Apply some fixes to get calibrations working and bump version.

Mostly namespace problems due to `from numpy import *` and the
like.  Things seem to work now.  I think we're ready for prime-time.

diff --git a/calibcant/T_analyze.py b/calibcant/T_analyze.py
index d52475d86c7d8cfef67823c5fa6258492c5a8c11..00804cd969568f1d74a8450f2f24c9f8ca21213b 100755 (executable)
--- a/calibcant/T_analyze.py
+++ b/calibcant/T_analyze.py
@@ -72,8 +72,8 @@ def T_save(T, log_dir=None) :
         log = data_logger.data_log(log_dir, noclobber_logsubdir=False,
                                    log_name="T_float")
         log.write_binary(T.tostring())
         log = data_logger.data_log(log_dir, noclobber_logsubdir=False,
                                    log_name="T_float")
         log.write_binary(T.tostring())

-    if LOG_DATA != None :
-        log = data_logger.data_log(LOG_DIR, noclobber_logsubdir=False,
+    if config.LOG_DATA != None :
+        log = data_logger.data_log(config.LOG_DIR, noclobber_logsubdir=False,

                                    log_name="T_float")
         log.write_binary(T.tostring())
         
                                    log_name="T_float")
         log.write_binary(T.tostring())
         


@@ -94,7 +94,7 @@ def T_plot(T, plotVerbose=False) :
     """
     Umm, just print the temperature?
     """
     """
     Umm, just print the temperature?
     """

-    if plotVerbose or PYLAB_VERBOSE or TEXT_VERBOSE :
+    if plotVerbose or config.PYLAB_VERBOSE or config.TEXT_VERBOSE :

         print "Temperature ", T
 
 @splittableKwargsFunction((T_analyze, 'T', 'convert_to_K'),
         print "Temperature ", T
 
 @splittableKwargsFunction((T_analyze, 'T', 'convert_to_K'),

diff --git a/calibcant/analyze.py b/calibcant/analyze.py
index 2e535efac835df4974fcdcee406cfd4a7c414e1f..7fafc04207358afe23c44367fe3eb28a96a90569 100755 (executable)
--- a/calibcant/analyze.py
+++ b/calibcant/analyze.py
@@ -49,6 +49,8 @@ Which are related by the parameters :
 import numpy
 from splittable_kwargs import splittableKwargsFunction, \
     make_splittable_kwargs_function
 import numpy
 from splittable_kwargs import splittableKwargsFunction, \
     make_splittable_kwargs_function

+import data_logger
+

 import common # common module for the calibcant package
 import config # config module for the calibcant package
 import T_analyze # T_analyze module for the calibcant package
 import common # common module for the calibcant package
 import config # config module for the calibcant package
 import T_analyze # T_analyze module for the calibcant package


@@ -173,7 +175,7 @@ def calib_save_analysis(k, k_s,
 @splittableKwargsFunction()
 def calib_plot(bumps, Ts, vibs, plotVerbose=False) :
     if plotVerbose or config.PYLAB_VERBOSE :
 @splittableKwargsFunction()
 def calib_plot(bumps, Ts, vibs, plotVerbose=False) :
     if plotVerbose or config.PYLAB_VERBOSE :

-        common.import_pylab()
+        common._import_pylab()

         common._pylab.figure(config.BASE_FIGNUM+4)
         common._pylab.subplot(311)
         common._pylab.plot(bumps, 'g.')
         common._pylab.figure(config.BASE_FIGNUM+4)
         common._pylab.subplot(311)
         common._pylab.plot(bumps, 'g.')

diff --git a/calibcant/calibrate.py b/calibcant/calibrate.py
index 64ac942bc6343108279bb88f77d3c5497c891089..2cfff35758eafd1cc3392c28eafe6fd15c74a286 100644 (file)
--- a/calibcant/calibrate.py
+++ b/calibcant/calibrate.py
@@ -84,6 +84,7 @@ import time
 import z_piezo_utils
 from splittable_kwargs import splittableKwargsFunction, \
     make_splittable_kwargs_function
 import z_piezo_utils
 from splittable_kwargs import splittableKwargsFunction, \
     make_splittable_kwargs_function

+import FFT_tools

 
 import common
 import config
 
 import common
 import config


@@ -109,9 +110,9 @@ def bump_aquire(zpiezo, push_depth=200, npoints=1024, freq=100e3) :
     start_pos = zpiezo.curPos()
     pos_dist = zpiezo.pos_nm2out(push_depth) - zpiezo.pos_nm2out(0)
     close_pos = start_pos + pos_dist
     start_pos = zpiezo.curPos()
     pos_dist = zpiezo.pos_nm2out(push_depth) - zpiezo.pos_nm2out(0)
     close_pos = start_pos + pos_dist

