forked from moreo/QuaPy
result file format check, read, load, and evaluation with pandas
This commit is contained in:
parent
646d21873f
commit
5f15b365fe
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@ -1,6 +1,12 @@
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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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@ -40,40 +46,162 @@ def gen_load_samples_T2B(path_dir:str, ground_truth_path:str = None):
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class ResultSubmission:
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def __init__(self, team_name, run_name, task_name):
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assert isinstance(team_name, str) and team_name, \
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f'invalid value encountered for team_name'
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assert isinstance(run_name, str) and run_name, \
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f'invalid value encountered for run_name'
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assert isinstance(task_name, str) and task_name in {'T1A', 'T1B', 'T2A', 'T2B'}, \
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f'invalid value encountered for task_name; valid values are T1A, T1B, T2A, and T2B'
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self.team_name = team_name
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self.run_name = run_name
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self.task_name = task_name
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self.data = {}
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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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# assert the result is a valid sample_name (not repeated)
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pass
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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.data)
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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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pass
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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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# assert all samples are covered (check for test and dev accordingly)
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pass
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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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pass
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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(ground_truth_prevs: ResultSubmission, submission_prevs: ResultSubmission):
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pass
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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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@ -31,8 +31,6 @@ dev_prev = pd.read_csv(os.path.join(path_binary_vector, 'public', 'dev_prevalenc
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print(dev_prev)
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scores = {}
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for quantifier in [CC]: #, ACC, PCC, PACC, EMQ, HDy]:
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@ -1,3 +1,4 @@
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from abc import abstractmethod
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from typing import List, Union
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import numpy as np
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@ -8,6 +9,112 @@ from sklearn.model_selection import train_test_split, RepeatedStratifiedKFold
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from quapy.functional import artificial_prevalence_sampling, strprev
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# class Sampling:
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#
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# @abstractmethod
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# def load(cls, path: str, loader_func: callable, classes=None): ...
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#
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# @abstractmethod
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# @property
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# def __len__(self): ...
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#
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# @abstractmethod
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# @property
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# def prevalence(self): ...
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#
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# @abstractmethod
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# @property
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# def n_classes(self):
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#
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# @property
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# def binary(self):
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# return self.n_classes == 2
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#
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# def uniform_sampling_index(self, size):
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# return np.random.choice(len(self), size, replace=False)
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#
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# def uniform_sampling(self, size):
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# unif_index = self.uniform_sampling_index(size)
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# return self.sampling_from_index(unif_index)
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#
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# def sampling(self, size, *prevs, shuffle=True):
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# prev_index = self.sampling_index(size, *prevs, shuffle=shuffle)
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# return self.sampling_from_index(prev_index)
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#
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# def sampling_from_index(self, index):
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# documents = self.instances[index]
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# labels = self.labels[index]
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# return LabelledCollection(documents, labels, classes_=self.classes_)
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#
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# def split_stratified(self, train_prop=0.6, random_state=None):
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# # with temp_seed(42):
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# tr_docs, te_docs, tr_labels, te_labels = \
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# train_test_split(self.instances, self.labels, train_size=train_prop, stratify=self.labels,
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# random_state=random_state)
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# return LabelledCollection(tr_docs, tr_labels), LabelledCollection(te_docs, te_labels)
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#
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# def artificial_sampling_generator(self, sample_size, n_prevalences=101, repeats=1):
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# dimensions = self.n_classes
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# for prevs in artificial_prevalence_sampling(dimensions, n_prevalences, repeats):
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# yield self.sampling(sample_size, *prevs)
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#
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# def artificial_sampling_index_generator(self, sample_size, n_prevalences=101, repeats=1):
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# dimensions = self.n_classes
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# for prevs in artificial_prevalence_sampling(dimensions, n_prevalences, repeats):
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# yield self.sampling_index(sample_size, *prevs)
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#
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# def natural_sampling_generator(self, sample_size, repeats=100):
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# for _ in range(repeats):
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# yield self.uniform_sampling(sample_size)
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#
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# def natural_sampling_index_generator(self, sample_size, repeats=100):
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# for _ in range(repeats):
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# yield self.uniform_sampling_index(sample_size)
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#
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# def __add__(self, other):
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# if other is None:
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# return self
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# elif issparse(self.instances) and issparse(other.instances):
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# join_instances = vstack([self.instances, other.instances])
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# elif isinstance(self.instances, list) and isinstance(other.instances, list):
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# join_instances = self.instances + other.instances
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# elif isinstance(self.instances, np.ndarray) and isinstance(other.instances, np.ndarray):
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# join_instances = np.concatenate([self.instances, other.instances])
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# else:
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# raise NotImplementedError('unsupported operation for collection types')
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# labels = np.concatenate([self.labels, other.labels])
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# return LabelledCollection(join_instances, labels)
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#
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# @property
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# def Xy(self):
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# return self.instances, self.labels
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#
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# def stats(self, show=True):
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# ninstances = len(self)
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# instance_type = type(self.instances[0])
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# if instance_type == list:
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# nfeats = len(self.instances[0])
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# elif instance_type == np.ndarray or issparse(self.instances):
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# nfeats = self.instances.shape[1]
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# else:
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# nfeats = '?'
