mirror of
https://github.com/fjosw/pyerrors.git
synced 2025-03-15 06:40:24 +01:00
[Feat] Added type hints to input modules
This commit is contained in:
Fabian Joswig
parent
3db8eb2989
commit
9fe375a747
7 changed files with 96 additions and 68 deletions
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@ -1,3 +1,4 @@
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from __future__ import annotations
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from collections import defaultdict
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import gzip
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import lxml.etree as et
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@ -11,10 +12,13 @@ from ..obs import Obs
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from ..obs import _merge_idx
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from ..covobs import Covobs
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from .. import version as pyerrorsversion
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from lxml.etree import _Element
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from numpy import ndarray
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from typing import Any, Dict, List, Optional, Tuple, Union
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# Based on https://stackoverflow.com/a/10076823
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def _etree_to_dict(t):
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def _etree_to_dict(t: _Element) -> Dict[str, Union[str, Dict[str, str], Dict[str, Union[str, Dict[str, str]]]]]:
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""" Convert the content of an XML file to a python dict"""
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d = {t.tag: {} if t.attrib else None}
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children = list(t)
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@ -38,7 +42,7 @@ def _etree_to_dict(t):
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return d
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def _dict_to_xmlstring(d):
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def _dict_to_xmlstring(d: Dict[str, Any]) -> str:
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if isinstance(d, dict):
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iters = ''
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for k in d:
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@ -66,7 +70,7 @@ def _dict_to_xmlstring(d):
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return iters
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def _dict_to_xmlstring_spaces(d, space=' '):
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def _dict_to_xmlstring_spaces(d: Dict[str, Dict[str, Dict[str, Union[str, Dict[str, str], List[Dict[str, str]]]]]], space: str=' ') -> str:
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s = _dict_to_xmlstring(d)
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o = ''
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c = 0
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@ -85,7 +89,7 @@ def _dict_to_xmlstring_spaces(d, space=' '):
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return o
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def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
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def create_pobs_string(obsl: List[Obs], name: str, spec: str='', origin: str='', symbol: Optional[List[Union[str, Any]]]=None, enstag: None=None) -> str:
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"""Export a list of Obs or structures containing Obs to an xml string
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according to the Zeuthen pobs format.
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@ -113,6 +117,8 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
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XML formatted string of the input data
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"""
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if symbol is None:
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symbol = []
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od = {}
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ename = obsl[0].e_names[0]
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names = list(obsl[0].deltas.keys())
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@ -176,7 +182,7 @@ def create_pobs_string(obsl, name, spec='', origin='', symbol=[], enstag=None):
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return rs
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def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], enstag=None, gz=True):
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def write_pobs(obsl: List[Obs], fname: str, name: str, spec: str='', origin: str='', symbol: Optional[List[Union[str, Any]]]=None, enstag: None=None, gz: bool=True):
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"""Export a list of Obs or structures containing Obs to a .xml.gz file
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according to the Zeuthen pobs format.
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@ -206,6 +212,8 @@ def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], enstag=None, gz
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-------
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None
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"""
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if symbol is None:
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symbol = []
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pobsstring = create_pobs_string(obsl, name, spec, origin, symbol, enstag)
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if not fname.endswith('.xml') and not fname.endswith('.gz'):
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@ -223,30 +231,30 @@ def write_pobs(obsl, fname, name, spec='', origin='', symbol=[], enstag=None, gz
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fp.close()
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def _import_data(string):
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def _import_data(string: str) -> List[Union[int, float]]:
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return json.loads("[" + ",".join(string.replace(' +', ' ').split()) + "]")
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def _check(condition):
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def _check(condition: bool):
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if not condition:
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raise Exception("XML file format not supported")
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class _NoTagInDataError(Exception):
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"""Raised when tag is not in data"""
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def __init__(self, tag):
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def __init__(self, tag: str):
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self.tag = tag
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super().__init__('Tag %s not in data!' % (self.tag))
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def _find_tag(dat, tag):
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def _find_tag(dat: _Element, tag: str) -> int:
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for i in range(len(dat)):
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if dat[i].tag == tag:
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return i
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raise _NoTagInDataError(tag)
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def _import_array(arr):
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def _import_array(arr: _Element) -> Union[List[Union[str, List[int], List[ndarray]]], ndarray]:
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name = arr[_find_tag(arr, 'id')].text.strip()
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index = _find_tag(arr, 'layout')
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try:
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@ -284,12 +292,12 @@ def _import_array(arr):
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_check(False)
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def _import_rdata(rd):
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def _import_rdata(rd: _Element) -> Tuple[List[ndarray], str, List[int]]:
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name, idx, mask, deltas = _import_array(rd)
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return deltas, name, idx
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def _import_cdata(cd):
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def _import_cdata(cd: _Element) -> Tuple[str, ndarray, ndarray]:
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_check(cd[0].tag == "id")
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_check(cd[1][0].text.strip() == "cov")
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cov = _import_array(cd[1])
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@ -297,7 +305,7 @@ def _import_cdata(cd):
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return cd[0].text.strip(), cov, grad
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def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
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def read_pobs(fname: str, full_output: bool=False, gz: bool=True, separator_insertion: None=None) -> Union[Dict[str, Union[str, Dict[str, str], List[Obs]]], List[Obs]]:
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"""Import a list of Obs from an xml.gz file in the Zeuthen pobs format.
