# Copyright 2020 MONAI Consortium # 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. import csv import os from collections import OrderedDict from typing import Dict, Optional, Union import numpy as np import torch class CSVSaver: """ Save the data in a dictionary format cache, and write to a CSV file finally. Typically, the data can be classification predictions, call `save` for single data or call `save_batch` to save a batch of data together, and call `finalize` to write the cached data into CSV file. If no meta data provided, use index from 0 to save data. """ def __init__(self, output_dir: str = "./", filename: str = "predictions.csv", overwrite: bool = True) -> None: """ Args: output_dir: output CSV file directory. filename: name of the saved CSV file name. overwrite: whether to overwriting existing CSV file content. If we are not overwriting, then we check if the results have been previously saved, and load them to the prediction_dict. """ self.output_dir = output_dir self._cache_dict: OrderedDict = OrderedDict() assert isinstance(filename, str) and filename[-4:] == ".csv", "filename must be a string with CSV format." self._filepath = os.path.join(output_dir, filename) self.overwrite = overwrite self._data_index = 0 def finalize(self) -> None: """ Writes the cached dict to a csv """ if not self.overwrite and os.path.exists(self._filepath): with open(self._filepath, "r") as f: reader = csv.reader(f) for row in reader: self._cache_dict[row[0]] = np.array(row[1:]).astype(np.float32) if not os.path.exists(self.output_dir): os.makedirs(self.output_dir) with open(self._filepath, "w") as f: for k, v in self._cache_dict.items(): f.write(k) for result in v.flatten(): f.write("," + str(result)) f.write("\n") def save(self, data: Union[torch.Tensor, np.ndarray], meta_data: Optional[Dict] = None) -> None: """Save data into the cache dictionary. The metadata should have the following key: - ``'filename_or_obj'`` -- save the data corresponding to file name or object. If meta_data is None, use the default index from 0 to save data instead. Args: data: target data content that save into cache. meta_data: the meta data information corresponding to the data. """ save_key = meta_data["filename_or_obj"] if meta_data else str(self._data_index) self._data_index += 1 if torch.is_tensor(data): data = data.detach().cpu().numpy() assert isinstance(data, np.ndarray) self._cache_dict[save_key] = data.astype(np.float32) def save_batch(self, batch_data: Union[torch.Tensor, np.ndarray], meta_data: Optional[Dict] = None) -> None: """Save a batch of data into the cache dictionary. Args: batch_data: target batch data content that save into cache. meta_data: every key-value in the meta_data is corresponding to 1 batch of data. """ for i, data in enumerate(batch_data): # save a batch of files self.save(data, {k: meta_data[k][i] for k in meta_data} if meta_data else None)