Merge pull request #53 from Imageomics/29-custom-bins

Add binning to custom label prediction

README.md

@@ -102,9 +102,29 @@ fish 2.932403668845507e-12
 bear 1.0
 ```
 
+### Predict from a list of classes with binning
+```python
+from bioclip import CustomLabelsBinningClassifier
+classifier = CustomLabelsBinningClassifier(cls_to_bin={
+  'dog': 'small',
+  'fish': 'small',
+  'bear': 'big',
+})
+predictions = classifier.predict("Ursus-arctos.jpeg")
+for prediction in predictions:
+   print(prediction["classification"], prediction["score"])
+```
+Output:
+```console
+big 0.99992835521698
+small 7.165559509303421e-05
+```
+
 ## Command Line Usage
 ```
-bioclip predict [-h] [--format {table,csv}] [--output OUTPUT] [--rank {kingdom,phylum,class,order,family,genus,species}] [--k K] [--cls CLS] [--device DEVICE] image_file [image_file ...]
+bioclip predict [-h] [--format {table,csv}] [--output OUTPUT]
+                [--rank {kingdom,phylum,class,order,family,genus,species} | --cls CLS | --bins BINS]
+                [--k K] [--device DEVICE] image_file [image_file ...]
 bioclip embed [-h] [--device=DEVICE] [--output=OUTPUT] [IMAGE_FILE...]
 
 Commands:
@@ -117,9 +137,13 @@ Arguments:
 Options:
   -h --help
   --format=FORMAT      format of the output (table or csv) for predict mode [default: csv]
-  --rank=RANK          rank of the classification (kingdom, phylum, class, order, family, genus, species) [default: species] 
-  --k=K                number of top predictions to show [default: 5]
-  --cls=CLS            classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the --rank argument is not allowed.
+  --rank {kingdom,phylum,class,order,family,genus,species}
+                        rank of the classification, default: species (when)
+  --cls CLS             classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the
+                        --rank and --bins arguments are not allowed.
+  --bins BINS           path to CSV file with two columns with the first being classes and second being bin names, when specified the --cls
+                        argument is not allowed.
+  --k K                 number of top predictions to show, default: 5
   --device=DEVICE      device to use matrix math (cpu or cuda or mps) [default: cpu]
   --output=OUTFILE     print output to file OUTFILE [default: stdout]
 ```
@@ -195,6 +219,29 @@ Ursus-arctos.jpeg,bird,3.051998476166773e-08
 Ursus-arctos.jpeg,bear,0.9999998807907104                                                                 
 ```
 
+### Predict from a binning CSV
+Create predictions for 3 classes (cat, bird, and bear) with 2 bins (one, two) for image `Ursus-arctos.jpeg`:
+
+Create a CSV file named `bins.csv` with the following contents:
+```
+cls,bin
+cat,one
+bird,one
+bear,two
+```
+The names of the columns do not matter. The first column values will be used as the classes. The second column values will be used for bin names.
+
+Run predict command:
+```console
+bioclip predict --bins bins.csv Ursus-arctos.jpeg
+```
+
+Output:
+```
+Ursus-arctos.jpeg,two,0.9999998807907104
+Ursus-arctos.jpeg,one,7.633736487377973e-08
+```
+
 ### Create embeddings
 
 #### Create embedding for an image

src/bioclip/__init__.py

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2024-present John Bradley <[email protected]>
 #
 # SPDX-License-Identifier: MIT
-from bioclip.predict import TreeOfLifeClassifier, Rank, CustomLabelsClassifier
+from bioclip.predict import TreeOfLifeClassifier, Rank, CustomLabelsClassifier, CustomLabelsBinningClassifier
 
-__all__ = ["TreeOfLifeClassifier", "Rank", "CustomLabelsClassifier"]
+__all__ = ["TreeOfLifeClassifier", "Rank", "CustomLabelsClassifier", "CustomLabelsBinningClassifier"]

src/bioclip/__main__.py

@@ -1,4 +1,4 @@
-from bioclip import TreeOfLifeClassifier, Rank, CustomLabelsClassifier
+from bioclip import TreeOfLifeClassifier, Rank, CustomLabelsClassifier, CustomLabelsBinningClassifier
 from .predict import BIOCLIP_MODEL_STR
 import open_clip as oc
 import os
@@ -32,17 +32,32 @@ def write_results_to_file(df, format, outfile):
         raise ValueError(f"Invalid format: {format}")
 
