V. 0.0.7 - Beta

- Moved sample signals
- Added sample signal loading module

README.md

@@ -59,7 +59,8 @@ if(__name__ == "__main__"):
 ### Requirements
 - Numpy
 - Scipy
-- peakutils
+- Peakutils
+- Matplotlib
 
 ## Credits
 

docs/conf.py

@@ -24,9 +24,9 @@
 author = 'Giulio Gabrieli'
 
 # The short X.Y version
-version = '0.0.6'
+version = '0.0.7'
 # The full version, including alpha/beta/rc tags
-release = '0.0.6 - Alpha version'
+release = '0.0.7 - Beta version'
 
 
 # -- General configuration ---------------------------------------------------

pysiology/__init__.py

@@ -1,5 +1,7 @@
 from . import heartrate
 from . import electromiography
 from . import electrodermalactivity
+from . import sampledata
+
+__version__ = '0.0.7' #Version Control
 
-__version__ = '0.0.6' #Version Control

pysiology/electrodermalactivity.py

@@ -248,8 +248,7 @@ def butter_highpass_filter(data, cutoff, fs, order):
     import pickle
     import os
     import pprint
-    fakesignal = [] 
-    with open(os.getcwd().replace('/pysiology/pysiology','/pysiology') + '/data/convertedEDA.pkl',"rb") as f:  # Python 3: open(..., 'rb')
-        fakesignal = pickle.load(f) #load a fake signal
-        GSRResults = analyzeGSR(fakesignal,1000) #analyze it
-        pprint.pprint(GSRResults) #print the results for each peak found
+    import sampledata
+    fakesignal = sampledata.loadsampleEDA()
+    GSRResults = analyzeGSR(fakesignal,1000) #analyze it
+    pprint.pprint(GSRResults) #print the results for each peak found

pysiology/electromiography.py

@@ -975,19 +975,15 @@ def analyzeEMG(rawEMGSignal, samplerate, preprocessing=True,lowpass=50,highpass=
     import os
     import pickle
     import pprint
-    basepath = os.path.dirname(os.path.realpath(__file__)) #This get the basepath of the script
-    datafolder = "/".join(basepath.split("/")[:-1])+"/data/"
-
-    fakesignal = []
-    with open(datafolder+"convertedEMG.pkl","rb") as f:  # Python 3: open(..., 'rb')
-        events = [30] #set a fake event
-        tmin = 0 #start from the beginning of the events
-        tmax = 5 #end from the beginning of the events
-        fakesignal = pickle.load(f) #load a fake signal
-        samplerate = 1000 #samplerate of the fake signal
-        for event in events: #for each event
-            smin = tmin*samplerate + event
-            smax = tmax*samplerate + event
-            eventSignal = fakesignal[smin:smax]
-            analyzedEMG = analyzeEMG(eventSignal,samplerate,preprocessing=False) #analyze it
-            pprint.pprint(analyzedEMG) #print the results of the analysis
+    import sampledata
+    fakesignal = sampledata.loadsampleEMG()
+    events = [30] #set a fake event
+    tmin = 0 #start from the beginning of the events
+    tmax = 5 #end from the beginning of the events
+    samplerate = 1000 #samplerate of the fake signal
+    for event in events: #for each event
+        smin = tmin*samplerate + event
+        smax = tmax*samplerate + event
+        eventSignal = fakesignal[smin:smax]
+        analyzedEMG = analyzeEMG(eventSignal,samplerate,preprocessing=False) #analyze it
+        pprint.pprint(analyzedEMG) #print the results of the analysis

