Can follow and update plot on fly

Makefile

@@ -1,15 +1,47 @@
-all: hex2binary anne-110126.zeo anne-110127.zeo anne-110128.zeo anne-110129.zeo anne-110130.zeo anne-110131.zeo anne-110201.zeo
+DATE ?= 110205
 
-%.zeo: hex/%.zeo
-	./hex2binary <$^ >$@
+ZEOS = $(wildcard *.zeo)
+CSVS = $(patsubst %.zeo,%.hypnogram.csv,$(ZEOS))
+
+all-csv: $(CSVS)
+
+#%.zeo: hex/%.zeo
+#	./hex2binary <$^ >$@
+
+%.hypnogram.csv: %.zeo
+	./raw2csv.py $^
+
+current: anne-$(DATE).hypnogram.csv
 
 sync:
 	rsync -av john-2.local:/Users/anne/education/bodytrack/zeologger/raw-data/\*.zeo .
-	rm *.csv
-	-./raw2csv.py
+
+connect:
+	connect.sh anne-$(DATE).zeo
+
+csv:
+	-./raw2csv.py -f anne-$(DATE).zeo
+
+plot-follow:
+	echo "set datafile separator ','" > gnuplot.script
+	echo "set xdata time" >> gnuplot.script
+	echo "set timefmt '%m/%d/%Y %H:%M:%S'" >> gnuplot.script
+	echo "set format x '%H:%M:%S'" >> gnuplot.script
+	echo "plot 'anne-$(DATE).hypnogram.csv' every ::2 using 1:6" >> gnuplot.script
+	echo "! sleep 5" >> gnuplot.script
+	echo "reread" >> gnuplot.script
+	gnuplot gnuplot.script
 
 plot:
-	./plot_hypnogram.pl hypnogram.csv
+	echo "set datafile separator ','" > gnuplot.script
+	echo "set xdata time" >> gnuplot.script
+	echo "set timefmt '%m/%d/%Y %H:%M:%S'" >> gnuplot.script
+	echo "set format x '%H:%M:%S'" >> gnuplot.script
+	echo "plot 'anne-$(DATE).hypnogram.csv' every ::2 using 1:6" >> gnuplot.script
+	gnuplot -p gnuplot.script
+
 
 hex2binary: hex2binary.c
 	gcc -Wall hex2binary.c -o hex2binary
+
+# plot 'anne-110202.spectrogram.csv' every ::2 using 1:6 with lines title '2-4 Hz', 'anne-110202.spectrogram.csv' every ::2 using 1:7 with lines title '4-8 Hz' smooth bezier, 'anne-110202.spectrogram.csv' every ::2 using 1:8 with lines title '8-13 Hz' smooth bezier, 'anne-110202.spectrogram.csv' every ::2 using 1:9 with lines title '11-14 Hz' smooth bezier, 'anne-110202.spectrogram.csv' every ::2 using 1:10 with lines title '13-18 Hz' smooth bezier, 'anne-110202.spectrogram.csv' every ::2 using 1:11 with lines title '18-21 Hz' smooth bezier, 'anne-110202.spectrogram.csv' every ::2 using 1:($12*10) with lines title "30-50 Hz (x10)" smooth bezier, 'anne-110202.hypnogram.csv' every ::2 using 1:($6*.1)

TODO

@@ -1,4 +1,10 @@
+Fix plot to include times
+
+-----------------------------
+DONE
+Commandline arg to block until new data, optionally
 Git setup
-Figure out how to remotely cat
 Commandline arg to select file
-Commandline arg to block until new data, optionally
+Figure out how to remotely cat
+Truncate CSV output files
+Different CSV output filename

connect.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+echo Connecting to $1
+ssh john-2.local tail -f -c +0 /Users/anne/education/bodytrack/zeologger/raw-data/$1 > $1

raw2csv.py

@@ -12,10 +12,14 @@
 
 from glob import glob
 
+
 sys.path.append("/Users/rsargent/projects/bodytrack/zeo/raw-data/raw2csv/ZeoRawData-2.0");
 
 from ZeoRawData import BaseLink, Parser
 
+global done
+done = False
+
 def scanPorts():
     portList = []
 
@@ -63,25 +67,33 @@ def flushInput(self):
         pass
 
 class FileReader:
-    def __init__(self, filename):
+    def __init__(self, filename, follow):
+        self.follow = follow
         self.file = open(filename, 'r')
-        # skip 5 lines
-        for i in range(5):
-            self.file.readline()
 
     def read(self, num):
-        return self.file.read(num)
+        global done
+        ret = self.file.read(num)
+        while len(ret) < num:
+            if not self.follow:
+                print "Done reading"
+                done = True
+                sys.exit(0)
+            time.sleep(1);
+            self.file.seek(0,1) # seek to current location to update buffer
+            ret += self.file.read(num - len(ret))
+        return ret
 
     def flushInput(self):
         pass
 
 
 class ZeoToCSV:
-    def __init__(self, parent=None):
-        samplesFileName = 'raw_samples.csv'
-        sgramFileName = 'spectrogram.csv'
-        hgramFileName = 'hypnogram.csv'
-        eventsFileName = 'events.csv'
+    def __init__(self, basename):
+        samplesFileName = basename + '.raw_samples.csv'
+        sgramFileName = basename + '.spectrogram.csv'
+        hgramFileName = basename + '.hypnogram.csv'
+        eventsFileName = basename + '.events.csv'
 
         self.hypToHeight = {'Undefined' : 0,
                             'Deep'      : 1,
@@ -96,39 +108,30 @@ def __init__(self, parent=None):
         hgramNeedHeader = False
         eventsNeedHeader = False
 