 
+def parse_bins_csv(bins_path):
+    if not os.path.exists(bins_path):
+        raise FileNotFoundError(f"File not found: {bins_path}")
+    bin_df = pd.read_csv(bins_path, index_col=0)
+    if len(bin_df.columns) == 0:
+        raise ValueError("CSV file must have at least two columns.")
+    return bin_df[bin_df.columns[0]].to_dict()
+
+
 def predict(image_file: list[str],
             format: str,
             output: str,
             cls_str: str,
             rank: Rank,
+            bins_path: str,
             k: int,
             **kwargs):
     if cls_str:
         classifier = CustomLabelsClassifier(cls_ary=cls_str.split(','), **kwargs)
         predictions = classifier.predict(image_paths=image_file, k=k)
         write_results(predictions, format, output)
+    elif bins_path:
+        cls_to_bin = parse_bins_csv(bins_path)
+        classifier = CustomLabelsBinningClassifier(cls_to_bin=cls_to_bin, **kwargs)
+        predictions = classifier.predict(image_paths=image_file, k=k)
+        write_results(predictions, format, output)
     else:
         classifier = TreeOfLifeClassifier(**kwargs)
         predictions = classifier.predict(image_paths=image_file, rank=rank, k=k)
@@ -81,11 +96,13 @@ def create_parser():
     predict_parser.add_argument('image_file', nargs='+', help='input image file(s)')
     predict_parser.add_argument('--format', choices=['table', 'csv'], default='csv', help='format of the output, default: csv')
     predict_parser.add_argument('--output', **output_arg)
-    predict_parser.add_argument('--rank', choices=['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'],
+    cls_group = predict_parser.add_mutually_exclusive_group(required=False)
+    cls_group.add_argument('--rank', choices=['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'],
                                 help='rank of the classification, default: species (when)')
+    cls_help = "classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the --rank and --bins arguments are not allowed."
+    cls_group.add_argument('--cls', help=cls_help)
+    cls_group.add_argument('--bins', help='path to CSV file with two columns with the first being classes and second being bin names, when specified the --cls argument is not allowed.')
     predict_parser.add_argument('--k', type=int, help='number of top predictions to show, default: 5')
-    cls_help = "classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the --rank argument is not allowed."
-    predict_parser.add_argument('--cls', help=cls_help)
 
     predict_parser.add_argument('--device', **device_arg)
     predict_parser.add_argument('--model', **model_arg)
@@ -115,11 +132,7 @@ def create_parser():
 def parse_args(input_args=None):
     args = create_parser().parse_args(input_args)
     if args.command == 'predict':
-        if args.cls:
-            # custom class list mode
-            if args.rank:
-                raise ValueError("Cannot use --cls with --rank")
-        else:
+        if not args.cls and not args.bins:
             # tree of life class list mode
             if args.model or args.pretrained:
                 raise ValueError("Custom model or checkpoints currently not supported for Tree-of-Life prediction")
@@ -155,6 +168,7 @@ def main():
                 output=args.output,
                 cls_str=cls_str,
                 rank=args.rank,
+                bins_path=args.bins,
                 k=args.k,
                 device=args.device,
                 model_str=args.model,
@@ -167,7 +181,7 @@ def main():
             for model_str in oc.list_models():
                 print(f"\t{model_str}")
     else:
-        raise ValueError("Invalid command")
+        create_parser().print_help()
 
 
 if __name__ == '__main__':