pysiology/heartrate.py

@@ -389,20 +389,15 @@ def analyzeECG(rawECGSignal,samplerate,preprocessing = True, highpass = 0.5, low
     import os
     import pickle
     import pprint
-
-    basepath = os.path.dirname(os.path.realpath(__file__)) #This get the basepath of the script
-    datafolder = "/".join(basepath.split("/")[:-1])+"/data/"
-
-    fakesignal = []
-    with open(datafolder+"convertedECG.pkl","rb") as f:  # Python 3: open(..., 'rb')
-        events = [30000] #set a list of fake fake events
-        tmin = 0 #start from the beginning of the events
-        tmax = 8 #end from the beginning of the events
-        fakesignal = pickle.load(f) #load a fake signal
-        samplerate = 1000 #samplerate of the fake signal
-        for event in events: #for each event
-            smin = tmin*samplerate + event
-            smax = tmax*samplerate + event
-            eventSignal = fakesignal[smin:smax]
-            analyzedECG = analyzeECG(eventSignal,samplerate) #analyze it
-            pprint.pprint(analyzedECG) #print the results of the analysis
+    import sampledata
+    fakesignal = sampledata.loadsampleECG()
+    events = [30000] #set a list of fake fake events
+    tmin = 0 #start from the beginning of the events
+    tmax = 8 #end from the beginning of the events
+    samplerate = 1000 #samplerate of the fake signal
+    for event in events: #for each event
+        smin = tmin*samplerate + event
+        smax = tmax*samplerate + event
+        eventSignal = fakesignal[smin:smax]
+        analyzedECG = analyzeECG(eventSignal,samplerate) #analyze it
+        pprint.pprint(analyzedECG) #print the results of the analysis

pysiology/sampledata.py

@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+""" This module is used to load sample data from the share/data folder. """
+import os
+import pickle
+import pkg_resources
+###############################################################################
+#                                                                             #
+#                                  DEBUG                                      #
+#                                                                             #
+###############################################################################
+
+def loadsampleECG():
+    fakesignal = os.stat(pkg_resources.resource_filename('pysiology','../share/data/convertedECG.pkl'))
+    with open(fakesignal,"rb") as f:  # Python 3: open(..., 'rb')
+        return(pickle.load(f)) #load a fake signal
+
+def loadsampleEMG():
+    fakesignal = os.stat(pkg_resources.resource_filename('pysiology','../share/data/convertedEMG.pkl'))
+    with open(fakesignal,"rb") as f:  # Python 3: open(..., 'rb')
+        return(pickle.load(f)) #load a fake signal
+
+def loadsampleEDA():
+    fakesignal = os.stat(pkg_resources.resource_filename('pysiology','../share/data/convertedEDA.pkl'))
+    with open(fakesignal,"rb") as f:  # Python 3: open(..., 'rb')
+        return(pickle.load(f)) #load a fake signal
+
+""" For debug purposes"""
+
+if(__name__=='__main__'):
+    ecg = loadsampleECG()
+    emg = loadsampleEMG()
+    eda = loadsampleEDA()

setup.py

@@ -1,14 +1,19 @@
 from setuptools import setup
+import os
+
+datadir = os.path.join("share","data")
+datafiles = [(d,[os.path.join(d,f) for f in files]) for d, folders, files in os.walk(datadir)]
+
 
 setup(name='pysiology',
-    version='0.0.6',
+    version='0.0.7',
     description='Physiological signal processing in Python',
-    long_description="A simple python package for physiological signal processing (ECG,EMG,GSR).",
+    long_description="A simple python package for physiological signal processing (ECG,EMG,GSR). Tutorial and documentation can be found on the Github Repository or at pysiology.rtfd.io.",
     url='https://github.com/Gabrock94/Pysiology',
     download_url='https://github.com/Gabrock94/Pysiology/archive/0.0.6.tar.gz',
     author='Giulio Gabrieli',
     author_email='[email protected]',
-    license='Apache2',
+    license='GPL-3.0',
     packages=['pysiology'],      
     install_requires=[
         'numpy',
@@ -22,10 +27,10 @@
         #   3 - Alpha
         #   4 - Beta
         #   5 - Production/Stable
-        'Development Status :: 3 - Alpha',
+        'Development Status :: 4 - Beta',
 
         # Pick your license as you wish (should match "license" above)
-         'License :: OSI Approved :: MIT License',
+        'License :: OSI Approved :: GNU General Public License (GPL)',
 
         # Specify the Python versions you support here. In particular, ensure
         # that you indicate whether you support Python 2, Python 3 or both.
@@ -37,4 +42,6 @@
         'Programming Language :: Python :: 3.3',
         'Programming Language :: Python :: 3.4',
     ],
-    zip_safe=False)
+    zip_safe=False,
+    include_package_data=True,
+    data_files = datafiles)