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PulseExtractionLogic.gated_extraction() B

↳ Parent: PulseExtractionLogic

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# -*- coding: utf-8 -*-
"""
This file contains the Qudi logic for the extraction of laser pulses.

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 scipy import ndimage
from logic.generic_logic import GenericLogic


class PulseExtractionLogic(GenericLogic):
    """unstable: Nikolas Tomek  """

    _modclass = 'PulseExtractionLogic'
    _modtype = 'logic'

    # declare connectors
    _out = {'pulseextractionlogic': 'PulseExtractionLogic'}

    def __init__(self, config, **kwargs):
        super().__init__(config=config, **kwargs)

        self.log.info('The following configuration was found.')
        # checking for the right configuration
        for key in config.keys():
            self.log.info('{0}: {1}'.format(key, config[key]))

    def on_activate(self, e):
        """ Initialisation performed during activation of the module.

        @param object e: Event class object from Fysom.
                         An object created by the state machine module Fysom,
                         which is connected to a specific event (have a look in
                         the Base Class). This object contains the passed event,
                         the state before the event happened and the destination
                         of the state which should be reached after the event
                         had happened.
        """
        self.extraction_method = None   # will later on be used to switch between different methods
        return

    def on_deactivate(self, e):
        """ Deinitialisation performed during deactivation of the module.

        @param object e: Event class object from Fysom. A more detailed
                         explanation can be found in method activation.
        """
        pass

    def gated_extraction(self, count_data, conv_std_dev):
        """ Detects the rising flank in the gated timetrace data and extracts
            just the laser pulses.

        @param numpy.ndarray count_data: 2D array, the raw timetrace data from a
                                         gated fast counter, dimensions:
                                            0: gate number,
                                            1: time bin)
        @param float conv_std_dev: standard deviation of the gaussian filter to be
                              applied for smoothing

        @return numpy.ndarray: The extracted laser pulses of the timetrace
                               dimensions:
                                    0: laser number,
                                    1: time bin
        """
        # sum up all gated timetraces to ease flank detection
        timetrace_sum = np.sum(count_data, 0)

        # apply gaussian filter to remove noise and compute the gradient of the
        # timetrace sum
        #FIXME: That option should be stated in the config, or should be
        #       choosable by the GUI, since it is not always desired.
        #       It should also be possible to display the bare laserpulse,
        #       without cutting away something.

        conv_deriv = self._convolve_derive(timetrace_sum.astype(float), conv_std_dev)
        # get indices of rising and falling flank

        rising_ind = conv_deriv.argmax()
        falling_ind = conv_deriv.argmin()
        # slice the data array to cut off anything but laser pulses
        laser_arr = count_data[:, rising_ind:falling_ind]
        return laser_arr.astype(int)

    def ungated_extraction(self, count_data, conv_std_dev, num_of_lasers):
        """ Detects the laser pulses in the ungated timetrace data and extracts
            them.

        @param numpy.ndarray count_data: 1D array the raw timetrace data from an
                                         ungated fast counter
        @param int num_of_lasers: The total number of laser pulses inside the
                                  pulse sequence
        @param float conv_std_dev: standard deviation of the gaussian filter to be
                              applied for smoothing

        @return 2D numpy.ndarray: 2D array, the extracted laser pulses of the
                                  timetrace, dimensions:
                                        0: laser number,
                                        1: time bin

        Procedure:
            Edge Detection:
            ---------------

            The count_data array with the laser pulses is smoothed with a
            gaussian filter (convolution), which used a defined standard
            deviation of 10 entries (bins). Then the derivation of the convolved
            time trace is taken to obtain the maxima and minima, which
            corresponds to the rising and falling edge of the pulses.

            The convolution with a gaussian removes nasty peaks due to count
            fluctuation within a laser pulse and at the same time ensures a
            clear distinction of the maxima and minima in the derived convolved
            trace.

