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QuaPy/quapy/data/_lequa2022.py

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2022-11-28 12:02:08 +01:00
from typing import Tuple, Union
import pandas as pd
import numpy as np
import os
from quapy.protocol import AbstractProtocol
DEV_SAMPLES = 1000
TEST_SAMPLES = 5000
ERROR_TOL = 1E-3
def load_category_map(path):
cat2code = {}
with open(path, 'rt') as fin:
for line in fin:
category, code = line.split()
cat2code[category] = int(code)
code2cat = [cat for cat, code in sorted(cat2code.items(), key=lambda x: x[1])]
return cat2code, code2cat
def load_raw_documents(path):
df = pd.read_csv(path)
documents = list(df["text"].values)
labels = None
if "label" in df.columns:
labels = df["label"].values.astype(int)
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return documents, labels
def load_vector_documents(path):
D = pd.read_csv(path).to_numpy(dtype=float)
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labelled = D.shape[1] == 301
if labelled:
X, y = D[:, 1:], D[:, 0].astype(int).flatten()
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else:
X, y = D, None
return X, y
class SamplesFromDir(AbstractProtocol):
def __init__(self, path_dir:str, ground_truth_path:str, load_fn):
self.path_dir = path_dir
self.load_fn = load_fn
self.true_prevs = ResultSubmission.load(ground_truth_path)
def __call__(self):
for id, prevalence in self.true_prevs.iterrows():
sample, _ = self.load_fn(os.path.join(self.path_dir, f'{id}.txt'))
yield sample, prevalence
class ResultSubmission:
def __init__(self):
self.df = None
def __init_df(self, categories: int):
if not isinstance(categories, int) or categories < 2:
raise TypeError('wrong format for categories: an int (>=2) was expected')
df = pd.DataFrame(columns=list(range(categories)))
df.index.set_names('id', inplace=True)
self.df = df
@property
def n_categories(self):
return len(self.df.columns.values)
def add(self, sample_id: int, prevalence_values: np.ndarray):
if not isinstance(sample_id, int):
raise TypeError(f'error: expected int for sample_sample, found {type(sample_id)}')
if not isinstance(prevalence_values, np.ndarray):
raise TypeError(f'error: expected np.ndarray for prevalence_values, found {type(prevalence_values)}')
if self.df is None:
self.__init_df(categories=len(prevalence_values))
if sample_id in self.df.index.values:
raise ValueError(f'error: prevalence values for "{sample_id}" already added')
if prevalence_values.ndim != 1 and prevalence_values.size != self.n_categories:
raise ValueError(f'error: wrong shape found for prevalence vector {prevalence_values}')
if (prevalence_values < 0).any() or (prevalence_values > 1).any():
raise ValueError(f'error: prevalence values out of range [0,1] for "{sample_id}"')
if np.abs(prevalence_values.sum() - 1) > ERROR_TOL:
raise ValueError(f'error: prevalence values do not sum up to one for "{sample_id}"'
f'(error tolerance {ERROR_TOL})')
self.df.loc[sample_id] = prevalence_values
def __len__(self):
return len(self.df)
@classmethod
def load(cls, path: str) -> 'ResultSubmission':
df = ResultSubmission.check_file_format(path)
r = ResultSubmission()
r.df = df
return r
def dump(self, path: str):
ResultSubmission.check_dataframe_format(self.df)
self.df.to_csv(path)
def prevalence(self, sample_id: int):
sel = self.df.loc[sample_id]
if sel.empty:
return None
else:
return sel.values.flatten()
def iterrows(self):
for index, row in self.df.iterrows():
prevalence = row.values.flatten()
yield index, prevalence
@classmethod
def check_file_format(cls, path) -> Union[pd.DataFrame, Tuple[pd.DataFrame, str]]:
try:
df = pd.read_csv(path, index_col=0)
except Exception as e:
print(f'the file {path} does not seem to be a valid csv file. ')
print(e)
return ResultSubmission.check_dataframe_format(df, path=path)
@classmethod
def check_dataframe_format(cls, df, path=None) -> Union[pd.DataFrame, Tuple[pd.DataFrame, str]]:
hint_path = '' # if given, show the data path in the error message
if path is not None:
hint_path = f' in {path}'
if df.index.name != 'id' or len(df.columns) < 2:
raise ValueError(f'wrong header{hint_path}, '
f'the format of the header should be "id,0,...,n-1", '
f'where n is the number of categories')
if [int(ci) for ci in df.columns.values] != list(range(len(df.columns))):
raise ValueError(f'wrong header{hint_path}, category ids should be 0,1,2,...,n-1, '
f'where n is the number of categories')
if df.empty:
raise ValueError(f'error{hint_path}: results file is empty')
elif len(df) != DEV_SAMPLES and len(df) != TEST_SAMPLES:
raise ValueError(f'wrong number of prevalence values found{hint_path}; '
f'expected {DEV_SAMPLES} for development sets and '
f'{TEST_SAMPLES} for test sets; found {len(df)}')
ids = set(df.index.values)
expected_ids = set(range(len(df)))
if ids != expected_ids:
missing = expected_ids - ids
if missing:
raise ValueError(f'there are {len(missing)} missing ids{hint_path}: {sorted(missing)}')
unexpected = ids - expected_ids
if unexpected:
raise ValueError(f'there are {len(missing)} unexpected ids{hint_path}: {sorted(unexpected)}')
for category_id in df.columns:
if (df[category_id] < 0).any() or (df[category_id] > 1).any():
raise ValueError(f'error{hint_path} column "{category_id}" contains values out of range [0,1]')
prevs = df.values
round_errors = np.abs(prevs.sum(axis=-1) - 1.) > ERROR_TOL
if round_errors.any():
raise ValueError(f'warning: prevalence values in rows with id {np.where(round_errors)[0].tolist()} '
f'do not sum up to 1 (error tolerance {ERROR_TOL}), '
f'probably due to some rounding errors.')
return df