577 lines
22 KiB
Python
577 lines
22 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# *****************************************************************************
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# This program is free software; you can redistribute it and/or modify it under
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# the terms of the GNU General Public License as published by the Free Software
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# Foundation; either version 2 of the License, or (at your option) any later
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# version.
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#
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# This program is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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# details.
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#
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# You should have received a copy of the GNU General Public License along with
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# this program; if not, write to the Free Software Foundation, Inc.,
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# 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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#
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# Module authors:
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# Markus Zolliker <markus.zolliker@psi.ch>
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# *****************************************************************************
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"""Software calibration"""
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import os
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import re
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from os.path import basename, dirname, exists, join
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import numpy as np
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from scipy.interpolate import PchipInterpolator, CubicSpline, PPoly # pylint: disable=import-error
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from frappy.errors import ProgrammingError, RangeError
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from frappy.lib import clamp
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to_scale = {
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'lin': lambda x: x,
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'log': lambda x: np.log10(x),
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}
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from_scale = {
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'lin': lambda x: x,
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'log': lambda x: 10 ** np.array(x),
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}
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TYPES = [ # lakeshore type, inp-type, loglog
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('DT', 'si', False), # Si diode
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('TG', 'gaalas', False), # GaAlAs diode
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('PT', 'pt250', False), # platinum, 250 Ohm range
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('PT', 'pt500', False), # platinum, 500 Ohm range
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('PT', 'pt2500', False), # platinum, 2500 Ohm range
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('RF', 'rhfe', False), # rhodium iron
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('CC', 'c', True), # carbon, LakeShore acronym unknown
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('CX', 'cernox', True), # Cernox
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('RX', 'ruox', True), # rutheniumm oxide
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('GE', 'ge', True), # germanium, LakeShore acronym unknown
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]
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OPTION_TYPE = {
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'loglog': 0, # boolean
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'extrange': 2, # tuple(min T, max T for extrapolation
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'calibrange': 2, # tuple(min T, max T)
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}
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class HasOptions:
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def insert_option(self, key, value):
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key = key.strip()
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argtype = OPTION_TYPE.get(key, 1)
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if argtype == 1: # one number or string
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try:
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value = float(value)
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except ValueError:
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value = value.strip()
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elif argtype == 0:
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if value.strip().lower() in ('false', '0'):
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value = False
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else:
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value = True
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else:
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value = [float(f) for f in value.split(',')]
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self.options[key] = value
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class StdParser(HasOptions):
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"""parser used for reading columns"""
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def __init__(self, **options):
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"""keys of options may be either 'x' or 'logx' and either 'y' or 'logy'
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default is x=0, y=1
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"""
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if 'logx' in options:
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self.xscale = 'log'
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self.xcol = options.pop('logx')
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else:
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self.xscale = 'lin'
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self.xcol = options.pop('x', 0)
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if 'logy' in options:
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self.yscale = 'log'
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self.ycol = options.pop('logy')
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else:
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self.yscale = 'lin'
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self.ycol = options.pop('y', 1)
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self.xdata, self.ydata = [], []
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self.options = options
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self.invalid_lines = []
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def parse(self, line):
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"""get numbers from a line and put them to self.xdata / self.ydata"""
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row = line.split()
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try:
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self.xdata.append(float(row[self.xcol]))
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self.ydata.append(float(row[self.ycol]))
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except (IndexError, ValueError):
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self.invalid_lines.append(line)
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return
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def finish(self):
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pass
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class InpParser(StdParser):
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"""M. Zollikers *.inp calcurve format"""
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HEADERLINE = re.compile(r'#?(?:(\w+)\s*=\s*([^!# \t\n]*)|curv.*)')
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INP_TYPES = {ityp: (ltyp, loglog) for ltyp, ityp, loglog in TYPES}
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def __init__(self, **options):
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options.update(x=0, y=1)
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super().__init__(**options)
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self.header = True
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def parse(self, line):
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"""scan header"""
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if self.header:
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match = self.HEADERLINE.match(line)
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if match:
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key, value = match.groups()
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if key is None:
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self.header = False
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else:
