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template_ffd

Code for paper Learning Free-Form Deformations for 3D Object Reconstruction in this repository.

Getting Started

cd /path/to/parent_dir
git clone https://github.com/jackd/template_ffd.git
# non-pip dependencies
git clone https://github.com/jackd/dids.git                  # framework for manipulating datasets
git clone https://github.com/jackd/util3d.git                # general 3d object utilities
git clone https://github.com/jackd/shapenet.git              # dataset access
git clone https://github.com/jackd/tf_nearest_neighbour.git  # for chamfer loss
git clone https://github.com/jackd/tf_toolbox.git            # optional

To run, ensure the parent directoy is on your PYTHON_PATH.

export PYTHONPATH=$PYTHONPATH:/path/to/parent_dir

So long as your PYTHONPATH is set as above, these repositories should work 'out of the box', except for tf_nearest_neighbour which requires the tensorflow op to be built. See the main repository for details.

Install pip dependencies

pip install h5py progress numpy pyemd

To use visualizations you'll also need mayavi.

pip install mayavi

See tensorflow documentation for installation. CUDA enabled GPU recommended.

Data

This repository depends on the Dictionary Interface to Datasets (dids) repository for dataset management and util3d for various 3d utility functions.

This code base is set up to train on the ShapeNet Core dataset. We cannot provide the data for this dataset, though it is freely available for registered users. We provide functionality for rendering, loading and converting data in the shapenet repository. For this project, most data accessing should "just work". There are, however, 2 manual steps that must be completed.

  1. Add the path to your shapenet core data to the environment variable SHAPENET_CORE_PATH,
export SHAPENET_CORE_PATH=/path/to/shapenet/dataset/ShapeNetCore.v1

This folder should contain the .zip files for each category, named by the category id, e.g. all plane obj files should be in 02691156.zip. 2. Render the images,

cd /path/to/parent_dir/shapenet/core/blender_renderings/scripts
python render_cat.py plane
python create_archive.py plane

Blender is required for this. The binary must either be on your path, or supplied via render_cat.py's --blender_path argument.

Other data preprocessing is required before training can begin (parsing mesh data, sampling meshes, calculating FFD decomposition), though this should be handled as the need arises.

In order to evaluate IoU scores, meshes must first be converted to voxels. To allow this, make the util3d binvox binary executable

chmod +x /path/to/parent_dir/util3d/bin/binvox

You can force any of this data processing for any category to occur by manually. See the example for generating plane data below.

cd /path/to/parent_dir/shapenet/core/meshes/scripts
python generate_mesh_data.py plane
cd ../../point_clouds/scripts
python create_point_clouds.py plane
cd ../../voxels/scripts
# For IoU data.
python create_voxels.py plane
python create_archive.py plane

Note evaluation of models produces a large amount of data. In particular, inferred meshes generated for IoU evaluation can be particularly large for a low edge_length_threshold. You can safely delete any data in inference/_inferences or eval/_eval and it will be regenerated if required.

Models

Different models can be built using different hyper-parameter sets. Models are built using the model.template_ffd_builder.TemplateFfdBuilder class. Each hyperparameter set should have a MODEL_ID and an associated model/params/MODEL_ID.json file. Default values are speficied where they are used in the code.

See paper/create_paper_params.py for the parameter sets used for the models presented in the paper.

Training

Training can be done via the scripts/train.py script. For example,

python train.py example -s 200000

will train the model with ID 'example' for 200000 steps (default is 100000).

To view training summaries, run

tensorboard --logdir=model/_model/MODEL_ID

Training to 100000 steps as done in the paper takes roughly 8 hours to an NVidia GTX-1070.

Evaluation

There are a number of steps to evaluation, depending on the metrics required.

  • To create predictions (network outputs, deformation parameters Delta P), run scripts/infer.py MODEL_ID
  • See also scripts/iou.py, scripts/chamfer.py and scripts/ffd_emd.py (slow).

Paper Figures

See the paper subdirectory for various scripts used to generate the figures presented in the paper.

Reference

If you find this code useful in your research, please cite the following paper.