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# stats_ = {'instances': ninstances,
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# 'type': instance_type,
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# 'features': nfeats,
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# 'classes': self.classes_,
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# 'prevs': strprev(self.prevalence())}
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# if show:
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# print(f'#instances={stats_["instances"]}, type={stats_["type"]}, #features={stats_["features"]}, '
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# f'#classes={stats_["classes"]}, prevs={stats_["prevs"]}')
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# return stats_
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#
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# def kFCV(self, nfolds=5, nrepeats=1, random_state=0):
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# kf = RepeatedStratifiedKFold(n_splits=nfolds, n_repeats=nrepeats, random_state=random_state)
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# for train_index, test_index in kf.split(*self.Xy):
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# train = self.sampling_from_index(train_index)
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# test = self.sampling_from_index(test_index)
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# yield train, test
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class LabelledCollection:
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'''
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A LabelledCollection is a set of objects each with a label associated to it.
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@ -176,104 +283,7 @@ class LabelledCollection:
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yield train, test
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class MultilingualLabelledCollection:
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def __init__(self, langs:List[str], labelledCollections:List[LabelledCollection]):
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assert len(langs) == len(labelledCollections), 'length mismatch for langs and labelledCollection lists'
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assert all(isinstance(lc, LabelledCollection) for lc in labelledCollections), 'unexpected type for labelledCollections'
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assert all(labelledCollections[0].classes_ == lc_i.classes_ for lc_i in labelledCollections[1:]), \
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'inconsistent classes found for some labelled collections'
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self.llc = {l: lc for l, lc in zip(langs, labelledCollections)}
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self.classes_=labelledCollections[0].classes_
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@classmethod
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def fromLangDict(cls, lang_labelledCollection:dict):
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return MultilingualLabelledCollection(*list(zip(*list(lang_labelledCollection.items()))))
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def langs(self):
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return list(sorted(self.llc.keys()))
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def __getitem__(self, lang)->LabelledCollection:
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return self.llc[lang]
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@classmethod
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def load(cls, path: str, loader_func: callable):
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return MultilingualLabelledCollection(*loader_func(path))
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def __len__(self):
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return sum(map(len, self.llc.values()))
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def prevalence(self):
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prev = np.asarray([lc.prevalence() * len(lc) for lc in self.llc.values()]).sum(axis=0)
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return prev / prev.sum()
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def language_prevalence(self):
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lang_count = np.asarray([len(self.llc[l]) for l in self.langs()])
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return lang_count / lang_count.sum()
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def counts(self):
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return np.asarray([lc.counts() for lc in self.llc.values()]).sum(axis=0)
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@property
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def n_classes(self):
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return len(self.classes_)
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@property
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def binary(self):
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return self.n_classes == 2
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def __check_langs(self, l_dict:dict):
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assert len(l_dict)==len(self.langs()), 'wrong number of languages'
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assert all(l in l_dict for l in self.langs()), 'missing languages in l_sizes'
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def __check_sizes(self, l_sizes: Union[int,dict]):
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assert isinstance(l_sizes, int) or isinstance(l_sizes, dict), 'unexpected type for l_sizes'
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if isinstance(l_sizes, int):
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return {l:l_sizes for l in self.langs()}
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self.__check_langs(l_sizes)
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return l_sizes
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def sampling_index(self, l_sizes: Union[int,dict], *prevs, shuffle=True):
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l_sizes = self.__check_sizes(l_sizes)
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return {l:lc.sampling_index(l_sizes[l], *prevs, shuffle=shuffle) for l,lc in self.llc.items()}
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def uniform_sampling_index(self, l_sizes: Union[int, dict]):
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l_sizes = self.__check_sizes(l_sizes)
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return {l: lc.uniform_sampling_index(l_sizes[l]) for l,lc in self.llc.items()}
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def uniform_sampling(self, l_sizes: Union[int, dict]):
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l_sizes = self.__check_sizes(l_sizes)
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return MultilingualLabelledCollection.fromLangDict(
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{l: lc.uniform_sampling(l_sizes[l]) for l,lc in self.llc.items()}
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)
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def sampling(self, l_sizes: Union[int, dict], *prevs, shuffle=True):
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l_sizes = self.__check_sizes(l_sizes)
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return MultilingualLabelledCollection.fromLangDict(
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{l: lc.sampling(l_sizes[l], *prevs, shuffle=shuffle) for l,lc in self.llc.items()}
|
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)
|
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|
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def sampling_from_index(self, l_index:dict):
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self.__check_langs(l_index)
|
||||
return MultilingualLabelledCollection.fromLangDict(
|
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{l: lc.sampling_from_index(l_index[l]) for l,lc in self.llc.items()}
|
||||
)
|
||||
|
||||
def split_stratified(self, train_prop=0.6, random_state=None):
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||||
train, test = list(zip(*[self[l].split_stratified(train_prop, random_state) for l in self.langs()]))
|
||||
return MultilingualLabelledCollection(self.langs(), train), MultilingualLabelledCollection(self.langs(), test)
|
||||
|
||||
def asLabelledCollection(self, return_langs=False):
|
||||
lXy_list = [([l]*len(lc),*lc.Xy) for l, lc in self.llc.items()] # a list with (lang_i, Xi, yi)
|
||||
ls,Xs,ys = list(zip(*lXy_list))
|
||||
ls = np.concatenate(ls)
|
||||
vertstack = vstack if issparse(Xs[0]) else np.vstack
|
||||
Xs = vertstack(Xs)
|
||||
ys = np.concatenate(ys)
|
||||
lc = LabelledCollection(Xs, ys, classes_=self.classes_)
|
||||
# return lc, ls if return_langs else lc
|
||||
#
|
||||
#
|
||||
#
|
||||
class Dataset:
|
||||
|
||||
def __init__(self, training: LabelledCollection, test: LabelledCollection, vocabulary: dict = None, name=''):
|
||||
|
|
|
|||
Loading…
Reference in New Issue