-    appr = linspace(start_pos, close_pos, npoints)
-    retr = linspace(close_pos, start_pos, npoints)
-    out = concatenate((appr, retr))
+    appr = numpy.linspace(start_pos, close_pos, npoints)
+    retr = numpy.linspace(close_pos, start_pos, npoints)
+    out = numpy.concatenate((appr, retr))

     # run the bump, and measure deflection
     if config.TEXT_VERBOSE :
         print "Bump %g nm" % push_depth
     # run the bump, and measure deflection
     if config.TEXT_VERBOSE :
         print "Bump %g nm" % push_depth


@@ -162,8 +163,8 @@ def T(**kwargs):
         T._splitargs(T, kwargs)
     T_raw = T_aquire(**T_aquire_kwargs)
     T_analyze.T_save(T_raw, **T_save_kwargs)
         T._splitargs(T, kwargs)
     T_raw = T_aquire(**T_aquire_kwargs)
     T_analyze.T_save(T_raw, **T_save_kwargs)

-    T_ret = T_analyze.T_analyze(T_raw, **T_analyze_kwargs)
-    return T_ret
+    T_ret = T_analyze.T_analyze(T_raw, **T_analyze_kwargs) # returns array
+    return T_ret[0]

 
 # vib family
 
 
 # vib family
 


@@ -173,14 +174,14 @@ def vib_aquire(zpiezo, time=1, freq=50e3) :
     Record data for TIME seconds at FREQ Hz from ZPIEZO at it's current position.
     """
     # round up to the nearest power of two, for efficient FFT-ing
     Record data for TIME seconds at FREQ Hz from ZPIEZO at it's current position.
     """
     # round up to the nearest power of two, for efficient FFT-ing

-    nsamps = ceil_pow_of_two(time*freq)
+    nsamps = FFT_tools.ceil_pow_of_two(time*freq)

     time = nsamps / freq
     # take some data, keeping the position voltage at it's current value
     time = nsamps / freq
     # take some data, keeping the position voltage at it's current value

-    out = ones((nsamps,), dtype=uint16) * zpiezo.curPos()
+    out = numpy.ones((nsamps,), dtype=numpy.uint16) * zpiezo.curPos()

     if config.TEXT_VERBOSE :
         print "get %g seconds of data" % time
     data = zpiezo.ramp(out, freq)
     if config.TEXT_VERBOSE :
         print "get %g seconds of data" % time
     data = zpiezo.ramp(out, freq)

-    data['sample frequency Hz'] = freq
+    data['sample frequency Hz'] = numpy.array([freq])

     return data
 
 @splittableKwargsFunction(vib_aquire,
     return data
 
 @splittableKwargsFunction(vib_aquire,


@@ -192,11 +193,12 @@ def vib(**kwargs) :
     """
     vib_aquire_kwargs,vib_save_kwargs,vib_analyze_kwargs = \
         vib._splitargs(vib, kwargs)
     """
     vib_aquire_kwargs,vib_save_kwargs,vib_analyze_kwargs = \
         vib._splitargs(vib, kwargs)

-    data = vib_aquire(freq=freq, **vib_aquire_kwargs)
+    data = vib_aquire(**vib_aquire_kwargs)

     vib_analyze.vib_save(data, **vib_save_kwargs)
     freq = data['sample frequency Hz']
     vib_analyze.vib_save(data, **vib_save_kwargs)
     freq = data['sample frequency Hz']

-    Vphoto_var = vib_analyze.vib_analyze(deflection_bits=data, freq=freq,
-                                         **vib_analyze_kwargs)
+    deflection_bits = data['Deflection input']
+    Vphoto_var = vib_analyze.vib_analyze(deflection_bits=deflection_bits,
+                                         freq=freq, **vib_analyze_kwargs)

     return Vphoto_var
 
 # A few positioning functions, so we can run bump_aquire() and vib_aquire()
     return Vphoto_var
 
 # A few positioning functions, so we can run bump_aquire() and vib_aquire()


@@ -257,8 +259,9 @@ def move_just_onto_surface(stepper, zpiezo, Depth_nm=100, setpoint=2) :
             print "get surf pos, with setpoint %g (%d)" % (setpoint, zpiezo.def_V2in(setpoint))
         for i in range(20) : # HACK, keep stepping back until we get a distance
             try :
             print "get surf pos, with setpoint %g (%d)" % (setpoint, zpiezo.def_V2in(setpoint))
         for i in range(20) : # HACK, keep stepping back until we get a distance
             try :