@article{jack2018learning,
  title={Learning Free-Form Deformations for 3D Object Reconstruction},
  author={Jack, Dominic and Pontes, Jhony K and Sridharan, Sridha and Fookes, Clinton and Shirazi, Sareh and Maire, Frederic and Eriksson, Anders},
  journal={arXiv preprint arXiv:1803.10932},
  year={2018}
}

CHANGELOG

Since the initial release, a small bug has been fixed where batch normalization was being applied both before and after activations in some cases. This shouldn't make a massive difference to performance, but may mean models previously trained can no longer be loaded properly. To revert to older functionality, add 'use_bn_bugged_version': true to the params file.

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template_ffd's Issues

Some questions about code and paper

Hi @jackd ,

These days I've looked into your work and got some questions.

  1. I never used tf.estimator before and there is few open source projects using it. It seems that TemplateFfdBulder.initilalize_variables calls get_estimator_spec with input [features=(one_example_id,image),labels=point_cloud]. Inside it, we get output of the network and define loss. But I think there is only one network and one loss. What if I would like to train two sub_network such as GAN, how can I define loss and train?

  2. According to your paper, you learn the offset of control points from the network. I think you got your result in TemplateFfdBulder.get_inference with output dict(example_id=example_id, probs=probs, dp=dp). And then I think you used probs to get entropy loss and dp to get inferred point clouds, but I don't know how and where you choose the final template to be deformed.

  3. keep looking into get_dataset but still stuck with dataset, where do you put it into network batch by batch?

Looking forward to your reply and thanks!

Cannot load json data: file does not exist at %s' % self._path)

It's me again..
I've trained successfully and next step is to get evaluation results.

After tpying this
scripts/infer.py plane
a plane.hdf5 file is generated in inference/_inferences/predictions, which means so far so good.

But when I type in the next line
scripts/chamfer.py
The error occurs.

File "template_ffd/scripts/chamfer.py", line 35, in <module>
    args.overwrite)
  File "template_ffd/scripts/chamfer.py", line 15, in create_and_report
    chamfer.report_chamfer_average(**kwargs)
  File "/media/tree/data1/projects/data_prepare/template_ffd/eval/chamfer.py", line 127, in report_chamfer_average
    with manager.get_saving_dataset('r') as ds:
  File "/media/tree/data1/projects/data_prepare/dids/core.py", line 105, in __enter__
    self.open()
  File "/media/tree/data1/projects/data_prepare/dids/core.py", line 136, in open
    self.open_connection(self)
  File "/media/tree/data1/projects/data_prepare/dids/core.py", line 122, in open_connection
    self._open_resource()
  File "/media/tree/data1/projects/data_prepare/dids/file_io/json_dataset.py", line 20, in _open_resource
    'Cannot load json data: file does not exist at %s' % self._path)

I checked in eval/_eval/chamfer/presampled/1024 and it is an empty folder. I suppose that it should be a json here. (But I can't find what the json is?)

Is there any other operations between this two scripts that you forgot to mention?

Question about mobilenet hack

Hi,
I was going over the code repository and found the hack for keras mobile net. If I understand correctly this hack is required because the resolution of images is 256X192 and imagenet weights are only trained for square images. I was thinking was there any reason for this resolution and not converting the images to 256X256 during preprocessing. This will avoid usage of mobile net hack.

Thanks for all the help.

InvalidArgumentError: 1-th value returned by pyfunc_1 is double, but expects float

Hi @jackd,
See you again here XD..
when trying to train the network, the issue occured.

