Does this repo's implementation of maskrcnn work with negative samples?

[rbavery]

❓ Questions and Help

I'm working with satellite imagery where some image tiles have over 100 objects to segment and some images have none (these are negative samples). The negative samples still provide information on what is not a segmentation (in my case, types of agriculture land cover). This issue on another facebookresearch repo seems to indicate that negative samples can be very useful but that they are not always supported out of the box: facebookresearch/maskrcnn-benchmark#169

Does this repo support negative samples? Does it depend on the maskrcnn model I pretrain from in the model zoo?

[ppwwyyxx]

We allow input images to have no objects, if that's what you mean.

However, the default data loader filter such images at

detectron2/detectron2/data/build.py

Lines 319 to 326 in cea5934

	dataset_dicts = get_detection_dataset_dicts(
	cfg.DATASETS.TRAIN,
	filter_empty=True,
	min_keypoints=cfg.MODEL.ROI_KEYPOINT_HEAD.MIN_KEYPOINTS_PER_IMAGE
	if cfg.MODEL.KEYPOINT_ON
	else 0,
	proposal_files=cfg.DATASETS.PROPOSAL_FILES_TRAIN if cfg.MODEL.LOAD_PROPOSALS else None,
	)

If you need to keep them, you need to write a custom data loader

[rbavery]

So if I wrote a data loader that accomplishes the same thing as setting filter_empty=False, would there be any other issues with training with negative samples? Or is this unknown? Thanks for the advice!

[rbavery]

I guess I'm wondering what the rationale is to filter out empty annotations by default, is this because some segmentation models like MaskRCNN can't make use of negative samples?

[ppwwyyxx]

would there be any other issues with training with negative samples

There shouldn't be. But we don't normally do this, so there might be things we are not aware of. If you found any issues please report to us.

what the rationale is to filter out empty annotations by default,

Mainly because that's the tradition I think.

[rbgirshick]

IIRC, the filtering was first added in detectron (v1) when we implemented keypoint prediction in Mask R-CNN. In that case only images that contain people annotated with keypoints are useful for training and this leaves a large number of images without positive examples. We found that training was faster and keypoint AP was no worse if the images without positives were filtered out. Since it had little impact on the usual COCO training data, filtering of these images was left on as the default. Detectron2 has inherited this choice, but in retrospect the design decision is a bit overfit to considerations of the COCO dataset.

@ppwwyyxx -- perhaps we should consider making this filtering configurable?

[rbavery]

Thanks both of you for the explanations. IMO then, the option should probably be configurable by default, since it's a bit of an unexpected and hidden behavior for folks looking to use Detectron2 on their own custom datasets. I'm happy to make a PR to make empty filtering a cfg attribute if the maintainers agree this would be valuable. I can also test this out on my own datasets to see if their are any errors that pop up and if including negative/empty samples improves segmentation accuracy.

[rbgirshick]

@rbavery -- sounds good, a PR is welcome!

[ppwwyyxx]

added in 62522b6.
Now, set cfg.DATALOADER.FILTER_EMPTY_ANNOTATIONS=False to include negative samples

[edwardchaos]

would there be any other issues with training with negative samples

There shouldn't be. But we don't normally do this, so there might be things we are not aware of. If you found any issues please report to us.

what the rationale is to filter out empty annotations by default,

Mainly because that's the tradition I think.

Hi, I'm using a custom dataset with torch DataLoader.
The model I'm using is ./model_final_a3ec72.pkl
Introducing negative samples fails in fast_rcnn.py(173):

File "/home/edwardchaos/detectron2_repo/detectron2/modeling/roi_heads/fast_rcnn.py", line 173, in _log_accuracy
pred_classes = self.pred_class_logits.argmax(dim=1)
RuntimeError: cannot perform reduction function argmax on a tensor with no elements because the operation does not have an identity

If I add a check to skip empty prediction in _log_accuracy function of fast_rcnn.py:

num_instances = self.gt_classes.numel()
if self.pred_class_logits.nelement() == 0:
return
pred_classes = self.pred_class_logits.argmax(dim=1)
bg_class_ind = self.pred_class_logits.shape[1] - 1

It then fails at:
File "/home/edwardchaos/anaconda3/envs/detectron2/lib/python3.7/site-packages/torch/nn/functional.py", line 1838, in nll_loss
ret = torch._C._nn.nll_loss(input, target, weight, _Reduction.get_enum(reduction), ignore_index)
RuntimeError: invalid argument 2: non-empty vector or matrix expected at /opt/conda/conda-bld/pytorch_1570711283072/work/aten/src/THCUNN/generic/ClassNLLCriterion.cu:31

[ppwwyyxx]

negative samples should not make self.pred_class_logits empty. Please provide exact steps to let others reproduce the issue if you think it is a detectron2 issue.