            The maxima and minima are not found sequentially, pulse by pulse,
            but are rather globally obtained. I.e. the convolved and derived
            array is searched iteratively for a maximum and a minimum, and after
            finding those the array entries within the 4 times
            self.conv_std_dev (2*self.conv_std_dev to the left and
            2*self.conv_std_dev) are set to zero.

            The crucial part is the knowledge of the number of laser pulses and
            the choice of the appropriate std_dev for the gauss filter.

            To ensure a good performance of the edge detection, you have to
            ensure a steep rising and falling edge of the laser pulse! Be also
            careful in choosing a large conv_std_dev value and using a small
            laser pulse (rule of thumb: conv_std_dev < laser_length/10).
        """

        # apply gaussian filter to remove noise and compute the gradient of the
        # timetrace

        conv_deriv = self._convolve_derive(count_data.astype(float), conv_std_dev)

        # use a reference for array, because the exact position of the peaks or
        # dips (i.e. maxima or minima, which are the inflection points in the
        # pulse) are distorted by a large conv_std_dev value.
        conv_deriv_ref = self._convolve_derive(count_data, 10)

        # initialize arrays to contain indices for all rising and falling
        # flanks, respectively
        rising_ind = np.empty([num_of_lasers],int)
        falling_ind = np.empty([num_of_lasers],int)

        # Find as many rising and falling flanks as there are laser pulses in
        # the trace:
        for i in range(num_of_lasers):

            # save the index of the absolute maximum of the derived time trace
            # as rising edge position
            rising_ind[i] = np.argmax(conv_deriv)

            # refine the rising edge detection, by using a small and fixed
            # conv_std_dev parameter to find the inflection point more precise
            start_ind = int(rising_ind[i]-conv_std_dev)
            if start_ind < 0:
                start_ind = 0

            stop_ind = int(rising_ind[i]+conv_std_dev)
            if stop_ind > len(conv_deriv):
                stop_ind = len(conv_deriv)

            if start_ind == stop_ind:
                stop_ind = start_ind+1

            rising_ind[i] = start_ind + np.argmax(conv_deriv_ref[start_ind:stop_ind])

            # set this position and the surrounding of the saved edge to 0 to
            # avoid a second detection
            if rising_ind[i] < 2*conv_std_dev:                del_ind_start = 0
            else:
                del_ind_start = rising_ind[i] - 2*conv_std_dev
            if (conv_deriv.size - rising_ind[i]) < 2*conv_std_dev:
                del_ind_stop = conv_deriv.size-1
            else:
                del_ind_stop = rising_ind[i] + 2*conv_std_dev
                conv_deriv[del_ind_start:del_ind_stop] = 0

            # save the index of the absolute minimum of the derived time trace
            # as falling edge position
            falling_ind[i] = np.argmin(conv_deriv)

            # refine the falling edge detection, by using a small and fixed
            # conv_std_dev parameter to find the inflection point more precise
            start_ind = int(falling_ind[i]-conv_std_dev)
            if start_ind < 0:
                start_ind = 0

            stop_ind = int(falling_ind[i]+conv_std_dev)
            if stop_ind > len(conv_deriv):
                stop_ind = len(conv_deriv)

            if start_ind == stop_ind:
                stop_ind = start_ind+1

            falling_ind[i] = start_ind + np.argmin(conv_deriv_ref[start_ind:stop_ind])

            # set this position and the sourrounding of the saved flank to 0 to
            #  avoid a second detection
            if falling_ind[i] < 2*conv_std_dev:                del_ind_start = 0
            else:
                del_ind_start = falling_ind[i] - 2*conv_std_dev
            if (conv_deriv.size - falling_ind[i]) < 2*conv_std_dev:
                del_ind_stop = conv_deriv.size-1
            else:
                del_ind_stop = falling_ind[i] + 2*conv_std_dev
            conv_deriv[del_ind_start:del_ind_stop] = 0