-                dist = zpiezo.pos_out2nm(getSurfPos(zpiezo, zpiezo.def_V2in(setpoint)))
-            except (tooClose, poorFit), string :
+                dist = zpiezo.pos_out2nm( \
+                    z_piezo_utils.getSurfPos(zpiezo,zpiezo.def_V2in(setpoint)))
+            except (z_piezo_utils.tooClose, z_piezo_utils.poorFit), string :

                 stepper.step_rel(-200)
                 stepper.step_rel(198)
                 continue
                 stepper.step_rel(-200)
                 stepper.step_rel(198)
                 continue


@@ -273,12 +276,14 @@ def move_just_onto_surface(stepper, zpiezo, Depth_nm=100, setpoint=2) :
     while dist < -stepper_tol : # step back if we need to
         stepper.step_rel(-200)
         stepper.step_rel(198)
     while dist < -stepper_tol : # step back if we need to
         stepper.step_rel(-200)
         stepper.step_rel(198)

-        dist = zpiezo.pos_out2nm(getSurfPos(zpiezo, zpiezo.def_V2in(setpoint)))
+        dist = zpiezo.pos_out2nm( \
+            z_piezo_utils.getSurfPos(zpiezo, zpiezo.def_V2in(setpoint)))

         if config.TEXT_VERBOSE :
             print 'distance to surface ', dist, ' nm, step back'
     while dist > stepper_tol : # and step forward if we need to
         stepper.step_rel(2)
         if config.TEXT_VERBOSE :
             print 'distance to surface ', dist, ' nm, step back'
     while dist > stepper_tol : # and step forward if we need to
         stepper.step_rel(2)

-        dist = zpiezo.pos_out2nm(getSurfPos(zpiezo, zpiezo.def_V2in(setpoint)))
+        dist = zpiezo.pos_out2nm( \
+            z_piezo_utils.getSurfPos(zpiezo, zpiezo.def_V2in(setpoint)))

         if config.TEXT_VERBOSE :
             print 'distance to surface ', dist, ' nm, step closer'
     # now adjust the zpiezo to place us just onto the surface
         if config.TEXT_VERBOSE :
             print 'distance to surface ', dist, ' nm, step closer'
     # now adjust the zpiezo to place us just onto the surface


@@ -310,7 +315,7 @@ def move_far_from_surface(stepper, um_back=50) :
                           (analyze.calib_save, 'bumps','Ts','vibs','log_dir'))
 def calib_aquire(stepper, zpiezo, num_bumps=10, num_Ts=10, num_vibs=20,
                  bump_freq=100e3,
                           (analyze.calib_save, 'bumps','Ts','vibs','log_dir'))
 def calib_aquire(stepper, zpiezo, num_bumps=10, num_Ts=10, num_vibs=20,
                  bump_freq=100e3,

-                 log_dir=config.LOG_DATA, Vphoto_in2V=config.Vphoto_in2V,
+                 log_dir=config.LOG_DIR, Vphoto_in2V=config.Vphoto_in2V,

                  **kwargs):
     """
     Aquire data for calibrating a cantilever in one function.
                  **kwargs):
     """
     Aquire data for calibrating a cantilever in one function.


@@ -334,26 +339,26 @@ def calib_aquire(stepper, zpiezo, num_bumps=10, num_Ts=10, num_vibs=20,
         calib_aquire._splitargs(calib_aquire, kwargs)
     # get bumps
     move_just_onto_surface(stepper, zpiezo, **move_just_onto_surface_kwargs)
         calib_aquire._splitargs(calib_aquire, kwargs)
     # get bumps
     move_just_onto_surface(stepper, zpiezo, **move_just_onto_surface_kwargs)

-    bumps=zeros((num_bumps,))
+    bumps = numpy.zeros((num_bumps,), dtype=numpy.float)

     for i in range(num_bumps) :
     for i in range(num_bumps) :

-        bumps[i] = bump(zpiezo, freq=bump_freq, log_dir=log_dir,
-                        Vphot_in2V=Vphoto_in2V, **bump_kwargs)
+        bumps[i] = bump(zpiezo=zpiezo, freq=bump_freq, log_dir=log_dir,
+                        Vphoto_in2V=Vphoto_in2V, **bump_kwargs)

     if config.TEXT_VERBOSE :
         print bumps
 
     move_far_from_surface(stepper, **move_far_from_surface_kwargs)
 
     # get Ts
     if config.TEXT_VERBOSE :
         print bumps
 
     move_far_from_surface(stepper, **move_far_from_surface_kwargs)
 
     # get Ts

-    Ts=zeros((num_Ts,), dtype=float)
+    Ts = numpy.zeros((num_Ts,), dtype=numpy.float)

     for i in range(num_Ts) :
         Ts[i] = T(**T_kwargs)
         time.sleep(1) # wait a bit to get an independent temperature measure
     print Ts
 
