BasicPulseAnalyzer.analyse_mean_norm() - Code Metrics - Inspection of "Pulsed 3.0" - Ulm-IQO/qudi - Measure and Improve Code Quality continuously with Scrutinizer

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Pull Request — master (#384)

unknown

created 2018-06-07 08:39 UTC

BasicPulseAnalyzer.analyse_mean_norm() C

↳ Parent: BasicPulseAnalyzer

Complexity

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Total Lines

Duplication

Lines	0
Ratio	0 %

Importance

Changes	2
Bugs	0	Features	0

Metric	Value
cc	9
c	2
b	0
f	0
dl	0
loc	55
rs	5.4159

How to fix Long Method

# -*- coding: utf-8 -*-
"""
This file contains basic pulse analysis methods for Qudi.

Qudi is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

Qudi is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with Qudi. If not, see <http://www.gnu.org/licenses/>.

Copyright (c) the Qudi Developers. See the COPYRIGHT.txt file at the
top-level directory of this distribution and at <https://github.com/Ulm-IQO/qudi/>
"""

import numpy as np

from logic.pulsed.pulse_analyzer import PulseAnalyzerBase


class BasicPulseAnalyzer(PulseAnalyzerBase):
    """

    """
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)

    def analyse_mean_norm(self, laser_data, signal_start=0.0, signal_end=200e-9, norm_start=300e-9,
                          norm_end=500e-9):
        """

        @param laser_data:
        @param signal_start:
        @param signal_end:
        @param norm_start:
        @param norm_end:
        @return:
        """
        # Get number of lasers
        num_of_lasers = laser_data.shape[0]
        # Get counter bin width
        bin_width = self.fast_counter_settings.get('bin_width')

        if not isinstance(bin_width, float):
            return np.zeros(num_of_lasers), np.zeros(num_of_lasers)

        # Convert the times in seconds to bins (i.e. array indices)
        signal_start_bin = round(signal_start / bin_width)
        signal_end_bin = round(signal_end / bin_width)
        norm_start_bin = round(norm_start / bin_width)
        norm_end_bin = round(norm_end / bin_width)

        # initialize data arrays for signal and measurement error
        signal_data = np.empty(num_of_lasers, dtype=float)
        error_data = np.empty(num_of_lasers, dtype=float)

        # loop over all laser pulses and analyze them
        for ii, laser_arr in enumerate(laser_data):
            # calculate the sum and mean of the data in the normalization window
            tmp_data = laser_arr[norm_start_bin:norm_end_bin]
            reference_sum = np.sum(tmp_data)
            reference_mean = (reference_sum / len(tmp_data)) if len(tmp_data) != 0 else 0.0

            # calculate the sum and mean of the data in the signal window
            tmp_data = laser_arr[signal_start_bin:signal_end_bin]
            signal_sum = np.sum(tmp_data)
            signal_mean = (signal_sum / len(tmp_data)) if len(tmp_data) != 0 else 0.0

            # Calculate normalized signal while avoiding division by zero
            if reference_mean > 0 and signal_mean >= 0:
                signal_data[ii] = signal_mean / reference_mean
            else:
                signal_data[ii] = 0.0

            # Calculate measurement error while avoiding division by zero
            if reference_sum > 0 and signal_sum > 0:
                # calculate with respect to gaussian error 'evolution'
                error_data[ii] = signal_data[ii] * np.sqrt(1 / signal_sum + 1 / reference_sum)
            else:
                error_data[ii] = 0.0

        return signal_data, error_data

    def analyse_mean(self, laser_data, signal_start=0.0, signal_end=200e-9):
        """

        @param laser_data:
        @param signal_start:
        @param signal_end:
        @return:
        """
        # Get number of lasers
        num_of_lasers = laser_data.shape[0]
        # Get counter bin width
        bin_width = self.fast_counter_settings.get('bin_width')

        if not isinstance(bin_width, float):
            return np.zeros(num_of_lasers), np.zeros(num_of_lasers)

        # Convert the times in seconds to bins (i.e. array indices)
        signal_start_bin = round(signal_start / bin_width)
        signal_end_bin = round(signal_end / bin_width)

        # initialize data arrays for signal and measurement error
        signal_data = np.empty(num_of_lasers, dtype=float)
        error_data = np.empty(num_of_lasers, dtype=float)

        # loop over all laser pulses and analyze them
        for ii, laser_arr in enumerate(laser_data):
            # calculate the sum and mean of the data in the signal window
            signal_mean = laser_arr[signal_start_bin:signal_end_bin].mean()

