Instance segmentation examples (#31084)

* Initial setup

* Metrics

* Overfit on two batches

* Train 40 epochs

* Memory leak debugging

* Trainer fine-tuning

* Draft

* Fixup

* Trained end-to-end

* Add requirements

* Rewrite evaluator

* nits

* Add readme

* Add instance-segmentation to the table

* Support void masks

* Remove sh

* Update docs

* Add pytorch test

* Add accelerate test

* Update examples/pytorch/instance-segmentation/README.md

* Update examples/pytorch/instance-segmentation/run_instance_segmentation.py

* Update examples/pytorch/instance-segmentation/run_instance_segmentation_no_trainer.py

* Update examples/pytorch/instance-segmentation/run_instance_segmentation_no_trainer.py

* Update examples/pytorch/instance-segmentation/run_instance_segmentation.py

* Fix consistency oneformer

* Fix imports

* Fix imports sort

* Apply suggestions from code review
Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com>

* Update examples/pytorch/instance-segmentation/run_instance_segmentation.py
Co-authored-by: Sangbum Daniel Choi <34004152+SangbumChoi@users.noreply.github.com>

* Add resources to docs

* Update examples/pytorch/instance-segmentation/README.md
Co-authored-by: amyeroberts <22614925+amyeroberts@users.noreply.github.com>

* Update examples/pytorch/instance-segmentation/README.md
Co-authored-by: amyeroberts <22614925+amyeroberts@users.noreply.github.com>

* Remove explicit model_type argument

* Fix tests

* Update readme

* Note about other models

---------
Co-authored-by: NielsRogge <48327001+NielsRogge@users.noreply.github.com>
Co-authored-by: Sangbum Daniel Choi <34004152+SangbumChoi@users.noreply.github.com>
Co-authored-by: amyeroberts <22614925+amyeroberts@users.noreply.github.com>

docs/source/en/model_doc/mask2former.md

@@ -41,6 +41,7 @@ This model was contributed by [Shivalika Singh](https://huggingface.co/shivi) an
 A list of official Hugging Face and community (indicated by 🌎) resources to help you get started with Mask2Former.
 
 - Demo notebooks regarding inference + fine-tuning Mask2Former on custom data can be found [here](https://github.com/NielsRogge/Transformers-Tutorials/tree/master/Mask2Former).
+- Scripts for finetuning [`Mask2Former`] with [`Trainer`] or [Accelerate](https://huggingface.co/docs/accelerate/index) can be found [here](https://github.com/huggingface/transformers/tree/main/examples/pytorch/instance-segmentation).
 
 If you're interested in submitting a resource to be included here, please feel free to open a Pull Request and we will review it.
 The resource should ideally demonstrate something new instead of duplicating an existing resource.

docs/source/en/model_doc/maskformer.md

@@ -51,6 +51,7 @@ This model was contributed by [francesco](https://huggingface.co/francesco). The
 <PipelineTag pipeline="image-segmentation"/>
 
 - All notebooks that illustrate inference as well as fine-tuning on custom data with MaskFormer can be found [here](https://github.com/NielsRogge/Transformers-Tutorials/tree/master/MaskFormer).
+- Scripts for finetuning [`MaskFormer`] with [`Trainer`] or [Accelerate](https://huggingface.co/docs/accelerate/index) can be found [here](https://github.com/huggingface/transformers/tree/main/examples/pytorch/instance-segmentation).
 
 ## MaskFormer specific outputs
 

examples/pytorch/README.md

@@ -47,6 +47,7 @@ Coming soon!
 | [**`image-classification`**](https://github.com/huggingface/transformers/tree/main/examples/pytorch/image-classification) | [CIFAR-10](https://huggingface.co/datasets/cifar10) | ✅ | ✅ |✅ | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/image_classification.ipynb)
 | [**`semantic-segmentation`**](https://github.com/huggingface/transformers/tree/main/examples/pytorch/semantic-segmentation) | [SCENE_PARSE_150](https://huggingface.co/datasets/scene_parse_150) | ✅ | ✅ |✅ | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/examples/semantic_segmentation.ipynb)
 | [**`object-detection`**](https://github.com/huggingface/transformers/tree/main/examples/pytorch/object-detection) | [CPPE-5](https://huggingface.co/datasets/cppe-5) | ✅ | ✅ |✅ | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/huggingface/notebooks/blob/main/transformers_doc/en/pytorch/object_detection.ipynb)
+| [**`instance-segmentation`**](https://github.com/huggingface/transformers/tree/main/examples/pytorch/instance-segmentation) | [ADE20K sample](https://huggingface.co/datasets/qubvel-hf/ade20k-mini) | ✅ | ✅ |✅ |
 