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Tags are not written or recovered automatically.
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@ -309,7 +317,7 @@ def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
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full_output : bool
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If True, a dict containing auxiliary information and the data is returned.
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If False, only the data is returned as list.
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separatior_insertion: str or int
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separator_insertion: str or int
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str: replace all occurences of "separator_insertion" within the replica names
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by "|%s" % (separator_insertion) when constructing the names of the replica.
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int: Insert the separator "|" at the position given by separator_insertion.
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@ -397,7 +405,7 @@ def read_pobs(fname, full_output=False, gz=True, separator_insertion=None):
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# this is based on Mattia Bruno's implementation at https://github.com/mbruno46/pyobs/blob/master/pyobs/IO/xml.py
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def import_dobs_string(content, full_output=False, separator_insertion=True):
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def import_dobs_string(content: bytes, full_output: bool=False, separator_insertion: bool=True) -> Union[Dict[str, Union[str, Dict[str, str], List[Obs]]], List[Obs]]:
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"""Import a list of Obs from a string in the Zeuthen dobs format.
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Tags are not written or recovered automatically.
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@ -409,7 +417,7 @@ def import_dobs_string(content, full_output=False, separator_insertion=True):
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full_output : bool
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If True, a dict containing auxiliary information and the data is returned.
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If False, only the data is returned as list.
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separatior_insertion: str, int or bool
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separator_insertion: str, int or bool
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str: replace all occurences of "separator_insertion" within the replica names
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by "|%s" % (separator_insertion) when constructing the names of the replica.
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int: Insert the separator "|" at the position given by separator_insertion.
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@ -571,7 +579,7 @@ def import_dobs_string(content, full_output=False, separator_insertion=True):
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return res
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def read_dobs(fname, full_output=False, gz=True, separator_insertion=True):
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def read_dobs(fname: str, full_output: bool=False, gz: bool=True, separator_insertion: bool=True) -> Union[Dict[str, Union[str, Dict[str, str], List[Obs]]], List[Obs]]:
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"""Import a list of Obs from an xml.gz file in the Zeuthen dobs format.
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Tags are not written or recovered automatically.
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@ -618,7 +626,7 @@ def read_dobs(fname, full_output=False, gz=True, separator_insertion=True):
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return import_dobs_string(content, full_output, separator_insertion=separator_insertion)
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def _dobsdict_to_xmlstring(d):
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def _dobsdict_to_xmlstring(d: Dict[str, Any]) -> str:
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if isinstance(d, dict):
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iters = ''
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for k in d:
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@ -658,7 +666,7 @@ def _dobsdict_to_xmlstring(d):
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return iters
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def _dobsdict_to_xmlstring_spaces(d, space=' '):
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def _dobsdict_to_xmlstring_spaces(d: Dict[str, Union[Dict[str, Union[Dict[str, str], Dict[str, Union[str, Dict[str, str]]], Dict[str, Union[str, Dict[str, Union[str, List[str]]], List[Dict[str, Union[str, int, List[Dict[str, str]]]]]]]]], Dict[str, Union[Dict[str, str], Dict[str, Union[str, Dict[str, str]]], Dict[str, Union[str, Dict[str, Union[str, List[str]]], List[Dict[str, Union[str, int, List[Dict[str, str]]]]], List[Dict[str, Union[str, List[Dict[str, str]]]]]]]]]]], space: str=' ') -> str:
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s = _dobsdict_to_xmlstring(d)
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o = ''
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c = 0
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@ -677,7 +685,7 @@ def _dobsdict_to_xmlstring_spaces(d, space=' '):
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return o
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def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=None, enstags=None):
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def create_dobs_string(obsl: List[Obs], name: str, spec: str='dobs v1.0', origin: str='', symbol: Optional[List[Union[str, Any]]]=None, who: None=None, enstags: Optional[Dict[Any, Any]]=None) -> str:
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"""Generate the string for the export of a list of Obs or structures containing Obs
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to a .xml.gz file according to the Zeuthen dobs format.
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@ -708,6 +716,8 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
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xml_str : str
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XML string generated from the data
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"""
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if symbol is None:
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symbol = []
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if enstags is None:
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enstags = {}
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od = {}
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@ -866,7 +876,7 @@ def create_dobs_string(obsl, name, spec='dobs v1.0', origin='', symbol=[], who=N
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return rs
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def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=None, enstags=None, gz=True):
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def write_dobs(obsl: List[Obs], fname: str, name: str, spec: str='dobs v1.0', origin: str='', symbol: Optional[List[Union[str, Any]]]=None, who: None=None, enstags: None=None, gz: bool=True):
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"""Export a list of Obs or structures containing Obs to a .xml.gz file
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according to the Zeuthen dobs format.
