decimer 2.3.0__tar.gz → 2.5.0__tar.gz

{decimer-2.3.0 → decimer-2.5.0}/DECIMER/Efficient_Net_encoder.py

@@ -1,37 +1,25 @@
 # EfficientNet-V2 config
 import tensorflow as tf
-import DECIMER.efficientnetv2 as efficientnetv2
+
+import DECIMER.efficientnetv2
+from DECIMER.efficientnetv2 import effnetv2_configs
+from DECIMER.efficientnetv2 import effnetv2_model
 
 BATCH_SIZE_DEBUG = 2
-MODEL = "efficientnetv2-b3"  # @param
+MODEL = "efficientnetv2-m"  # @param
 
 
 # Define encoder
 def get_efficientnetv2_backbone(
-    model_name, include_top=False, input_shape=(299, 299, 3), pooling=None, weights=None
+    model_name, include_top=False, input_shape=(512, 512, 3), pooling=None, weights=None
 ):
-    """Initiate and get the desired Efficient-Net V2 backbone as encoder
-
-    Args:
-        model_name (str): Name of the Efficient-Net V2 model
-        include_top (bool, optional):  Defaults to False.
-        input_shape (tuple, optional): Image shape. Defaults to (299, 299, 3).
-        pooling (int, optional): Max pooling values. Defaults to None.
-        weights ( optional): Pretrained weights. Defaults to None.
-
-    Raises:
-        NotImplementedError: At this time we only want to use the raw
-
-    Returns:
-        Efficient Net V2 backbone
-    """
     # Catch unsupported arguments
     if pooling or weights or include_top:
         raise NotImplementedError(
             "\n...At this time we only want to use the raw "
             "(no pretraining), headless, features with no pooling ...\n"
         )
-    backbone = efficientnetv2.effnetv2_model.EffNetV2Model(model_name=model_name)
+    backbone = effnetv2_model.EffNetV2Model(model_name=model_name)
     backbone(
         tf.ones((BATCH_SIZE_DEBUG, *input_shape)), training=False, features_only=True
     )
@@ -39,12 +27,6 @@ def get_efficientnetv2_backbone(
 
 
 class Encoder(tf.keras.Model):
-    """Encoder class
-
-    Args:
-        tf (_type_): tensorflow model module
-    """
-
     def __init__(
         self,
         image_embedding_dim,
@@ -56,7 +38,6 @@ class Encoder(tf.keras.Model):
         pretrained_weights=None,
         scale_factor=0,
     ):
-
         super(Encoder, self).__init__()
 