 
 ## Running quick tests

examples/pytorch/instance-segmentation/README.md

+<!---
+Copyright 2024 The HuggingFace Team. All rights reserved.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+
+# Instance Segmentation Examples
+
+This directory contains two scripts that demonstrate how to fine-tune [MaskFormer](https://huggingface.co/docs/transformers/model_doc/maskformer) and [Mask2Former](https://huggingface.co/docs/transformers/model_doc/mask2former) for instance segmentation using PyTorch.
+For other instance segmentation models, such as [DETR](https://huggingface.co/docs/transformers/model_doc/detr) and [Conditional DETR](https://huggingface.co/docs/transformers/model_doc/conditional_detr), the scripts need to be adjusted to properly handle input and output data.
+
+Content:
+- [PyTorch Version with Trainer](#pytorch-version-with-trainer)
+- [PyTorch Version with Accelerate](#pytorch-version-with-accelerate)
+- [Reload and Perform Inference](#reload-and-perform-inference)
+- [Note on Custom Data](#note-on-custom-data)
+
+## PyTorch Version with Trainer
+
+This example is based on the script [`run_instance_segmentation.py`](https://github.com/huggingface/transformers/blob/main/examples/pytorch/instance-segmentation/run_instance_segmentation.py).
+
+The script uses the [🤗 Trainer API](https://huggingface.co/docs/transformers/main_classes/trainer) to manage training automatically, including distributed environments.
+
+Here, we show how to fine-tune a [Mask2Former](https://huggingface.co/docs/transformers/model_doc/mask2former) model on a subsample of the [ADE20K](https://huggingface.co/datasets/zhoubolei/scene_parse_150) dataset. We created a [small dataset](https://huggingface.co/datasets/qubvel-hf/ade20k-mini) with approximately 2,000 images containing only "person" and "car" annotations; all other pixels are marked as "background."
+
+Here is the `label2id` mapping for this dataset:
+
+```python
+label2id = {
+    "background": 0,
+    "person": 1,
+    "car": 2,
+}
+```
+
+Since the `background` label is not an instance and we don't want to predict it, we will use `do_reduce_labels` to remove it from the data.
+
+Run the training with the following command:
+
+```bash
+python run_instance_segmentation.py \
+    --model_name_or_path facebook/mask2former-swin-tiny-coco-instance \
+    --output_dir finetune-instance-segmentation-ade20k-mini-mask2former \
+    --dataset_name qubvel-hf/ade20k-mini \
+    --do_reduce_labels \
+    --image_height 256 \
+    --image_width 256 \
+    --do_train \
+    --fp16 \
+    --num_train_epochs 40 \
+    --learning_rate 1e-5 \
+    --lr_scheduler_type constant \
+    --per_device_train_batch_size 8 \
+    --gradient_accumulation_steps 2 \
+    --dataloader_num_workers 8 \
+    --dataloader_persistent_workers \
+    --dataloader_prefetch_factor 4 \
+    --do_eval \
+    --evaluation_strategy epoch \
+    --logging_strategy epoch \
+    --save_strategy epoch \
+    --save_total_limit 2 \
+    --push_to_hub
+```
+
+The resulting model can be viewed [here](https://huggingface.co/qubvel-hf/finetune-instance-segmentation-ade20k-mini-mask2former). Always refer to the original paper for details on training hyperparameters. To improve model quality, consider:
+- Changing image size parameters (`--image_height`/`--image_width`)
+- Adjusting training parameters such as learning rate, batch size, warmup, optimizer, and more (see [TrainingArguments](https://huggingface.co/docs/transformers/main_classes/trainer#transformers.TrainingArguments))
+- Adding more image augmentations (we created a helpful [HF Space](https://huggingface.co/spaces/qubvel-hf/albumentations-demo) to choose some)
+
+You can also replace the model [checkpoint](https://huggingface.co/models?search=maskformer).
+
+## PyTorch Version with Accelerate
+
+This example is based on the script [`run_instance_segmentation_no_trainer.py`](https://github.com/huggingface/transformers/blob/main/examples/pytorch/instance-segmentation/run_instance_segmentation_no_trainer.py).
+
+The script uses [🤗 Accelerate](https://github.com/huggingface/accelerate) to write your own training loop in PyTorch and run it on various environments, including CPU, multi-CPU, GPU, multi-GPU, and TPU, with support for mixed precision.
+
+First, configure the environment:
+
+```bash
+accelerate config
+```
+
+Answer the questions regarding your training environment. Then, run:
+
+```bash
+accelerate test
+```
+
+This command ensures everything is ready for training. Finally, launch training with:
+
+```bash
+accelerate launch run_instance_segmentation_no_trainer.py \
+    --model_name_or_path facebook/mask2former-swin-tiny-coco-instance \
+    --output_dir finetune-instance-segmentation-ade20k-mini-mask2former-no-trainer \
+    --dataset_name qubvel-hf/ade20k-mini \
+    --do_reduce_labels \
+    --image_height 256 \
+    --image_width 256 \
+    --num_train_epochs 40 \
+    --learning_rate 1e-5 \
+    --lr_scheduler_type constant \