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@ -900,6 +910,8 @@ def write_dobs(obsl, fname, name, spec='dobs v1.0', origin='', symbol=[], who=No
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-------
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None
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"""
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if symbol is None:
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symbol = []
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if enstags is None:
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enstags = {}
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@ -1,3 +1,4 @@
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from __future__ import annotations
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import rapidjson as json
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import gzip
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import getpass
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@ -12,9 +13,11 @@ from ..covobs import Covobs
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from ..correlators import Corr
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from ..misc import _assert_equal_properties
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from .. import version as pyerrorsversion
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from numpy import float32, float64, int64, ndarray
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from typing import Any, Dict, List, Optional, Tuple, Union
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def create_json_string(ol, description='', indent=1):
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def create_json_string(ol: Any, description: Union[str, Dict[str, Union[str, Dict[str, Union[Dict[str, Union[str, Dict[str, Union[int, str]]]], Dict[str, Optional[Union[str, List[str], float]]]]]]], Dict[str, Union[str, Dict[Optional[Union[int, bool]], str], float32]], Dict[str, Dict[str, Dict[str, str]]], Dict[str, Union[str, Dict[Optional[Union[int, bool]], str], Dict[int64, float64]]]]='', indent: int=1) -> str:
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"""Generate the string for the export of a list of Obs or structures containing Obs
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to a .json(.gz) file
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@ -216,7 +219,7 @@ def create_json_string(ol, description='', indent=1):
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return json.dumps(d, indent=indent, ensure_ascii=False, default=_jsonifier, write_mode=json.WM_COMPACT)
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def dump_to_json(ol, fname, description='', indent=1, gz=True):
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def dump_to_json(ol: Union[Corr, List[Union[Obs, List[Obs], Corr, ndarray]], ndarray, List[Union[Obs, List[Obs], ndarray]], List[Obs]], fname: str, description: Union[str, Dict[str, Union[str, Dict[str, Union[Dict[str, Union[str, Dict[str, Union[int, str]]]], Dict[str, Optional[Union[str, List[str], float]]]]]]], Dict[str, Union[str, Dict[Optional[Union[int, bool]], str], float32]], Dict[str, Dict[str, Dict[str, str]]], Dict[str, Union[str, Dict[Optional[Union[int, bool]], str], Dict[int64, float64]]]]='', indent: int=1, gz: bool=True):
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"""Export a list of Obs or structures containing Obs to a .json(.gz) file.
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Dict keys that are not JSON-serializable such as floats are converted to strings.
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@ -258,7 +261,7 @@ def dump_to_json(ol, fname, description='', indent=1, gz=True):
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fp.close()
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def _parse_json_dict(json_dict, verbose=True, full_output=False):
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def _parse_json_dict(json_dict: Dict[str, Any], verbose: bool=True, full_output: bool=False) -> Any:
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"""Reconstruct a list of Obs or structures containing Obs from a dict that
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was built out of a json string.
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@ -470,7 +473,7 @@ def _parse_json_dict(json_dict, verbose=True, full_output=False):
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return ol
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def import_json_string(json_string, verbose=True, full_output=False):
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def import_json_string(json_string: str, verbose: bool=True, full_output: bool=False) -> Union[Obs, List[Obs], Corr]:
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"""Reconstruct a list of Obs or structures containing Obs from a json string.
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The following structures are supported: Obs, list, numpy.ndarray, Corr
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@ -500,7 +503,7 @@ def import_json_string(json_string, verbose=True, full_output=False):
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return _parse_json_dict(json.loads(json_string), verbose, full_output)
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def load_json(fname, verbose=True, gz=True, full_output=False):
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def load_json(fname: str, verbose: bool=True, gz: bool=True, full_output: bool=False) -> Any:
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"""Import a list of Obs or structures containing Obs from a .json(.gz) file.
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The following structures are supported: Obs, list, numpy.ndarray, Corr
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@ -545,7 +548,7 @@ def load_json(fname, verbose=True, gz=True, full_output=False):
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return _parse_json_dict(d, verbose, full_output)
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def _ol_from_dict(ind, reps='DICTOBS'):
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def _ol_from_dict(ind: Union[Dict[Optional[Union[int, bool]], str], Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]], str]], Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]], List[str]]], Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]]]]], reps: str='DICTOBS') -> Union[Tuple[List[Any], Dict[Optional[Union[int, bool]], str]], Tuple[List[Union[Obs, List[Obs], Corr, ndarray]], Dict[str, Union[Dict[str, Union[str, Dict[str, Union[int, str]]]], Dict[str, Optional[Union[str, List[str], float]]]]]]]:
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"""Convert a dictionary of Obs objects to a list and a dictionary that contains
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placeholders instead of the Obs objects.