         self.image_embedding_dim = image_embedding_dim

decimer-2.5.0/DECIMER/Predictor_usingCheckpoints.py

@@ -0,0 +1,275 @@
+import os
+import pickle
+import sys
+from typing import List
+from typing import Tuple
+
+import pystow
+import tensorflow as tf
+import Transformer_decoder
+
+if int(tf.__version__.split(".")[1]) <= 10:
+    import Efficient_Net_encoder
+else:
+    raise ImportError("Please use tensorflow 2.10 when working with the checkpoints.")
+import config
+import utils
+
+print(tf.__version__)
+
+# Set GPU
+os.environ["CUDA_VISIBLE_DEVICES"] = ""
+"""
+gpus = tf.config.experimental.list_physical_devices("GPU")
+for gpu in gpus:
+    tf.config.experimental.set_memory_growth(gpu, True)
+"""
+# Set path
+default_path = pystow.join("DECIMER-V2")
+
+# model download location
+checkpoint_url = "https://zenodo.org/record/8093783/files/DECIMER_512_checkpoints.zip"
+checkpoint_path = str(default_path) + "/DECIMER_checkpoints/"
+
+if not os.path.exists(checkpoint_path):
+    config.download_trained_weights(checkpoint_url, default_path)
+
+# load assets
+
+tokenizer = pickle.load(
+    open(
+        default_path.as_posix() + "/DECIMER_model/assets/tokenizer_SMILES.pkl",
+        "rb",
+    )
+)
+
+max_length = 302
+
+# Image partameters
+IMG_EMB_DIM = (16, 16, 512)
+IMG_EMB_DIM = (IMG_EMB_DIM[0] * IMG_EMB_DIM[1], IMG_EMB_DIM[2])
+IMG_SHAPE = (512, 512, 3)
+PE_INPUT = IMG_EMB_DIM[0]
+IMG_SEQ_LEN, IMG_EMB_DEPTH = IMG_EMB_DIM
+D_MODEL = 512
+
+# Network parameters
+N_LAYERS = 6
+D_MODEL = 512
+D_FF = 2048
+N_HEADS = 8
+DROPOUT_RATE = 0.1
+
+# Misc
+MAX_LEN = max_length
+VOCAB_LEN = len(tokenizer.word_index)
+PE_OUTPUT = MAX_LEN
+TARGET_V_SIZE = VOCAB_LEN
+REPLICA_BATCH_SIZE = 1
+
+# Config Encoder
+PREPROCESSING_FN = tf.keras.applications.efficientnet.preprocess_input
+BB_FN = Efficient_Net_encoder.get_efficientnetv2_backbone
+
+# Config Model
+testing_config = config.Config()
+
+testing_config.initialize_encoder_config(
+    image_embedding_dim=IMG_EMB_DIM,
+    preprocessing_fn=PREPROCESSING_FN,
+    backbone_fn=BB_FN,
+    image_shape=IMG_SHAPE,
+    do_permute=IMG_EMB_DIM[1] < IMG_EMB_DIM[0],
+)
+testing_config.initialize_transformer_config(
+    vocab_len=VOCAB_LEN,
+    max_len=MAX_LEN,
+    n_transformer_layers=N_LAYERS,
+    transformer_d_dff=D_FF,
+    transformer_n_heads=N_HEADS,
+    image_embedding_dim=D_MODEL,
+)
+
+# print(f"Encoder config:\n\t -> {testing_config.encoder_config}\n")
+# print(f"Transformer config:\n\t -> {testing_config.transformer_config}\n")
+
+# Prepare model
+optimizer, encoder, transformer = config.prepare_models(
+    encoder_config=testing_config.encoder_config,
+    transformer_config=testing_config.transformer_config,
+    replica_batch_size=REPLICA_BATCH_SIZE,
+    verbose=0,
+)
+
+# Load trained model checkpoint
+ckpt = tf.train.Checkpoint(
+    encoder=encoder, transformer=transformer, optimizer=optimizer
+)
+ckpt_manager = tf.train.CheckpointManager(ckpt, checkpoint_path, max_to_keep=50)
+if ckpt_manager.latest_checkpoint:
+    ckpt.restore(tf.train.latest_checkpoint(checkpoint_path))
+    start_epoch = int(ckpt_manager.latest_checkpoint.split("-")[-1])
+
+
+def main():
+    if len(sys.argv) != 2:
+        print("Usage: {} $image_path".format(sys.argv[0]))
+    else:
+        SMILES = predict_SMILES(sys.argv[1])
+        print(SMILES)
+        SMILES_with_confidence = predict_SMILES_with_confidence(sys.argv[1])
+        for tup in SMILES_with_confidence:
+            print(tup)
+
+
+class DECIMER_Predictor(tf.Module):
+    def __init__(self, encoder, tokenizer, transformer, max_length):
+        self.encoder = encoder
+        self.tokenizer = tokenizer
+        self.transformer = transformer
+        self.max_length = max_length
+
+    def __call__(self, Decoded_image):
+        """
+        Run the DECIMER predictor model when called.
+        Usage of predict_SMILES or predict_SMILES_with_confidence is recommended instead
+
+        Args:
+            Decoded_image (_type_): output of config.decode_image
+
+        Returns:
+            Tuple[tf.Tensor, tf.Tensor]: predicted tokens, confidence values
+        """
+        assert isinstance(Decoded_image, tf.Tensor)
+
+        _image_batch = tf.expand_dims(Decoded_image, 0)
+        _image_embedding = encoder(_image_batch, training=False)
+
+        start_token = tf.cast(
+            tf.convert_to_tensor([tokenizer.word_index["<start>"]]), tf.int32
+        )
+        end_token = tf.cast(
+            tf.convert_to_tensor([tokenizer.word_index["<end>"]]), tf.int32
+        )
+
+        output_array = tf.TensorArray(dtype=tf.int32, size=0, dynamic_size=True)
+        output_array = output_array.write(0, start_token)
+        confidence_array = tf.TensorArray(dtype=tf.float32, size=0, dynamic_size=True)
+
+        for t in tf.range(max_length):
+            output = tf.transpose(output_array.stack())
+            combined_mask = Transformer_decoder.create_masks_decoder(output)
+
+            # predictions.shape == (batch_size, seq_len, vocab_size)
+            prediction_batch = transformer(
+                output, _image_embedding, training=False, look_ahead_mask=combined_mask
+            )
+
+            # select the last word from the seq_len dimension
+            predictions = prediction_batch[:, -1:, :]  # (batch_size, 1, vocab_size)
+
+            predicted_id = tf.cast(tf.argmax(predictions, axis=-1), tf.int32)
+            confidence = predictions[-1][-1][int(predicted_id)]
+            output_array = output_array.write(t + 1, predicted_id[0])
+            confidence_array = confidence_array.write(t + 1, confidence)
+            if predicted_id == end_token:
+                break
+        output = tf.transpose(output_array.stack())
+
+        return output, confidence_array.stack()
+
+
+def detokenize_output(predicted_array: tf.Tensor) -> str:
+    """
+    This function takes the predicted array of tokens and returns the predicted SMILES
+    string.
+
+    Args:
+        predicted_array (tf.Tensor): Transformer Decoder output array (predicted tokens)
+
+    Returns:
+        str: SMILES string
+    """
+    outputs = [tokenizer.index_word[i] for i in predicted_array[0].numpy()]
+    prediction = (
+        "".join([str(elem) for elem in outputs])
+        .replace("<start>", "")
+        .replace("<end>", "")
+    )
+    return prediction
+
+
+def detokenize_output_add_confidence(
+    predicted_array: tf.Tensor,
+    confidence_array: tf.Tensor,
+) -> List[Tuple[str, float]]:
+    """
+    This function takes the predicted array of tokens as well as the confidence values
+    returned by the Transformer Decoder and returns a list of tuples
+    that contain each token of the predicted SMILES string and the confidence
+    value.
+
+    Args:
+        predicted_array (tf.Tensor): Transformer Decoder output array (predicted tokens)
+
+    Returns:
+        str: SMILES string
+    """
+    prediction_with_confidence = [
+        (
+            tokenizer.index_word[predicted_array[0].numpy()[i]],
+            confidence_array[i].numpy(),
+        )
+        for i in range(len(confidence_array))
+    ]
+    decoded_prediction_with_confidence = list(
+        [(utils.decoder(tok), conf) for tok, conf in prediction_with_confidence[1:-1]]
+    )
+    decoded_prediction_with_confidence.append(prediction_with_confidence[-1])
+    return decoded_prediction_with_confidence
+
+
+# Initiate the DECIMER class
+DECIMER = DECIMER_Predictor(encoder, tokenizer, transformer, MAX_LEN)
+
+
+def predict_SMILES_with_confidence(image_path: str) -> List[Tuple[str, float]]:
+    """
+    This function takes an image path (str) and returns a list of tuples
+    that contain each token of the predicted SMILES string and the confidence
+    level from the last layer of the Transformer decoder.
+
+    Args:
+        image_path (str): Path of chemical structure depiction image
+
+    Returns:
+        (List[Tuple[str, float]]): Tuples that contain the tokens and the confidence
+            values of the predicted SMILES
+    """
+    decodedImage = config.decode_image(image_path)
+    predicted_tokens, confidence_values = DECIMER(tf.constant(decodedImage))
+    predicted_SMILES_with_confidence = detokenize_output_add_confidence(
+        predicted_tokens, confidence_values
+    )
+    return predicted_SMILES_with_confidence
+
+
+def predict_SMILES(image_path: str) -> str:
+    """
+    This function takes an image path (str) and returns the SMILES
+    representation of the depicted molecule (str).
+
+    Args:
+        image_path (str): Path of chemical structure depiction image
+
+    Returns:
+        (str): SMILES representation of the molecule in the input image
+    """
+    decodedImage = config.decode_image(image_path)
+    predicted_tokens, _ = DECIMER(tf.constant(decodedImage))
+    predicted_SMILES = utils.decoder(detokenize_output(predicted_tokens))
+    return predicted_SMILES
+
+
+if __name__ == "__main__":
+    main()