-        if not os.path.isfile(samplesFileName):
-            samplesNeedHeader = True
-
-        if not os.path.isfile(sgramFileName):
-            sgramNeedHeader = True
-
-        if not os.path.isfile(hgramFileName):
-            hgramNeedHeader = True
-
-        if not os.path.isfile(eventsFileName):
-            eventsNeedHeader = True
-
-        self.rawSamples = csv.writer(open(samplesFileName, 'a+b'), delimiter=',',
+        self.rawSamplesFile = open(samplesFileName, 'wb')
+        self.rawSamples = csv.writer(self.rawSamplesFile, delimiter=',',
                                 quotechar='"', quoting=csv.QUOTE_MINIMAL)
-        self.spectrogram = csv.writer(open(sgramFileName, 'a+b'), delimiter=',',
+
+        self.spectrogramFile = open(sgramFileName, 'wb')
+        self.spectrogram = csv.writer(self.spectrogramFile, delimiter=',',
                                 quotechar='"', quoting=csv.QUOTE_MINIMAL)
-        self.hypnogram = csv.writer(open(hgramFileName, 'a+b'), delimiter=',',
+
+        self.hypnogramFile = open(hgramFileName, 'wb')
+        self.hypnogram = csv.writer(self.hypnogramFile, delimiter=',',
                                 quotechar='"', quoting=csv.QUOTE_MINIMAL)
-        self.eventsOut = csv.writer(open(eventsFileName, 'a+b'), delimiter=',',
+
+        self.eventsOutFile = open(eventsFileName, 'wb')
+        self.eventsOut = csv.writer(self.eventsOutFile, delimiter=',',
                                 quotechar='"', quoting=csv.QUOTE_MINIMAL)
 
-        if samplesNeedHeader:
-            self.rawSamples.writerow(["Time Stamp","Version","SQI","Impedance","Bad Signal (Y/N)","Voltage (uV)"])
+        self.rawSamples.writerow(["Time Stamp","Version","SQI","Impedance","Bad Signal (Y/N)","Voltage (uV)"])
 
-        if sgramNeedHeader:
-            self.spectrogram.writerow(["Time Stamp","Version","SQI","Impedance","Bad Signal (Y/N)",
-                                    "2-4 Hz","4-8 Hz","8-13 Hz","11-14 Hz","13-18 Hz","18-21 Hz","30-50 Hz"])
+        self.spectrogram.writerow(["Time Stamp","Version","SQI","Impedance","Bad Signal (Y/N)",
+                                   "2-4 Hz","4-8 Hz","8-13 Hz","11-14 Hz","13-18 Hz","18-21 Hz","30-50 Hz"])
 
-        if hgramNeedHeader:
-            self.hypnogram.writerow(["Time Stamp","Version","SQI","Impedance","Bad Signal (Y/N)","State (0-4)","State (named)"])
+        self.hypnogram.writerow(["Time Stamp","Version","SQI","Impedance","Bad Signal (Y/N)","State (0-4)","State (named)"])
 
-        if eventsNeedHeader:
-            self.eventsOut.writerow(["Time Stamp","Version","Event"])
+        self.eventsOut.writerow(["Time Stamp","Version","Event"])
 
     def updateSlice(self, slice):
 
@@ -150,19 +153,33 @@ def updateSlice(self, slice):
             badSignal = 'N'
         if not slice['Waveform'] == []:
             self.rawSamples.writerow([timestamp,ver,sqi,imp,badSignal] + slice['Waveform'])
+            self.rawSamplesFile.flush()
         if len(slice['FrequencyBins'].values()) == 7:
             f = slice['FrequencyBins']
             bins = [f['2-4'],f['4-8'],f['8-13'],f['11-14'],f['13-18'],f['18-21'],f['30-50']]
             self.spectrogram.writerow([timestamp,ver,sqi,imp,badSignal] + bins)
+            self.spectrogramFile.flush()
         if not slice['SleepStage'] == None:
             stage = slice['SleepStage']
             self.hypnogram.writerow([timestamp,ver,sqi,imp,badSignal] +
                                      [self.hypToHeight[stage],str(stage)])
+            self.hypnogramFile.flush()
 
     def updateEvent(self, timestamp, version, event):
         self.eventsOut.writerow([timestamp,version,event])
+        self.eventsOutFile.flush()
 
 if __name__ == '__main__':
+
+    follow = False
+    zeofile = ""
+
+    for arg in sys.argv[1:]:
+        if arg == "-f":
+            follow = True
+        else:
+            zeofile = arg
+
     # Find ports.
     # TODO: offer a command line option for selecting ports.
 
@@ -178,10 +195,12 @@ def updateEvent(self, timestamp, version, event):
 #    else:
 #        sys.exit("No serial ports found.")
 
+
+    print "Generating CSV files from " + zeofile + ", follow=", follow
     # Initialize
-    output = ZeoToCSV()
+    output = ZeoToCSV(os.path.splitext(zeofile)[0])
 
-    reader = FileReader("anne-110202.zeo")
+    reader = FileReader(zeofile, follow)
 
     link = BaseLink.BaseLink(reader)
 
@@ -194,8 +213,10 @@ def updateEvent(self, timestamp, version, event):
     link.start()
 
     # TODO: perhaps use a more forgiving key?  This would require polling the keyboard without blocking.
-    print "Hit ctrl-C at any time to stop."
-    while True:
-        time.sleep(5)
-
+    if follow:
+        print "Following; hit ctrl-C at any time to stop."
+    while not done:
+        time.sleep(.2)
+    print "Exiting"
+
     sys.exit()