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@ -625,7 +628,7 @@ def _ol_from_dict(ind, reps='DICTOBS'):
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return ol, nd
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def dump_dict_to_json(od, fname, description='', indent=1, reps='DICTOBS', gz=True):
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def dump_dict_to_json(od: Union[Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]], str]], Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]], List[str]]], List[Union[Obs, List[Obs], Corr, ndarray]], Dict[Optional[Union[int, bool]], str], Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]]]]], fname: str, description: Union[str, float32, Dict[int64, float64]]='', indent: int=1, reps: str='DICTOBS', gz: bool=True):
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"""Export a dict of Obs or structures containing Obs to a .json(.gz) file
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Parameters
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@ -665,7 +668,7 @@ def dump_dict_to_json(od, fname, description='', indent=1, reps='DICTOBS', gz=Tr
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dump_to_json(ol, fname, description=desc_dict, indent=indent, gz=gz)
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def _od_from_list_and_dict(ol, ind, reps='DICTOBS'):
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def _od_from_list_and_dict(ol: List[Union[Obs, List[Obs], Corr, ndarray]], ind: Dict[str, Dict[str, Optional[Union[str, Dict[str, Union[int, str]], List[str], float]]]], reps: str='DICTOBS') -> Dict[str, Dict[str, Any]]:
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"""Parse a list of Obs or structures containing Obs and an accompanying
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dict, where the structures have been replaced by placeholders to a
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dict that contains the structures.
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@ -728,7 +731,7 @@ def _od_from_list_and_dict(ol, ind, reps='DICTOBS'):
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return nd
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def load_json_dict(fname, verbose=True, gz=True, full_output=False, reps='DICTOBS'):
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def load_json_dict(fname: str, verbose: bool=True, gz: bool=True, full_output: bool=False, reps: str='DICTOBS') -> Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]], str, Dict[str, Union[Dict[str, Union[Obs, List[Obs], Dict[str, Union[int, Obs, Corr, ndarray]]]], Dict[str, Optional[Union[str, List[str], Obs, float]]]]]]]:
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"""Import a dict of Obs or structures containing Obs from a .json(.gz) file.
|
||||
|
||||
The following structures are supported: Obs, list, numpy.ndarray, Corr
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
from __future__ import annotations
|
||||
import os
|
||||
import fnmatch
|
||||
import re
|
||||
|
|
@ -8,9 +9,10 @@ import matplotlib.pyplot as plt
|
|||
from matplotlib import gridspec
|
||||
from ..obs import Obs
|
||||
from ..fits import fit_lin
|
||||
from typing import Dict, Optional
|
||||
|
||||
|
||||
def fit_t0(t2E_dict, fit_range, plot_fit=False, observable='t0'):
|
||||
def fit_t0(t2E_dict: Dict[float, Obs], fit_range: int, plot_fit: Optional[bool]=False, observable: str='t0') -> Obs:
|
||||
"""Compute the root of (flow-based) data based on a dictionary that contains
|
||||
the necessary information in key-value pairs a la (flow time: observable at flow time).
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
from __future__ import annotations
|
||||
import os
|
||||
import fnmatch
|
||||
import struct
|
||||
|
|
@ -8,9 +9,11 @@ from ..obs import CObs
|
|||
from ..correlators import Corr
|
||||
from .misc import fit_t0
|
||||
from .utils import sort_names
|
||||
from io import BufferedReader
|
||||
from typing import Dict, List, Optional, Tuple, Union
|
||||
|
||||
|
||||
def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
|
||||
def read_rwms(path: str, prefix: str, version: str='2.0', names: Optional[List[str]]=None, **kwargs) -> List[Obs]:
|
||||
"""Read rwms format from given folder structure. Returns a list of length nrw
|
||||
|
||||
Parameters
|
||||
|
|
@ -229,7 +232,7 @@ def read_rwms(path, prefix, version='2.0', names=None, **kwargs):
|
|||
return result
|
||||
|
||||
|
||||
def _extract_flowed_energy_density(path, prefix, dtr_read, xmin, spatial_extent, postfix='ms', **kwargs):
|
||||
def _extract_flowed_energy_density(path: str, prefix: str, dtr_read: int, xmin: int, spatial_extent: int, postfix: str='ms', **kwargs) -> Dict[float, Obs]:
|
||||
"""Extract a dictionary with the flowed Yang-Mills action density from given .ms.dat files.
|
||||
Returns a dictionary with Obs as values and flow times as keys.
|
||||
|
||||
|
|
@ -422,7 +425,7 @@ def _extract_flowed_energy_density(path, prefix, dtr_read, xmin, spatial_extent,
|
|||
return E_dict
|
||||
|
||||
|
||||
def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, postfix='ms', c=0.3, **kwargs):
|
||||
def extract_t0(path: str, prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int=5, postfix: str='ms', c: Union[float, int]=0.3, **kwargs) -> Obs:
|
||||
"""Extract t0/a^2 from given .ms.dat files. Returns t0 as Obs.