            # Avoid numpy C type variables overflow and NaN values
            if signal_mean < 0 or signal_mean != signal_mean:
                signal_data[ii] = 0.0
                error_data[ii] = 0.0
            else:
                signal_data[ii] = signal_mean
                error_data[ii] = np.sqrt(signal_mean)

        return signal_data, error_data


1			# -- coding: utf-8 --
2			"""
3			This file contains basic pulse analysis methods for Qudi.
4
5			Qudi is free software: you can redistribute it and/or modify
6			it under the terms of the GNU General Public License as published by
7			the Free Software Foundation, either version 3 of the License, or
8			(at your option) any later version.
9
10			Qudi is distributed in the hope that it will be useful,
11			but WITHOUT ANY WARRANTY; without even the implied warranty of
12			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13			GNU General Public License for more details.
14
15			You should have received a copy of the GNU General Public License
16			along with Qudi. If not, see <http://www.gnu.org/licenses/>.
17
18			Copyright (c) the Qudi Developers. See the COPYRIGHT.txt file at the
19			top-level directory of this distribution and at <https://github.com/Ulm-IQO/qudi/>
20			"""
21
22			import numpy as np
23
24			from logic.pulsed.pulse_analyzer import PulseAnalyzerBase
25
26
27			class BasicPulseAnalyzer(PulseAnalyzerBase):
28			"""
29
30			"""
31			def __init__(self, args, *kwargs):
32			super().__init__(args, *kwargs)
33
34			def analyse_mean_norm(self, laser_data, signal_start=0.0, signal_end=200e-9, norm_start=300e-9,
35			norm_end=500e-9):
36			"""
37
38			@param laser_data:
39			@param signal_start:
40			@param signal_end:
41			@param norm_start:
42			@param norm_end:
43			@return:
44			"""
45			# Get number of lasers
46			num_of_lasers = laser_data.shape[0]
47			# Get counter bin width
48			bin_width = self.fast_counter_settings.get('bin_width')
49
50			if not isinstance(bin_width, float):
51			return np.zeros(num_of_lasers), np.zeros(num_of_lasers)
52
53			# Convert the times in seconds to bins (i.e. array indices)
54			signal_start_bin = round(signal_start / bin_width)
55			signal_end_bin = round(signal_end / bin_width)
56			norm_start_bin = round(norm_start / bin_width)
57			norm_end_bin = round(norm_end / bin_width)
58
59			# initialize data arrays for signal and measurement error
60			signal_data = np.empty(num_of_lasers, dtype=float)
61			error_data = np.empty(num_of_lasers, dtype=float)
62
63			# loop over all laser pulses and analyze them
64			for ii, laser_arr in enumerate(laser_data):
65			# calculate the sum and mean of the data in the normalization window
66			tmp_data = laser_arr[norm_start_bin:norm_end_bin]
67			reference_sum = np.sum(tmp_data)
68			reference_mean = (reference_sum / len(tmp_data)) if len(tmp_data) != 0 else 0.0
69
70			# calculate the sum and mean of the data in the signal window
71			tmp_data = laser_arr[signal_start_bin:signal_end_bin]
72			signal_sum = np.sum(tmp_data)
73			signal_mean = (signal_sum / len(tmp_data)) if len(tmp_data) != 0 else 0.0
74
75			# Calculate normalized signal while avoiding division by zero
76			if reference_mean > 0 and signal_mean >= 0:
77			signal_data[ii] = signal_mean / reference_mean
78			else:
79			signal_data[ii] = 0.0
80
81			# Calculate measurement error while avoiding division by zero
82			if reference_sum > 0 and signal_sum > 0:
83			# calculate with respect to gaussian error 'evolution'
84			error_data[ii] = signal_data[ii] * np.sqrt(1 / signal_sum + 1 / reference_sum)
85			else:
86			error_data[ii] = 0.0
87
88			return signal_data, error_data
89
90			def analyse_mean(self, laser_data, signal_start=0.0, signal_end=200e-9):
91			"""
92
93			@param laser_data:
94			@param signal_start:
95			@param signal_end:
96			@return:
97			"""
98			# Get number of lasers
99			num_of_lasers = laser_data.shape[0]
100			# Get counter bin width
101			bin_width = self.fast_counter_settings.get('bin_width')
102
103			if not isinstance(bin_width, float):
104			return np.zeros(num_of_lasers), np.zeros(num_of_lasers)
105
106			# Convert the times in seconds to bins (i.e. array indices)
107			signal_start_bin = round(signal_start / bin_width)
108			signal_end_bin = round(signal_end / bin_width)
109
110			# initialize data arrays for signal and measurement error
111			signal_data = np.empty(num_of_lasers, dtype=float)
112			error_data = np.empty(num_of_lasers, dtype=float)
113
114			# loop over all laser pulses and analyze them
115			for ii, laser_arr in enumerate(laser_data):
116			# calculate the sum and mean of the data in the signal window
117			signal_mean = laser_arr[signal_start_bin:signal_end_bin].mean()
118
119			# Avoid numpy C type variables overflow and NaN values
120			if signal_mean < 0 or signal_mean != signal_mean:
121			signal_data[ii] = 0.0
122			error_data[ii] = 0.0
123			else:
124			signal_data[ii] = signal_mean
125			error_data[ii] = np.sqrt(signal_mean)
126
127			return signal_data, error_data
128

Ulm-IQO / qudi

Pull Request — master (#384)

BasicPulseAnalyzer.analyse_mean_norm() C

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How to fix Long Method

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