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key = key.lower()
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value = value.strip()
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if key == 'type':
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type_, loglog = self.INP_TYPES.get(value.lower(), (None, None))
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if type_ is not None:
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self.options['type'] = type_
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if loglog is not None:
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self.options['loglog'] = loglog
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else:
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self.insert_option(key, value)
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return
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elif line.startswith('!'):
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return
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super().parse(line)
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class Parser340(StdParser):
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"""parser for LakeShore *.340 files"""
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HEADERLINE = re.compile(r'([^:]*):\s*([^(]*)')
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CALIBHIGH = dict(L=325, M=420, H=500, B=40)
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def __init__(self, **options):
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options.update(x=1, y=2)
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super().__init__(**options)
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self.header = True
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def parse(self, line):
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"""scan header"""
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if self.header:
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match = self.HEADERLINE.match(line)
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if match:
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key, value = match.groups()
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key = ''.join(key.split()).lower()
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value = value.strip()
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if key == 'dataformat':
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if value[0:1] == '4':
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self.xscale, self.yscale = 'log', 'lin' # logOhm
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self.options['loglog'] = True
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elif value[0:1] == '5':
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self.xscale, self.yscale = 'log', 'log' # logOhm, logK
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self.options['loglog'] = True
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elif value[0:1] in ('1', '2', '3'):
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self.options['loglog'] = False
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else:
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raise ValueError('invalid Data Format')
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self.options['scale'] = self.xscale + self.yscale
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self.insert_option(key, value)
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return
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if 'No.' in line:
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self.header = False
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return
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if len(line.split()) != 3:
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return
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super().parse(line)
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if self.header and self.xdata:
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# valid line detected
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self.header = False
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def finish(self):
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model = self.options.get('sensormodel', '').split('-')
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if model[0]:
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self.options['type'] = model[0]
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if 'calibrange' not in self.options:
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if len(model) > 2:
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try: # e.g. model[-1] == 1.4M -> calibrange = 1.4, 420
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self.options['calibrange'] = float(model[-1][:-1]), self.CALIBHIGH[model[-1][-1]]
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return
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except (ValueError, KeyError):
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pass
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class CaldatParser(StdParser):
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"""parser for format from sea/tcl/startup/calib_ext.tcl"""
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def __init__(self, options):
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options.update(x=1, y=2)
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super().__init__(options)
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PARSERS = {
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"340": Parser340,
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"inp": InpParser,
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"caldat": CaldatParser,
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"dat": StdParser, # lakeshore raw data *.dat format
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}
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def check(x, y, islog):
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# check interpolation error
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yi = y[:-2] + (x[1:-1] - x[:-2]) * (y[2:] - y[:-2]) / (x[2:] - x[:-2])
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if islog:
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return sum((yi - y[1:-1]) ** 2)
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return sum((np.log10(yi) - np.log10(y[1:-1])) ** 2)
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def get_curve(newscale, curves):
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"""get curve from curve cache (converts not existing ones)
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:param newscale: the new scale to get
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:param curves: a dict <scale> of <array> storing available scales
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:return: the retrieved or converted curve
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"""
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if newscale in curves:
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return curves[newscale]
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for scale, array in curves.items():
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curves[newscale] = curve = to_scale[newscale](from_scale[scale](array))
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return curve
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class CalCurve(HasOptions):
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EXTRAPOLATION_AMOUNT = 0.1
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MAX_EXTRAPOLATION_FACTOR = 2
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def __init__(self, calibspec=None, *, x=None, y=None, cubic_spline=True, **options):
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"""calibration curve
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:param calibspec: a string with name or filename, options
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lookup path for files in env. variable FRAPPY_CALIB_PATH
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calibspec format:
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[<full path> | <name>][,<key>=<value> ...]
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for <key>/<value> as in parser arguments
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:param x, y: x and y arrays (given instead of calibspec)
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:param cubic_split: set to False for always using Pchip interpolation
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:param options: options for parsers
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"""
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self.options = options
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if calibspec is None:
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parser = StdParser()
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parser.xdata = x
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parser.ydata = y
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else:
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if x or y:
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raise ProgrammingError('can not give both calibspec and x,y ')
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sensopt = calibspec.split(',')
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calibname = sensopt.pop(0)
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_, dot, ext = basename(calibname).rpartition('.')