|
||||
|
||||
It is assumed that all boundary effects have
|
||||
|
|
@ -495,7 +498,7 @@ def extract_t0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, postfi
|
|||
return fit_t0(t2E_dict, fit_range, plot_fit=kwargs.get('plot_fit'))
|
||||
|
||||
|
||||
def extract_w0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, postfix='ms', c=0.3, **kwargs):
|
||||
def extract_w0(path: str, prefix: str, dtr_read: int, xmin: int, spatial_extent: int, fit_range: int=5, postfix: str='ms', c: Union[float, int]=0.3, **kwargs) -> Obs:
|
||||
"""Extract w0/a from given .ms.dat files. Returns w0 as Obs.
|
||||
|
||||
It is assumed that all boundary effects have
|
||||
|
|
@ -577,7 +580,7 @@ def extract_w0(path, prefix, dtr_read, xmin, spatial_extent, fit_range=5, postfi
|
|||
return np.sqrt(fit_t0(tdtt2E_dict, fit_range, plot_fit=kwargs.get('plot_fit'), observable='w0'))
|
||||
|
||||
|
||||
def _parse_array_openQCD2(d, n, size, wa, quadrupel=False):
|
||||
def _parse_array_openQCD2(d: int, n: Tuple[int, int], size: int, wa: Union[Tuple[float, float, float, float, float, float, float, float], Tuple[float, float]], quadrupel: bool=False) -> List[List[float]]:
|
||||
arr = []
|
||||
if d == 2:
|
||||
for i in range(n[0]):
|
||||
|
|
@ -596,7 +599,7 @@ def _parse_array_openQCD2(d, n, size, wa, quadrupel=False):
|
|||
return arr
|
||||
|
||||
|
||||
def _find_files(path, prefix, postfix, ext, known_files=[]):
|
||||
def _find_files(path: str, prefix: str, postfix: str, ext: str, known_files: Union[str, List[str]]=[]) -> List[str]:
|
||||
found = []
|
||||
files = []
|
||||
|
||||
|
|
@ -636,7 +639,7 @@ def _find_files(path, prefix, postfix, ext, known_files=[]):
|
|||
return files
|
||||
|
||||
|
||||
def _read_array_openQCD2(fp):
|
||||
def _read_array_openQCD2(fp: BufferedReader) -> Dict[str, Union[int, Tuple[int, int], List[List[float]]]]:
|
||||
t = fp.read(4)
|
||||
d = struct.unpack('i', t)[0]
|
||||
t = fp.read(4 * d)
|
||||
|
|
@ -662,7 +665,7 @@ def _read_array_openQCD2(fp):
|
|||
return {'d': d, 'n': n, 'size': size, 'arr': arr}
|
||||
|
||||
|
||||
def read_qtop(path, prefix, c, dtr_cnfg=1, version="openQCD", **kwargs):
|
||||
def read_qtop(path: str, prefix: str, c: float, dtr_cnfg: int=1, version: str="openQCD", **kwargs) -> Obs:
|
||||
"""Read the topologial charge based on openQCD gradient flow measurements.
|
||||
|
||||
Parameters
|
||||
|
|
@ -715,7 +718,7 @@ def read_qtop(path, prefix, c, dtr_cnfg=1, version="openQCD", **kwargs):
|
|||
return _read_flow_obs(path, prefix, c, dtr_cnfg=dtr_cnfg, version=version, obspos=0, **kwargs)
|
||||
|
||||
|
||||
def read_gf_coupling(path, prefix, c, dtr_cnfg=1, Zeuthen_flow=True, **kwargs):
|
||||
def read_gf_coupling(path: str, prefix: str, c: float, dtr_cnfg: int=1, Zeuthen_flow: bool=True, **kwargs) -> Obs:
|
||||
"""Read the gradient flow coupling based on sfqcd gradient flow measurements. See 1607.06423 for details.
|
||||
|
||||
Note: The current implementation only works for c=0.3 and T=L. The definition of the coupling in 1607.06423 requires projection to topological charge zero which is not done within this function but has to be performed in a separate step.
|
||||
|
|
@ -787,7 +790,7 @@ def read_gf_coupling(path, prefix, c, dtr_cnfg=1, Zeuthen_flow=True, **kwargs):
|
|||
return t * t * (5 / 3 * plaq - 1 / 12 * C2x1) / normdict[L]
|
||||
|
||||
|
||||
def _read_flow_obs(path, prefix, c, dtr_cnfg=1, version="openQCD", obspos=0, sum_t=True, **kwargs):
|
||||
def _read_flow_obs(path: str, prefix: str, c: float, dtr_cnfg: int=1, version: str="openQCD", obspos: int=0, sum_t: bool=True, **kwargs) -> Obs:
|
||||
"""Read a flow observable based on openQCD gradient flow measurements.
