diff --git a/.idea/.gitignore b/.idea/.gitignore new file mode 100644 index 0000000..73f69e0 --- /dev/null +++ b/.idea/.gitignore @@ -0,0 +1,8 @@ +# Default ignored files +/shelf/ +/workspace.xml +# Datasource local storage ignored files +/dataSources/ +/dataSources.local.xml +# Editor-based HTTP Client requests +/httpRequests/ diff --git a/.idea/deployment.xml b/.idea/deployment.xml new file mode 100644 index 0000000..acde663 --- /dev/null +++ b/.idea/deployment.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/easy_attribute_prediction.iml b/.idea/easy_attribute_prediction.iml new file mode 100644 index 0000000..473daa9 --- /dev/null +++ b/.idea/easy_attribute_prediction.iml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml new file mode 100644 index 0000000..105ce2d --- /dev/null +++ b/.idea/inspectionProfiles/profiles_settings.xml @@ -0,0 +1,6 @@ + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..9895fb8 --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 0000000..32a26be --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..94a25f7 --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/README.md b/README.md index 5ca4083..7bc3dbb 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,14 @@ # easy_attribute_prediction easy to train and infer object based attribute prediction + +## Install + +``` +conda create -n attr +conda activate attr +conda install python=3.8.5 +pip install h5py==2.10 hickle pycocotools +``` + +## training data format + diff --git a/data_processing/mcs/Readme.md b/data_processing/mcs/Readme.md new file mode 100644 index 0000000..86388bd --- /dev/null +++ b/data_processing/mcs/Readme.md @@ -0,0 +1,11 @@ +# prepare data for evaluation 3 DARPA MCS project + +## Install +``` +conda create -n attr +conda activate attr +conda install python=3.8.5 +pip install h5py==2.10 hickle pycocotools +pip install git+https://github.com/NextCenturyCorporation/MCS@0.3.3 +``` + diff --git a/data_processing/mcs/mcs_process.py b/data_processing/mcs/mcs_process.py new file mode 100644 index 0000000..64b0143 --- /dev/null +++ b/data_processing/mcs/mcs_process.py @@ -0,0 +1,228 @@ +""" +This tool processes passive data for eval 3 and dumps it in a valid format to train a derender +""" +import argparse +import os +import random +import shutil +import sys +from itertools import repeat, chain, product +from multiprocessing import Process, Queue +from concurrent.futures.thread import ThreadPoolExecutor +from pathlib import Path + +import numpy as np +import hickle as hkl +from pycocotools import mask as mask_util +from PIL import Image + +import machine_common_sense as mcs + +sys.path.insert(0, './') +from easy_attributes.utils.io import write_serialized +from easy_attributes.utils.meta_data import get_continuous_metadata, get_discrete_metadata + +MIN_AREA = 100 + + +def parse_args(): + parser = argparse.ArgumentParser() + parser.add_argument('--mcs_executable', type=str) + parser.add_argument('--output_dir', type=str) + parser.add_argument('--data_path', type=str) + # parser.add_argument('--parallel', action='store_true') + parser.add_argument('--num_parallel_controllers', type=int) + args = parser.parse_args() + args.data_path = Path(args.data_path) + args.input_dir = Path(args.mcs_executable) + args.output_dir = Path(args.output_dir) + return args + + +def get_attributes(obj: mcs.object_metadata.ObjectMetadata): + attributes = {} + + attributes['shape'] = obj.shape + + [attributes.__setitem__('position_' + k, v) for k, v in obj.position.items()] + + [attributes.__setitem__('rotation_' + k, v) for k, v in obj.rotation.items()] + + [attributes.