        # sort all indices of rising and falling flanks
        rising_ind.sort()
        falling_ind.sort()

        # find the maximum laser length to use as size for the laser array
        laser_length = np.max(falling_ind-rising_ind)

        #Todo: Find better method, here the idea is to take a histogram to find
        # length of pulses
        #diff = (falling_ind-rising_ind)[np.where( falling_ind-rising_ind > 0)]
        #self.histo = np.histogram(diff)
        #laser_length = int(self.histo[1][self.histo[0].argmax()])

        # initialize the empty output array
        laser_arr = np.zeros([num_of_lasers, laser_length],int)
        # slice the detected laser pulses of the timetrace and save them in the
        # output array according to the found rising edge
        for i in range(num_of_lasers):
            if (rising_ind[i]+laser_length > count_data.size):
                lenarr = count_data[rising_ind[i]:].size
                laser_arr[i, 0:lenarr] = count_data[rising_ind[i]:]
            else:
                laser_arr[i] = count_data[rising_ind[i]:rising_ind[i]+laser_length]
        return laser_arr.astype(int)


    def _convolve_derive(self, data, std_dev):
        """ Smooth the input data by applying a gaussian filter.

        @param numpy.ndarray timetrace: 1D array, the raw data to be smoothed
                                        and derived
        @param float std_dev: standard deviation of the gaussian filter to be
                              applied for smoothing


        @return numpy.ndarray: 1D array, the smoothed and derived data

        The convolution is applied with specified standard deviation. The
        derivative of the smoothed data is computed afterwards and returned. If
        the input data is some kind of rectangular signal containing high
        frequency noise, the output data will show sharp peaks corresponding to
        the rising and falling flanks of the input signal.
        """
        conv = ndimage.filters.gaussian_filter1d(data, std_dev)
        conv_deriv = np.gradient(conv)
        return conv_deriv



    def get_data_laserpulses(self, num_of_lasers, conv_std_dev):
        """ Capture the fast counter data and extracts the laser pulses.

        @param int num_of_lasers: The total number of laser pulses inside the
                                  pulse sequence
        @param int conv_std_dev: Standard deviation of gaussian convolution


        @return tuple (numpy.ndarray, numpy.ndarray):
                    Explanation of the return value:

                    numpy.ndarray: 2D array, the extracted laser pulses of the
                                   timetrace, with the dimensions:
                                        0: laser number
                                        1: time bin
                    numpy.ndarray: 1D or 2D, the raw timetrace from the fast
                                   counter
        """
        # poll data from the fast counting device, netobtain is needed for
        # getting numpy array over network
        raw_data = netobtain(self._fast_counter_device.get_data_trace())
        if self.old_raw_data is not None:
            #if raw_data.shape == self.old_raw_data.shape:
            raw_data = np.add(raw_data, self.old_raw_data)

        # Saving data for testing

        # name = str(self._iter) + '.dat'
        # self._iter = self._iter + 1
        # np.savetxt(name, raw_data.transpose())

        # call appropriate laser extraction method depending on if the fast
        # counter is gated or not.
        if self.is_counter_gated:
            laser_data = self._gated_extraction(raw_data, conv_std_dev)
        else:
            laser_data = self._ungated_extraction(raw_data, num_of_lasers, conv_std_dev)
        return laser_data.astype(dtype=int), raw_data.astype(dtype=int)


    def _check_if_counter_gated(self):
        '''Check the fast counter if it is gated or not
        '''
        self.is_counter_gated = self._fast_counter_device.is_gated()
        return


