ValueError: operands could not be broadcast together with shapes (4,224,224) (3,) #12

dbl001 · 2022-05-11T18:22:06Z

Running a Concept example on OS S Monterey 12.3.1
...Transformers/Image_utils #143:
return (image - mean) / std

image is (4,224,224)
mean is (3,)
std is (3,)

Python 3.8.13 
% pip show tensorflow_macos
WARNING: Ignoring invalid distribution -umpy (/Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages)
Name: tensorflow-macos
Version: 2.8.0
Summary: TensorFlow is an open source machine learning framework for everyone.
Home-page: https://www.tensorflow.org/
Author: Google Inc.
Author-email: [email protected]
License: Apache 2.0
Location: /Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages
Requires: absl-py, astunparse, flatbuffers, gast, google-pasta, grpcio, h5py, keras, keras-preprocessing, libclang, numpy, opt-einsum, protobuf, setuptools, six, tensorboard, termcolor, tf-estimator-nightly, typing-extensions, wrapt
Required-by: 

pip show sentence_transformers
WARNING: Ignoring invalid distribution -umpy (/Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages)
Name: sentence-transformers
Version: 2.1.0
Summary: Sentence Embeddings using BERT / RoBERTa / XLM-R
Home-page: https://github.com/UKPLab/sentence-transformers
Author: Nils Reimers
Author-email: [email protected]
License: Apache License 2.0
Location: /Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages
Requires: huggingface-hub, nltk, numpy, scikit-learn, scipy, sentencepiece, tokenizers, torch, torchvision, tqdm, transformers
Required-by: bertopic, concept

% pip show transformers
WARNING: Ignoring invalid distribution -umpy (/Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages)
Name: transformers
Version: 4.11.3
Summary: State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
Home-page: https://github.com/huggingface/transformers
Author: Thomas Wolf, Lysandre Debut, Victor Sanh, Julien Chaumond, Sam Shleifer, Patrick von Platen, Sylvain Gugger, Suraj Patil, Stas Bekman, Google AI Language Team Authors, Open AI team Authors, Facebook AI Authors, Carnegie Mellon University Authors
Author-email: [email protected]
License: Apache
Location: /Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages
Requires: filelock, huggingface-hub, numpy, packaging, pyyaml, regex, requests, sacremoses, tokenizers, tqdm
Required-by: sentence-transformers

Here's the code:

import os
import glob
import zipfile
from tqdm import tqdm
from sentence_transformers import util

# 25k images from Unsplash
img_folder = 'photos/'
if not os.path.exists(img_folder) or len(os.listdir(img_folder)) == 0:
    os.makedirs(img_folder, exist_ok=True)

    photo_filename = 'unsplash-25k-photos.zip'
    if not os.path.exists(photo_filename):  # Download dataset if does not exist
        util.http_get('http://sbert.net/datasets/' + photo_filename, photo_filename)

    # Extract all images
    with zipfile.ZipFile(photo_filename, 'r') as zf:
        for member in tqdm(zf.infolist(), desc='Extracting'):
            zf.extract(member, img_folder)
img_names = list(glob.glob('photos/*.jpg'))

from concept import ConceptModel
concept_model = ConceptModel()
concepts = concept_model.fit_transform(img_names)

B/s]
  0%|                                                   | 0/196 [00:00<?, ?it/s]/Users/davidlaxer/tensorflow-metal/lib/python3.8/site-packages/transformers/feature_extraction_utils.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor. (Triggered internally at  ../torch/csrc/utils/tensor_new.cpp:201.)
  tensor = as_tensor(value)
  5%|█▉                                         | 9/196 [02:21<48:54, 15.69s/it]
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Input In [2], in <cell line: 3>()
      1 from concept import ConceptModel
      2 concept_model = ConceptModel()
----> 3 concepts = concept_model.fit_transform(img_names)

File ~/Concept/concept/_model.py:120, in ConceptModel.fit_transform(self, images, docs, image_names, image_embeddings)
    118 # Calculate image embeddings if not already generated
    119 if image_embeddings is None:
--> 120     image_embeddings = self._embed_images(images)
    122 # Reduce dimensionality and cluster images into concepts
    123 reduced_embeddings = self._reduce_dimensionality(image_embeddings)