     # get vibs
     for i in range(num_Ts) :
         Ts[i] = T(**T_kwargs)
         time.sleep(1) # wait a bit to get an independent temperature measure
     print Ts
 
     # get vibs

-    vibs=zeros((num_vibs,))
+    vibs = numpy.zeros((num_vibs,), dtype=numpy.float)

     for i in range(num_vibs) :
     for i in range(num_vibs) :

-        vibs[i] = vib(zpiezo, log_dir=log_dir, Vphoto_in2V=Vphoto_in2V,
+        vibs[i] = vib(zpiezo=zpiezo, log_dir=log_dir, Vphoto_in2V=Vphoto_in2V,

                       **vib_kwargs)
     print vibs
     
                       **vib_kwargs)
     print vibs
     


@@ -365,7 +370,7 @@ def calib_aquire(stepper, zpiezo, num_bumps=10, num_Ts=10, num_vibs=20,
 @splittableKwargsFunction( \
     (calib_aquire, 'log_dir'),
     (analyze.calib_analyze, 'bumps','Ts','vibs'))
 @splittableKwargsFunction( \
     (calib_aquire, 'log_dir'),
     (analyze.calib_analyze, 'bumps','Ts','vibs'))

-def calib(log_dir=None, **kwargs) :
+def calib(log_dir=config.LOG_DIR, **kwargs) :

     """
     Calibrate a cantilever in one function.
     The I-don't-care-about-the-details black box version :p.
     """
     Calibrate a cantilever in one function.
     The I-don't-care-about-the-details black box version :p.


@@ -383,8 +388,7 @@ def calib(log_dir=None, **kwargs) :
         calib._splitargs(calib, kwargs)
     a, T, vib = calib_aquire(**calib_aquire_kwargs)
     k,k_s,ps2_m, ps2_s,T_m,T_s,one_o_Vp2_m,one_o_Vp2_s = \
         calib._splitargs(calib, kwargs)
     a, T, vib = calib_aquire(**calib_aquire_kwargs)
     k,k_s,ps2_m, ps2_s,T_m,T_s,one_o_Vp2_m,one_o_Vp2_s = \

-        analyze.calib_analyze(a, T, vib, log_dir=log_dir,
-                              **calib_analyze_kwargs)
+        analyze.calib_analyze(a, T, vib, **calib_analyze_kwargs)

     analyze.calib_save_analysis(k, k_s, ps2_m, ps2_s, T_m, T_s,
                                 one_o_Vp2_m, one_o_Vp2_s, log_dir)
     return (k, k_s)
     analyze.calib_save_analysis(k, k_s, ps2_m, ps2_s, T_m, T_s,
                                 one_o_Vp2_m, one_o_Vp2_s, log_dir)
     return (k, k_s)

diff --git a/calibcant/common.py b/calibcant/common.py
index 2db32e1bc7d23adbcd83f7c15f18ded9c21b1c73..c58e06b9a1208a627e796854d69bc9da92632c5e 100644 (file)
--- a/calibcant/common.py
+++ b/calibcant/common.py
@@ -23,7 +23,7 @@
 
 import config
 
 
 import config
 

-VERSION="0.2"
+VERSION="0.3"

 
 # handle extra verbose input modules, only imported if we need them
 _flush_plot = None
 
 # handle extra verbose input modules, only imported if we need them
 _flush_plot = None

diff --git a/calibcant/vib_analyze.py b/calibcant/vib_analyze.py
index c6bc70fa4c66db285f94163ab921d9d91e9da393..a98ea0534b9008e129d4176d1158487da8351b22 100755 (executable)
--- a/calibcant/vib_analyze.py
+++ b/calibcant/vib_analyze.py
@@ -231,10 +231,10 @@ def fit_psd(freq_axis, psd_data, minFreq=500, maxFreq=7000) :
                                       args=(psd_data[imin:imax],
                                             freq_axis[imin:imax]),
                                       full_output=True, maxfev=10000)
                                       args=(psd_data[imin:imax],
                                             freq_axis[imin:imax]),
                                       full_output=True, maxfev=10000)

-        if config.TEXT_VERBOSE :
+        if config.TEXT_VERBOSE:

             print "Fitted params:",p
             print "Covariance mx:",cov
             print "Fitted params:",p
             print "Covariance mx:",cov

-            print "Info:", info
+            #print "Info:", info  # too much information :p

             print "mesg:", mesg
             if ier == 1 :
                 print "Solution converged"
             print "mesg:", mesg
             if ier == 1 :
                 print "Solution converged"