import glob import json import os import trimesh import numpy as np import traceback class NpEncoder(json.JSONEncoder): def default(self, obj): if isinstance(obj, np.integer): return int(obj) if isinstance(obj, np.floating): return float(obj) if isinstance(obj, np.ndarray): return obj.tolist() return super(NpEncoder, self).default(obj) class ScanSegmentation(): # SegmentationAlgorithm is not inherited in this class anymore def __init__(self): """ Write your own input validators here Initialize your model etc. """ #self.model = load_model() #sef.device = "cuda" pass @staticmethod def load_input(input_dir): """ Read from /input/ Check https://grand-challenge.org/algorithms/interfaces/ """ # iterate over files in input_dir, assuming only 1 file available inputs = glob.glob(f'{input_dir}/*.obj') print("scan to process:", inputs) return inputs @staticmethod def write_output(labels, instances, jaw): """ Write to /output/dental-labels.json your predicted labels and instances Check https://grand-challenge.org/components/interfaces/outputs/ """ pred_output = {'id_patient': "", 'jaw': jaw, 'labels': labels, 'instances': instances } # just for testing with open('./test/test_local/expected_output.json', 'w') as fp: # with open('/output/dental-labels.json', 'w') as fp: json.dump(pred_output, fp, cls=NpEncoder) return @staticmethod def get_jaw(scan_path): try: # read jaw from filename _, jaw = os.path.basename(scan_path).split('.')[0].split('_') except: # read from first line in obj file try: with open(scan_path, 'r') as f: jaw = f.readline()[2:-1] if jaw not in ["upper", "lower"]: return None except Exception as e: print(str(e)) print(traceback.format_exc()) return None return jaw def predict(self, inputs): """ Your algorithm goes here """ try: assert len(inputs) == 1, f"Expected only one path in inputs, got {len(inputs)}" except AssertionError as e: raise Exception(e.args) scan_path = inputs[0] print(f"loading scan : {scan_path}") # read input 3D scan .obj try: # you can use trimesh or other any loader we keep the same order mesh = trimesh.load(scan_path, process=False) jaw = self.get_jaw(scan_path) print("jaw processed is:", jaw) except Exception as e: print(str(e)) print(traceback.format_exc()) raise # preprocessing if needed # prep_data = preprocess_function(mesh) # inference data here # labels, instances = self.model(mesh, jaw=None) # extract number of vertices from mesh nb_vertices = mesh.vertices.shape[0] # just for testing : generate dummy output instances and labels instances = [2] * nb_vertices labels = [43] * nb_vertices try: assert (len(labels) == len(instances) and len(labels) == mesh.vertices.shape[0]),\ "length of output labels and output instances should be equal" except AssertionError as e: raise Exception(e.args) return labels, instances, jaw def process(self): """ Read input from /input, process with your algorithm and write to /output assumption /input contains only 1 file """ input = self.load_input(input_dir='/input') labels, instances, jaw = self.predict(input) self.write_output(labels=labels, instances=instances, jaw=jaw) if __name__ == "__main__": ScanSegmentation().process()