[edwardchaos]

I found this comment in fast_rcnn.py:

proposals (list[Instances]): A list of N Instances, where Instances i stores the
proposals for image i, in the field "proposal_boxes".
When training, each Instances must have ground-truth labels
stored in the field "gt_classes" and "gt_boxes".

Maybe mask rcnn accepts negative samples, i'll just use sample with gt labels for my purposes.

[MLaurenceFournier]

I'm working on project based on Torchvision where negative samples also cause problems. Since Torchvision currently don't support them, I'm wondering if it would be worth switching to Detectron2. As of today, what is the answer to this issue's title: "Does this repo's implementation of maskrcnn work with negative samples?" What about faster-rcnn? I understand a data loader option has been added, but it's still unclear if the models support negative samples.

[ppwwyyxx]

Images without annotations are supported in R-CNN.

[Hvorost]

Hi, maybe someone can help me. I try to implement this process https://github.com/TannerGilbert/Microcontroller-Detection-with Detectron2/blob/master/Detectron2_Detect_Microcontrollers.ipynb with some modification, in which I try to train model without filtering empty annotations, for that, I modify the value of this variable DATALOADER.FILTER_EMPTY_ANNOTATIONS = False , my dataset looks like
and my code
`def get_watermark_dicts(csv_file, img_dir):
df = pd.read_csv(csv_file)
df['filename'] = df['filename'].map(lambda x: img_dir+x)

classes = ['watermark', 'not']

df['class_int'] = df['class'].map(lambda x: classes.index(x))

dataset_dicts = []
for filename in df['filename'].unique().tolist():

    record = {}
    
    height, width = cv2.imread(filename).shape[:2]
    
    record["file_name"] = filename
    record["height"] = height
    record["width"] = width

    objs = []
    for index, row in df[(df['filename']==filename)].iterrows():
        obj= {
            'bbox': [row['xmin'], row['ymin'], row['xmax'], row['ymax']],
            'bbox_mode': BoxMode.XYXY_ABS,
            'category_id': row['class_int'],
            "iscrowd": 0
        }
        objs.append(obj)
    record["annotations"] = objs
    dataset_dicts.append(record)
return dataset_dicts

cfg = get_cfg()
cfg.merge_from_file("detectron2_repo/configs/COCO-Detection/faster_rcnn_R_50_FPN_3x.yaml")
cfg.DATASETS.TRAIN = ('/home/ubuntu/watermark/train',)
cfg.DATASETS.TEST = () # no metrics implemented for this dataset
cfg.DATALOADER.NUM_WORKERS = 4
cfg.MODEL.WEIGHTS = "detectron2://COCO-Detection/faster_rcnn_R_50_FPN_3x/137849458/model_final_280758.pkl" # initialize from model zoo
cfg.SOLVER.IMS_PER_BATCH = 2
cfg.SOLVER.MAX_ITER = 2000
cfg.MODEL.ROI_HEADS.NUM_CLASSES = 2
cfg.DATALOADER.FILTER_EMPTY_ANNOTATIONS = False

os.makedirs(cfg.OUTPUT_DIR, exist_ok=True)
trainer = DefaultTrainer(cfg)
trainer.resume_or_load(resume=False)
trainer.train()`