+    --per_device_train_batch_size 8 \
+    --gradient_accumulation_steps 2 \
+    --dataloader_num_workers 8 \
+    --push_to_hub
+```
+
+With this setup, you can train on multiple GPUs, log everything to trackers (like Weights and Biases, Tensorboard), and regularly push your model to the hub (with the repo name set to `args.output_dir` under your HF username).
+With the default settings, the script fine-tunes a [Mask2Former](https://huggingface.co/docs/transformers/model_doc/mask2former) model on the sample of [ADE20K](https://huggingface.co/datasets/qubvel-hf/ade20k-mini) dataset. The resulting model can be viewed [here](https://huggingface.co/qubvel-hf/finetune-instance-segmentation-ade20k-mini-mask2former-no-trainer).
+
+## Reload and Perform Inference
+
+After training, you can easily load your trained model and perform inference as follows:
+
+```python
+import torch
+import requests
+import matplotlib.pyplot as plt
+
+from PIL import Image
+from transformers import Mask2FormerForUniversalSegmentation, Mask2FormerImageProcessor
+
+# Load image
+image = Image.open(requests.get("http://farm4.staticflickr.com/3017/3071497290_31f0393363_z.jpg", stream=True).raw)
+
+# Load model and image processor
+device = "cuda"
+checkpoint = "qubvel-hf/finetune-instance-segmentation-ade20k-mini-mask2former"
+
+model = Mask2FormerForUniversalSegmentation.from_pretrained(checkpoint, device_map=device)
+image_processor = Mask2FormerImageProcessor.from_pretrained(checkpoint)
+
+# Run inference on image
+inputs = image_processor(images=[image], return_tensors="pt").to(device)
+with torch.no_grad():
+    outputs = model(**inputs)
+
+# Post-process outputs
+outputs = image_processor.post_process_instance_segmentation(outputs, target_sizes=[image.size[::-1]])
+
+print("Mask shape: ", outputs[0]["segmentation"].shape)
+print("Mask values: ", outputs[0]["segmentation"].unique())
+for segment in outputs[0]["segments_info"]:
+    print("Segment: ", segment)
+```
+
+```
+Mask shape:  torch.Size([427, 640])
+Mask values:  tensor([-1.,  0.,  1.,  2.,  3.,  4.,  5.,  6.])
+Segment:  {'id': 0, 'label_id': 0, 'was_fused': False, 'score': 0.946127}
+Segment:  {'id': 1, 'label_id': 1, 'was_fused': False, 'score': 0.961582}
+Segment:  {'id': 2, 'label_id': 1, 'was_fused': False, 'score': 0.968367}
+Segment:  {'id': 3, 'label_id': 1, 'was_fused': False, 'score': 0.819527}
+Segment:  {'id': 4, 'label_id': 1, 'was_fused': False, 'score': 0.655761}
+Segment:  {'id': 5, 'label_id': 1, 'was_fused': False, 'score': 0.531299}
+Segment:  {'id': 6, 'label_id': 1, 'was_fused': False, 'score': 0.929477}
+```
+
+Use the following code to visualize the results:
+
+```python
+import numpy as np
+import matplotlib.pyplot as plt
+
+segmentation = outputs[0]["segmentation"].numpy()
+
+plt.figure(figsize=(10, 10))
+plt.subplot(1, 2, 1)
+plt.imshow(np.array(image))
+plt.axis("off")
+plt.subplot(1, 2, 2)
+plt.imshow(segmentation)
+plt.axis("off")
+plt.show()
+```
+
+![Result](https://i.imgur.com/rZmaRjD.png)
+
+## Note on Custom Data
+
+Here is a short script demonstrating how to create your own dataset for instance segmentation and push it to the hub:
+
+> Note: Annotations should be represented as 3-channel images (similar to the [scene_parsing_150](https://huggingface.co/datasets/zhoubolei/scene_parse_150#instance_segmentation-1) dataset). The first channel is a semantic-segmentation map with values corresponding to `label2id`, the second is an instance-segmentation map where each instance has a unique value, and the third channel should be empty (filled with zeros).
+
+```python
+from datasets import Dataset, DatasetDict
+from datasets import Image as DatasetImage
+
+label2id = {
+    "background": 0,
+    "person": 1,
+    "car": 2,
+}
+
+train_split = {
+    "image": [<PIL Image 1>, <PIL Image 2>, <PIL Image 3>, ...],
+    "annotation": [<PIL Image ann 1>, <PIL Image ann 2>, <PIL Image ann 3>, ...],
+}
+
+validation_split = {
+    "image": [<PIL Image 101>, <PIL Image 102>, <PIL Image 103>, ...],
+    "annotation": [<PIL Image ann 101>, <PIL Image ann 102>, <PIL Image ann 103>, ...],
+}
+
+def create_instance_segmentation_dataset(label2id, **splits):
+    dataset_dict = {}
+    for split_name, split in splits.items():
+        split["semantic_class_to_id"] = [label2id] * len(split["image"])
+        dataset_split = (
+            Dataset.from_dict(split)
+            .cast_column("image", DatasetImage())
+            .cast_column("annotation", DatasetImage())
+        )
+        dataset_dict[split_name] = dataset_split
+    return DatasetDict(dataset_dict)
+
+dataset = create_instance_segmentation_dataset(label2id, train=train_split, validation=validation_split)
+dataset.push_to_hub("qubvel-hf/ade20k-nano")
+```
+
+Use this dataset for fine-tuning by specifying its name with `--dataset_name <your_dataset_repo>`.
+
+See also: [Dataset Creation Guide](https://huggingface.co/docs/datasets/image_dataset#create-an-image-dataset)
\ No newline at end of file

