forked from moreo/QuaPy
210 lines
8.3 KiB
Python
210 lines
8.3 KiB
Python
import os.path
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from typing import List, Tuple, Union
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import pandas as pd
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import quapy as qp
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import numpy as np
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import sklearn
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import re
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# def load_binary_raw_document(path):
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# documents, labels = qp.data.from_text(path, verbose=0, class2int=True)
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# labels = np.asarray(labels)
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# labels[np.logical_or(labels == 1, labels == 2)] = 0
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# labels[np.logical_or(labels == 4, labels == 5)] = 1
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# return documents, labels
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# def load_multiclass_raw_document(path):
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# return qp.data.from_text(path, verbose=0, class2int=False)
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def load_binary_vectors(path, nF=None):
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return sklearn.datasets.load_svmlight_file(path, n_features=nF)
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def gen_load_samples_T1A(path_dir:str, ground_truth_path:str = None):
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# for ... : yield
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pass
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def gen_load_samples_T1B(path_dir:str, ground_truth_path:str = None):
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# for ... : yield
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pass
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def gen_load_samples_T2A(path_dir:str, ground_truth_path:str = None):
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# for ... : yield
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pass
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def gen_load_samples_T2B(path_dir:str, ground_truth_path:str = None):
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# for ... : yield
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pass
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class ResultSubmission:
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DEV_LEN = 1000
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TEST_LEN = 5000
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ERROR_TOL = 1E-3
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def __init__(self, categories: List[str]):
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if not isinstance(categories, list) or len(categories) < 2:
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raise TypeError('wrong format for categories; a list with at least two category names (str) was expected')
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self.categories = categories
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self.df = pd.DataFrame(columns=['filename'] + list(categories))
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self.inferred_type = None
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def add(self, sample_name:str, prevalence_values:np.ndarray):
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if not isinstance(sample_name, str):
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raise TypeError(f'error: expected str for sample_sample, found {type(sample_name)}')
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if not isinstance(prevalence_values, np.ndarray):
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raise TypeError(f'error: expected np.ndarray for prevalence_values, found {type(prevalence_values)}')
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if self.inferred_type is None:
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if sample_name.startswith('test'):
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self.inferred_type = 'test'
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elif sample_name.startswith('dev'):
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self.inferred_type = 'dev'
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else:
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if not sample_name.startswith(self.inferred_type):
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raise ValueError(f'error: sample "{sample_name}" is not a valid entry for type "{self.inferred_type}"')
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if not re.match("(test|dev)_sample_\d+\.txt", sample_name):
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raise ValueError(f'error: wrong format "{sample_name}"; right format is (test|dev)_sample_<number>.txt')
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if sample_name in self.df.filename.values:
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raise ValueError(f'error: prevalence values for "{sample_name}" already added')
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if prevalence_values.ndim!=1 and prevalence_values.size != len(self.categories):
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raise ValueError(f'error: wrong shape found for prevalence vector {prevalence_values}')
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if (prevalence_values<0).any() or (prevalence_values>1).any():
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raise ValueError(f'error: prevalence values out of range [0,1] for "{sample_name}"')
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if np.abs(prevalence_values.sum()-1) > ResultSubmission.ERROR_TOL:
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raise ValueError(f'error: prevalence values do not sum up to one for "{sample_name}"'
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f'(error tolerance {ResultSubmission.ERROR_TOL})')
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new_entry = dict([('filename',sample_name)]+[(col_i,prev_i) for col_i, prev_i in zip(self.categories, prevalence_values)])
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self.df = self.df.append(new_entry, ignore_index=True)
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def __len__(self):
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return len(self.df)
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@classmethod
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def load(cls, path: str) -> 'ResultSubmission':
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df, inferred_type = ResultSubmission.check_file_format(path, return_inferred_type=True)
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r = ResultSubmission(categories=df.columns.values.tolist())
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r.inferred_type = inferred_type
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r.df = df
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return r
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def dump(self, path:str):
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ResultSubmission.check_dataframe_format(self.df)
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self.df.to_csv(path)
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def get(self, sample_name:str):
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sel = self.df.loc[self.df['filename'] == sample_name]
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if sel.empty:
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return None