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kind = None
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pathlist = os.environ.get('FRAPPY_CALIB_PATH', '').split(':')
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pathlist.append(join(dirname(__file__), 'calcurves'))
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for path in pathlist:
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# first try without adding kind
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filename = join(path.strip(), calibname)
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if exists(filename):
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kind = ext if dot else None
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break
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# then try adding all kinds as extension
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for nam in calibname, calibname.upper(), calibname.lower():
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for kind in PARSERS:
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filename = join(path.strip(), '%s.%s' % (nam, kind))
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if exists(filename):
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break
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else:
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continue
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break
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else:
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continue
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break
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else:
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raise FileNotFoundError(calibname)
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sensopt = iter(sensopt)
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for opt in sensopt:
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key, _, value = opt.lower().partition('=')
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if OPTION_TYPE.get(key) == 2:
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self.options[key] = float(value), float(next(sensopt))
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else:
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self.insert_option(key, value)
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kind = self.options.pop('kind', kind)
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cls = PARSERS.get(kind, StdParser)
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try:
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parser = cls(**self.options)
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with open(filename, encoding='utf-8') as f:
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for line in f:
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parser.parse(line)
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parser.finish()
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except Exception as e:
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raise ValueError('error parsing calib curve %s %r' % (calibspec, e)) from e
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# take defaults from parser options
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self.options = dict(parser.options, **self.options)
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x = np.asarray(parser.xdata)
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y = np.asarray(parser.ydata)
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if len(x) < 2:
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raise ValueError('calib file %s has less than 2 points' % calibspec)
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if x[0] > x[-1]:
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x = np.flip(np.array(x))
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y = np.flip(np.array(y))
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else:
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x = np.array(x)
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y = np.array(y)
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not_incr_idx = np.argwhere(x[1:] <= x[:-1])
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if len(not_incr_idx):
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raise RangeError('x not monotonic at x=%.4g' % x[not_incr_idx[0]])
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self.x = {parser.xscale: x}
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self.y = {parser.yscale: y}
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self.lin_forced = [parser.yscale == 'lin' and (y[0] <= 0 or y[-1] <= 0),
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parser.xscale == 'lin' and x[0] <= 0]
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if sum(self.lin_forced):
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self.loglog = False
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else:
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self.loglog = self.options.get('loglog', y[0] > y[-1]) # loglog defaults to True for NTC
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newscale = 'log' if self.loglog else 'lin'
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self.scale = newscale
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x = get_curve(newscale, self.x)
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y = get_curve(newscale, self.y)
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self.convert_x = to_scale[newscale]
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self.convert_y = from_scale[newscale]
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self.calibrange = self.options.get('calibrange')
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dirty = set()
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self.extra_points = False
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self.cutted = False
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if self.calibrange:
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self.calibrange = sorted(self.calibrange)
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# determine indices (ibeg, iend) of first and last well calibrated point
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ylin = get_curve('lin', self.y)
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beg, end = self.calibrange
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if y[0] > y[-1]:
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ylin = -ylin
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beg, end = -end, -beg
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ibeg, iend = np.searchsorted(ylin, (beg, end))
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if ibeg > 0 and abs(ylin[ibeg-1] - beg) < 0.1 * (ylin[ibeg] - ylin[ibeg-1]):
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# add previous point, if close
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ibeg -= 1
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if iend < len(ylin) and abs(ylin[iend] - end) < 0.1 * (ylin[iend] - ylin[iend-1]):
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# add next point, if close
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iend += 1
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if self.options.get('cut', False):
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self.cutted = True
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x = x[ibeg:iend]
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y = y[ibeg:iend]
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self.x = {newscale: x}
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self.y = {newscale: y}
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ibeg = 0
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iend = len(x)
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dirty.add('xy')