examples/pytorch/instance-segmentation/requirements.txt

+albumentations >= 1.4.5
+timm
+datasets
+torchmetrics
+pycocotools

examples/pytorch/instance-segmentation/run_instance_segmentation.py

+#!/usr/bin/env python
+# coding=utf-8
+# Copyright 2024 The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+
+"""Finetuning 🤗 Transformers model for instance segmentation leveraging the Trainer API."""
+
+import logging
+import os
+import sys
+from dataclasses import dataclass, field
+from functools import partial
+from typing import Any, Dict, List, Mapping, Optional
+
+import albumentations as A
+import numpy as np
+import torch
+from datasets import load_dataset
+from torchmetrics.detection.mean_ap import MeanAveragePrecision
+
+import transformers
+from transformers import (
+    AutoImageProcessor,
+    AutoModelForUniversalSegmentation,
+    HfArgumentParser,
+    Trainer,
+    TrainingArguments,
+)
+from transformers.image_processing_utils import BatchFeature
+from transformers.trainer import EvalPrediction
+from transformers.trainer_utils import get_last_checkpoint
+from transformers.utils import check_min_version, send_example_telemetry
+from transformers.utils.versions import require_version
+
+
+logger = logging.getLogger(__name__)
+
+# Will error if the minimal version of Transformers is not installed. Remove at your own risks.
+check_min_version("4.42.0.dev0")
+require_version("datasets>=2.0.0", "To fix: pip install -r examples/pytorch/instance-segmentation/requirements.txt")
+
+
+@dataclass
+class Arguments:
+    """
+    Arguments pertaining to what data we are going to input our model for training and eval.
+    Using `HfArgumentParser` we can turn this class into argparse arguments to be able to specify
+    them on the command line.
+    """
+
+    model_name_or_path: str = field(
+        default="facebook/mask2former-swin-tiny-coco-instance",
+        metadata={"help": "Path to pretrained model or model identifier from huggingface.co/models"},
+    )
+    dataset_name: str = field(
+        default="qubvel-hf/ade20k-mini",
+        metadata={
+            "help": "Name of a dataset from the hub (could be your own, possibly private dataset hosted on the hub)."
+        },
+    )
+    image_height: Optional[int] = field(default=512, metadata={"help": "Image height after resizing."})
+    image_width: Optional[int] = field(default=512, metadata={"help": "Image width after resizing."})
+    token: str = field(
+        default=None,
+        metadata={
+            "help": (
+                "The token to use as HTTP bearer authorization for remote files. If not specified, will use the token "
+                "generated when running `huggingface-cli login` (stored in `~/.huggingface`)."
+            )
+        },
+    )
+    do_reduce_labels: bool = field(
+        default=False,
+        metadata={
+            "help": (
+                "If background class is labeled as 0 and you want to remove it from the labels, set this flag to True."
+            )
+        },
+    )
+
+
+def augment_and_transform_batch(
+    examples: Mapping[str, Any], transform: A.Compose, image_processor: AutoImageProcessor
+) -> BatchFeature:
+    batch = {
+        "pixel_values": [],
+        "mask_labels": [],
+        "class_labels": [],
+    }
+
+    for pil_image, pil_annotation in zip(examples["image"], examples["annotation"]):
+        image = np.array(pil_image)
+        semantic_and_instance_masks = np.array(pil_annotation)[..., :2]
+
+        # Apply augmentations
+        output = transform(image=image, mask=semantic_and_instance_masks)
+
+        aug_image = output["image"]
+        aug_semantic_and_instance_masks = output["mask"]
+        aug_instance_mask = aug_semantic_and_instance_masks[..., 1]
+
+        # Create mapping from instance id to semantic id
+        unique_semantic_id_instance_id_pairs = np.unique(aug_semantic_and_instance_masks.reshape(-1, 2), axis=0)
+        instance_id_to_semantic_id = {
+            instance_id: semantic_id for semantic_id, instance_id in unique_semantic_id_instance_id_pairs
+        }
+
+        # Apply the image processor transformations: resizing, rescaling, normalization
+        model_inputs = image_processor(
+            images=[aug_image],
+            segmentation_maps=[aug_instance_mask],
+            instance_id_to_semantic_id=instance_id_to_semantic_id,
+            return_tensors="pt",
+        )
+
+        batch["pixel_values"].append(model_inputs.pixel_values[0])
+        batch["mask_labels"].append(model_inputs.mask_labels[0])
+        batch["class_labels"].append(model_inputs.class_labels[0])
+
+    return batch
+
+
+def collate_fn(examples):
+    batch = {}
+    batch["pixel_values"] = torch.stack([example["pixel_values"] for example in examples])
+    batch["class_labels"] = [example["class_labels"] for example in examples]
+    batch["mask_labels"] = [example["mask_labels"] for example in examples]
+    if "pixel_mask" in examples[0]:
+        batch["pixel_mask"] = torch.stack([example["pixel_mask"] for example in examples])
+    return batch
+
+
+@dataclass
+class ModelOutput:
+    class_queries_logits: torch.Tensor
+    masks_queries_logits: torch.Tensor
+
+
+def nested_cpu(tensors):
+    if isinstance(tensors, (list, tuple)):
+        return type(tensors)(nested_cpu(t) for t in tensors)
+    elif isinstance(tensors, Mapping):
+        return type(tensors)({k: nested_cpu(t) for k, t in tensors.items()})
+    elif isinstance(tensors, torch.Tensor):
+        return tensors.cpu().detach()
+    else:
+        return tensors
+
+
+class Evaluator:
+    """
+    Compute metrics for the instance segmentation task.
+    """
+
+    def __init__(
+        self,
+        image_processor: AutoImageProcessor,
+        id2label: Mapping[int, str],
+        threshold: float = 0.0,
+    ):
+        """
+        Initialize evaluator with image processor, id2label mapping and threshold for filtering predictions.
+
+        Args:
+            image_processor (AutoImageProcessor): Image processor for
+                `post_process_instance_segmentation` method.
+            id2label (Mapping[int, str]): Mapping from class id to class name.
+            threshold (float): Threshold to filter predicted boxes by confidence. Defaults to 0.0.
+        """
+        self.image_processor = image_processor
+        self.id2label = id2label
+        self.threshold = threshold
+        self.metric = self.get_metric()
+