2018-05-16 12:25:02.195364: W tensorflow/core/framework/op_kernel.cc:1192] Invalid argument: 1-th value returned by pyfunc_1 is double, but expects float
	 [[Node: PyFuncStateless = PyFuncStateless[Tin=[DT_STRING], Tout=[DT_UINT8, DT_FLOAT], token="pyfunc_1"](arg0)]]
Traceback (most recent call last):
  File "train.py", line 19, in <module>
    train(args.model_id, max_steps=args.max_steps)
  File "train.py", line 8, in train
    builder.train(max_steps=max_steps)
  File "/media/tree/data1/projects/data_prepare/template_ffd/model/builder.py", line 242, in train
    estimator.train(self.get_train_inputs, **train_kwargs)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/estimator/estimator.py", line 302, in train
    loss = self._train_model(input_fn, hooks, saving_listeners)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/estimator/estimator.py", line 783, in _train_model
    _, loss = mon_sess.run([estimator_spec.train_op, estimator_spec.loss])
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/monitored_session.py", line 521, in run
    run_metadata=run_metadata)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/monitored_session.py", line 892, in run
    run_metadata=run_metadata)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/monitored_session.py", line 967, in run
    raise six.reraise(*original_exc_info)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/monitored_session.py", line 952, in run
    return self._sess.run(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/monitored_session.py", line 1024, in run
    run_metadata=run_metadata)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/monitored_session.py", line 827, in run
    return self._sess.run(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 889, in run
    run_metadata_ptr)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 1120, in _run
    feed_dict_tensor, options, run_metadata)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 1317, in _do_run
    options, run_metadata)
  File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 1336, in _do_call
    raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.InvalidArgumentError: 1-th value returned by pyfunc_1 is double, but expects float
	 [[Node: PyFuncStateless = PyFuncStateless[Tin=[DT_STRING], Tout=[DT_UINT8, DT_FLOAT], token="pyfunc_1"](arg0)]]
	 [[Node: IteratorGetNext = IteratorGetNext[output_shapes=[[?], [?,192,256,3], [?,1024,3]], output_types=[DT_STRING, DT_FLOAT, DT_FLOAT], _device="/job:localhost/replica:0/task:0/device:CPU:0"](OneShotIterator)]]
	 [[Node: IteratorGetNext/_2101 = _Recv[client_terminated=false, recv_device="/job:localhost/replica:0/task:0/device:GPU:0", send_device="/job:localhost/replica:0/task:0/device:CPU:0", send_device_incarnation=1, tensor_name="edge_193_IteratorGetNext", tensor_type=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:GPU:0"]()]]

It seems like input shape went wrong and it didn't get the batch size?Or my setting went wrong?

I am running at

Ubuntu16.04
Python2.7
TensorFlow1.4

And for more private request, could you release an example to load your dataset and finally get input tensor to tensorflow?

Thanks for your amazing job and looking forward to your reply!

Question about chamfer evaluation

Hi @jackd ,

I used your data as the input of PSGN, and I got 0.00039 chamfer distance with test split of plane in PSGN, while got 0.031 in your work. At the same time, the author of DN got 0.14 in PSGN according to their paper. I suppose that the results rely on different evaluating methods, so I tried to use your chamfer calculating method in PSGN.

I suppose that your method is np_metrics.chamfer(c0,c1)/n_samples in template_ffd.metrics while c0, c1 are np arrays of GT point clouds and infered point cloud. So I added this line in PSGN but it didn't get the correct result.

dis=np_metrics.chamfer(pred,pt_gt.eval())/1024

here pred is an np array and pt_gt is a tensor.

I also tried tf_metrics.chamfer but got AttributeError: 'tuple' object has no attribute 'as_list'. I looked into your implement and found it was similar to nn_distance of PSGN so I was wondering why I used got inappropriate results in PSGN

plane has 803 test example but when it iterate to 400 and it got me an OutOfRangeError. And the result of the first 400 examples still are strange like 0.0041 because it is supposed to be 0.14..

So could you tell me how to use your chamfer metrics?

Thanks a lot!

Getting warnings in preprocessing

Hi,
While trying to execute

python render_cat.py plane

I am getting warnings. "Invalid clnors in this fan!". Should I ignore this warning?
PS:- Images are still generated

Build the model

Hi,
Sorry to bother you again.
I used "python create_paper_params.py" and there were many json files created in the model/params folder.However, its could't be trained.
Can you tell me more detail about creating the json file ?
Thank you very much.

Evaluation error

Hi,
I have trained the b_plane model but I got some errors when I ran " python iou.py " and
" python chamfer.py "

Here is the detailed description of the error.
Running " python iou.py " :