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else:
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self.extra_points = ibeg, len(x) - iend
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else:
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ibeg = 0
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iend = len(x)
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ylin = get_curve('lin', self.y)
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self.calibrange = tuple(sorted([ylin[0], ylin[-1]]))
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if cubic_spline:
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# fit well calibrated part with spline
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# determine slopes of calibrated part with CubicSpline
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spline = CubicSpline(x[ibeg:iend], y[ibeg:iend])
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roots = spline.derivative().roots(extrapolate=False)
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if len(roots):
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cubic_spline = False
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self.cubic_spline = cubic_spline
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if cubic_spline:
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coeff = spline.c
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if self.extra_points:
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p = PchipInterpolator(x, y).c
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# use Pchip outside left and right of calibrange
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# remark: first derivative at end of calibrange is not continuous
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coeff = np.concatenate((p[:, :ibeg], coeff, p[:, iend-1:]), axis=1)
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else:
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spline = PchipInterpolator(x, y)
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coeff = spline.c
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# extrapolation extension
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# linear extrapolation is more robust than spline extrapolation
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x1, x2 = x[0], x[-1]
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# take slope at end of calibrated range for extrapolation
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slopes = spline([x[ibeg], x[iend-1]], 1)
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for i, j in enumerate([ibeg, iend-2]):
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# slope of last interval in calibrange
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si = (y[j+1] - y[j])/(x[j+1] - x[j])
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# make sure slope is not more than a factor 2 different
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# from the slope calculated at the outermost calibrated intervals
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slopes[i] = clamp(slopes[i], 2*si, 0.5 * si)
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dx = 0.1 if self.loglog else (x2 - x1) * 0.1
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xe = np.concatenate(([x1 - dx], x, [x2 + dx]))
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# x3 = np.append(x, x2 + dx)
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# y3 = np.append(y, y[-1] + slope * dx)
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y0 = y[0] - slopes[0] * dx
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coeff = np.concatenate(([[0], [0], [slopes[0]], [y0]], coeff, [[0], [0], [slopes[1]], [y[-1]]]), axis=1)
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self.spline = PPoly(coeff, xe)
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# ranges without extrapolation:
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self.xrange = get_curve('lin', self.x)[[0, -1]]
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self.yrange = sorted(get_curve('lin', self.y)[[0, -1]])
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self.calibrange = [max(self.calibrange[0], self.yrange[0]),
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min(self.calibrange[1], self.yrange[1])]
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self.set_extrapolation()
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# check
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# ys = self.spline(xe)
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# ye = np.concatenate(([y0], y, [y[-1] + slope2 * dx]))
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# assert np.all(np.abs(ys - ye) < 1e-5 * (0.1 + np.abs(ys + ye)))
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def set_extrapolation(self, extleft=None, extright=None):
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"""set default extrapolation range for export method
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:param extleft: y value for the lower end of the extrapolation
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:param extright: y value for the upper end of the extrapolation
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if arguments omitted or None are replaced by a default extrapolation scheme
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on return self.extx and self.exty are set to the extrapolated ranges
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"""
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yc1, yc2 = self.calibrange
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y1, y2 = to_scale[self.scale]([yc1, yc2])
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d = (y2 - y1) * self.EXTRAPOLATION_AMOUNT
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yex1, yex2 = tuple(from_scale[self.scale]([y1 - d, y2 + d]))
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t1, t2 = tuple(from_scale[self.scale]([y1, y2]))
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# raw units, excluding extrapolation points at end
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xrng = self.spline.x[1], self.spline.x[-2]
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# first and last point
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yp1, yp2 = sorted(from_scale[self.scale](self.spline(xrng)))
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xrng = from_scale[self.scale](xrng)
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# limit by maximal factor
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f = self.MAX_EXTRAPOLATION_FACTOR
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# but ext range should be at least to the points in curve
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self.exty = [min(yp1, max(yex1, min(t1 / f, t1 * f))),
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max(yp2, min(yex2, max(t2 * f, t2 / f)))]
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if extleft is not None:
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self.exty[0] = min(extleft, yp1)
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if extright is not None:
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self.exty[1] = max(extright, yp2)
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self.extx = sorted(self.invert(*yd) for yd in zip(self.exty, xrng))
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# check that sensor range is not extended by more than a factor f
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extnew = [max(self.extx[0], min(xrng[0] / f, xrng[0] * f)),
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min(self.extx[1], max(xrng[1] / f, xrng[1] * f))]
|
|
if extnew != self.extx:
|
|
# need further reduction
|
|
self.extx = extnew
|
|
self.exty = sorted(self(extnew))
|
|
|
|
def convert(self, value):
|
|
"""convert a single value
|
|
|
|
return a tuple (converted value, boolean: was it clamped?)
