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base repository: RoboDoig/pypulse
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head repository: warnerwarner/pypulse
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Commits on Jan 17, 2019

  1. Add anti pulse

    @warnerwarner
    warnerwarner committed Jan 17, 2019
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  2. Debugging

    @warnerwarner
    warnerwarner committed Jan 17, 2019
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  3. add int casting

    @warnerwarner
    warnerwarner committed Jan 17, 2019
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  4. fixed typo

    @warnerwarner
    warnerwarner committed Jan 17, 2019
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  5. casting to int

    @warnerwarner
    warnerwarner committed Jan 17, 2019
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  6. removed length prints

    @warnerwarner
    warnerwarner committed Jan 17, 2019
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Commits on Jun 18, 2019

  1. Add binary pulse

    @warnerwarner
    warnerwarner committed Jun 18, 2019
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Commits on Jun 19, 2019

  1. Add binary pulse type

    @warnerwarner
    warnerwarner committed Jun 19, 2019
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  2. Correct parmas to params

    @warnerwarner
    warnerwarner committed Jun 19, 2019
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  3. correct var names

    @warnerwarner
    warnerwarner committed Jun 19, 2019
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  4. ditto

    @warnerwarner
    warnerwarner committed Jun 19, 2019
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  5. spelling mistake and some pep

    @warnerwarner
    warnerwarner committed Jun 19, 2019
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  6. remove resampling

    @warnerwarner
    warnerwarner committed Jun 19, 2019
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Commits on Jul 12, 2019

  1. update binary pulse generation 

    Now takes a value between 2^num_of_bins and 0, instead of binary array
    @warnerwarner
    warnerwarner committed Jul 12, 2019
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Commits on Feb 25, 2020

  1. Add binary pulse shatter test

    @warnerwarner
    warnerwarner committed Feb 25, 2020
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  2. Include binary shattering

    @warnerwarner
    warnerwarner committed Feb 25, 2020
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  3. Merge pull request #1 from warnerwarner/binary_test 

    Binary test
    @warnerwarner
    warnerwarner authored Feb 25, 2020

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Commits on Feb 27, 2020

  1. remove print params

    @warnerwarner
    warnerwarner committed Feb 27, 2020
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Commits on Jun 17, 2020

  1. Cast linspace num of points to int

    @warnerwarner
    warnerwarner committed Jun 17, 2020
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  2. more int castings

    @warnerwarner
    warnerwarner committed Jun 17, 2020
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Commits on Feb 19, 2021

  1. Add invert valve option

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  2. Merge branch 'binary_test' of https://github.com/warnerwarner/pypulse … 

    …into binary_test
    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  3. Merge remote-tracking branch 'origin/binary_test'

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  4. Merge branch 'master' of https://github.com/warnerwarner/pypulse

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  5. debug print

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  6. invert full pulse

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  7. attempt 2 at full invert

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  8. attempt numero three

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  9. 4

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  10. retry 5

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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  11. limit inversions to length of blank valves

    @warnerwarner
    warnerwarner committed Feb 19, 2021
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Commits on Mar 1, 2021

  1. switched valve inversion 

    Updated valve inversion so that the pulses are unchanged but that the onset and offset are the only thing inverted
    @warnerwarner
    warnerwarner committed Mar 1, 2021
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  2. print debug removal

    @warnerwarner
    warnerwarner committed Mar 1, 2021
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Commits on Mar 2, 2021

  1. add old binary pulse fix

    @warnerwarner
    warnerwarner committed Mar 2, 2021
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  2. cast all onsets and offsets to ints

    @warnerwarner
    warnerwarner committed Mar 2, 2021
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Commits on May 3, 2021

  1. updated inverted channels

    @warnerwarner
    warnerwarner committed May 3, 2021
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Commits on Feb 11, 2022

  1. fix inversion

    @warnerwarner
    warnerwarner committed Feb 11, 2022
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Showing with 165 additions and 40 deletions.
  1. +131 −35 PulseGeneration.py
  2. +34 −5 PulseInterface.py
166 changes: 131 additions & 35 deletions PulseGeneration.py
View file
Original file line number Diff line number Diff line change
@@ -1,12 +1,14 @@
import scipy.signal as signal
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as sio


def square_pulse(sampling_rate, duration, frequency, duty):
t = np.linspace(0, duration, sampling_rate * duration, endpoint=False)
return (np.array(signal.square(2 * np.pi * frequency * t, duty=duty)) / 2) + 0.5, t
def square_pulse(sampling_rate, duration, frequency, duty, inverted=False):
t = np.linspace(0, duration, int(sampling_rate * duration), endpoint=False)
square_pulse = (np.array(signal.square(2 * np.pi * frequency * t, duty=duty)) / 2) + 0.5
if inverted:
square_pulse = -square_pulse + 1
return square_pulse, t


def extended_square_pulse(sampling_rate, duration, frequency, duty):
@@ -25,17 +27,20 @@ def extended_square_pulse(sampling_rate, duration, frequency, duty):
return pulse, t


def shatter_pulse(sampling_rate, duration, frequency, duty, shatter_frequency, shatter_duty):
def shatter_pulse(sampling_rate, duration, frequency, duty, shatter_frequency, shatter_duty, inverted=False):

if shatter_frequency < frequency:
raise ValueError('Shatter frequency must not be lower than major frequency.')