1		# -- coding: utf-8 --
2		"""
3		This file contains the Qudi logic for the extraction of laser pulses.
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		from scipy import ndimage
24		from logic.generic_logic import GenericLogic
25
26
27		class PulseExtractionLogic(GenericLogic):
28		"""unstable: Nikolas Tomek """
29
30		_modclass = 'PulseExtractionLogic'
31		_modtype = 'logic'
32
33		# declare connectors
34		_out = {'pulseextractionlogic': 'PulseExtractionLogic'}
35
36		def __init__(self, config, **kwargs):
37		super().__init__(config=config, **kwargs)
38
39		self.log.info('The following configuration was found.')
40		# checking for the right configuration
41		for key in config.keys():
42		self.log.info('{0}: {1}'.format(key, config[key]))
43
44		def on_activate(self, e):
45		""" Initialisation performed during activation of the module.
46
47		@param object e: Event class object from Fysom.
48		An object created by the state machine module Fysom,
49		which is connected to a specific event (have a look in
50		the Base Class). This object contains the passed event,
51		the state before the event happened and the destination
52		of the state which should be reached after the event
53		had happened.
54		"""
55		self.extraction_method = None # will later on be used to switch between different methods
56		return
57
58		def on_deactivate(self, e):
59		""" Deinitialisation performed during deactivation of the module.
60
61		@param object e: Event class object from Fysom. A more detailed
62		explanation can be found in method activation.
63		"""
64		pass
65
66		def gated_extraction(self, count_data, conv_std_dev):
67		""" Detects the rising flank in the gated timetrace data and extracts
68		just the laser pulses.
69
70		@param numpy.ndarray count_data: 2D array, the raw timetrace data from a
71		gated fast counter, dimensions:
72		0: gate number,
73		1: time bin)
74		@param float conv_std_dev: standard deviation of the gaussian filter to be
75		applied for smoothing
76
77		@return numpy.ndarray: The extracted laser pulses of the timetrace
78		dimensions:
79		0: laser number,
80		1: time bin
81		"""
82		# sum up all gated timetraces to ease flank detection
83		timetrace_sum = np.sum(count_data, 0)
84
85		# apply gaussian filter to remove noise and compute the gradient of the
86		# timetrace sum
87		#FIXME: That option should be stated in the config, or should be
88		# choosable by the GUI, since it is not always desired.
89		# It should also be possible to display the bare laserpulse,
90		# without cutting away something.
91
92		conv_deriv = self._convolve_derive(timetrace_sum.astype(float), conv_std_dev)
93		# get indices of rising and falling flank
94
95		rising_ind = conv_deriv.argmax()
96		falling_ind = conv_deriv.argmin()
97		# slice the data array to cut off anything but laser pulses
98		laser_arr = count_data[:, rising_ind:falling_ind]
99		return laser_arr.astype(int)
100
101		def ungated_extraction(self, count_data, conv_std_dev, num_of_lasers):
102		""" Detects the laser pulses in the ungated timetrace data and extracts
103		them.
104
105		@param numpy.ndarray count_data: 1D array the raw timetrace data from an
106		ungated fast counter
107		@param int num_of_lasers: The total number of laser pulses inside the
108		pulse sequence
109		@param float conv_std_dev: standard deviation of the gaussian filter to be
110		applied for smoothing
111
112		@return 2D numpy.ndarray: 2D array, the extracted laser pulses of the
113		timetrace, dimensions:
114		0: laser number,
115		1: time bin
116
117		Procedure:
118		Edge Detection:
119		---------------
120
121		The count_data array with the laser pulses is smoothed with a
122		gaussian filter (convolution), which used a defined standard
123		deviation of 10 entries (bins). Then the derivation of the convolved
124		time trace is taken to obtain the maxima and minima, which
125		corresponds to the rising and falling edge of the pulses.
126