+    def get_metric(self):
+        metric = MeanAveragePrecision(iou_type="segm", class_metrics=True)
+        return metric
+
+    def reset_metric(self):
+        self.metric.reset()
+
+    def postprocess_target_batch(self, target_batch) -> List[Dict[str, torch.Tensor]]:
+        """Collect targets in a form of list of dictionaries with keys "masks", "labels"."""
+        batch_masks = target_batch[0]
+        batch_labels = target_batch[1]
+        post_processed_targets = []
+        for masks, labels in zip(batch_masks, batch_labels):
+            post_processed_targets.append(
+                {
+                    "masks": masks.to(dtype=torch.bool),
+                    "labels": labels,
+                }
+            )
+        return post_processed_targets
+
+    def get_target_sizes(self, post_processed_targets) -> List[List[int]]:
+        target_sizes = []
+        for target in post_processed_targets:
+            target_sizes.append(target["masks"].shape[-2:])
+        return target_sizes
+
+    def postprocess_prediction_batch(self, prediction_batch, target_sizes) -> List[Dict[str, torch.Tensor]]:
+        """Collect predictions in a form of list of dictionaries with keys "masks", "labels", "scores"."""
+
+        model_output = ModelOutput(class_queries_logits=prediction_batch[0], masks_queries_logits=prediction_batch[1])
+        post_processed_output = self.image_processor.post_process_instance_segmentation(
+            model_output,
+            threshold=self.threshold,
+            target_sizes=target_sizes,
+            return_binary_maps=True,
+        )
+
+        post_processed_predictions = []
+        for image_predictions, target_size in zip(post_processed_output, target_sizes):
+            if image_predictions["segments_info"]:
+                post_processed_image_prediction = {
+                    "masks": image_predictions["segmentation"].to(dtype=torch.bool),
+                    "labels": torch.tensor([x["label_id"] for x in image_predictions["segments_info"]]),
+                    "scores": torch.tensor([x["score"] for x in image_predictions["segments_info"]]),
+                }
+            else:
+                # for void predictions, we need to provide empty tensors
+                post_processed_image_prediction = {
+                    "masks": torch.zeros([0, *target_size], dtype=torch.bool),
+                    "labels": torch.tensor([]),
+                    "scores": torch.tensor([]),
+                }
+            post_processed_predictions.append(post_processed_image_prediction)
+
+        return post_processed_predictions
+
+    @torch.no_grad()
+    def __call__(self, evaluation_results: EvalPrediction, compute_result: bool = False) -> Mapping[str, float]:
+        """
+        Update metrics with current evaluation results and return metrics if `compute_result` is True.
+
+        Args:
+            evaluation_results (EvalPrediction): Predictions and targets from evaluation.
+            compute_result (bool): Whether to compute and return metrics.
+
+        Returns:
+            Mapping[str, float]: Metrics in a form of dictionary {<metric_name>: <metric_value>}
+        """
+        prediction_batch = nested_cpu(evaluation_results.predictions)
+        target_batch = nested_cpu(evaluation_results.label_ids)
+
+        # For metric computation we need to provide:
+        #  - targets in a form of list of dictionaries with keys "masks", "labels"
+        #  - predictions in a form of list of dictionaries with keys "masks", "labels", "scores"
+        post_processed_targets = self.postprocess_target_batch(target_batch)
+        target_sizes = self.get_target_sizes(post_processed_targets)
+        post_processed_predictions = self.postprocess_prediction_batch(prediction_batch, target_sizes)
+
+        # Compute metrics
+        self.metric.update(post_processed_predictions, post_processed_targets)
+
+        if not compute_result:
+            return
+
+        metrics = self.metric.compute()
+
+        # Replace list of per class metrics with separate metric for each class
+        classes = metrics.pop("classes")
+        map_per_class = metrics.pop("map_per_class")
+        mar_100_per_class = metrics.pop("mar_100_per_class")
+        for class_id, class_map, class_mar in zip(classes, map_per_class, mar_100_per_class):
+            class_name = self.id2label[class_id.item()] if self.id2label is not None else class_id.item()
+            metrics[f"map_{class_name}"] = class_map
+            metrics[f"mar_100_{class_name}"] = class_mar
+
+        metrics = {k: round(v.item(), 4) for k, v in metrics.items()}
+
+        # Reset metric for next evaluation
+        self.reset_metric()
+
+        return metrics
+
+
+def setup_logging(training_args: TrainingArguments) -> None:
+    """Setup logging according to `training_args`."""
+
+    logging.basicConfig(
+        format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
+        datefmt="%m/%d/%Y %H:%M:%S",
+        handlers=[logging.StreamHandler(sys.stdout)],
+    )
+
+    if training_args.should_log:
+        # The default of training_args.log_level is passive, so we set log level at info here to have that default.
+        transformers.utils.logging.set_verbosity_info()
+
+    log_level = training_args.get_process_log_level()
+    logger.setLevel(log_level)
+    transformers.utils.logging.set_verbosity(log_level)
+    transformers.utils.logging.enable_default_handler()
+    transformers.utils.logging.enable_explicit_format()
+
+
+def find_last_checkpoint(training_args: TrainingArguments) -> Optional[str]:
+    """Find the last checkpoint in the output directory according to parameters specified in `training_args`."""
+
+    checkpoint = None
+    if training_args.resume_from_checkpoint is not None:
+        checkpoint = training_args.resume_from_checkpoint
+    elif os.path.isdir(training_args.output_dir) and not training_args.overwrite_output_dir:
+        checkpoint = get_last_checkpoint(training_args.output_dir)
+        if checkpoint is None and len(os.listdir(training_args.output_dir)) > 0:
+            raise ValueError(
+                f"Output directory ({training_args.output_dir}) already exists and is not empty. "
+                "Use --overwrite_output_dir to overcome."
+            )
+        elif checkpoint is not None and training_args.resume_from_checkpoint is None:
+            logger.info(
