def main(argv=None):
#Importer.loadFromRaw(argv[1], numFiles = 2)
DataFormatter.formatData('.', argv[2])
tmp = h5py.File("{0}.hdf5".format(argv[2]), "r+")
data = []
for dataset in tmp["raw_data"].keys():
data.append(tmp["raw_data"][dataset])
print tmp["raw_data"][dataset][0]
datavisualization.analyze8x8data(data=data, samprate=20000, time=2)
tmp.close()
def main(argv=None):
if argv is None:
argv = sys.argv
run_importer = True
run_formatter = True
run_analysis = True
try:
try:
opts, args = getopt.getopt(argv[1:], "h", ["help", "skip-importer", "skip-formatter", "skip-analysis"])
print "got args"
except getopt.error, msg:
raise Usage(msg)
for option, data in opts:
if('-h' == option or '--help' == option):
print "LSCE test script. Usage: \"python testscript.py [--skip-importer] [--skip-formatter] [--skip-analysis]" +\
" mat_source hdf5_dest" +\
"\"\n\nSupply the following arguments to run pipeline:\n\n\tmat_source: " +\
"The path to the raw .mat files to be imported.\n\thdf5_dest: the name to save hdf5 output file under" +\
"\n\nAvailable modes:\n\t--skip-importer: skip importation step. Formatter wil still run using" +\
" mat_source as src directory." +\
"\n\t--skip-formatter: skip formatting step. Importer will use mat_source as usual. \n\t\t\t Analysis will" +\
" use hdf5_dest if it exists." + \
"\n\t--skip-analysis: skip computation of analysis data. Formatter will still output to hdf5_dest. "
return
if('--skip-importer' == option):
run_importer = False
if('--skip-formatter' == option):
run_formatter = False
if('--skip-analysis' == option):
run_analysis = False
if(len(args) < 2):
raise Usage("Insufficient arguments supplied.")
else:
print args.__repr__()
print "Welcome to LSCE test script.\nThis script will perform a " + \
"complete iteration of our pipeline, starting with the data importer."
if(run_importer):
print "Importing data from directory "+args[0]
Importer.loadFromMat(args[0])
else:
print "Skipped importing data."
if(run_formatter):
print "Formatting data as hdf5 in "+args[1]+".hdf5"
DataFormatter.formatData(args[0], args[1])
else:
print "Skipped formatting data."
os.system("PAUSE")
testing = None
raw_data = None
if(run_analysis):
dtool = DataAnalysis.data_analysis()
dtool.load_hdf5(args[1], dataset_name="Electrode_12_master", group_name="raw_data")
dtool.sampling_rate = 1000
testing = dtool.high_demo_filter(20)
raw_data = dtool.f["raw_data"]["Electrode_12_master"]
else:
print "Skipped data analysis.\nPlaceholder groups " + \
"\"/data_analysis/demo_filter_results\" and \"/raw_data/Electrode_12_master\" will be used."
hdfile = h5py.File(args[1]+".hdf5", "r+")
if("data_analysis" not in hdfile or "demo_filter_results" not in hdfile["data_analysis"]):
print "Skipping graphs..."
return
testing = hdfile["data_analysis"]["demo_filter_results"]
raw_data = hdfile["raw_data"]["Electrode_12_master"]
os.system("PAUSE")
plt.subplot(2, 1, 1)
plt.plot(testing)
plt.subplot(2, 1, 2)
plt.plot(raw_data)
plt.show()
if(run_analysis):
dtool.close()
def main(argv=None):
if argv is None:
argv = sys.argv
run_importer = True
run_formatter = True
run_analysis = True
try:
try:
opts, args = getopt.getopt(
argv[1:], "h",
["help", "skip-importer", "skip-formatter", "skip-analysis"])
print "got args"
except getopt.error, msg:
raise Usage(msg)
for option, data in opts:
if ('-h' == option or '--help' == option):
print "LSCE test script. Usage: \"python testscript.py [--skip-importer] [--skip-formatter] [--skip-analysis]" +\
" mat_source hdf5_dest" +\
"\"\n\nSupply the following arguments to run pipeline:\n\n\tmat_source: " +\
"The path to the raw .mat files to be imported.\n\thdf5_dest: the name to save hdf5 output file under" +\
"\n\nAvailable modes:\n\t--skip-importer: skip importation step. Formatter wil still run using" +\
" mat_source as src directory." +\
"\n\t--skip-formatter: skip formatting step. Importer will use mat_source as usual. \n\t\t\t Analysis will" +\
" use hdf5_dest if it exists." + \
"\n\t--skip-analysis: skip computation of analysis data. Formatter will still output to hdf5_dest. "
return
if ('--skip-importer' == option):
run_importer = False
if ('--skip-formatter' == option):
run_formatter = False
if ('--skip-analysis' == option):
run_analysis = False
if (len(args) < 2):
raise Usage("Insufficient arguments supplied.")
else:
print args.__repr__()
print "Welcome to LSCE test script.\nThis script will perform a " + \
"complete iteration of our pipeline, starting with the data importer."
if (run_importer):
print "Importing data from directory " + args[0]
Importer.loadFromMat(args[0])
else:
print "Skipped importing data."
if (run_formatter):
print "Formatting data as hdf5 in " + args[1] + ".hdf5"
DataFormatter.formatData(args[0], args[1])
else:
print "Skipped formatting data."
os.system("PAUSE")
testing = None
raw_data = None
if (run_analysis):
dtool = DataAnalysis.data_analysis()
dtool.load_hdf5(args[1],
dataset_name="Electrode_12_master",
group_name="raw_data")
dtool.sampling_rate = 1000
testing = dtool.high_demo_filter(20)
raw_data = dtool.f["raw_data"]["Electrode_12_master"]
else:
print "Skipped data analysis.\nPlaceholder groups " + \
"\"/data_analysis/demo_filter_results\" and \"/raw_data/Electrode_12_master\" will be used."
hdfile = h5py.File(args[1] + ".hdf5", "r+")
if ("data_analysis" not in hdfile
or "demo_filter_results" not in hdfile["data_analysis"]):
print "Skipping graphs..."
return
testing = hdfile["data_analysis"]["demo_filter_results"]
raw_data = hdfile["raw_data"]["Electrode_12_master"]
os.system("PAUSE")
plt.subplot(2, 1, 1)
plt.plot(testing)
plt.subplot(2, 1, 2)
plt.plot(raw_data)
plt.show()
if (run_analysis):
dtool.close()
