# Copyright (c) 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. from __future__ import annotations import os import warnings from collections import OrderedDict from pathlib import Path import numpy as np import torch from monai.config.type_definitions import PathLike from monai.utils import ImageMetaKey as Key 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 metadata provided, use index from 0 to save data. Note that this saver can't support multi-processing because it reads / writes single CSV file and can't guarantee the data order in multi-processing situation. """ def __init__( self, output_dir: PathLike = "./", filename: str = "predictions.csv", overwrite: bool = True, flush: bool = False, delimiter: str = ",", ) -> 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 True, will clear the file before saving. otherwise, will append new content to the CSV file. flush: whether to write the cache data to CSV file immediately when `save_batch` and clear the cache. default to False. delimiter: the delimiter character in the saved file, default to "," as the default output type is `csv`. to be consistent with: https://docs.python.org/3/library/csv.html#csv.Dialect.delimiter. """ self.output_dir = Path(output_dir) self._cache_dict: OrderedDict = OrderedDict() if not (isinstance(filename, str) and filename[-4:] == ".csv"): warnings.warn("CSV filename is not a string ends with '.csv'.") self._filepath = self.output_dir / filename if self._filepath.exists() and overwrite: os.remove(self._filepath) self.flush = flush self.delimiter = delimiter self._data_index = 0 def finalize(self) -> None: """ Writes the cached dict to a csv """ if not self.output_dir.exists(): self.output_dir.mkdir(parents=True, exist_ok=True) with open(self._filepath, "a") as f: for k, v in self._cache_dict.items(): f.write(k) for result in v.flatten(): f.write(self.delimiter + str(result)) f.write("\n") # clear cache content after writing self.reset_cache() def save(self, data: torch.Tensor | np.ndarray, meta_data: dict | None = 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 metadata information corresponding to the data. """ save_key = meta_data[Key.FILENAME_OR_OBJ] if meta_data else str(self._data_index) self._data_index += 1 if isinstance(data, torch.Tensor): data = data.detach().cpu().numpy() self._cache_dict[save_key] = np.asarray(data, dtype=float) def save_batch(self, batch_data: torch.Tensor | np.ndarray, meta_data: dict | None = 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) if self.flush: self.finalize() def get_cache(self) -> OrderedDict: """Get the cache dictionary, key is filename and value is the corresponding data""" return self._cache_dict def reset_cache(self) -> None: """Clear the cache dictionary content""" self._cache_dict.clear()