src/bioclip/predict.py

@@ -5,6 +5,7 @@
 import open_clip as oc
 import torch.nn.functional as F
 import numpy as np
+import pandas as pd
 import collections
 import heapq
 import PIL.Image
@@ -253,13 +254,41 @@ def predict(self, image_paths: List[str] | str, k: int = None) -> dict[str, floa
             img_probs = probs[image_path]
             if not k or k > len(self.classes):
                 k = len(self.classes)
-            topk = img_probs.topk(k)
-            for i, prob in zip(topk.indices, topk.values):
-                result.append({
-                    PRED_FILENAME_KEY: image_path,
-                    PRED_CLASSICATION_KEY: self.classes[i],
-                    PRED_SCORE_KEY: prob.item()
-                })
+            result.extend(self.group_probs(image_path, img_probs, k))
+        return result
+
+    def group_probs(self, image_path: str, img_probs: torch.Tensor, k: int = None) -> List[dict[str, float]]:
+        result = []
+        topk = img_probs.topk(k)
+        for i, prob in zip(topk.indices, topk.values):
+            result.append({
+                PRED_FILENAME_KEY: image_path,
+                PRED_CLASSICATION_KEY: self.classes[i],
+                PRED_SCORE_KEY: prob.item()
+            })
+        return result
+
+
+class CustomLabelsBinningClassifier(CustomLabelsClassifier):
+    def __init__(self, cls_to_bin: dict, **kwargs):
+        super().__init__(cls_ary=cls_to_bin.keys(), **kwargs)
+        self.cls_to_bin = cls_to_bin
+        if any([pd.isna(x) or not x for x in cls_to_bin.values()]):
+            raise ValueError("Empty, null, or nan are not allowed for bin values.")
+
+    def group_probs(self, image_path: str, img_probs: torch.Tensor, k: int = None) -> List[dict[str, float]]:
+        result = []
+        output = collections.defaultdict(float)
+        for i in range(len(self.classes)):
+            name = self.cls_to_bin[self.classes[i]]
+            output[name] += img_probs[i]
+        topk_names = heapq.nlargest(k, output, key=output.get)
+        for name in topk_names:
+            result.append({
+                PRED_FILENAME_KEY: image_path,
+                PRED_CLASSICATION_KEY: name,
+                PRED_SCORE_KEY: output[name].item()
+            })
         return result
 
 

tests/test_main.py

@@ -1,7 +1,8 @@
 import unittest
 from unittest.mock import mock_open, patch
 import argparse
-from bioclip.__main__ import parse_args, Rank, create_classes_str, main
+import pandas as pd
+from bioclip.__main__ import parse_args, Rank, create_classes_str, main, parse_bins_csv
 
 
 class TestParser(unittest.TestCase):
@@ -15,6 +16,7 @@ def test_parse_args(self):
         self.assertEqual(args.rank, Rank.SPECIES)
         self.assertEqual(args.k, 5)
         self.assertEqual(args.cls, None)
+        self.assertEqual(args.bins, None)
         self.assertEqual(args.device, 'cpu')
 
         args = parse_args(['predict', 'image.jpg', 'image2.png'])
@@ -41,12 +43,29 @@ def test_parse_args(self):
         self.assertEqual(args.rank, None) # default ignored for the --cls variation
         self.assertEqual(args.k, None)
         self.assertEqual(args.cls, 'class1,class2')
+        self.assertEqual(args.bins, None)
+        self.assertEqual(args.device, 'cuda')
+
+        # test binning version of predict
+        args = parse_args(['predict', 'image.jpg', '--format', 'table', '--output', 'output.csv', '--bins', 'bins.csv', '--device', 'cuda'])
+        self.assertEqual(args.command, 'predict')
+        self.assertEqual(args.image_file, ['image.jpg'])
+        self.assertEqual(args.format, 'table')
+        self.assertEqual(args.output, 'output.csv')
+        self.assertEqual(args.rank, None) # default ignored for the --cls variation
+        self.assertEqual(args.k, None)
+        self.assertEqual(args.cls, None)
+        self.assertEqual(args.bins, 'bins.csv')
         self.assertEqual(args.device, 'cuda')
 
         # test error when using --cls with --rank
-        with self.assertRaises(ValueError):
+        with self.assertRaises(SystemExit):
             parse_args(['predict', 'image.jpg', '--cls', 'class1,class2', '--rank', 'genus'])
 
+        # test error when using --cls with --bins
+        with self.assertRaises(SystemExit):
+            parse_args(['predict', 'image.jpg', '--cls', 'class1,class2', '--bins', 'somefile.csv'])
+
         # not an error when using --cls with --k
         args = parse_args(['predict', 'image.jpg', '--cls', 'class1,class2', '--k', '10'])
         self.assertEqual(args.k, 10)
@@ -77,10 +96,10 @@ def test_create_classes_str(self):
     def test_predict_no_class(self, mock_parse_args, mock_predict):
         mock_parse_args.return_value = argparse.Namespace(command='predict', image_file='image.jpg', format='csv',
                                                           output='stdout', rank=Rank.SPECIES, k=5, cls=None, device='cpu',
-                                                          model=None, pretrained=None)
+                                                          model=None, pretrained=None, bins=None)
         main()
-        mock_predict.assert_called_with('image.jpg', format='csv', output='stdout', cls_str=None, rank=Rank.SPECIES, k=5,
-                                        device='cpu', model_str=None, pretrained_str=None)
+        mock_predict.assert_called_with('image.jpg', format='csv', output='stdout', cls_str=None, rank=Rank.SPECIES,
+                                        bins_path=None, k=5, device='cpu', model_str=None, pretrained_str=None)
 
