    Returns:
-        True if we're running in WSL.
-    """
-
-    if sys.platform not in ('linux','posix'):
-        return False
-    platform_string = ' '.join(platform.uname()).lower()
-    return 'microsoft' in platform_string and 'wsl' in platform_string
-
+#%% WSL utilities
 
 def wsl_path_to_windows_path(filename, failure_behavior='none'):
     r"""
@@ -731,6 +718,8 @@ def windows_path_to_wsl_path(filename, failure_behavior='none'):
 # ...def window_path_to_wsl_path(...)
 
 
+#%% Platform-independent file openers
+
 def open_file_in_chrome(filename):
     """
     Open a file in chrome, regardless of file type.  I typically use this to open

megadetector/utils/wi_utils.py

@@ -1869,22 +1869,30 @@ country_code_to_country = None
 
 #%% Functions related to geofencing and taxonomy mapping
 
-def taxonomy_info_to_taxonomy_string(taxonomy_info):
+def taxonomy_info_to_taxonomy_string(taxonomy_info, include_taxon_id_and_common_name=False):
     """
-    Convert a taxonomy record in dict format to a semicolon-delimited string
+    Convert a taxonomy record in dict format to a five- or seven-token semicolon-delimited string
 
     Args:
         taxonomy_info (dict): dict in the format stored in, e.g., taxonomy_string_to_taxonomy_info
+        include_taxon_id_and_common_name (bool, optional): by default, this function returns a
+            five-token string of latin names; if this argument is True, it includes the leading
+            (GUID) and trailing (common name) tokens
 
     Returns:
         str: string in the format used as keys in, e.g., taxonomy_string_to_taxonomy_info
     """
-    return taxonomy_info['class'] + ';' + \
+    s = taxonomy_info['class'] + ';' + \
         taxonomy_info['order'] + ';'  + \
         taxonomy_info['family'] + ';'  + \
         taxonomy_info['genus'] + ';'  + \
         taxonomy_info['species']
 
+    if include_taxon_id_and_common_name:
+        s = taxonomy_info['taxon_id'] + ';' + s + ';' + taxonomy_info['common_name']
+
+    return s
+
 
 def initialize_taxonomy_info(taxonomy_file,force_init=False,encoding='cp1252'):
     """
@@ -2504,7 +2512,7 @@ if False:
     initialize_geofencing(geofencing_file, country_code_file, force_init=True)
     initialize_taxonomy_info(taxonomy_file, force_init=True, encoding=encoding)
 
-    from megadetector.utils.path_utils import open_file; open_file(geofencing_file)
+    # from megadetector.utils.path_utils import open_file; open_file(geofencing_file)
 
 
     #%% Generate a block list
@@ -2530,6 +2538,14 @@ if False:
     print(rows)
 
 
+    #%% Look up taxonomy info for a common name
+
+    common_name = 'domestic horse'
+    info = common_name_to_taxonomy_info[common_name]
+    s = taxonomy_info_to_taxonomy_string(info,include_taxon_id_and_common_name=True)
+    print(s)
+
+
     #%% Generate a block-except list
 
     block_except_list = 'ALB,AND,ARM,AUT,AZE,BEL,BGR,BIH,BLR,CHE,CYP,CZE,DEU,DNK,ESP,EST,FIN,FRA,GBR,GEO,GRC,HRV,HUN,IRL,IRN,IRQ,ISL,ISR,ITA,KAZ,LIE,LTU,LUX,LVA,MDA,MKD,MLT,MNE,NLD,NOR,POL,PRT,ROU,RUS,SMR,SRB,SVK,SVN,SWE,TUR,UKR,UZB'

megadetector/visualization/visualization_utils.py

@@ -552,7 +552,7 @@ def render_detection_bounding_boxes(detections,
         custom_strings (list of str, optional): optional set of strings to append to detection labels, should
             have the same length as [detections].  Appended before any classification labels.
         box_sort_order (str, optional): sorting scheme for detection boxes, can be None, "confidence", or
-            "reverse_confidence".
+            "reverse_confidence".  "confidence" puts the highest-confidence boxes on top.
         verbose (bool, optional): enable additional debug output
     """
 

megadetector/visualization/visualize_db.py

@@ -321,7 +321,7 @@ def visualize_db(db_path, output_dir, image_base_dir, options=None):
         box_classes = []
         box_score_strings = []
 