t = np.linspace(0, duration, sampling_rate * duration, endpoint=False)

guide_pulse, _ = square_pulse(sampling_rate, duration, frequency, duty)
t = np.linspace(0, duration, int(sampling_rate * duration), endpoint=False)
if inverted:
shatter_duty = 1-shatter_duty
guide_pulse, _ = square_pulse(sampling_rate, duration, frequency, duty, inverted=False)
shattered_pulse = (np.array(signal.square(2 * np.pi * shatter_frequency * t, duty=shatter_duty)) / 2) + 0.5

return guide_pulse * shattered_pulse, t
out_pulse = guide_pulse * shattered_pulse
if inverted:
out_pulse = out_pulse * -1 + 1
return out_pulse, t


def random_shatter_pulse(sampling_rate, duration, frequency, duty, shatter_frequency, target_duty, amp_min, amp_max, extend=False):
@@ -51,7 +56,7 @@ def random_shatter_pulse(sampling_rate, duration, frequency, duty, shatter_frequ
else:
guide_pulse, _ = square_pulse(sampling_rate, duration, frequency, duty)

t = np.linspace(0, duration, sampling_rate * duration, endpoint=False)
t = np.linspace(0, duration, int(sampling_rate * duration), endpoint=False)

if target_duty == 1.0:
return guide_pulse, t
@@ -108,8 +113,12 @@ def random_simple_pulse(sampling_rate, params):
pulse, t = square_pulse(sampling_rate, duration, frequency, duty)

# Attach onset and offset
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))
if params['inversion']:
onset = np.ones(int(sampling_rate * params['onset']))
offset = np.ones(int(sampling_rate * params['offset']))
else:
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))

# if we want to shadow the pulse, add this in here (repeat the pulse at a compensating duty)
if params['shadow']:
@@ -180,8 +189,12 @@ def spec_time_pulse(sampling_rate, params):
pulse = pulse[::-1]

# Attach onset and offset
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))
if params['inversion']:
onset = np.ones(int(sampling_rate * params['onset']))
offset = np.ones(int(sampling_rate * params['offset']))
else:
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))

pulse = np.hstack((onset, pulse, offset))

@@ -212,21 +225,25 @@ def simple_pulse(sampling_rate, params):
duration = (1.0 / frequency) * params['repeats']

if params['isClean']:
pulse, t = square_pulse(sampling_rate, duration, frequency, duty)
pulse, t = square_pulse(sampling_rate, duration, frequency, duty, inverted=params['inversion'])
else:
assert params['isShatter']
pulse, t = shatter_pulse(sampling_rate, duration, frequency, duty, params['shatter_frequency'],
params['shatter_duty'])
params['shatter_duty'], inverted=params['inversion'])

# Attach onset and offset
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))
if params['inversion']:
onset = np.ones(int(int(sampling_rate * params['onset'])))
offset = np.ones(int(int(sampling_rate * params['offset'])))
else:
onset = np.zeros(int(int(sampling_rate * params['onset'])))
offset = np.zeros(int(int(sampling_rate * params['offset'])))

pulse = np.hstack((onset, pulse, offset))

total_length = round(duration + params['onset'] + params['offset'], 10) # N.B. Have to round here due to floating point representation problem

return pulse, np.linspace(0, total_length, total_length*sampling_rate)
return pulse, np.linspace(0, total_length, int(total_length*sampling_rate))


def multi_simple_pulse(sampling_rate, global_onset, global_offset, params_list):
@@ -264,7 +281,7 @@ def noise_pulse(sampling_rate, params):
amp_min = params['amp_min']
amp_max = params['amp_max']

t = np.linspace(0, duration, sampling_rate * duration)
t = np.linspace(0, duration, int(sampling_rate * duration))
np.random.seed(int(params['seed']))
while len(guide_pulse) < len(t):
rand_param = np.random.uniform(amp_min, amp_max)
@@ -275,8 +292,12 @@ def noise_pulse(sampling_rate, params):
pulse = (np.array(signal.square(2 * np.pi * params['shatter_frequency'] * t, duty=guide_pulse)) / 2) + 0.5

# Attach onset and offset
onset = np.zeros(sampling_rate * params['onset'])
offset = np.zeros(sampling_rate * params['offset'])
if params['inversion']:
onset = np.ones(int(sampling_rate * params['onset']))
offset = np.ones(int(sampling_rate * params['offset']))
else:
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))

total_length = round(duration + params['onset'] + params['offset'], 10)
return np.hstack((onset, pulse, offset)), np.linspace(0, total_length, total_length * sampling_rate)
@@ -287,24 +308,97 @@ def plume_pulse(sampling_rate, params):
plume = plume['plume'][0]

# resample to match sampling rate
resampled = signal.resample(plume, len(plume)*(sampling_rate / params['data_fs']))
resampled = signal.resample(plume, int(len(plume)*(sampling_rate / params['data_fs'])))
# zero out negative values
resampled[resampled < 0] = 0
# normalise
resampled = (resampled - min(resampled)) / (max(resampled) - min(resampled))
resampled = resampled * params['target_max']

duration = len(resampled) / sampling_rate
t = np.linspace(0, duration, sampling_rate * duration)
t = np.linspace(0, duration, int(sampling_rate * duration))
pulse = (np.array(signal.square(2 * np.pi * params['shatter_frequency'] * t, duty=resampled)) / 2) + 0.5
print(len(pulse))

# Attach onset and offset
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))
if params['inversion']:
onset = np.ones(int(sampling_rate * params['onset']))
offset = np.ones(int(sampling_rate * params['offset']))
else:
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))

total_length = round(params['onset'] + params['offset'] + len(pulse) / sampling_rate, 10)
return np.hstack((onset, pulse, offset)), np.linspace(0, total_length, total_length * sampling_rate)
return np.hstack((onset, pulse, offset)), np.linspace(0, total_length, int(total_length * sampling_rate))

def anti_plume_pulse(sampling_rate, params):
plume = sio.loadmat(params['data_path'])
plume = plume['plume'][0]

# resample to match sampling rate
resampled = signal.resample(plume, int(len(plume)*(sampling_rate / params['data_fs'])))
# zero out negative values
resampled[resampled < 0] = 0
# normalise
resampled = (resampled - min(resampled)) / (max(resampled) - min(resampled))
resampled = resampled * params['target_max']

duration = len(resampled) / sampling_rate
t = np.linspace(0, duration, int(sampling_rate * duration))
pulse = (np.array(signal.square(2 * np.pi * params['shatter_frequency'] * t, duty=resampled)) / 2) + 0.5
anti_pulse = [1 - i for i in pulse]

# Attach onset and offset
if params['inversion']:
onset = np.ones(int(int(sampling_rate * params['onset'])))
offset = np.ones(int(int(sampling_rate * params['offset'])))
else:
onset = np.zeros(int(int(sampling_rate * params['onset'])))
offset = np.zeros(int(int(sampling_rate * params['offset'])))

total_length = round(params['onset'] + params['offset'] + len(pulse) / sampling_rate, 10)
return np.hstack((onset, anti_pulse, offset)), np.linspace(0, total_length, int(total_length * sampling_rate))


def binary_pulse(sampling_rate, params):
'''
Creates a pulse from a value passed to it
'''

binary = params['value_to_binarise']

assert binary >= 0, 'Binary minimum should be zero'
assert binary <= 2**params['num_of_bins'] - 1, 'Binary maximum should be less than %s' % str(2**params['num_of_bins'])
bin_width = params['bin_size']*sampling_rate
binned = bin(binary)[2:]
while len(binned) < params['num_of_bins']:
binned = '0' + binned
bin_output = []
bin_pulse = [int(i) for i in binned for j in range(int(bin_width))]


duration = len(bin_pulse) / sampling_rate
t = np.linspace(0, duration, int(sampling_rate * duration))

if 'isShatter' in params:
if params['isShatter'] is True:
if params['inversion']:
shatter_duty = 1 - params['shatter_duty']
else:
shatter_duty = params['shatter_duty']
shattered_pulse = (np.array(signal.square(2 * np.pi * params["shatter_frequency"] * t, duty=shatter_duty)) / 2) + 0.5
bin_pulse = bin_pulse * shattered_pulse

bin_pulse = np.array(bin_pulse)
if params['inversion']:
onset = np.ones(int(sampling_rate * params['onset']))
offset = np.ones(int(sampling_rate * params['offset']))
bin_pulse = bin_pulse * -1 + 1
else:
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))

total_length = round(params['onset'] + params['offset'] + len(bin_pulse)/sampling_rate, 10)
return np.hstack((onset, bin_pulse, offset)), np.linspace(0, total_length, int(total_length * sampling_rate))


def dummy_noise_pulse(sampling_rate, params):
@@ -322,18 +416,22 @@ def dummy_noise_pulse(sampling_rate, params):
amp_min = params['amp_min']
amp_max = params['amp_max']

t = np.linspace(0, duration, sampling_rate * duration)
t = np.linspace(0, duration, int(sampling_rate * duration))

guide_pulse = np.ones(sampling_rate*duration)

pulse = (np.array(signal.square(2 * np.pi * params['shatter_frequency'] * t, duty=guide_pulse)) / 2) + 0.5

# Attach onset and offset
onset = np.zeros(sampling_rate * params['onset'])
offset = np.zeros(sampling_rate * params['offset'])
if params['inversion']:
onset = np.ones(int(sampling_rate * params['onset']))
offset = np.ones(int(sampling_rate * params['offset']))
else:
onset = np.zeros(int(sampling_rate * params['onset']))
offset = np.zeros(int(sampling_rate * params['offset']))

total_length = round(duration + params['onset'] + params['offset'], 10)
return np.hstack((onset, pulse, offset)), np.linspace(0, total_length, total_length * sampling_rate)
return np.hstack((onset, pulse, offset)), np.linspace(0, total_length, int(total_length * sampling_rate))


def multi_noise_pulse(sampling_rate, global_onset, global_offset, params_list):
@@ -371,5 +469,3 @@ def multi_noise_pulse(sampling_rate, global_onset, global_offset, params_list):
# plt.xlim((-0.1, 2.1))
# plt.ylim((-0.1, 1.1))
# plt.show()


39 changes: 34 additions & 5 deletions PulseInterface.py
View file
Original file line number Diff line number Diff line change
@@ -2,11 +2,15 @@
import numpy as np


def make_pulse(sampling_rate, global_onset, global_offset, params_list):
def make_pulse(sampling_rate, global_onset, global_offset, params_list, *,invert_chan_list=[]):
longest_t = []
pulses = list()

for params in params_list:
for param_index, params in enumerate(params_list):
if param_index in invert_chan_list:
params['inversion'] = True
else:
params['inversion'] = False
if params['type'] == 'Simple':
this_pulse, t = PulseGeneration.simple_pulse(sampling_rate, params)
elif params['type'] == 'Noise':
@@ -19,18 +23,43 @@ def make_pulse(sampling_rate, global_onset, global_offset, params_list):
this_pulse, t = PulseGeneration.plume_pulse(sampling_rate, params)
elif params['type'] == 'ContCorr':
this_pulse, t = PulseGeneration.spec_time_pulse(sampling_rate, params)
elif params['type'] == 'Anti Plume':
this_pulse, t = PulseGeneration.anti_plume_pulse(sampling_rate, params)
elif params['type'] == 'Binary':
this_pulse, t = PulseGeneration.binary_pulse(sampling_rate, params)
else:
raise ValueError

pulses.append(this_pulse)
if len(t) > len(longest_t):
longest_t = t

# pulse_matrix = []
# print(invert_chan_list)
# for pulse_index, this_pulse in enumerate(pulses):
# if pulse_index in invert_chan_list:
# full_pulse = np.ones(len(longest_t)+ int((global_onset + global_offset) * sampling_rate))
# else:
# full_pulse = np.zeros(len(longest_t)+ int((global_onset + global_offset) * sampling_rate))
# pulse_matrix.append(full_pulse)
# pulse_matrix = np.array(pulse_matrix)

pulse_matrix = np.zeros((len(pulses), len(longest_t) + int((global_onset + global_offset) * sampling_rate)))

# invert_vect = np.ones(len(pulses))
# offset_vect = np.zeros(len(pulses))
# for i in invert_chan_list:
# if i < len(invert_vect):
# invert_vect[i] = -1
# offset_vect[i] = 1
pulse_matrix = []
for pulse_index, pulse in enumerate(pulses):
if pulse_index in invert_chan_list:
pulse_matrix.append(np.ones(len(longest_t) + int((global_onset + global_offset) * sampling_rate)))
else:
pulse_matrix.append(np.zeros(len(longest_t) + int((global_onset + global_offset) * sampling_rate)))
pulse_matrix = np.array(pulse_matrix)
for p, pulse in enumerate(pulses):
pulse_matrix[p][int(global_onset * sampling_rate):int(global_onset * sampling_rate)+len(pulse)] = pulse

# pulse_matrix = pulse_matrix * invert_vect[:, np.newaxis] + offset_vect[:, np.newaxis]
t = np.linspace(0, pulse_matrix.shape[1] / sampling_rate, pulse_matrix.shape[1])

return pulse_matrix, t