Fixed non-interactive pylab plotting setup in common.py

Also fixed spacing in analyze.py from last change and removed some
.pyc files from versioning.

diff --git a/calibcant/T_analyze.py b/calibcant/T_analyze.py
index 4b94002dd6e8e6e712b23384cd470e2d3c780183..7d46993ed9a9eca9e48f0934ca7125a4257ee104 100755 (executable)
--- a/calibcant/T_analyze.py
+++ b/calibcant/T_analyze.py
@@ -36,7 +36,6 @@ import numpy
 import common # common module for the calibcant package
 import config # config module for the calibcant package
 import data_logger
-import z_piezo_utils
 import linfit
 
 def C_to_K(celsius) :

diff --git a/calibcant/T_analyze.pyc b/calibcant/T_analyze.pyc
deleted file mode 100644 (file)
index 83a3781..0000000
Binary files a/calibcant/T_analyze.pyc and /dev/null differ

diff --git a/calibcant/analyze.py b/calibcant/analyze.py
index f61f9305ed8d36248e3f9314536cf94fdcf6f126..797a78a5a91e4e2785cc37b31573ebe7526853b4 100755 (executable)
--- a/calibcant/analyze.py
+++ b/calibcant/analyze.py
@@ -118,7 +118,7 @@ def string_errors(k_m, k_s,
     T_r = T_s / T_m
     one_o_Vphoto2_r = one_o_Vphoto2_s / one_o_Vphoto2_m
     string  = "Variable (units)              : mean +/- std. dev. (relative error)\n"
-    string += "Cantilever k (N/m)          : %g +/- %g (%g)\n" \
+    string += "Cantilever k (N/m)            : %g +/- %g (%g)\n" \
               % (k_m, k_s, k_r)
     string += "photoSensitivity**2 (V/nm)**2 : %g +/- %g (%g)\n" \
               % (photoSensitivity2_m, photoSensitivity2_s, photoSensitivity2_r)

diff --git a/calibcant/common.py b/calibcant/common.py
index 24e5f1d9449c926c2fbe4ae523c3e4eff553b4ac..2db32e1bc7d23adbcd83f7c15f18ded9c21b1c73 100644 (file)
--- a/calibcant/common.py
+++ b/calibcant/common.py
@@ -29,6 +29,7 @@ VERSION="0.2"
 _flush_plot = None
 _final_flush_plot = None
 _pylab = None
+def _dummy_fn(): pass
 
 def _import_pylab() :
     """Import pylab plotting functions for when we need to plot.  This
@@ -46,12 +47,12 @@ def _import_pylab() :
         if config.PYLAB_INTERACTIVE :
             _flush_plot = _pylab.draw
         else :
-            def _flush_plot () : pass
+            _flush_plot = _pylab.show #_dummy_fn
     if _final_flush_plot == None :
         if config.PYLAB_INTERACTIVE :
             _final_flush_plot = _pylab.draw
         else :
-            _final_flush_plot = _pylab.show
+            _final_flush_plot = _dummy_fn # _pylab.show
 
 def write_array(ofile, array, seperator):
     """Erite an iterable array seperated by seperator.

diff --git a/calibcant/common.pyc b/calibcant/common.pyc
deleted file mode 100644 (file)
index cfa016f..0000000
Binary files a/calibcant/common.pyc and /dev/null differ

diff --git a/calibcant/config.py b/calibcant/config.py
index 2374ba659a55a0de8ceff707c2b5d9994f50086f..14af67b5fa340b188b06e32fc4c683e90ca66047 100644 (file)
--- a/calibcant/config.py
+++ b/calibcant/config.py
@@ -1,7 +1,7 @@
 """Define some variables to configure the package for a particular lab
 and workflow."""
 
-import z_piezo_utils
+import z_piezo
 
 DEFAULT_TEMP = 22  # assume 22 deg C
 LOG_DATA = True  # quietly grab all real-world data and log to LOG_DIR
@@ -14,12 +14,12 @@ PYLAB_INTERACTIVE = True # select between draw() and show() for flushing plots
 BASE_FIGNUM = 20 # to avoid writing to already existing figures
 