{decimer-2.3.0 → decimer-2.5.0}/DECIMER/Repack_model.py

@@ -1,11 +1,13 @@
 import os
+import pickle
+from typing import List
+from typing import Tuple
+
 import tensorflow as tf
 
-import pickle
-import Transformer_decoder
-import Efficient_Net_encoder
-import config
-import utils
+import DECIMER.config as config
+import DECIMER.Efficient_Net_encoder as Efficient_Net_encoder
+import DECIMER.Transformer_decoder as Transformer_decoder
 
 print(tf.__version__)
 
@@ -16,19 +18,19 @@ for gpu in gpus:
     tf.config.experimental.set_memory_growth(gpu, True)
 
 # load assets
-tokenizer = pickle.load(open("tokenizer_TPU_Stereo.pkl", "rb"))
-max_length = pickle.load(open("max_length_TPU_Stereo.pkl", "rb"))
+tokenizer = pickle.load(open("tokenizer.pkl", "rb"))
+max_length = pickle.load(open("max_length.pkl", "rb"))
 
 # Image parameters
-IMG_EMB_DIM = (16, 16, 232)
+IMG_EMB_DIM = (16, 16, 512)
 IMG_EMB_DIM = (IMG_EMB_DIM[0] * IMG_EMB_DIM[1], IMG_EMB_DIM[2])
 IMG_SHAPE = (512, 512, 3)
 PE_INPUT = IMG_EMB_DIM[0]
 IMG_SEQ_LEN, IMG_EMB_DEPTH = IMG_EMB_DIM
-D_MODEL = IMG_EMB_DEPTH
+D_MODEL = 512
 