but my training process crushed with:
AssertionError: Caught AssertionError in DataLoader worker process 1.
Original Traceback (most recent call last):
File "/home/ubuntu/.local/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py", line 178, in _worker_loop
data = fetcher.fetch(index)
File "/home/ubuntu/.local/lib/python3.6/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/ubuntu/.local/lib/python3.6/site-packages/torch/utils/data/_utils/fetch.py", line 44, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/ubuntu/detectron2_repo/detectron2/data/common.py", line 39, in getitem
data = self._map_func(self._dataset[cur_idx])
File "/home/ubuntu/detectron2_repo/detectron2/utils/serialize.py", line 23, in call
return self._obj(*args, **kwargs)
File "/home/ubuntu/detectron2_repo/detectron2/data/dataset_mapper.py", line 131, in call
annos, image_shape, mask_format=self.mask_format
File "/home/ubuntu/detectron2_repo/detectron2/data/detection_utils.py", line 234, in annotations_to_instances
boxes.clip(image_size)
File "/home/ubuntu/detectron2_repo/detectron2/structures/boxes.py", line 130, in clip
assert torch.isfinite(self.tensor).all()
AssertionError
Maybe someone can help I would be very grateful .

[ppwwyyxx]

It does not allow boxes with NaNs.

[Hvorost]

It does not allow boxes with NaNs.

I understand it, but how I can train the model with negative samples? How can I use the images which haven't boxes? If you can explain I would be very grateful.

[ppwwyyxx]

You can train with an image whose "annotations" is an empty list.

[Hvorost]

Thanks, I'll try.

[Hvorost]

I still got the same issue. As I understand it, I don't need to clip boxes in boxes.clip(image_size) function, because I haven't coordinates to clip, but the process still the same as in case when I have nan in bbox list. Now I use an empty list for negative sample images. The question is open, please help.

[Hvorost]

full traceback

AssertionError Traceback (most recent call last)
in
16 trainer = DefaultTrainer(cfg)
17 trainer.resume_or_load(resume=False)
---> 18 trainer.train()

~/detectron2_repo/detectron2/engine/defaults.py in train(self)
367 OrderedDict of results, if evaluation is enabled. Otherwise None.
368 """
--> 369 super().train(self.start_iter, self.max_iter)
370 if hasattr(self, "_last_eval_results") and comm.is_main_process():
371 verify_results(self.cfg, self._last_eval_results)

~/detectron2_repo/detectron2/engine/train_loop.py in train(self, start_iter, max_iter)
130 for self.iter in range(start_iter, max_iter):
131 self.before_step()
--> 132 self.run_step()
133 self.after_step()
134 finally:

~/detectron2_repo/detectron2/engine/train_loop.py in run_step(self)
204 If your want to do something with the data, you can wrap the dataloader.
205 """
--> 206 data = next(self._data_loader_iter)
207 data_time = time.perf_counter() - start
208

~/.local/lib/python3.6/site-packages/torch/utils/data/dataloader.py in next(self)
799 if len(self._task_info[self._rcvd_idx]) == 2:
800 data = self._task_info.pop(self._rcvd_idx)[1]
--> 801 return self._process_data(data)
802
803 assert not self._shutdown and self._tasks_outstanding > 0

~/.local/lib/python3.6/site-packages/torch/utils/data/dataloader.py in _process_data(self, data)
844 self._try_put_index()
845 if isinstance(data, ExceptionWrapper):
--> 846 data.reraise()
847 return data
848

~/.local/lib/python3.6/site-packages/torch/_utils.py in reraise(self)
383 # (https://bugs.python.org/issue2651), so we work around it.
384 msg = KeyErrorMessage(msg)
--> 385 raise self.exc_type(msg)

AssertionError: Caught AssertionError in DataLoader worker process 1.
Original Traceback (most recent call last):
File "/home/ubuntu/.local/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py", line 178, in _worker_loop
data = fetcher.fetch(index)
File "/home/ubuntu/.local/lib/python3.6/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/ubuntu/.local/lib/python3.6/site-packages/torch/utils/data/_utils/fetch.py", line 44, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/ubuntu/detectron2_repo/detectron2/data/common.py", line 39, in getitem
data = self._map_func(self._dataset[cur_idx])
File "/home/ubuntu/detectron2_repo/detectron2/utils/serialize.py", line 23, in call
return self._obj(*args, **kwargs)
File "/home/ubuntu/detectron2_repo/detectron2/data/dataset_mapper.py", line 131, in call
annos, image_shape, mask_format=self.mask_format
File "/home/ubuntu/detectron2_repo/detectron2/data/detection_utils.py", line 234, in annotations_to_instances
boxes.clip(image_size)
File "/home/ubuntu/detectron2_repo/detectron2/structures/boxes.py", line 130, in clip
assert torch.isfinite(self.tensor).all()
AssertionError