 # zpGain      zpiezo applied voltage per output Volt
-zpGain = z_piezo_utils._usual_zpGain
+zpGain = z_piezo.DEFAULT_GAIN
 # zpSensitivity  nm zpiezo response per applied Volt
-zpSensitivity = z_piezo_utils._usual_zpSensitivity
+zpSensitivity = z_piezo.DEFAULT_SENSITIVITY
 # Vzp_out2V   function that converts output DAC bits to Volts
-Vzp_out2V = z_piezo_utils._usual_Vzp_out2V
+Vzp_out2V = z_piezo.DEFAULT_VZP_OUT_2_VOLTS
 # Vphoto_in2V function that converts input ADC bits to Volts
-Vphoto_in2V = z_piezo_utils._usual_Vphoto_in2V
+Vphoto_in2V = z_piezo.DEFAULT_VPHOTO_IN_2_VOLTS
 # zeroVphoto_bits  ADC bit output for a 0V input
-zeroVphoto_bits = z_piezo_utils._usual_zeroVphoto_bits
+zeroVphoto_bits = z_piezo.DEFAULT_ZERO_PHOTODIODE_BITS

diff --git a/calibcant/config.pyc b/calibcant/config.pyc
deleted file mode 100644 (file)
index f8711bb..0000000
Binary files a/calibcant/config.pyc and /dev/null differ

diff --git a/calibcant/vib_analyze.py b/calibcant/vib_analyze.py
index a100edeed26d884ec78960d0feb97db750ddbccf..f7d8033e2678f45f146f2c5fb3ecca3d96ad2891 100755 (executable)
--- a/calibcant/vib_analyze.py
+++ b/calibcant/vib_analyze.py
@@ -250,23 +250,24 @@ def vib_plot(deflection_bits, freq_axis, power, A, B, C,
      FFTed Vphoto data (Vphoto vs Frequency) (show major noise components).
     """
     if plotVerbose or config.PYLAB_VERBOSE :
+        print "plotting"
         common._import_pylab()
+        common._pylab.figure(config.BASE_FIGNUM+2)
         common._pylab.hold(False)
-        common._pylab.figure(BASE_FIGNUM+2)
 
         # plot time series
         common._pylab.subplot(311)
-        common._pylab.plot(data["Deflection input"], 'r.')
+        common._pylab.plot(deflection_bits, 'r.')
         common._pylab.title("free oscillation")
 
         # plot histogram distribution and gaussian fit
         common._pylab.subplot(312)
         n, bins, patches = \
-            common._pylab.hist(data["Deflection input"], bins=30,
-                        normed=1, align='center')
+            common._pylab.hist(deflection_bits, bins=30,
+                               normed=1, align='center')
         gaus = numpy.zeros((len(bins),))
-        mean = data["Deflection input"].mean()
-        std = data["Deflection input"].std()
+        mean = deflection_bits.mean()
+        std = deflection_bits.std()
         pi = numpy.pi
         exp = numpy.exp
         for i in range(len(bins)) :
@@ -279,7 +280,7 @@ def vib_plot(deflection_bits, freq_axis, power, A, B, C,
         common._pylab.subplot(313)
         common._pylab.semilogy(freq_axis, power, 'r.-')
         common._flush_plot()
-    if (plotVerbose or config.GNUPLOT_VERBOSE) and False : # TODO, clean up and double check...
+    if (plotVerbose or config.GNUPLOT_VERBOSE):
         # write all the ft data now
         fd = file(datafilename, 'w')
         for i in range(len(freq_axis)) :
@@ -379,6 +380,9 @@ if __name__ == '__main__' :
     parser.add_option('-g', '--gnuplot', dest='gnuplot', action='store_true',
                       help='Print gnuplot fit check script to stderr',
                       default=False)
+    parser.add_option('-p', '--pylab', dest='pylab', action='store_true',
+                      help='Produce pylab fit checks during execution',
+                      default=False)
     parser.add_option('-t', '--tweak-mode', dest='tweakmode', action='store_true',
                       help='Run in tweak-file mode',
                       default=False)
@@ -401,7 +405,8 @@ if __name__ == '__main__' :
     else :
         vfile = None
     config.TEXT_VERBOSE = options.verbose
-    config.PYLAB_VERBOSE = False
+    config.PYLAB_INTERACTIVE = False
+    config.PYLAB_VERBOSE = options.pylab
     config.GNUPLOT_VERBOSE = options.gnuplot
 
     if options.tweakmode == False :
@@ -421,5 +426,9 @@ if __name__ == '__main__' :
             sep = '\n'
         common.write_array(ofile, Vphoto_vars, sep)
 
+    if common._final_flush_plot != None:
+        common._final_flush_plot()
+    
     if options.ofilename != None :
         ofile.close()
+