__setitem__(f'dimension_{i}_{c}', obj.dimensions[i][c]) for i,c in product(range(8), 'xyz')] + + return attributes + + +def dump_for_detectron(step_data, out_path, index): + # print(step_data) + depth: np.ndarray = step_data.depth_map_list[0] + depth = 1 / (1 + depth) + rgb = np.array(step_data.image_list[0], dtype=np.float32) / 255.0 + input = np.concatenate([rgb, depth[..., np.newaxis]], axis=2) + input = input.swapaxes(2, 0).swapaxes(1, 2) # now it is C, H, W + + input_to_file = out_path / 'inputs' / (str(index).zfill(9) + '.hkl') + hkl.dump(input, input_to_file, mode='w', compression='gzip') + + masks = np.array(step_data.object_mask_list[0]) + masks = masks[:, :, 0] + masks[:, :, 1] * 256 + masks[:, :, 2] * 256 ** 2 + assert not (masks == 0).any() + + foreground_objects = {e.color['r'] + e.color['g'] * 256 + e.color['b'] * 256 ** 2: e + for e in step_data.structural_object_list + if not (e.uuid.startswith('wall') or e.uuid.startswith('floor'))} + + foreground_objects.update({e.color['r'] + e.color['g'] * 256 + e.color['b'] * 256 ** 2: e + for e in step_data.object_list}) + + objects = [] + for v in foreground_objects.keys(): + mask = masks == v + if mask.sum() < MIN_AREA: + continue + + mask_y, mask_x = mask.nonzero() + bbox = list(map(int, [mask_x.min(), mask_y.min(), mask_x.max(), mask_y.max()])) + if bbox[3] <= bbox[1] + 2 and bbox[2] <= bbox[0] + 2: # width and height shouldn't be too small + continue + + mask = mask_util.encode(np.asarray(mask, order="F")) + mask['counts'] = mask['counts'].decode('ascii') + attributes = get_attributes(foreground_objects[v]) + + objects.append({'mask': mask, + 'bbox': bbox, + **attributes, + 'filename': str(input_to_file), + **{'agent_position_' + k: v for k, v in step_data.position.items()}, + 'agent_rotation': step_data.rotation}) + + return objects + + +def process_scene(controller, scene_path, output_path, vid_index, concurrent, tp: ThreadPoolExecutor): + config_data, _ = mcs.load_config_json_file(scene_path) + + jobs = [] + frame_id = 0 + step_data = controller.start_scene(config_data) + if concurrent: + jobs.append(tp.submit(dump_for_detectron, step_data, + output_path, + vid_index * 500 + frame_id)) + else: + jobs.append(dump_for_detectron(step_data, output_path, vid_index * 500 + frame_id)) + + frame_id += 1 + actions = config_data['goal']['action_list'] + for a in actions: + assert len(a) == 1, "there must be an action" + step_data = controller.step(a[0]) + if concurrent: + jobs.append(tp.submit(dump_for_detectron, step_data, + output_path, + vid_index * 500 + frame_id)) + else: + jobs.append(dump_for_detectron(step_data, output_path, vid_index * 500 + frame_id)) + + frame_id += 1 + + controller.end_scene("classification", 0.0) + if concurrent: + jobs = [j.result() for j in jobs] + return chain.from_iterable(jobs) + + +class SequentialSceneProcessor: + def __init__(self, mcs_executable: Path, concurrent_dump: bool): + self.controller = mcs.create_controller(str(mcs_executable), + depth_maps=True, + object_masks=True, + history_enabled=False) + + self.concurrent = concurrent_dump + self.tp = ThreadPoolExecutor(4) + + def process(self, w_arg): + (s, _, o, v) = w_arg + return process_scene(self.controller, s, o, v, self.concurrent, self.tp) + + +def ParallelSceneProcess(work_q: Queue, result_q: Queue, mcs_executable: Path, concurrent_dump): + controller = mcs.create_controller(str(mcs_executable), + depth_maps=True, + object_masks=True, + history_enabled=False) + with ThreadPoolExecutor(4) as p: + while True: + w_arg = work_q.get() + if w_arg is None: + break + (s, _, o, v) = w_arg + results = process_scene(controller, s, o, v, concurrent_dump, p) + result_q.put(results) + + +if __name__ == "__main__": + args = parse_args() + scene_files = [args.data_path / a for a in args.data_path.iterdir()] + + shutil.rmtree(args.output_dir, ignore_errors=True) + + (args.output_dir / 'inputs').mkdir(parents=True, exist_ok=True) + + w_args = [(s, e, o, i) for i, (s, e, o) in enumerate(zip(scene_files, + repeat(args.mcs_executable), + repeat(args.output_dir)))] + + + if args.num_parallel_controllers > 0: + work_queue = Queue() + result_queue = Queue() + + workers = [Process(target=ParallelSceneProcess, + args=(work_queue, result_queue, args.mcs_executable, True)) for _ in + range(args.num_parallel_controllers)] + [w.start() for