     @patch('bioclip.__main__.predict')
     @patch('bioclip.__main__.parse_args')
@@ -89,10 +108,10 @@ def test_predict_class_list(self, mock_os, mock_parse_args, mock_predict):
         mock_os.path.exists.return_value = False
         mock_parse_args.return_value = argparse.Namespace(command='predict', image_file='image.jpg', format='csv',
                                                           output='stdout', rank=Rank.SPECIES, k=5, cls='dog,fish,bird',
-                                                          device='cpu', model=None, pretrained=None)
+                                                          device='cpu', model=None, pretrained=None, bins=None)
         main()
         mock_predict.assert_called_with('image.jpg', format='csv', output='stdout', cls_str='dog,fish,bird', rank=Rank.SPECIES,
-                                        k=5, device='cpu', model_str=None, pretrained_str=None)
+                                        bins_path=None, k=5, device='cpu', model_str=None, pretrained_str=None)
 
     @patch('bioclip.__main__.predict')
     @patch('bioclip.__main__.parse_args')
@@ -101,8 +120,38 @@ def test_predict_class_file(self, mock_os, mock_parse_args, mock_predict):
         mock_os.path.exists.return_value = True
         mock_parse_args.return_value = argparse.Namespace(command='predict', image_file='image.jpg', format='csv', 
                                                           output='stdout', rank=Rank.SPECIES, k=5, cls='somefile.txt',
-                                                          device='cpu', model=None, pretrained=None)
+                                                          device='cpu', model=None, pretrained=None, bins=None)
         with patch("builtins.open", mock_open(read_data='dog\nfish\nbird')) as mock_file:
             main()
         mock_predict.assert_called_with('image.jpg', format='csv', output='stdout', cls_str='dog,fish,bird', rank=Rank.SPECIES,
-                                        k=5, device='cpu', model_str=None, pretrained_str=None)
+                                        bins_path=None, k=5, device='cpu', model_str=None, pretrained_str=None)
+
+    @patch('bioclip.__main__.predict')
+    @patch('bioclip.__main__.parse_args')
+    @patch('bioclip.__main__.os')
+    def test_predict_bins(self, mock_os, mock_parse_args, mock_predict):
+        mock_os.path.exists.return_value = True
+        mock_parse_args.return_value = argparse.Namespace(command='predict', image_file='image.jpg', format='csv', 
+                                                          output='stdout', rank=None, k=5, cls=None, 
+                                                          device='cpu', model=None, pretrained=None,
+                                                          bins='some.csv')
+        with patch("builtins.open", mock_open(read_data='dog\nfish\nbird')) as mock_file:
+            main()
+        mock_predict.assert_called_with('image.jpg', format='csv', output='stdout', cls_str=None, rank=None,
+                                        bins_path='some.csv', k=5, device='cpu', model_str=None, pretrained_str=None)
+    @patch('bioclip.__main__.os.path')
+    def test_parse_bins_csv_file_missing(self, mock_path):
+        mock_path.exists.return_value = False
+        with self.assertRaises(FileNotFoundError) as raised_exception:
+            parse_bins_csv("somefile.csv")
+        self.assertEqual(str(raised_exception.exception), 'File not found: somefile.csv')
+
+    @patch('bioclip.__main__.pd')
+    @patch('bioclip.__main__.os.path')
+    def test_parse_bins_csv(self, mock_path, mock_pd):
+        mock_path.exists.return_value = True
+        data = {'bin': ['a', 'b']}
+        mock_pd.read_csv.return_value = pd.DataFrame(data=data, index=['dog', 'cat'])
+        with patch("builtins.open", mock_open(read_data='dog\nfish\nbird')) as mock_file:
+            cls_to_bin = parse_bins_csv("somefile.csv")
+        self.assertEqual(cls_to_bin, {'cat': 'b', 'dog': 'a'})