|
||||
|
||||
Parameters
|
||||
|
|
@ -1059,7 +1062,7 @@ def _read_flow_obs(path, prefix, c, dtr_cnfg=1, version="openQCD", obspos=0, sum
|
|||
return result
|
||||
|
||||
|
||||
def qtop_projection(qtop, target=0):
|
||||
def qtop_projection(qtop: Obs, target: int=0) -> Obs:
|
||||
"""Returns the projection to the topological charge sector defined by target.
|
||||
|
||||
Parameters
|
||||
|
|
@ -1085,7 +1088,7 @@ def qtop_projection(qtop, target=0):
|
|||
return reto
|
||||
|
||||
|
||||
def read_qtop_sector(path, prefix, c, target=0, **kwargs):
|
||||
def read_qtop_sector(path: str, prefix: str, c: float, target: int=0, **kwargs) -> Obs:
|
||||
"""Constructs reweighting factors to a specified topological sector.
|
||||
|
||||
Parameters
|
||||
|
|
@ -1143,7 +1146,7 @@ def read_qtop_sector(path, prefix, c, target=0, **kwargs):
|
|||
return qtop_projection(qtop, target=target)
|
||||
|
||||
|
||||
def read_ms5_xsf(path, prefix, qc, corr, sep="r", **kwargs):
|
||||
def read_ms5_xsf(path: str, prefix: str, qc: str, corr: str, sep: str="r", **kwargs) -> Corr:
|
||||
"""
|
||||
Read data from files in the specified directory with the specified prefix and quark combination extension, and return a `Corr` object containing the data.
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
from __future__ import annotations
|
||||
import warnings
|
||||
import gzip
|
||||
import sqlite3
|
||||
|
|
@ -6,9 +7,11 @@ from ..obs import Obs
|
|||
from ..correlators import Corr
|
||||
from .json import create_json_string, import_json_string
|
||||
import numpy as np
|
||||
from pandas.core.frame import DataFrame
|
||||
from pandas.core.series import Series
|
||||
|
||||
|
||||
def to_sql(df, table_name, db, if_exists='fail', gz=True, **kwargs):
|
||||
def to_sql(df: DataFrame, table_name: str, db: str, if_exists: str='fail', gz: bool=True, **kwargs):
|
||||
"""Write DataFrame including Obs or Corr valued columns to sqlite database.
|
||||
|
||||
Parameters
|
||||
|
|
@ -34,7 +37,7 @@ def to_sql(df, table_name, db, if_exists='fail', gz=True, **kwargs):
|
|||
con.close()
|
||||
|
||||
|
||||
def read_sql(sql, db, auto_gamma=False, **kwargs):
|
||||
def read_sql(sql: str, db: str, auto_gamma: bool=False, **kwargs) -> DataFrame:
|
||||
"""Execute SQL query on sqlite database and obtain DataFrame including Obs or Corr valued columns.
|
||||
|
||||
Parameters
|
||||
|
|
@ -58,7 +61,7 @@ def read_sql(sql, db, auto_gamma=False, **kwargs):
|
|||
return _deserialize_df(extract_df, auto_gamma=auto_gamma)
|
||||
|
||||
|
||||
def dump_df(df, fname, gz=True):
|
||||
def dump_df(df: DataFrame, fname: str, gz: bool=True):
|
||||
"""Exports a pandas DataFrame containing Obs valued columns to a (gzipped) csv file.
|
||||
|
||||
Before making use of pandas to_csv functionality Obs objects are serialized via the standardized
|
||||
|
|
@ -97,7 +100,7 @@ def dump_df(df, fname, gz=True):
|
|||
out.to_csv(fname, index=False)
|
||||
|
||||
|
||||
def load_df(fname, auto_gamma=False, gz=True):
|
||||
def load_df(fname: str, auto_gamma: bool=False, gz: bool=True) -> DataFrame:
|
||||
"""Imports a pandas DataFrame from a csv.(gz) file in which Obs objects are serialized as json strings.
|
||||
|
||||
Parameters
|
||||
|
|
@ -131,7 +134,7 @@ def load_df(fname, auto_gamma=False, gz=True):
|
|||
return _deserialize_df(re_import, auto_gamma=auto_gamma)
|
||||
|
||||
|
||||
def _serialize_df(df, gz=False):
|
||||
def _serialize_df(df: DataFrame, gz: bool=False) -> DataFrame:
|
||||
"""Serializes all Obs or Corr valued columns into json strings according to the pyerrors json specification.
|
||||
|
||||
Parameters
|
||||
|
|
@ -152,7 +155,7 @@ def _serialize_df(df, gz=False):
|
|||
return out
|
||||
|
||||
|
||||
def _deserialize_df(df, auto_gamma=False):
|
||||
def _deserialize_df(df: DataFrame, auto_gamma: bool=False) -> DataFrame:
|
||||
"""Deserializes all pyerrors json strings into Obs or Corr objects according to the pyerrors json specification.