File ~/Concept/concept/_model.py:224, in ConceptModel._embed_images(self, images)
    221 end_index = (i * batch_size) + batch_size
    223 images_to_embed = [Image.open(filepath) for filepath in images[start_index:end_index]]
--> 224 img_emb = self.embedding_model.encode(images_to_embed, show_progress_bar=False)
    225 embeddings.extend(img_emb.tolist())
    227 # Close images

File ~/tensorflow-metal/lib/python3.8/site-packages/sentence_transformers/SentenceTransformer.py:153, in SentenceTransformer.encode(self, sentences, batch_size, show_progress_bar, output_value, convert_to_numpy, convert_to_tensor, device, normalize_embeddings)
    151 for start_index in trange(0, len(sentences), batch_size, desc="Batches", disable=not show_progress_bar):
    152     sentences_batch = sentences_sorted[start_index:start_index+batch_size]
--> 153     features = self.tokenize(sentences_batch)
    154     features = batch_to_device(features, device)
    156     with torch.no_grad():

File ~/tensorflow-metal/lib/python3.8/site-packages/sentence_transformers/SentenceTransformer.py:311, in SentenceTransformer.tokenize(self, texts)
    307 def tokenize(self, texts: Union[List[str], List[Dict], List[Tuple[str, str]]]):
    308     """
    309     Tokenizes the texts
    310     """
--> 311     return self._first_module().tokenize(texts)

File ~/tensorflow-metal/lib/python3.8/site-packages/sentence_transformers/models/CLIPModel.py:71, in CLIPModel.tokenize(self, texts)
     68 if len(images) == 0:
     69     images = None
---> 71 inputs = self.processor(text=texts_values, images=images, return_tensors="pt", padding=True)
     72 inputs['image_text_info'] = image_text_info
     73 return inputs

File ~/tensorflow-metal/lib/python3.8/site-packages/transformers/models/clip/processing_clip.py:148, in CLIPProcessor.__call__(self, text, images, return_tensors, **kwargs)
    145     encoding = self.tokenizer(text, return_tensors=return_tensors, **kwargs)
    147 if images is not None:
--> 148     image_features = self.feature_extractor(images, return_tensors=return_tensors, **kwargs)
    150 if text is not None and images is not None:
    151     encoding["pixel_values"] = image_features.pixel_values

File ~/tensorflow-metal/lib/python3.8/site-packages/transformers/models/clip/feature_extraction_clip.py:150, in CLIPFeatureExtractor.__call__(self, images, return_tensors, **kwargs)
    148     images = [self.center_crop(image, self.crop_size) for image in images]
    149 if self.do_normalize:
--> 150     images = [self.normalize(image=image, mean=self.image_mean, std=self.image_std) for image in images]
    152 # return as BatchFeature
    153 data = {"pixel_values": images}

File ~/tensorflow-metal/lib/python3.8/site-packages/transformers/models/clip/feature_extraction_clip.py:150, in <listcomp>(.0)
    148     images = [self.center_crop(image, self.crop_size) for image in images]
    149 if self.do_normalize:
--> 150     images = [self.normalize(image=image, mean=self.image_mean, std=self.image_std) for image in images]
    152 # return as BatchFeature
    153 data = {"pixel_values": images}

File ~/tensorflow-metal/lib/python3.8/site-packages/transformers/image_utils.py:143, in ImageFeatureExtractionMixin.normalize(self, image, mean, std)
    141     return (image - mean[:, None, None]) / std[:, None, None]
    142 else:
--> 143     return (image - mean) / std

ValueError: operands could not be broadcast together with shapes (4,224,224) (3,)

The exception is in the normalize() function ... I believe in the 9th Pil image:

The text was updated successfully, but these errors were encountered:

dbl001 · 2022-05-11T18:32:31Z

Was the image corrupted during download?

MaartenGr · 2022-05-12T06:15:59Z

That indeed does sound familiar. I can remember having trouble with some of the images when starting out developing the packages but I cannot find the code for fixing this. I believe you are indeed correct that some of the images are either corrupted or in a different format.

