-
Notifications
You must be signed in to change notification settings - Fork 38
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Started python-only features, added initburst_sahp as first example #132
Merged
Merged
Changes from all commits
Commits
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,31 @@ | ||
"""Python implementation of features""" | ||
|
||
""" | ||
Copyright (c) 2015, Blue Brain Project/EPFL | ||
|
||
All rights reserved. | ||
|
||
Redistribution and use in source and binary forms, with or without | ||
modification, are permitted provided that the following conditions are met: | ||
* Redistributions of source code must retain the above copyright | ||
notice, this list of conditions and the following disclaimer. | ||
* Redistributions in binary form must reproduce the above copyright | ||
notice, this list of conditions and the following disclaimer in the | ||
documentation and/or other materials provided with the distribution. | ||
* Neither the name of the copyright holder nor the | ||
names of its contributors may be used to endorse or promote products | ||
derived from this software without specific prior written permission. | ||
|
||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND | ||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED | ||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE | ||
DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY | ||
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES | ||
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; | ||
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND | ||
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS | ||
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
""" | ||
|
||
from .pyfeatures import * # NOQA |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,183 @@ | ||
"""Python implementation of features""" | ||
|
||
""" | ||
Copyright (c) 2015, Blue Brain Project/EPFL | ||
|
||
All rights reserved. | ||
|
||
Redistribution and use in source and binary forms, with or without | ||
modification, are permitted provided that the following conditions are met: | ||
* Redistributions of source code must retain the above copyright | ||
notice, this list of conditions and the following disclaimer. | ||
* Redistributions in binary form must reproduce the above copyright | ||
notice, this list of conditions and the following disclaimer in the | ||
documentation and/or other materials provided with the distribution. | ||
* Neither the name of the copyright holder nor the | ||
names of its contributors may be used to endorse or promote products | ||
derived from this software without specific prior written permission. | ||
|
||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND | ||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED | ||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE | ||
DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY | ||
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES | ||
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; | ||
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND | ||
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS | ||
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
""" | ||
|
||
|
||
import numpy | ||
import efel.cppcore | ||
|
||
|
||
all_pyfeatures = [ | ||
'voltage', | ||
'time', | ||
'ISIs', | ||
'initburst_sahp', | ||
'initburst_sahp_vb', | ||
'initburst_sahp_ssse'] | ||
|
||
|
||
def voltage(): | ||
"""Get voltage trace""" | ||
return _get_cpp_feature("voltage") | ||
|
||
|
||
def time(): | ||
"""Get time trace""" | ||
return _get_cpp_feature("time") | ||
|
||
|
||
def ISIs(): | ||
"""Get all ISIs""" | ||
|
||
peak_times = _get_cpp_feature("peak_time") | ||
|
||
return numpy.diff(peak_times) | ||
|
||
|
||
def initburst_sahp_vb(): | ||
"""SlowAHP voltage from voltage base after initial burst""" | ||
|
||
# Required cpp features | ||
initburst_sahp_value = initburst_sahp() | ||
voltage_base = _get_cpp_feature("voltage_base") | ||
|
||
if initburst_sahp_value is None or voltage_base is None or \ | ||
len(initburst_sahp_value) != 1 or len(voltage_base) != 1: | ||
return None | ||
else: | ||
return numpy.array([initburst_sahp_value[0] - voltage_base[0]]) | ||
|
||
|
||
def initburst_sahp_ssse(): | ||
"""SlowAHP voltage from steady_state_voltage_stimend after initial burst""" | ||
|
||
# Required cpp features | ||
initburst_sahp_value = initburst_sahp() | ||
ssse = _get_cpp_feature("steady_state_voltage_stimend") | ||
|
||
if initburst_sahp_value is None or ssse is None or \ | ||
len(initburst_sahp_value) != 1 or len(ssse) != 1: | ||
return None | ||
else: | ||
return numpy.array([initburst_sahp_value[0] - ssse[0]]) | ||
|
||
|
||
def initburst_sahp(): | ||
"""SlowAHP voltage after initial burst""" | ||
|
||
# Required cpp features | ||
voltage = _get_cpp_feature("voltage") | ||
time = _get_cpp_feature("time") | ||
peak_times = _get_cpp_feature("peak_time") | ||
|
||
# Required python features | ||
all_isis = ISIs() | ||
|
||
# Required trace data | ||
stim_end = _get_cpp_data("stim_end") | ||
|
||
# Required settings | ||
initburst_freq_thresh = _get_cpp_data("initburst_freq_threshold") | ||
initburst_sahp_start = _get_cpp_data("initburst_sahp_start") | ||
initburst_sahp_end = _get_cpp_data("initburst_sahp_end") | ||
|
||
last_isi = None | ||
|
||
# Loop over ISIs until frequency higher than initburst_freq_threshold | ||
for isi_counter, isi in enumerate(all_isis): | ||
# Convert to Hz | ||
freq = 1000.0 / isi | ||
if freq < initburst_freq_thresh: | ||
# Threshold reached | ||
break | ||
else: | ||
# Add isi to initburst | ||
last_isi = isi_counter | ||
|
||
if last_isi is None: | ||
# No initburst found | ||
return None | ||
else: | ||
# Get index of second peak of last ISI | ||
last_peak = last_isi + 1 | ||
|
||
# Get time of last peak | ||
last_peak_time = peak_times[last_peak] | ||
|
||
# Determine start of sahp interval | ||
sahp_interval_start = min( | ||
last_peak_time + | ||
initburst_sahp_start, | ||
stim_end) | ||
|
||
# Get next peak, we wont search beyond that | ||
next_peak = last_peak + 1 | ||
|
||
# Determine end of sahp interval | ||
# Add initburst_slow_ahp_max to last peak time | ||
# If next peak or stim_end is earlier, use these | ||
# If no next peak, use stim end | ||
if next_peak < len(peak_times): | ||
next_peak_time = peak_times[next_peak] | ||
|
||
sahp_interval_end = min( | ||
last_peak_time + initburst_sahp_end, next_peak_time, stim_end) | ||
else: | ||
sahp_interval_end = min( | ||
last_peak_time + initburst_sahp_end, stim_end) | ||
|
||
if sahp_interval_end <= sahp_interval_start: | ||
return None | ||
else: | ||
sahp_interval = voltage[numpy.where( | ||
(time <= sahp_interval_end) & | ||
(time >= sahp_interval_start))] | ||
|
||
min_volt_index = numpy.argmin(sahp_interval) | ||
|
||
slow_ahp = sahp_interval[min_volt_index] | ||
|
||
return numpy.array([slow_ahp]) | ||
|
||
|
||
def _get_cpp_feature(feature_name): | ||
"""Get cpp feature""" | ||
cppcoreFeatureValues = list() | ||
exitCode = efel.cppcore.getFeature(feature_name, cppcoreFeatureValues) | ||
|
||
if exitCode < 0: | ||
return None | ||
else: | ||
return numpy.array(cppcoreFeatureValues) | ||
|
||
|
||
def _get_cpp_data(data_name): | ||
"""Get cpp data value""" | ||
|
||
return efel.cppcore.getMapDoubleData(data_name)[0] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
from efel import cppcore, pyfeatures ?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yeah, Werner implemented some new features just in Python. One issue I found in using Python-only features is that getDistance function knows only about c++ features names.
(https://github.com/BlueBrain/eFEL/blob/master/efel/api.py#L196)
I can try to think about a work-around.