-        # All the class labels we've seen for this image (with out without bboxes)
+        # All the class labels we've seen for this image (with or without bboxes)
         image_categories = set()
 
         extra_annotation_field_string = ''
@@ -368,6 +368,7 @@ def visualize_db(db_path, output_dir, image_base_dir, options=None):
                 category_name = category_name.replace('"','')
                 category_name = '<a href="https://www.google.com/search?tbm=isch&q={}">{}</a>'.format(
                     category_name,category_name)
+
             image_categories.add(category_name)
 
             assert not ('bbox' in anno and 'bbox_relative' in anno), \
@@ -522,7 +523,7 @@ def visualize_db(db_path, output_dir, image_base_dir, options=None):
 
         return True
 
-    # ...def render_image_info
+    # ...def render_image_info(...)
 
     print('Rendering images')
     start_time = time.time()
@@ -589,7 +590,7 @@ def visualize_db(db_path, output_dir, image_base_dir, options=None):
 
     return html_output_file,image_db
 
-# def visualize_db(...)
+# ...def visualize_db(...)
 
 
 #%% Command-line driver
@@ -603,8 +604,10 @@ def _args_to_object(args, obj):
         if not n.startswith('_'):
             setattr(obj, n, v)
 
-
-def main(): # noqa
+def main():
+    """
+    Command-line driver for visualize_db
+    """
 
     parser = argparse.ArgumentParser()
     parser.add_argument('db_path', action='store', type=str,
@@ -642,20 +645,3 @@ def main(): # noqa
 
 if __name__ == '__main__':
     main()
-
-
-#%% Interactive driver
-
-if False:
-
-    #%%
-
-    db_path = r'e:\wildlife_data\missouri_camera_traps\missouri_camera_traps_set1.json'
-    output_dir = r'e:\wildlife_data\missouri_camera_traps\preview'
-    image_base_dir = r'e:\wildlife_data\missouri_camera_traps'
-
-    options = DbVizOptions()
-    options.num_to_visualize = 100
-
-    html_output_file, db = visualize_db(db_path,output_dir,image_base_dir,options)
-    # os.startfile(html_output_file)

megadetector/visualization/visualize_detector_output.py

@@ -24,10 +24,13 @@ from megadetector.detection.run_detector import get_typical_confidence_threshold
 from megadetector.utils.ct_utils import get_max_conf
 from megadetector.utils import write_html_image_list
 from megadetector.utils.path_utils import path_is_abs
+from megadetector.utils.path_utils import open_file
 from megadetector.utils.wi_utils import load_md_or_speciesnet_file
 from megadetector.visualization import visualization_utils as vis_utils
 from megadetector.visualization.visualization_utils import blur_detections
 
+default_box_sort_order = 'confidence'
+
 
 #%% Constants
 
@@ -49,7 +52,7 @@ def _render_image(entry,
                   out_dir,
                   images_dir,
                   output_image_width,
-                  box_sort_order=None,
+                  box_sort_order=default_box_sort_order,
                   category_names_to_blur=None):
     """
     Internal function for rendering a single image.
@@ -153,7 +156,7 @@ def visualize_detector_output(detector_output_path,
                               parallelize_rendering=False,
                               parallelize_rendering_n_cores=10,
                               parallelize_rendering_with_threads=True,
-                              box_sort_order=None,
+                              box_sort_order=default_box_sort_order,
                               category_names_to_blur=None):
     """
     Draws bounding boxes on images given the output of a detector.
@@ -397,7 +400,7 @@ def main(): # noqa
         '--category_names_to_blur', default=None, type=str,
         help='Comma-separated list of category names to blur (or a single category name, typically "person")')
     parser.add_argument(
-        '--classification_confidence', type=float, default=0.1,
+        '--classification_confidence', type=float, default=0.3,
         help='If classification results are present, render results above this threshold')
 
     if len(sys.argv[1:]) == 0:
@@ -424,8 +427,7 @@ def main(): # noqa
         html_output_file=args.html_output_file,
         category_names_to_blur=category_names_to_blur)
 
-    if args.html_output_file is not None and args.open_html_output_file:
-        from megadetector.utils.path_utils import open_file
+    if (args.html_output_file is not None) and args.open_html_output_file:
         open_file(args.html_output_file)
 
 if __name__ == '__main__':