 # Network parameters
-N_LAYERS = 4
+N_LAYERS = 6
 D_MODEL = 512
 D_FF = 2048
 N_HEADS = 8
@@ -56,14 +58,13 @@ testing_config.initialize_encoder_config(
     image_shape=IMG_SHAPE,
     do_permute=IMG_EMB_DIM[1] < IMG_EMB_DIM[0],
 )
-
 testing_config.initialize_transformer_config(
     vocab_len=VOCAB_LEN,
     max_len=MAX_LEN,
     n_transformer_layers=N_LAYERS,
     transformer_d_dff=D_FF,
     transformer_n_heads=N_HEADS,
-    image_embedding_dim=IMG_EMB_DIM,
+    image_embedding_dim=D_MODEL,
 )
 
 # Prepare model
@@ -85,17 +86,56 @@ if ckpt_manager.latest_checkpoint:
     start_epoch = int(ckpt_manager.latest_checkpoint.split("-")[-1])
 
 
-def detokenize_output(predicted_array):
+def detokenize_output(predicted_array: tf.Tensor) -> str:
+    """
+    This function takes the predicted array of tokens and returns the predicted SMILES
+    string.
+
+    Args:
+        predicted_array (tf.Tensor): Transformer Decoder output array (predicted tokens)
+
+    Returns:
+        str: SMILES string
+    """
     outputs = [tokenizer.index_word[i] for i in predicted_array[0].numpy()]
     prediction = (
         "".join([str(elem) for elem in outputs])
         .replace("<start>", "")
         .replace("<end>", "")
     )
-
     return prediction
 
 
+def detokenize_output_add_confidence(
+    predicted_array: tf.Tensor,
+    confidence_array: tf.Tensor,
+) -> List[Tuple[str, float]]:
+    """
+    This function takes the predicted array of tokens as well as the confidence values
+    returned by the Transformer Decoder and returns a list of tuples
+    that contain each token of the predicted SMILES string and the confidence
+    value.
+
+    Args:
+        predicted_array (tf.Tensor): Transformer Decoder output array (predicted tokens)
+
+    Returns:
+        str: SMILES string
+    """
+    prediction_with_confidence = [
+        (
+            tokenizer.index_word[predicted_array[0].numpy()[i]],
+            confidence_array[i].numpy(),
+        )
+        for i in range(len(confidence_array))
+    ]
+    decoded_prediction_with_confidence = list(
+        [(utils.decoder(tok), conf) for tok, conf in prediction_with_confidence[1:-1]]
+    )
+    decoded_prediction_with_confidence.append(prediction_with_confidence[-1])
+    return decoded_prediction_with_confidence
+
+
 class DECIMER_Predictor(tf.Module):
     """This is a class which takes care of inference. It loads the saved checkpoint and the necessary
     tokenizers. The inference begins with the start token (<start>) and ends when the end token(<end>)
@@ -129,8 +169,6 @@ class DECIMER_Predictor(tf.Module):
             output (tf.Tensor[tf.int64]): predicted output as an array.
         """
         assert isinstance(Decoded_image, tf.Tensor)
-        if len(Decoded_image.shape) == 0:
-            sentence = Decoded_image[tf.newaxis]
 
         _image_batch = tf.expand_dims(Decoded_image, 0)
         _image_embedding = encoder(_image_batch, training=False)
@@ -144,28 +182,29 @@ class DECIMER_Predictor(tf.Module):
 
         output_array = tf.TensorArray(dtype=tf.int32, size=0, dynamic_size=True)
         output_array = output_array.write(0, start_token)
+        confidence_array = tf.TensorArray(dtype=tf.float32, size=0, dynamic_size=True)
 
         for t in tf.range(max_length):
             output = tf.transpose(output_array.stack())
-            combined_mask = Transformer_decoder.create_mask(None, output)
+            combined_mask = Transformer_decoder.create_masks_decoder(output)
 
             # predictions.shape == (batch_size, seq_len, vocab_size)
-            prediction_batch, _ = transformer(
-                _image_embedding, output, training=False, look_ahead_mask=combined_mask
+            prediction_batch = transformer(
+                output, _image_embedding, training=False, look_ahead_mask=combined_mask
             )
 
             # select the last word from the seq_len dimension
             predictions = prediction_batch[:, -1:, :]  # (batch_size, 1, vocab_size)
 
             predicted_id = tf.cast(tf.argmax(predictions, axis=-1), tf.int32)
-
+            confidence = predictions[0, 0, int(predicted_id[0, 0])]
             output_array = output_array.write(t + 1, predicted_id[0])
-
+            confidence_array = confidence_array.write(t + 1, confidence)
             if predicted_id == end_token:
                 break
         output = tf.transpose(output_array.stack())
 
-        return output
+        return output, confidence_array.stack()
 
 
 DECIMER = DECIMER_Predictor(encoder, tokenizer, transformer, MAX_LEN)