127		The convolution with a gaussian removes nasty peaks due to count
128		fluctuation within a laser pulse and at the same time ensures a
129		clear distinction of the maxima and minima in the derived convolved
130		trace.
131
132		The maxima and minima are not found sequentially, pulse by pulse,
133		but are rather globally obtained. I.e. the convolved and derived
134		array is searched iteratively for a maximum and a minimum, and after
135		finding those the array entries within the 4 times
136		self.conv_std_dev (2*self.conv_std_dev to the left and
137		2*self.conv_std_dev) are set to zero.
138
139		The crucial part is the knowledge of the number of laser pulses and
140		the choice of the appropriate std_dev for the gauss filter.
141
142		To ensure a good performance of the edge detection, you have to
143		ensure a steep rising and falling edge of the laser pulse! Be also
144		careful in choosing a large conv_std_dev value and using a small
145		laser pulse (rule of thumb: conv_std_dev < laser_length/10).
146		"""
147
148		# apply gaussian filter to remove noise and compute the gradient of the
149		# timetrace
150
151		conv_deriv = self._convolve_derive(count_data.astype(float), conv_std_dev)
152
153		# use a reference for array, because the exact position of the peaks or
154		# dips (i.e. maxima or minima, which are the inflection points in the
155		# pulse) are distorted by a large conv_std_dev value.
156		conv_deriv_ref = self._convolve_derive(count_data, 10)
157
158		# initialize arrays to contain indices for all rising and falling
159		# flanks, respectively
160		rising_ind = np.empty([num_of_lasers],int)
161		falling_ind = np.empty([num_of_lasers],int)
162
163		# Find as many rising and falling flanks as there are laser pulses in
164		# the trace:
165		for i in range(num_of_lasers):
166
167		# save the index of the absolute maximum of the derived time trace
168		# as rising edge position
169		rising_ind[i] = np.argmax(conv_deriv)
170
171		# refine the rising edge detection, by using a small and fixed
172		# conv_std_dev parameter to find the inflection point more precise
173		start_ind = int(rising_ind[i]-conv_std_dev)
174		if start_ind < 0:
175		start_ind = 0
176
177		stop_ind = int(rising_ind[i]+conv_std_dev)
178		if stop_ind > len(conv_deriv):
179		stop_ind = len(conv_deriv)
180
181		if start_ind == stop_ind:
182		stop_ind = start_ind+1
183
184		rising_ind[i] = start_ind + np.argmax(conv_deriv_ref[start_ind:stop_ind])
185
186		# set this position and the surrounding of the saved edge to 0 to
187		# avoid a second detection
188		if rising_ind[i] < 2*conv_std_dev: del_ind_start = 0
189		else:
190		del_ind_start = rising_ind[i] - 2*conv_std_dev
191		if (conv_deriv.size - rising_ind[i]) < 2*conv_std_dev:
192		del_ind_stop = conv_deriv.size-1
193		else:
194		del_ind_stop = rising_ind[i] + 2*conv_std_dev
195		conv_deriv[del_ind_start:del_ind_stop] = 0
196
197		# save the index of the absolute minimum of the derived time trace
198		# as falling edge position
199		falling_ind[i] = np.argmin(conv_deriv)
200
201		# refine the falling edge detection, by using a small and fixed
202		# conv_std_dev parameter to find the inflection point more precise
203		start_ind = int(falling_ind[i]-conv_std_dev)
204		if start_ind < 0:
205		start_ind = 0
206
207		stop_ind = int(falling_ind[i]+conv_std_dev)
208		if stop_ind > len(conv_deriv):
209		stop_ind = len(conv_deriv)
210
211		if start_ind == stop_ind:
212		stop_ind = start_ind+1
213
214		falling_ind[i] = start_ind + np.argmin(conv_deriv_ref[start_ind:stop_ind])
215
216		# set this position and the sourrounding of the saved flank to 0 to
217		# avoid a second detection
218		if falling_ind[i] < 2*conv_std_dev: del_ind_start = 0
219		else:
220		del_ind_start = falling_ind[i] - 2*conv_std_dev
221		if (conv_deriv.size - falling_ind[i]) < 2*conv_std_dev:
222		del_ind_stop = conv_deriv.size-1
223		else:
224		del_ind_stop = falling_ind[i] + 2*conv_std_dev
225		conv_deriv[del_ind_start:del_ind_stop] = 0
226