+                f"Checkpoint detected, resuming training at {checkpoint}. To avoid this behavior, change "
+                "the `--output_dir` or add `--overwrite_output_dir` to train from scratch."
+            )
+
+    return checkpoint
+
+
+def main():
+    # See all possible arguments in https://huggingface.co/docs/transformers/main_classes/trainer#transformers.TrainingArguments
+    # or by passing the --help flag to this script.
+
+    parser = HfArgumentParser([Arguments, TrainingArguments])
+    if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
+        # If we pass only one argument to the script and it's the path to a json file,
+        # let's parse it to get our arguments.
+        args, training_args = parser.parse_json_file(json_file=os.path.abspath(sys.argv[1]))
+    else:
+        args, training_args = parser.parse_args_into_dataclasses()
+
+    # Set default training arguments for instance segmentation
+    training_args.eval_do_concat_batches = False
+    training_args.batch_eval_metrics = True
+    training_args.remove_unused_columns = False
+
+    # # Sending telemetry. Tracking the example usage helps us better allocate resources to maintain them. The
+    # # information sent is the one passed as arguments along with your Python/PyTorch versions.
+    send_example_telemetry("run_instance_segmentation", args)
+
+    # Setup logging and log on each process the small summary:
+    setup_logging(training_args)
+    logger.warning(
+        f"Process rank: {training_args.local_rank}, device: {training_args.device}, n_gpu: {training_args.n_gpu}, "
+        + f"distributed training: {training_args.parallel_mode.value == 'distributed'}, 16-bits training: {training_args.fp16}"
+    )
+    logger.info(f"Training/evaluation parameters {training_args}")
+
+    # Load last checkpoint from output_dir if it exists (and we are not overwriting it)
+    checkpoint = find_last_checkpoint(training_args)
+
+    # ------------------------------------------------------------------------------------------------
+    # Load dataset, prepare splits
+    # ------------------------------------------------------------------------------------------------
+
+    dataset = load_dataset(args.dataset_name)
+
+    # We need to specify the label2id mapping for the model
+    # it is a mapping from semantic class name to class index.
+    # In case your dataset does not provide it, you can create it manually:
+    # label2id = {"background": 0, "cat": 1, "dog": 2}
+    label2id = dataset["train"][0]["semantic_class_to_id"]
+
+    if args.do_reduce_labels:
+        label2id = {name: idx for name, idx in label2id.items() if idx != 0}  # remove background class
+        label2id = {name: idx - 1 for name, idx in label2id.items()}  # shift class indices by -1
+
+    id2label = {v: k for k, v in label2id.items()}
+
+    # ------------------------------------------------------------------------------------------------
+    # Load pretrained config, model and image processor
+    # ------------------------------------------------------------------------------------------------
+    model = AutoModelForUniversalSegmentation.from_pretrained(
+        args.model_name_or_path,
+        label2id=label2id,
+        id2label=id2label,
+        ignore_mismatched_sizes=True,
+        token=args.token,
+    )
+
+    image_processor = AutoImageProcessor.from_pretrained(
+        args.model_name_or_path,
+        do_resize=True,
+        size={"height": args.image_height, "width": args.image_width},
+        do_reduce_labels=args.do_reduce_labels,
+        reduce_labels=args.do_reduce_labels,  # TODO: remove when mask2former support `do_reduce_labels`
+        token=args.token,
+    )
+
+    # ------------------------------------------------------------------------------------------------
+    # Define image augmentations and dataset transforms
+    # ------------------------------------------------------------------------------------------------
+    train_augment_and_transform = A.Compose(
+        [
+            A.HorizontalFlip(p=0.5),
+            A.RandomBrightnessContrast(p=0.5),
+            A.HueSaturationValue(p=0.1),
+        ],
+    )
+    validation_transform = A.Compose(
+        [A.NoOp()],
+    )
+
+    # Make transform functions for batch and apply for dataset splits
+    train_transform_batch = partial(
+        augment_and_transform_batch, transform=train_augment_and_transform, image_processor=image_processor
+    )
+    validation_transform_batch = partial(
+        augment_and_transform_batch, transform=validation_transform, image_processor=image_processor
+    )
+
+    dataset["train"] = dataset["train"].with_transform(train_transform_batch)
+    dataset["validation"] = dataset["validation"].with_transform(validation_transform_batch)
+
+    # ------------------------------------------------------------------------------------------------
+    # Model training and evaluation with Trainer API
+    # ------------------------------------------------------------------------------------------------
+
+    compute_metrics = Evaluator(image_processor=image_processor, id2label=id2label, threshold=0.0)
+
+    trainer = Trainer(
+        model=model,
+        args=training_args,
+        train_dataset=dataset["train"] if training_args.do_train else None,
+        eval_dataset=dataset["validation"] if training_args.do_eval else None,
+        tokenizer=image_processor,
+        data_collator=collate_fn,
+        compute_metrics=compute_metrics,
+    )
+
+    # Training
+    if training_args.do_train:
+        train_result = trainer.train(resume_from_checkpoint=checkpoint)
+        trainer.save_model()
+        trainer.log_metrics("train", train_result.metrics)
+        trainer.save_metrics("train", train_result.metrics)
+        trainer.save_state()
+
+    # Final evaluation
+    if training_args.do_eval:
+        metrics = trainer.evaluate(eval_dataset=dataset["validation"], metric_key_prefix="test")
+        trainer.log_metrics("test", metrics)
+        trainer.save_metrics("test", metrics)
+
+    # Write model card and (optionally) push to hub
+    kwargs = {
+        "finetuned_from": args.model_name_or_path,
+        "dataset": args.dataset_name,
+        "tags": ["image-segmentation", "instance-segmentation", "vision"],
+    }
+    if training_args.push_to_hub:
+        trainer.push_to_hub(**kwargs)
+    else:
+        trainer.create_model_card(**kwargs)
+
+
+if __name__ == "__main__":
+    main()