I would have to do some digging but it indeed seems that this might not be the best dataset to be used unless some images are removed...

dbl001 · 2022-05-12T20:29:12Z

Not an elegant solution ... but it was quick:

       # Prepare images
        batch_size = 1
        nr_iterations = int(np.ceil(len(images) / batch_size))

        # Embed images per batch
        embeddings = []
        for i in tqdm(range(nr_iterations)):
            start_index = i * batch_size
            end_index = (i * batch_size) + batch_size

            images_to_embed = [Image.open(filepath) for filepath in images[start_index:end_index]]
            try:
                img_emb = self.embedding_model.encode(images_to_embed, show_progress_bar=False)
                embeddings.extend(img_emb.tolist())
                # Close images
                for image in images_to_embed:
                    image.close()
            except Exception:
                print("Skipping: %s", images[start_index:end_index])
                # Close images
                for image in images_to_embed:
                    image.close()
            continue

        return np.array(embeddings)

dbl001 · 2022-05-13T20:04:17Z

Is this what you get?

MaartenGr · 2022-05-14T07:26:09Z

I just tried out the following code in a Kaggle session and I had no issues:

import os
import glob
import zipfile
from tqdm import tqdm
from sentence_transformers import util
from concept import ConceptModel

# 25k images from Unsplash
img_folder = 'photos/'
if not os.path.exists(img_folder) or len(os.listdir(img_folder)) == 0:
    os.makedirs(img_folder, exist_ok=True)

    photo_filename = 'unsplash-25k-photos.zip'
    if not os.path.exists(photo_filename):  # Download dataset if does not exist
        util.http_get('http://sbert.net/datasets/' + photo_filename, photo_filename)

    # Extract all images
    with zipfile.ZipFile(photo_filename, 'r') as zf:
        for member in tqdm(zf.infolist(), desc='Extracting'):
            zf.extract(member, img_folder)
img_names = list(glob.glob('photos/*.jpg'))

# Train model
concept_model = ConceptModel()
concepts = concept_model.fit_transform(img_names)

It might mean that something indeed went wrong when trying to load the images in your environment.

Is this what you get?

Concept uses UMAP, which is stocastisch by natures, which means that every run you will get different results. So comparing outputs is not easily done unless you set a random_state in UMAP which might hurt performance.

dbl001 · 2022-05-14T16:21:43Z

Its something in the inner workings of SentenceTransformer('clip-ViT-B-32').
Possibly an issue with tensorflow_macos/tensorflow_metal and torch.
Investigating ...

dbl001 · 2022-05-14T16:43:59Z

It appears that the images which cause the exceptions int the normailze() methods have 4 channels (not 3).

numpy 1.20.3
transformers 4.11.3
sentence_transformers 2.1.0

Are you using the same versions?

these defaults in class CLIPFeatureExtractor(FeatureExtractionMixin, ImageFeatureExtractionMixin): look odd.

       do_normalize (:obj:`bool`, `optional`, defaults to :obj:`True`):
            Whether or not to normalize the input with :obj:`image_mean` and :obj:`image_std`.
        image_mean (:obj:`List[int]`, defaults to :obj:`[0.485, 0.456, 0.406]`):
            The sequence of means for each channel, to be used when normalizing images.
        image_std (:obj:`List[int]`, defaults to :obj:`[0.229, 0.224, 0.225]`):
            The sequence of standard deviations for each channel, to be used when normalizing images.
...
       self.do_normalize = do_normalize
        self.image_mean = image_mean if image_mean is not None else [0.48145466, 0.4578275, 0.40821073]
        self.image_std = image_std if image_std is not None else [0.26862954, 0.26130258, 0.27577711]

But why doesn't your system generate these exceptions?

dbl001 · 2022-05-15T01:44:50Z

openai/CLIP#20

MaartenGr · 2022-05-16T06:39:38Z

But why doesn't your system generate these exceptions?

Indeed, this is quite strange as it is working perfectly fine for me in a Kaggle session with the following packages:

transformers==4.15.0
tokenizers==0.10.3
sentence-transformers==1.2.0
numpy==1.20.3

Hopefully, the issue you posted on the CLIP page gives a bit more insight.

dbl001 mentioned this issue May 15, 2022

ValueError: operands could not be broadcast together with shapes (4,224,224) (3,) openai/CLIP#244

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ValueError: operands could not be broadcast together with shapes (4,224,224) (3,) #12

ValueError: operands could not be broadcast together with shapes (4,224,224) (3,) #12

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ValueError: operands could not be broadcast together with shapes (4,224,224) (3,) #12

ValueError: operands could not be broadcast together with shapes (4,224,224) (3,) #12

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