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else:
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return sel.loc[:,self.df.columns[1]:].values.flatten()
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@classmethod
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def check_file_format(cls, path, return_inferred_type=False) -> Union[pd.DataFrame, Tuple[pd.DataFrame, str]]:
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df = pd.read_csv(path, index_col=0)
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return ResultSubmission.check_dataframe_format(df, path=path, return_inferred_type=return_inferred_type)
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@classmethod
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def check_dataframe_format(cls, df, path=None, return_inferred_type=False) -> Union[pd.DataFrame, Tuple[pd.DataFrame, str]]:
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hint_path = '' # if given, show the data path in the error messages
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if path is not None:
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hint_path = f' in {path}'
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if 'filename' not in df.columns or len(df.columns) < 3:
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raise ValueError(f'wrong header{hint_path}, the format of the header should be ",filename,<cat_1>,...,<cat_n>"')
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if df.empty:
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raise ValueError(f'error{hint_path}: results file is empty')
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elif len(df) == ResultSubmission.DEV_LEN:
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inferred_type = 'dev'
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expected_len = ResultSubmission.DEV_LEN
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elif len(df) == ResultSubmission.TEST_LEN:
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inferred_type = 'test'
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expected_len = ResultSubmission.TEST_LEN
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else:
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raise ValueError(f'wrong number of prevalence values found{hint_path}; '
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f'expected {ResultSubmission.DEV_LEN} for development sets and '
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f'{ResultSubmission.TEST_LEN} for test sets; found {len(df)}')
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set_names = frozenset(df.filename)
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for i in range(expected_len):
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if f'{inferred_type}_sample_{i}.txt' not in set_names:
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raise ValueError(f'{hint_path} a file with {len(df)} entries is assumed to be of type '
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f'"{inferred_type}" but entry {inferred_type}_sample_{i}.txt is missing '
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f'(among perhaps many others)')
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for category_name in df.columns[1:]:
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if (df[category_name] < 0).any() or (df[category_name] > 1).any():
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raise ValueError(f'{hint_path} column "{category_name}" contains values out of range [0,1]')
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prevs = df.loc[:, df.columns[1]:].values
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round_errors = np.abs(prevs.sum(axis=-1) - 1.) > ResultSubmission.ERROR_TOL
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if round_errors.any():
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raise ValueError(f'warning: prevalence values in rows with id {np.where(round_errors)[0].tolist()} '
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f'do not sum up to 1 (error tolerance {ResultSubmission.ERROR_TOL}), '
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f'probably due to some rounding errors.')
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if return_inferred_type:
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return df, inferred_type
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else:
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return df
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def sort_categories(self):
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self.df = self.df.reindex([self.df.columns[0]] + sorted(self.df.columns[1:]), axis=1)
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self.categories = sorted(self.categories)
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def evaluate_submission(true_prevs: ResultSubmission, predicted_prevs: ResultSubmission, sample_size=1000, average=True):
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if len(true_prevs) != len(predicted_prevs):
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raise ValueError(f'size mismatch, groun truth has {len(true_prevs)} entries '
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f'while predictions contain {len(predicted_prevs)} entries')
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true_prevs.sort_categories()
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predicted_prevs.sort_categories()
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if true_prevs.categories != predicted_prevs.categories:
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raise ValueError(f'these result files are not comparable since the categories are different')
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ae, rae = [], []
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for sample_name in true_prevs.df.filename.values:
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ae.append(qp.error.mae(true_prevs.get(sample_name), predicted_prevs.get(sample_name)))
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rae.append(qp.error.mrae(true_prevs.get(sample_name), predicted_prevs.get(sample_name), eps=sample_size))
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ae = np.asarray(ae)
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rae = np.asarray(rae)
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if average:
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return ae.mean(), rae.mean()
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else:
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return ae, rae
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# r = ResultSubmission(['negative', 'positive'])
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# from tqdm import tqdm
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# for i in tqdm(range(1000), total=1000):
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# r.add(f'dev_sample_{i}.txt', np.asarray([0.5, 0.5]))
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# r.dump('./path.csv')
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r = ResultSubmission.load('./data/T1A/public/dummy_submission.csv')
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t = ResultSubmission.load('./data/T1A/public/dummy_submission (copy).csv')
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# print(r.df)
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# print(r.get('dev_sample_10.txt'))
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print(evaluate_submission(r, t))
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# s = ResultSubmission.load('./data/T1A/public/dummy_submission.csv')
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#
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# print(s)
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