Creating filled voxels
| | 1/803Traceback (most recent call last):
File "iou.py", line 32, in
args.overwrite)
File "iou.py", line 13, in create_and_report
iou.report_iou_average(**kwargs)
File "/home/howard/TF_14/FFD-template/template_ffd/eval/iou.py", line 129, in report_iou_average
filled=filled) as ds:
File "/home/howard/TF_14/FFD-template/template_ffd/eval/iou.py", line 123, in get_iou_dataset
manager.save_all()
File "/home/howard/TF_14/FFD-template/dids/auto_save.py", line 77, in save_all
with self.get_auto_saving_dataset('a') as ds:
File "/home/howard/TF_14/FFD-template/dids/auto_save.py", line 69, in get_auto_saving_dataset
self.get_lazy_dataset(),
File "/home/howard/TF_14/FFD-template/template_ffd/eval/iou.py", line 92, in get_lazy_dataset
filled=self._filled, example_ids=example_ids)
File "/home/howard/TF_14/FFD-template/template_ffd/inference/voxels.py", line 31, in get_voxel_dataset
create_voxel_data(example_ids=example_ids, overwrite=False, **kwargs)
File "/home/howard/TF_14/FFD-template/template_ffd/inference/voxels.py", line 104, in create_voxel_data
_create_filled_voxel_data(**kwargs)
File "/home/howard/TF_14/FFD-template/template_ffd/inference/voxels.py", line 90, in _create_filled_voxel_data
unfilled, dst, message=message, overwrite=overwrite)
File "/home/howard/TF_14/FFD-template/template_ffd/data/voxels.py", line 23, in create_filled_data
dst.save_dataset(src, overwrite=overwrite, message=message)
File "/home/howard/TF_14/FFD-template/dids/core.py", line 204, in save_dataset
value = dataset[key]
File "/home/howard/TF_14/FFD-template/dids/core.py", line 477, in getitem
return self._map_fn(self._base[key])
File "/home/howard/TF_14/FFD-template/template_ffd/data/voxels.py", line 19, in map_fn
voxels.axis_order)
AttributeError: 'RleVoxels' object has no attribute 'axis_order'

Running " python chamfer.py ":

RuntimeWarning: Mean of empty slice.
out=out, **kwargs)
/home/howard/TF_14/local/lib/python2.7/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)

How can I test on a new image?

Thanks for your work, but your README does not provide a way to reconstruct a mesh from a new image. How can I achieve this? Thank you.

OSError: [Errno 2] No such file or directory

Hi,
Sorry to bother you, I got an error while running the "python render_cat.py plane"
I have downloaded the ShapeNet Core dataset and exported the path

Here is the detailed description of the error.

Rendering 4045 images for cat 02691156
| | 1/4045
2018-07-13 11:24:01.861504
Rendering 8504e370736b26604d210d9468aedaf2
Traceback (most recent call last):
File "render_cat.py", line 106, in
args.example_ids, args.fixed_meshes, args.blender_path)
File "render_cat.py", line 86, in render_cat
overwrite, call_kwargs, blender_path=blender_path)
File "render_cat.py", line 60, in render_example
config, obj_path, cat_dir, call_kwargs, blender_path=blender_path)
File "render_cat.py", line 31, in render_obj
], **call_kwargs)
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Some questions about paper

How do you guarantee that the deformed mesh is still manifold(keeps the topolopy)?
In training, if we do not restrict the range that the control points of FFD vary, the mesh will be no more manifold. Do we have to consider this and if yes, where is the corresponding code?

can't find where the CD was calculated..

Hi @jackd,
I firstly went through the training pipiline in scripts/train.py and so far so good to understand it.
But when I tried to do the same thing in scripts/chamfer.py, it didn't go well..

it seems that eval.chamfer.report_chamfer_average() directly get the final json file which includes {example_id : CD_value} in it. I know that get_saving_dataset or get_saved_dataset should lead me to where the prediction and the GT are saved and where they get calculated, but I really can't find when I jumped between .py here and there. Would you give me some help?

Another question I have is that CD should have been defined in d(GT(16384)->PRED(1024)) + d(PRED(1024)->GT(16384)) in PSGN and your paper. I wonder if you use 1024 points to resample GT will affect the results.
But after I tried it, I got 0.031 in resample 1024 points but got 0.016 in resample 16384 for model plane. I think that it's weird and still working on figuring out what happened and then I am stuck on reading chamfer.py...

Question about implementation

I was going over the code and I had few questions.

  1. Are the weights for mobile net trainable
  2. get_mobilenet_features will initialize mobile net with imagenet weights once but what will happen when weights=None

Why is emd much larger than cd?

Hi @jackd ,
Thanks for your help months ago and I finally came out with sth. but still have a question.
For two point clouds, I got a emd value 1e6 larger than cd. Maybe the normalization influences the ratio but the emd is still much larger than cd. How can that happen?
cd is finding a nearest point in S2 for a point in S1 and add all distance between point pairs. emd is finding point to point mapping between two point clouds and add these distances all together too. Am I right?

Pretrained weights

Hi,
I am looking for pretrained weights for firearm category for comparison purpose. Is it possible to get access to pretrained weights.
I tried to re implement the paper and train the pistol/firearm category and the final loss was at 15 with batch size of 32. However the test deformations were not satisfactory.