|
||||
|
||||
Parameters
|
||||
|
|
@ -188,7 +191,7 @@ def _deserialize_df(df, auto_gamma=False):
|
|||
return df
|
||||
|
||||
|
||||
def _need_to_serialize(col):
|
||||
def _need_to_serialize(col: Series) -> bool:
|
||||
serialize = False
|
||||
i = 0
|
||||
while i < len(col) and col[i] is None:
|
||||
|
|
|
|||
|
|
@ -1,3 +1,4 @@
|
|||
from __future__ import annotations
|
||||
import os
|
||||
import fnmatch
|
||||
import re
|
||||
|
|
@ -5,12 +6,14 @@ import numpy as np # Thinly-wrapped numpy
|
|||
from ..obs import Obs
|
||||
from .utils import sort_names, check_idl
|
||||
import itertools
|
||||
from numpy import ndarray
|
||||
from typing import Any, Dict, List, Tuple, Union
|
||||
|
||||
|
||||
sep = "/"
|
||||
|
||||
|
||||
def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0, wf2=0, version="1.0c", cfg_separator="n", silent=False, **kwargs):
|
||||
def read_sfcf(path: str, prefix: str, name: str, quarks: str='.*', corr_type: str="bi", noffset: int=0, wf: int=0, wf2: int=0, version: str="1.0c", cfg_separator: str="n", silent: bool=False, **kwargs) -> List[Obs]:
|
||||
"""Read sfcf files from given folder structure.
|
||||
|
||||
Parameters
|
||||
|
|
@ -75,7 +78,7 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0,
|
|||
return ret[name][quarks][str(noffset)][str(wf)][str(wf2)]
|
||||
|
||||
|
||||
def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=['bi'], noffset_list=[0], wf_list=[0], wf2_list=[0], version="1.0c", cfg_separator="n", silent=False, keyed_out=False, **kwargs):
|
||||
def read_sfcf_multi(path: str, prefix: str, name_list: List[str], quarks_list: List[str]=['.*'], corr_type_list: List[str]=['bi'], noffset_list: List[int]=[0], wf_list: List[int]=[0], wf2_list: List[int]=[0], version: str="1.0c", cfg_separator: str="n", silent: bool=False, keyed_out: bool=False, **kwargs) -> Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, List[Obs]]]]]]:
|
||||
"""Read sfcf files from given folder structure.
|
||||
|
||||
Parameters
|
||||
|
|
@ -407,22 +410,22 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
|
|||
return result_dict
|
||||
|
||||
|
||||
def _lists2key(*lists):
|
||||
def _lists2key(*lists) -> List[str]:
|
||||
keys = []
|
||||
for tup in itertools.product(*lists):
|
||||
keys.append(sep.join(tup))
|
||||
return keys
|
||||
|
||||
|
||||
def _key2specs(key):
|
||||
def _key2specs(key: str) -> List[str]:
|
||||
return key.split(sep)
|
||||
|
||||
|
||||
def _specs2key(*specs):
|
||||
def _specs2key(*specs) -> str:
|
||||
return sep.join(specs)
|
||||
|
||||
|
||||
def _read_o_file(cfg_path, name, needed_keys, intern, version, im):
|
||||
def _read_o_file(cfg_path: str, name: str, needed_keys: List[str], intern: Dict[str, Dict[str, Union[bool, Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[int, str]]]]]], int]]], version: str, im: int) -> Dict[str, List[float]]:
|
||||
return_vals = {}
|
||||
for key in needed_keys:
|
||||
file = cfg_path + '/' + name
|
||||
|
|
@ -447,7 +450,7 @@ def _read_o_file(cfg_path, name, needed_keys, intern, version, im):
|
|||
return return_vals
|
||||
|
||||
|
||||
def _extract_corr_type(corr_type):
|
||||
def _extract_corr_type(corr_type: str) -> Tuple[bool, bool]:
|
||||
if corr_type == 'bb':
|
||||
b2b = True
|
||||
single = True
|
||||
|
|
@ -460,7 +463,7 @@ def _extract_corr_type(corr_type):
|
|||
return b2b, single
|
||||
|
||||
|
||||
def _find_files(rep_path, prefix, compact, files=[]):
|
||||
def _find_files(rep_path: str, prefix: str, compact: bool, files: List[Union[range, str, Any]]=[]) -> List[str]:
|
||||
sub_ls = []
|
||||
if not files == []:
|
||||
files.sort(key=lambda x: int(re.findall(r'\d+', x)[-1]))
|
||||
|
|
@ -487,7 +490,7 @@ def _find_files(rep_path, prefix, compact, files=[]):
|
|||
return files
|
||||
|
||||
|
||||
def _make_pattern(version, name, noffset, wf, wf2, b2b, quarks):
|
||||
def _make_pattern(version: str, name: str, noffset: str, wf: str, wf2: Union[str, int], b2b: bool, quarks: str) -> str:
|
||||
if version == "0.0":
|
||||
pattern = "# " + name + " : offset " + str(noffset) + ", wf " + str(wf)
|
||||
if b2b:
|
||||
|
|
@ -501,7 +504,7 @@ def _make_pattern(version, name, noffset, wf, wf2, b2b, quarks):
|
|||
return pattern
|
||||
|
||||
|
||||
def _find_correlator(file_name, version, pattern, b2b, silent=False):
|
||||
def _find_correlator(file_name: str, version: str, pattern: str, b2b: bool, silent: bool=False) -> Tuple[int, int]:
|
||||
T = 0
|
||||
|
||||
with open(file_name, "r") as my_file:
|
||||
|
|
@ -527,7 +530,7 @@ def _find_correlator(file_name, version, pattern, b2b, silent=False):
|
|||
return start_read, T
|
||||
|
||||
|
||||
def _read_compact_file(rep_path, cfg_file, intern, needed_keys, im):
|
||||
def _read_compact_file(rep_path: str, cfg_file: str, intern: Dict[str, Dict[str, Union[bool, Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[int, str]]]]]], int]]], needed_keys: List[str], im: int) -> Dict[str, List[float]]:
|
||||
return_vals = {}
|
||||
with open(rep_path + cfg_file) as fp:
|
||||
lines = fp.readlines()
|
||||
|
|
@ -558,7 +561,7 @@ def _read_compact_file(rep_path, cfg_file, intern, needed_keys, im):
|
|||
return return_vals
|
||||
|
||||
|
||||
def _read_compact_rep(path, rep, sub_ls, intern, needed_keys, im):
|
||||
def _read_compact_rep(path: str, rep: str, sub_ls: List[str], intern: Dict[str, Dict[str, Union[bool, Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[int, str]]]]]], int]]], needed_keys: List[str], im: int) -> Dict[str, List[ndarray]]:
|
||||
rep_path = path + '/' + rep + '/'
|
||||
no_cfg = len(sub_ls)
|
||||
|
||||
|
|
@ -580,7 +583,7 @@ def _read_compact_rep(path, rep, sub_ls, intern, needed_keys, im):
|
|||
return return_vals
|
||||
|
||||
|
||||
def _read_chunk(chunk, gauge_line, cfg_sep, start_read, T, corr_line, b2b, pattern, im, single):
|
||||
def _read_chunk(chunk: List[str], gauge_line: int, cfg_sep: str, start_read: int, T: int, corr_line: int, b2b: bool, pattern: str, im: int, single: bool) -> Tuple[int, List[float]]:
|
||||
try:
|
||||
idl = int(chunk[gauge_line].split(cfg_sep)[-1])
|
||||
except Exception:
|
||||
|
|
@ -597,7 +600,7 @@ def _read_chunk(chunk, gauge_line, cfg_sep, start_read, T, corr_line, b2b, patte
|
|||
return idl, data
|
||||
|
||||
|
||||
def _read_append_rep(filename, pattern, b2b, cfg_separator, im, single):
|
||||
def _read_append_rep(filename: str, pattern: str, b2b: bool, cfg_separator: str, im: int, single: bool) -> Tuple[int, List[int], List[List[float]]]:
|
||||
with open(filename, 'r') as fp:
|
||||
content = fp.readlines()
|
||||
data_starts = []
|
||||
|
|
@ -646,7 +649,7 @@ def _read_append_rep(filename, pattern, b2b, cfg_separator, im, single):
|
|||
return T, rep_idl, data
|
||||
|
||||
|
||||
def _get_rep_names(ls, ens_name=None):
|
||||
def _get_rep_names(ls: List[str], ens_name: None=None) -> List[str]:
|
||||
new_names = []
|
||||
for entry in ls:
|
||||
try:
|
||||
|
|
@ -661,7 +664,7 @@ def _get_rep_names(ls, ens_name=None):
|
|||
return new_names
|
||||
|
||||
|
||||
def _get_appended_rep_names(ls, prefix, name, ens_name=None):
|
||||
def _get_appended_rep_names(ls: List[str], prefix: str, name: str, ens_name: None=None) -> List[str]:
|
||||
new_names = []
|
||||
for exc in ls:
|
||||
if not fnmatch.fnmatch(exc, prefix + '*.' + name):
|
||||
|
|
|
|||
|
|
@ -1,11 +1,13 @@
|
|||
"""Utilities for the input"""
|
||||
|
||||
from __future__ import annotations
|
||||
import re
|
||||
import fnmatch
|
||||
import os
|
||||
from typing import List
|
||||
|
||||
|
||||
def sort_names(ll):
|
||||
def sort_names(ll: List[str]) -> List[str]:
|
||||
"""Sorts a list of names of replika with searches for `r` and `id` in the replikum string.
|
||||
If this search fails, a fallback method is used,
|
||||
where the strings are simply compared and the first diffeing numeral is used for differentiation.
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue