SDNN reflects all the cyclic components responsible for variability in the period of recording, therefore it represents total variability
- SDNN = sqrt((1/N-1) * sum(i=1 --> N)(rri - rrmean)^2
+ SDNN = sqrt((1/N-1) * sum(i=1 --> N)(rri - rrmean)^2)
Input: peaks of the ECG signal,samplerate of the signal
@@ -458,14 +467,12 @@ Source code for electrocardiography
Quick search
-
-
@@ -487,7 +494,7 @@ Navigation
\ No newline at end of file
diff --git a/docs/html/_modules/electrodermalactivity.html b/docs/html/_modules/electrodermalactivity.html
index 61afded..75e27e0 100644
--- a/docs/html/_modules/electrodermalactivity.html
+++ b/docs/html/_modules/electrodermalactivity.html
@@ -4,19 +4,28 @@
-
electrodermalactivity — Pysiology 0.0.9 - Beta version documentation
-
+
-
+
+
Navigation
@@ -50,14 +59,14 @@ Source code for electrodermalactivity
###############################################################################
[docs]def phasicGSRFilter(rawGSRSignal,samplerate,seconds=4):
- """ Apply a phasic filter to the signal, with +- X seconds from each sample. Default is 10 seconds
+ """ Apply a phasic filter to the signal, with +- X seconds from each sample. Default is 4 seconds
* Input:
* rawGSRSignal = gsr signal as list
* samplerate = samplerate of the signal
* seconds = number of seconds before and after each timepoint to use in order to compute the filtered value
* Output:
- * phasic filtered signal
+ * phasic signal
:param rawGSRSignal: raw GSR Signal
:type rawGSRSignal: list
@@ -67,6 +76,7 @@ Source code for electrodermalactivity
:param seconds: int
:return: filtered signal
:rtype: list
+
"""
phasicSignal = []
@@ -84,6 +94,68 @@ Source code for electrodermalactivity
phasicSignal.append(newsample)
return(phasicSignal)
+
+[docs]def tonicGSRFilter(rawGSRSignal,samplerate,seconds=4):
+ """ Apply a modified filter to the signal, with +- X seconds from each sample, in order to extract the tonic component. Default is 4 seconds
+
+ * Input:
+ * rawGSRSignal = gsr signal as list
+ * samplerate = samplerate of the signal
+ * seconds = number of seconds before and after each timepoint to use in order to compute the filtered value
+ * Output:
+ * tonic signal
+
+ :param rawGSRSignal: raw GSR Signal
+ :type rawGSRSignal: list
+ :param samplerate: samplerate of the GSR signal in Hz
+ :type samplerate: int
+ :param seconds: seconds to use to apply the phasic filter
+ :param seconds: int
+ :return: filtered signal
+ :rtype: list
+
+ """
+
+ tonicSignal = []
+ for sample in range(0,len(rawGSRSignal)):
+ smin = sample - seconds * samplerate #min sample index
+ smax = sample + seconds * samplerate #max sample index
+ #is smin is < 0 or smax > signal length, fix it to the closest real sample
+ if(smin < 0):
+ smin = sample
+ if(smax > len(rawGSRSignal)):
+ smax = sample
+ #substract the mean of the segment
+ newsample = np.mean(rawGSRSignal[smin:smax])
+ #move to th
+ tonicSignal.append(newsample)
+ return(tonicSignal)
+
+[docs]def getPhasicAndTonic(rawGSRSignal, samplerate, seconds = 4):
+ """ This function returns the phasic and tonic components of a singnal.
+
+ * Input:
+ * rawGSRSignal = gsr signal as list
+ * samplerate = samplerate of the signal
+ * seconds = number of seconds before and after each timepoint to use in order to compute the filtered value
+ * Output:
+ * List containing the phasic and tonic components
+
+ :param rawGSRSignal: raw GSR Signal
+ :type rawGSRSignal: list
+ :param samplerate: samplerate of the GSR signal in Hz
+ :type samplerate: int
+ :param seconds: seconds to use to apply the phasic filter
+ :param seconds: int
+ :return: phasic and tonic signals
+ :rtype: list
+
+ """
+
+ phasic = phasicGSRFilter(rawGSRSignal, samplerate, seconds)
+ tonic = tonicGSRFilter(rawGSRSignal, samplerate, seconds)
+ return(phasic, tonic)
+
[docs]def findPeakOnsetAndOffset(rawGSRSignal,onset=0.01,offset=0):
""" This functions finds the peaks of a GSR signal
@@ -279,7 +351,6 @@ Source code for electrodermalactivity
y = lfilter(b, a, data)
return(y)
-
###############################################################################
# #
# DEBUG #
@@ -292,7 +363,8 @@ Source code for electrodermalactivity
import os
import pprint
import sampledata
- fakesignal =sampledata.loadsampleEDA() #load the sample GSR Signal
+ fakesignal = '/home/giulio/Desktop/EDAPhasic/convertedEDA.pkl'
+ fakesignal = pickle.load(open(fakesignal,'rb'))
GSRResults = analyzeGSR(fakesignal[1500:9500],1000,preprocessing=False,phasic_seconds=8) #analyze it
pprint.pprint(GSRResults) #print the results for each peak found
@@ -304,14 +376,12 @@ Source code for electrodermalactivity
Quick search
-
-
@@ -333,7 +403,7 @@ Navigation
\ No newline at end of file
diff --git a/docs/html/_modules/electromyography.html b/docs/html/_modules/electromyography.html
index ff2e237..244513a 100644
--- a/docs/html/_modules/electromyography.html
+++ b/docs/html/_modules/electromyography.html
@@ -4,19 +4,28 @@
-
electromyography — Pysiology 0.0.9 - Beta version documentation
-
+
-
+
+
Navigation
@@ -1032,14 +1041,12 @@ Source code for electromyography
Quick search
-
-
@@ -1061,7 +1068,7 @@ Navigation
\ No newline at end of file
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
index 2bda045..6429284 100644
--- a/docs/html/_modules/index.html
+++ b/docs/html/_modules/index.html
@@ -4,19 +4,28 @@
-
Overview: module code — Pysiology 0.0.9 - Beta version documentation
-
+
-
+
+
Navigation
@@ -48,14 +57,12 @@ All modules for which code is available
Quick search
-
-
@@ -76,7 +83,7 @@ Navigation
\ No newline at end of file
diff --git a/docs/html/_static/basic.css b/docs/html/_static/basic.css
index 19ced10..607b5f5 100644
--- a/docs/html/_static/basic.css
+++ b/docs/html/_static/basic.css
@@ -82,21 +82,9 @@ div.sphinxsidebar input {
}
div.sphinxsidebar #searchbox input[type="text"] {
- float: left;
- width: 80%;
- padding: 0.25em;
- box-sizing: border-box;
-}
-
-div.sphinxsidebar #searchbox input[type="submit"] {
- float: left;
- width: 20%;
- border-left: none;
- padding: 0.25em;
- box-sizing: border-box;
+ width: 170px;
}
-
img {
border: 0;
max-width: 100%;
@@ -211,11 +199,6 @@ table.modindextable td {
/* -- general body styles --------------------------------------------------- */
-div.body {
- min-width: 450px;
- max-width: 800px;
-}
-
div.body p, div.body dd, div.body li, div.body blockquote {
-moz-hyphens: auto;
-ms-hyphens: auto;
diff --git a/docs/html/_static/jquery.js b/docs/html/_static/jquery.js
index 644d35e..ba171ca 100644
--- a/docs/html/_static/jquery.js
+++ b/docs/html/_static/jquery.js
@@ -1,4 +1,10253 @@
-/*! jQuery v3.2.1 | (c) JS Foundation and other contributors | jquery.org/license */
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+
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Navigation
@@ -26,6 +37,12 @@ Navigation
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+ previous |
- Pysiology 0.0.9 - Beta version documentation »
@@ -38,7 +55,7 @@ Navigation
Cite¶
If you use PySiology in your work, please cite:
-Gabrieli G., Azhari A., Esposito G. (in press), PySiology: a Python Package for Physiological Feature Extraction, Special issue of Smart Innovation, Systems and Technologies.
+Gabrieli G., Azhari A., Esposito G. (in press), PySiology: a Python Package for Physiological Feature Extraction, Special issue of Smart Innovation, Systems and Technologies.
@@ -49,6 +66,12 @@ Cite¶
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@@ -58,14 +81,12 @@ This Page
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@@ -81,12 +102,18 @@ Navigation
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