|
|
"""
|
|
x = clamp(value, *self.extx)
|
|
return self(x), x == value
|
|
|
|
def __call__(self, value):
|
|
"""convert value or numpy array without checking extrapolation range"""
|
|
return self.convert_y(self.spline(self.convert_x(value)))
|
|
|
|
def invert(self, y, defaultx=None, xscale=True, yscale=True):
|
|
"""invert y, return defaultx if no solution is found"""
|
|
if yscale:
|
|
y = to_scale[self.scale](y)
|
|
r = self.spline.solve(y)
|
|
try:
|
|
if xscale:
|
|
return from_scale[self.scale](r[0])
|
|
return r[0]
|
|
except IndexError:
|
|
return defaultx
|
|
|
|
def export(self, logformat=False, nmax=199, yrange=None, extrapolate=True, xlimits=None):
|
|
"""export curve for downloading to hardware
|
|
|
|
:param nmax: max number of points. if the number of given points is bigger,
|
|
the points with the lowest interpolation error are omitted
|
|
:param logformat: a list with two elements of None, True or False
|
|
True: use log, False: use line, None: use log if self.loglog
|
|
values None are replaced with the effectively used format
|
|
False / True are replaced by [False, False] / [True, True]
|
|
default is False
|
|
:param yrange: to reduce or extrapolate to this interval (extrapolate is ignored when given)
|
|
:param extrapolate: a flag indicating whether the curves should be extrapolated
|
|
to the preset extrapolation range
|
|
:param xlimits: max x range
|
|
:return: numpy array with 2 dimensions returning the curve
|
|
"""
|
|
|
|
if logformat in (True, False):
|
|
logformat = [logformat, logformat]
|
|
try:
|
|
scales = []
|
|
for idx, logfmt in enumerate(logformat):
|
|
if logfmt and self.lin_forced[idx]:
|
|
raise ValueError('%s must contain positive values only' % 'xy'[idx])
|
|
logformat[idx] = linlog = self.loglog if logfmt is None else logfmt
|
|
scales.append('log' if linlog else 'lin')
|
|
xscale, yscale = scales
|
|
except (TypeError, AssertionError):
|
|
raise ValueError('logformat must be a 2 element list or a boolean')
|
|
|
|
x = self.spline.x[1:-1] # raw units, excluding extrapolated points
|
|
x1, x2 = xmin, xmax = x[0], x[-1]
|
|
y1, y2 = sorted(self.spline([x1, x2]))
|
|
|
|
if extrapolate and not yrange:
|
|
yrange = self.exty
|
|
if yrange is not None:
|
|
xmin, xmax = sorted(self.invert(*yd, xscale=False) for yd in zip(yrange, [x1, x2]))
|
|
if xlimits is not None:
|
|
lim = to_scale[self.scale](xlimits)
|
|
xmin = clamp(xmin, *lim)
|
|
xmax = clamp(xmax, *lim)
|
|
if xmin != x1 or xmax != x2:
|
|
ibeg, iend = np.searchsorted(x, (xmin, xmax))
|
|
if abs(x[ibeg] - xmin) < 0.1 * (x[ibeg + 1] - x[ibeg]):
|
|
# remove first point, if close
|
|
ibeg += 1
|
|
if abs(x[iend - 1] - xmax) < 0.1 * (x[iend - 1] - x[iend - 2]):
|
|
# remove last point, if close
|
|
iend -= 1
|
|
x = np.concatenate(([xmin], x[ibeg:iend], [xmax]))
|
|
y = self.spline(x)
|
|
|
|
# convert to exported scale
|
|
if xscale != self.scale:
|
|
x = to_scale[xscale](from_scale[self.scale](x))
|
|
if yscale != self.scale:
|
|
y = to_scale[yscale](from_scale[self.scale](y))
|
|
|
|
# reduce number of points, if needed
|
|
n = len(x)
|
|
i, j = 1, n - 1 # index range for calculating interpolation deviation
|
|
deviation = np.zeros(n)
|
|
while True:
|
|
# calculate interpolation error when a single point is omitted
|
|
ym = y[i-1:j-1] + (x[i:j] - x[i-1:j-1]) * (y[i+1:j+1] - y[i-1:j-1]) / (x[i+1:j+1] - x[i-1:j-1])
|
|
if yscale == 'log':
|
|
deviation[i:j] = np.abs(ym - y[i:j])
|
|
else:
|
|
deviation[i:j] = np.abs(ym - y[i:j]) / (np.abs(ym + y[i:j]) + 1e-10)
|
|
if n <= nmax:
|
|
break
|
|
idx = np.argmin(deviation[1:-1]) + 1 # find index of the smallest error
|
|
y = np.delete(y, idx)
|
|
x = np.delete(x, idx)
|
|
deviation = np.delete(deviation, idx)
|
|
n -= 1
|
|
# index range to recalculate
|
|
i, j = max(1, idx - 1), min(n - 1, idx + 1)
|
|
self.deviation = deviation # for debugging purposes
|
|
return np.stack([x, y], axis=1)
|