w in workers] + + w_args = [work_queue.put(w) for w in w_args] + + data_dicts = [result_queue.get() for _ in range(len(w_args))] + + [work_queue.put(None) for _ in range(args.num_parallel_controllers)] + [w.join() for w in workers] + work_queue.close() + result_queue.close() + else: + worker = SequentialSceneProcessor(args.mcs_executable, False) + data_dicts = [worker.process(w_arg) for w_arg in w_args] + + data_dicts = list(chain.from_iterable(data_dicts)) + + all_indices = set(range(len(data_dicts))) + val_indices = random.sample(all_indices, 6000) + train_indices = all_indices.difference(val_indices) + + val_dicts = [data_dicts[i] for i in val_indices] + train_dicts = [data_dicts[i] for i in train_indices] + + meta_data = {'inputs': {'file_name': {'type': 'input_tensor', + 'num_channels': 4, + 'height': 400, + 'width': 600}, + 'mask': {'type': 'bitmask'}, + 'bbox': {'type': 'bounding_box'}}, + 'outputs': {**{e: get_continuous_metadata(val_dicts, e) + for e in [*[c[0] + c[1] for c in product(['rotation_', 'position_', 'agent_position_'], + 'xyz')], + *[f'dimension_{c[0]}_{c[1]}' for c in product(range(8), 'xyz')], + 'agent_rotation']}, + 'shape': get_discrete_metadata(data_dicts, 'shape')} + } + + write_serialized(val_dicts, args.output_dir / 'val.json') + write_serialized(train_dicts, args.output_dir / 'train.json') + write_serialized(meta_data, args.output_dir / 'metadata.yml') + + # kill stalling controllers + os.system('pkill -f MCS-AI2-THOR-Unity-App -9') diff --git a/easy_attributes/__init__.py b/easy_attributes/__init__.py new file mode 100644 index 0000000..e29c188 --- /dev/null +++ b/easy_attributes/__init__.py @@ -0,0 +1 @@ +from easy_attributes.utils import istarmap_tqdm_patch diff --git a/easy_attributes/attributes_dataset.py b/easy_attributes/attributes_dataset.py new file mode 100644 index 0000000..3294f56 --- /dev/null +++ b/easy_attributes/attributes_dataset.py @@ -0,0 +1,85 @@ + +from itertools import repeat +from pathlib import Path + +import numpy as np +from torch.utils.data import Dataset, DataLoader +import torch +from pycocotools import mask as mask_util +from yacs.config import CfgNode + +from easy_attributes.utils.io import read_serialized, load_input +from easy_attributes.utils.istarmap_tqdm_patch import array_apply + + +def data_dict_from_serialized(d, cfg, metadata): + for input in cfg.DATASET.INPUTS: + if metadata['inputs'][input]['type'] == 'bitmask': + d[input]['counts'] = d[input]['counts'].encode('ascii') + for output in cfg.DATASET.OUTPUTS: + meta_out = metadata['outputs'][output] + if meta_out['type'] == 'discrete': + d[output] = meta_out['class_to_index_map'][d[output]] + elif meta_out['type'] == 'continuous': + d[output] = np.float32(d[output]) + return d + + +class AttributeDataset(Dataset): + def __init__(self, dataset_json_path: Path, cfg): + self.metadata = read_serialized(dataset_json_path.parent / 'metadata.yml') + self.cfg = cfg + data = read_serialized(dataset_json_path) + self.data = array_apply(data_dict_from_serialized, zip(data, repeat(cfg), repeat(self.metadata)), + parallel=True, + total=len(data), + description='data_dict_from_serialized') + + def __getitem__(self, idx): + d = self.data[idx] + tensor_input = [] + base_input = load_input(d['filename']) + tensor_input.append(base_input) + for input in sorted(self.cfg.DATASET.INPUTS): + in_type = self.metadata['inputs'][input]['type'] + if in_type == 'input_tensor': + continue + elif in_type == 'bounding_box': + box = d[input] + segmented = np.zeros_like(base_input.numpy(), dtype=np.float32) + segmented[:, box[1]:box[3] + 1, box[0]:box[2] + 1] = \ + base_input[:, box[1]:box[3] + 1, box[0]:box[2] + 1] + tensor_input.append(torch.FloatTensor(segmented)) + elif in_type == 'bitmask': + mask = d[input] + mask = mask_util.decode(mask) + segmented = base_input * torch.FloatTensor(mask) + tensor_input.append(segmented) + else: + raise NotImplementedError + + tensor_input = torch.cat(tensor_input, dim=0) + + outputs = {k: d[k] for k in self.cfg.DATASET.OUTPUTS} + + return {'inputs': {'input_tensor': tensor_input}, + 'outputs': outputs} + + def __len__(self): + return len(self.data) + + +if __name__ == "__main__": + import argparse + parser = argparse.ArgumentParser() + parser.add_argument("--data_path", type=str) + data_path = Path(parser.parse_args().data_path) + metadata = read_serialized(data_path / 'metadata.yml') + cfg = CfgNode() + cfg.DATASET = CfgNode() + cfg.DATASET.INPUTS = ('file_name', 'mask', 'bbox') + cfg.DATASET.OUTPUTS = tuple(metadata['outputs'].keys()) + + dataset = AttributeDataset(data_path / 'val.json', cfg) + loader = DataLoader(dataset,batch_size=2,num_workers=0, shuffle=True) + print(iter(loader).next()) diff --git a/easy_attributes/utils/__init__.py b/easy_attributes/utils/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/easy_attributes/utils/io.py b/easy_attributes/utils/io.py new file mode 100644 index 0000000..307553b --- /dev/null +++ b/easy_attributes/utils/io.py @@ -0,0 +1,44 @@ +import json +from pathlib import Path + +import numpy as np +import torch +import yaml +import hickle as hkl + + +def read_serialized(file_path: Path): + with open(file_path, "r") as f: + if file_path.name.endswith(".json"): + return json.load(f) + elif file_path.name.endswith(".yml"): + return yaml.full_load(f) + else: + raise NotImplementedError + + +def write_serialized(data, file_path: Path): + """Write json and yaml file""" + assert file_path is not None + if file_path.name.endswith(".json"): + with open(file_path, "w") as f: + json.dump(data, f, indent=4) + elif file_path.name.endswith('.yml'): + with open(file_path, "w") as f: + yaml.safe_dump(data, f, indent=4) + else: + raise ValueError("Unrecognized filename extension", file_path) + + +def load_input(input_path: Path) -> torch.FloatTensor: + if not isinstance(input_path, Path): + input_path = Path(input_path) + ext = input_path.suffix + if ext == '.npy': + input = np.load(input_path) + elif ext == '.hkl': + input = hkl.load(str(input_path)) + else: + raise NotImplementedError + + return torch.FloatTensor(input) diff --git a/easy_attributes/utils/istarmap_tqdm_patch.py b/easy_attributes/utils/istarmap_tqdm_patch.py new file mode 100644 index 0000000..2c3d1f5 --- /dev/null +++ b/easy_attributes/utils/istarmap_tqdm_patch.py @@ -0,0 +1,56 @@ +# istarmap.py for Python 3.8+ +import multiprocessing.pool as mpp + +from tqdm import tqdm + + +def istarmap(self, func, iterable, chunksize=1): + """starmap-version of imap + """ + self._check_running() + if chunksize < 1: + raise ValueError( + "Chunksize must be 1+, not {0:n}".format( + chunksize)) + + task_batches = mpp.Pool._get_tasks(func, iterable, chunksize) + result = mpp.IMapIterator(self) + self._taskqueue.put( + ( + self._guarded_task_generation(result._job, + mpp.starmapstar, + task_batches), + result._set_length + )) + return (item for chunk in result for item in chunk) + + +mpp.Pool.istarmap = istarmap + +from multiprocessing import Pool, cpu_count + + +def array_apply(func, args, parallel, cpu_frac=1, use_tqdm=True, chunksize=None, total=None, unpack=True, description=None): + progress = tqdm if use_tqdm else lambda x, total, desc: x + total = len(args) if total is None else total + + if not parallel: + results = [] + for a in progress(args, total=total, desc=description): + r = func(*a) if unpack else func(a) + results.append(r) + return results + else: + num_processes = cpu_count() // cpu_frac + chunksize = total // num_processes if chunksize is None else chunksize + with Pool(num_processes) as p: + applier = p.istarmap if unpack else p.imap + return [a for a in progress(applier(func, args, chunksize), total=total, desc=description)] + +if __name__ == "__main__": + def h(v): + return v ** 2 + + + x = array_apply(h, [[e] for e in range(1000)], True) + print(x) diff --git a/easy_attributes/utils/meta_data.py b/easy_attributes/utils/meta_data.py new file mode 100644 