227		# sort all indices of rising and falling flanks
228		rising_ind.sort()
229		falling_ind.sort()
230
231		# find the maximum laser length to use as size for the laser array
232		laser_length = np.max(falling_ind-rising_ind)
233
234		#Todo: Find better method, here the idea is to take a histogram to find
235		# length of pulses
236		#diff = (falling_ind-rising_ind)[np.where( falling_ind-rising_ind > 0)]
237		#self.histo = np.histogram(diff)
238		#laser_length = int(self.histo[1][self.histo[0].argmax()])
239
240		# initialize the empty output array
241		laser_arr = np.zeros([num_of_lasers, laser_length],int)
242		# slice the detected laser pulses of the timetrace and save them in the
243		# output array according to the found rising edge
244		for i in range(num_of_lasers):
245		if (rising_ind[i]+laser_length > count_data.size):
246		lenarr = count_data[rising_ind[i]:].size
247		laser_arr[i, 0:lenarr] = count_data[rising_ind[i]:]
248		else:
249		laser_arr[i] = count_data[rising_ind[i]:rising_ind[i]+laser_length]
250		return laser_arr.astype(int)
251
252
253		def _convolve_derive(self, data, std_dev):
254		""" Smooth the input data by applying a gaussian filter.
255
256		@param numpy.ndarray timetrace: 1D array, the raw data to be smoothed
257		and derived
258		@param float std_dev: standard deviation of the gaussian filter to be
259	View Code Duplication	applied for smoothing
		0 ignored issues – show Duplication introduced 2016-09-08 17:03 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
260
261		@return numpy.ndarray: 1D array, the smoothed and derived data
262
263		The convolution is applied with specified standard deviation. The
264		derivative of the smoothed data is computed afterwards and returned. If
265		the input data is some kind of rectangular signal containing high
266		frequency noise, the output data will show sharp peaks corresponding to
267		the rising and falling flanks of the input signal.
268		"""
269		conv = ndimage.filters.gaussian_filter1d(data, std_dev)
270		conv_deriv = np.gradient(conv)
271		return conv_deriv
272
273
274
275		def get_data_laserpulses(self, num_of_lasers, conv_std_dev):
276		""" Capture the fast counter data and extracts the laser pulses.
277
278		@param int num_of_lasers: The total number of laser pulses inside the
279		pulse sequence
280		@param int conv_std_dev: Standard deviation of gaussian convolution
281
282
283		@return tuple (numpy.ndarray, numpy.ndarray):
284		Explanation of the return value:
285
286		numpy.ndarray: 2D array, the extracted laser pulses of the
287		timetrace, with the dimensions:
288		0: laser number
289		1: time bin
290		numpy.ndarray: 1D or 2D, the raw timetrace from the fast
291		counter
292		"""
293		# poll data from the fast counting device, netobtain is needed for
294		# getting numpy array over network
295		raw_data = netobtain(self._fast_counter_device.get_data_trace())
296		if self.old_raw_data is not None:
297		#if raw_data.shape == self.old_raw_data.shape:
298		raw_data = np.add(raw_data, self.old_raw_data)
299
300		# Saving data for testing
301
302		# name = str(self._iter) + '.dat'
303		# self._iter = self._iter + 1
304		# np.savetxt(name, raw_data.transpose())
305
306		# call appropriate laser extraction method depending on if the fast
307		# counter is gated or not.
308		if self.is_counter_gated:
309		laser_data = self._gated_extraction(raw_data, conv_std_dev)
310		else:
311		laser_data = self._ungated_extraction(raw_data, num_of_lasers, conv_std_dev)
312		return laser_data.astype(dtype=int), raw_data.astype(dtype=int)
313
314
315		def _check_if_counter_gated(self):
316		'''Check the fast counter if it is gated or not
317		'''
318		self.is_counter_gated = self._fast_counter_device.is_gated()
319		return
320

Ulm-IQO / qudi

Push — pulsed_with_queued_connections ( cddfb2...d3c1fc )

PulseExtractionLogic.gated_extraction() B

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

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