examples/pytorch/test_accelerate_examples.py

@@ -355,3 +355,28 @@ class ExamplesTestsNoTrainer(TestCasePlus):
         run_command(self._launch_args + testargs)
         result = get_results(tmp_dir)
         self.assertGreaterEqual(result["test_map"], 0.10)
+
+    @slow
+    @mock.patch.dict(os.environ, {"WANDB_MODE": "offline", "DVCLIVE_TEST": "true"})
+    def test_run_instance_segmentation_no_trainer(self):
+        stream_handler = logging.StreamHandler(sys.stdout)
+        logger.addHandler(stream_handler)
+
+        tmp_dir = self.get_auto_remove_tmp_dir()
+        testargs = f"""
+            {self.examples_dir}/pytorch/instance-segmentation/run_instance_segmentation_no_trainer.py
+            --model_name_or_path qubvel-hf/finetune-instance-segmentation-ade20k-mini-mask2former
+            --output_dir {tmp_dir}
+            --dataset_name qubvel-hf/ade20k-nano
+            --do_reduce_labels
+            --image_height 256
+            --image_width 256
+            --num_train_epochs 1
+            --per_device_train_batch_size 2
+            --per_device_eval_batch_size 1
+            --seed 1234
+        """.split()
+
+        run_command(self._launch_args + testargs)
+        result = get_results(tmp_dir)
+        self.assertGreaterEqual(result["test_map"], 0.1)