index 0000000..3e52502 --- /dev/null +++ b/easy_attributes/utils/meta_data.py @@ -0,0 +1,19 @@ +import numpy as np + + +def get_continuous_metadata(data_dicts, attribute_name): + values = np.array([d[attribute_name] for d in data_dicts]) + std = values.std() + std = 1.0 if std == 0 else std + return {'type': 'continuous', + 'average': float(values.mean()), + 'std': float(std)} + + +def get_discrete_metadata(data_dicts, attribute_name): + values = [d[attribute_name] for d in data_dicts] + possible_values = sorted(list(set(values))) + class_to_index_map = {k: i for i, k in enumerate(possible_values)} + + return {'type': 'discrete', + 'class_to_index_map': class_to_index_map} \ No newline at end of file diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..81de9ed --- /dev/null +++ b/environment.yml @@ -0,0 +1,12 @@ +name: attr +channels: + - defaults +dependencies: + - python=3.8.5=h7579374_1 + - pip: + - torch==1.6.0 + - pyyaml==5.3.1 + - h5py==2.10.0 + - hickle==4.0.1 + - pycocotools==2.0.2 + - tqdm==4.51.0 \ No newline at end of file diff --git a/example_data/inputs/000000000.hkl b/example_data/inputs/000000000.hkl new file mode 100644 index 0000000..ee954c7 Binary files /dev/null and b/example_data/inputs/000000000.hkl differ diff --git a/example_data/inputs/000000001.hkl b/example_data/inputs/000000001.hkl new file mode 100644 index 0000000..1d2c290 Binary files /dev/null and b/example_data/inputs/000000001.hkl differ diff 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a/example_data/metadata.yml b/example_data/metadata.yml new file mode 100644 index 0000000..f70a039 --- /dev/null +++ b/example_data/metadata.yml @@ -0,0 +1,55 @@ +inputs: + bbox: + type: bounding_box + file_name: + num_channels: 4 + type: input_tensor + mask: + type: bitmask +outputs: + agent_position_x: + average: 0.0 + std: 1.0 + type: continuous + agent_position_y: + average: 1.5 + std: 1.0 + type: continuous + agent_position_z: + average: -4.5 + std: 1.0 + type: continuous + agent_rotation: + average: 0.0 + std: 1.0 + type: continuous + position_x: + average: 0.73337250617 + std: 2.9321969255678364 + type: continuous + position_y: + average: 0.99018177435 + std: 0.5151446769694885 + type: continuous + position_z: + average: 1.147998528 + std: 0.5970700013718997 + type: continuous + rotation_x: + average: 2.699802320850862 + std: 12.436859773303427 + type: continuous + rotation_y: + average: 6.299644327876399 + std: 38.71820759510201 + type: continuous + rotation_z: + average: 37.80000006640219 + std: 44.42026558880523 + type: continuous + shape: + class_to_index_map: + car: 0 + cube: 1 + structural: 2 + type: discrete diff --git a/example_data/train.json b/example_data/train.json new file mode 100644 index 0000000..ae546b8 --- /dev/null +++ b/example_data/train.json @@ -0,0 +1,11612 @@ +[ + { + "mask": { + "size": [ + 400, + 600 + ], + "counts": "Zeo59W<0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000fG" + }, + "bbox": [ + 490, + 266, + 599, + 274 + ], + "shape": "structural", + "position_x": 5.01724148, + "position_y": 0.75, + "position_z": 1.0, + "rotation_x": 0.0, + "rotation_y": 0.0, + "rotation_z": 90.0, + "filename": "/home/aldo/disk1/mcs_physics_data/inputs/000000000.hkl", + "agent_position_x": 0.0, + "agent_position_y": 1.5, + "agent_position_z": -4.5, + "agent_rotation": 0.0 + }, + { + "mask": { + "size": [ + 400, + 600 + ], + "counts": "Z89W<00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000fam4" + }, + "bbox": [ + 0, + 266, + 195, + 274 + ], + "shape": "structural", + "position_x": -4.10057449, + "position_y": 0.75, + "position_z": 1.0, + "rotation_x": 0.0, + "rotation_y": 0.0, + "rotation_z": 90.0, + "filename": "/home/aldo/disk1/mcs_physics_data/inputs/000000000.hkl", + "agent_position_x": 0.0, + "agent_position_y": 1.5, + "agent_position_z": -4.5, + "agent_rotation": 0.0 + }, + { + "mask": { + "size": [ + 400, + 600 + ], + "counts": 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