Questions about KeyError

Hi @jackd ๏ผŒ
I encountered a problem when I was learning your code. I read it in issues for a long time, and no one encountered this problem. I think I made a mistake in which step, but I didn't know about it, so I want to consult you, I would appreciate it if you could help me T^T
I encountered the following problem when I was training create_voxel.py:

Traceback (most recent call last):
  File "create_voxels.py", line 35, in <module>
    cat_desc=args.cat)
  File "create_voxels.py", line 19, in create_voxels
    overwrite=overwrite)
  File "/home/louise/FFD/template_ffd/inference/voxels.py", line 137, in create_voxel_data
    _create_unfilled_voxel_data(**kwargs)
  File "/home/louise/FFD/template_ffd/inference/voxels.py", line 77, in _create_unfilled_voxel_data
    model_id, edge_length_threshold)
  File "/home/louise/FFD/template_ffd/inference/meshes.py", line 46, in get_inferred_mesh_dataset
    return manager.get_lazy_dataset()
  File "/home/louise/FFD/template_ffd/inference/meshes.py", line 32, in get_lazy_dataset
    self._edge_length_threshold)
  File "/home/louise/FFD/template_ffd/model/template_ffd_builder.py", line 450, in get_prediction_to_mesh_fn
    edge_length_threshold=edge_length_threshold) as d:
  File "/home/louise/FFD/template_ffd/templates/ffd.py", line 94, in get_ffd_dataset
    datasets = {c: _get_ffd_dataset(c, **kwargs) for c in cat_ids}
  File "/home/louise/FFD/template_ffd/templates/ffd.py", line 94, in <dictcomp>
    datasets = {c: _get_ffd_dataset(c, **kwargs) for c in cat_ids}
  File "/home/louise/FFD/template_ffd/templates/ffd.py", line 83, in _get_ffd_dataset
    return manager.get_saved_dataset()
  File "/home/louise/FFD/dids/auto_save.py", line 81, in get_saved_dataset
    self.save_all()
  File "/home/louise/FFD/dids/auto_save.py", line 77, in save_all
    with self.get_auto_saving_dataset('a') as ds:
  File "/home/louise/FFD/dids/auto_save.py", line 69, in get_auto_saving_dataset
    self.get_lazy_dataset(),
  File "/home/louise/FFD/template_ffd/templates/ffd.py", line 58, in get_lazy_dataset
    self._cat_id, self._edge_length_threshold)
  File "/home/louise/FFD/template_ffd/templates/mesh_ffd.py", line 68, in get_template_mesh_dataset
    return _get_template_mesh_dataset(cat_id, edge_length_threshold)
  File "/home/louise/FFD/template_ffd/templates/mesh_ffd.py", line 58, in _get_template_mesh_dataset
    edge_length_threshold=edge_length_threshold)
  File "/home/louise/FFD/template_ffd/templates/mesh_ffd.py", line 48, in get_split_template_mesh_dataset
    cat_id, edge_length_threshold).get_saved_dataset()
  File "/home/louise/FFD/dids/auto_save.py", line 81, in get_saved_dataset
    self.save_all()
  File "/home/louise/FFD/dids/auto_save.py", line 77, in save_all
    with self.get_auto_saving_dataset('a') as ds:
  File "/home/louise/FFD/dids/core.py", line 45, in __enter__
    self.open()
  File "/home/louise/FFD/dids/core.py", line 70, in open
    self.open_connection(self)
  File "/home/louise/FFD/dids/core.py", line 56, in open_connection
    self._open_resource()
  File "/home/louise/FFD/dids/auto_save.py", line 47, in _open_resource
    self.src.open_connection(self)
  File "/home/louise/FFD/dids/core.py", line 56, in open_connection
    self._open_resource()
  File "/home/louise/FFD/dids/core.py", line 369, in _open_resource
    self._base.open_connection(self)
  File "/home/louise/FFD/dids/core.py", line 56, in open_connection
    self._open_resource()
  File "/home/louise/FFD/dids/core.py", line 630, in _open_resource
    self._check_keys()
  File "/home/louise/FFD/dids/core.py", line 594, in _check_keys
    raise KeyError('key %s not present in base' % str(key))
KeyError: 'key 9c1b448ec62cb9fb36dd029536673b0b not present in base'

Hope you can give me some advice, I've been stuck in preprocessing for a long time. Thanks a lot!

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