examples/pytorch/test_pytorch_examples.py

@@ -49,6 +49,7 @@ SRC_DIRS = [
         "image-pretraining",
         "semantic-segmentation",
         "object-detection",
+        "instance-segmentation",
     ]
 ]
 sys.path.extend(SRC_DIRS)
@@ -60,6 +61,7 @@ if SRC_DIRS is not None:
     import run_generation
     import run_glue
     import run_image_classification
+    import run_instance_segmentation
     import run_mae
     import run_mlm
     import run_ner
@@ -639,3 +641,33 @@ class ExamplesTests(TestCasePlus):
             run_object_detection.main()
             result = get_results(tmp_dir)
             self.assertGreaterEqual(result["test_map"], 0.1)
+
+    @patch.dict(os.environ, {"WANDB_DISABLED": "true"})
+    def test_run_instance_segmentation(self):
+        tmp_dir = self.get_auto_remove_tmp_dir()
+        testargs = f"""
+            run_instance_segmentation.py
+            --model_name_or_path qubvel-hf/finetune-instance-segmentation-ade20k-mini-mask2former
+            --output_dir {tmp_dir}
+            --dataset_name qubvel-hf/ade20k-nano
+            --do_reduce_labels
+            --image_height 256
+            --image_width 256
+            --do_train
+            --num_train_epochs 1
+            --learning_rate 1e-5
+            --lr_scheduler_type constant
+            --per_device_train_batch_size 2
+            --per_device_eval_batch_size 1
+            --do_eval
+            --evaluation_strategy epoch
+            --seed 32
+        """.split()
+
+        if is_torch_fp16_available_on_device(torch_device):
+            testargs.append("--fp16")
+
+        with patch.object(sys, "argv", testargs):
+            run_instance_segmentation.main()
+            result = get_results(tmp_dir)
+            self.assertGreaterEqual(result["test_map"], 0.1)

src/transformers/models/mask2former/image_processing_mask2former.py

@@ -283,7 +283,12 @@ def convert_segmentation_map_to_binary_masks(
 
     # Generate a binary mask for each object instance
     binary_masks = [(segmentation_map == i) for i in all_labels]
-    binary_masks = np.stack(binary_masks, axis=0)  # (num_labels, height, width)
+
+    # Stack the binary masks
+    if binary_masks:
+        binary_masks = np.stack(binary_masks, axis=0)
+    else:
+        binary_masks = np.zeros((0, *segmentation_map.shape))
 
     # Convert instance ids to class ids
     if instance_id_to_semantic_id is not None:
@@ -969,11 +974,15 @@ class Mask2FormerImageProcessor(BaseImageProcessor):
                 )
                 # We add an axis to make them compatible with the transformations library
                 # this will be removed in the future
-                masks = [mask[None, ...] for mask in masks]
-                masks = [
-                    self._pad_image(image=mask, output_size=pad_size, constant_values=ignore_index) for mask in masks
-                ]
-                masks = np.concatenate(masks, axis=0)
+                if masks.shape[0] > 0:
+                    masks = [mask[None, ...] for mask in masks]
+                    masks = [
+                        self._pad_image(image=mask, output_size=pad_size, constant_values=ignore_index)
+                        for mask in masks
+                    ]
+                    masks = np.concatenate(masks, axis=0)
+                else:
+                    masks = np.zeros((0, *pad_size), dtype=np.float32)
                 mask_labels.append(torch.from_numpy(masks))
                 class_labels.append(torch.from_numpy(classes))
 

src/transformers/models/maskformer/image_processing_maskformer.py

@@ -286,7 +286,12 @@ def convert_segmentation_map_to_binary_masks(
 
     # Generate a binary mask for each object instance
     binary_masks = [(segmentation_map == i) for i in all_labels]
-    binary_masks = np.stack(binary_masks, axis=0)  # (num_labels, height, width)
+
+    # Stack the binary masks
+    if binary_masks:
+        binary_masks = np.stack(binary_masks, axis=0)
+    else:
+        binary_masks = np.zeros((0, *segmentation_map.shape))
 
     # Convert instance ids to class ids
     if instance_id_to_semantic_id is not None:
@@ -982,17 +987,20 @@ class MaskFormerImageProcessor(BaseImageProcessor):
                 )
                 # We add an axis to make them compatible with the transformations library
                 # this will be removed in the future
-                masks = [mask[None, ...] for mask in masks]
-                masks = [
-                    self._pad_image(
-                        image=mask,
-                        output_size=pad_size,
-                        constant_values=ignore_index,
-                        input_data_format=ChannelDimension.FIRST,
-                    )
-                    for mask in masks
-                ]
-                masks = np.concatenate(masks, axis=0)
+                if masks.shape[0] > 0:
+                    masks = [mask[None, ...] for mask in masks]
+                    masks = [
+                        self._pad_image(
+                            image=mask,
+                            output_size=pad_size,
+                            constant_values=ignore_index,
+                            input_data_format=ChannelDimension.FIRST,
+                        )
+                        for mask in masks
+                    ]
+                    masks = np.concatenate(masks, axis=0)
+                else:
+                    masks = np.zeros((0, *pad_size), dtype=np.float32)
                 mask_labels.append(torch.from_numpy(masks))
                 class_labels.append(torch.from_numpy(classes))
 

src/transformers/models/oneformer/image_processing_oneformer.py

@@ -285,7 +285,12 @@ def convert_segmentation_map_to_binary_masks(
 
     # Generate a binary mask for each object instance
     binary_masks = [(segmentation_map == i) for i in all_labels]
-    binary_masks = np.stack(binary_masks, axis=0)  # (num_labels, height, width)
+
+    # Stack the binary masks
+    if binary_masks:
+        binary_masks = np.stack(binary_masks, axis=0)
+    else:
+        binary_masks = np.zeros((0, *segmentation_map.shape))
 
     # Convert instance ids to class ids
     if instance_id_to_semantic_id is not None: