Merged

ADQ14.py

@@ -3,6 +3,11 @@
 Created on Tue Apr  9 11:33:36 2019
 
 @author: Oscar
+v1.2.2 - OSC:
+    - inserted wait for WFA completion in the acquire data function
+v1.2.1 - OSC:
+    - implemented connection to multiple boards when more than one is in the 
+    chassis
 v1.2.0 - OSC:
     - removed 'SW' trigger mode (useless and it wasn't implemented correctly in this library) and Trigger function
     - removed 'ChannelUsed' and relative function (it is always asked in the AcquireData function)
@@ -24,8 +29,9 @@ class ADQ14(object):
     import ctypes as ct
     import numpy as np
     import copy
+    import time
     
-    version='1.2.0'
+    version='1.2.2'
     
     def __init__(self,board_num = 1):
         import os
@@ -48,7 +54,7 @@ class ADQ14(object):
         self.ADQAPI.ADQControlUnit_FindDevices.argtypes = [self.ct.c_void_p]
         
         self.Connect(board_num)
-        self.Print_adq_device_revisions()
+        
 
         self.__ADCSF = 1.0 #GSamples/s
         
@@ -129,11 +135,29 @@ class ADQ14(object):
     
     #---------------------------------        
     def Connect(self,board_num=1):
+        
+        class stwrapper(self.ct.Structure):
+            """ creates a struct to match emxArray_real_T """
+        
+            _fields_ = [('HWIFType', self.ct.c_int),
+                        ('ProductID', self.ct.c_int),
+                        ('VendorID', self.ct.c_uint),
+                        ('AddressField1', self.ct.c_int),
+                        ('AddressField2', self.ct.c_int),
+                        ('DevFile', (self.ct.c_char*64)),
+                        ('DeviceInterfaceOpened', self.ct.c_uint),
+                        ('DeviceSetupCompleted', self.ct.c_uint)]
+                
         self._adq = self.ct.c_void_p(self.ADQAPI.CreateADQControlUnit())
-        self.ADQAPI.ADQControlUnit_FindDevices(self._adq)
-        DEV_NUM=self.ADQAPI.ADQControlUnit_NofADQ(self._adq)
 
-        if DEV_NUM==0:
+        nof_devices = self.ct.c_int(0)
+        e = stwrapper()
+        
+        success = self.ADQAPI.ADQControlUnit_ListDevices(self._adq,self.ct.pointer(e),self.ct.pointer(nof_devices))
+        nof_devices = nof_devices.value
+
+
+        if nof_devices==0:
             print("WARNING: No device has been found")
             return 0
         
@@ -143,15 +167,23 @@ class ADQ14(object):
             print('Error: board_num can\'t be negative!')
             return 0
         
-        if board_num > DEV_NUM:
-            print("Erro: Selected board number {}, but only {} boards have been found!".format(board_num,DEV_NUM))
+        if board_num > nof_devices:
+            print("Erro: Selected board number {}, but only {} boards have been found!".format(board_num,nof_devices))
             return 0
         
-        self.devnum = board_num
+        success = success and self.ADQAPI.ADQControlUnit_OpenDeviceInterface(self._adq,board_num-1)
+        success = success and self.ADQAPI.ADQControlUnit_SetupDevice(self._adq, board_num-1)
+        
+        self.devnum = 1
         self.id = 'ADQ14' #to implement better
         
         # Print ADQAPI revision
         print('ADQAPI loaded, revision {:d}.'.format(self.ADQAPI.ADQAPI_GetRevision()))   
+        rev=self.Print_adq_device_revisions()
+        
+        if rev<30e3:
+            print('WARNING: FPGA revision is not in the correct range, are you sure you are using the right board?\n')
+        
         
         self.Clock_ref() #ext ref activated by def
         
@@ -183,7 +215,11 @@ class ADQ14(object):
                 print('Mixed Revision\n')
             else :
                 print('SVN Updated\n')
+        
+        return revision[0]
                 
+    def Blink(self):
+        self.ADQAPI.ADQ_Blink(self._adq,self.devnum)
 
     def Reset(self,Type='COMM'):
         '''function reset([Type='COMM']):
@@ -721,7 +757,7 @@ http://localhost:8988/edit/python_repo/ADQ14.py#                        tmp = tm
         return data_32bit       
     """
     
-    def Acquire_data(self,channel_mask = 3,conversion_to_volt=True):
+    def Acquire_data(self,channel_mask = 3,conversion_to_volt=True,timeout=5):
         '''This function start the acquisition, it will wait for the trigger.
         '''
         
@@ -742,6 +778,13 @@ http://localhost:8988/edit/python_repo/ADQ14.py#                        tmp = tm
         if success == 0:
             self.__ADQEXC('STARTERR','ADQ_ATDStartWFA failed!')
         
+        
+        #Waiting for WFA
+        start_time = self.time.time()
+        while(not self.ADQAPI.ADQ_ATDWaitForWFACompletion(self._adq,self.devnum)):
+            if (self.time.time()-start_time) > timeout:
+                self.__BASEEXC('TIMEOUT','WFA failed!')
+        
         #getting data
         
         #init only what is necessary:

AWGSIGD.py

@@ -4,6 +4,11 @@
 Created on Wed Sep  6 18:09:39 2017
 
 @author: oscar
+v2.5.3 - OSC:
+    - when loading waves in memory, the channels queue is cleaned. Now after 
+    calling the function load_waves_in_AWG_memory, they will be re-queued 
+    automatically
+    
 v2.5.2 - OSC:
     - inserted the stop_multiple function
     - inserted ext port setup functions
@@ -462,7 +467,7 @@ class AWGChannel(object):
 ##------------------------------------------------------------------------------------------ a00 AWG class --------------------------------    
         
 class Awgsigd(object):
-    version = '2.5.2'
+    version = '2.5.3'
     import keysightSD1 as sigd
     import numpy as np
     import matplotlib.pyplot as plt
@@ -1028,6 +1033,8 @@ class Awgsigd(object):
             self.__check_command( self._awg.waveformLoad(wave,n))
             del wave #bugfix
         
+        for i in range(4):
+            self.__load_waves_in_channel(i)
         #self.time.sleep(0.1)
     
     def __change_offset_slow(self,channel):
@@ -1099,8 +1106,6 @@ class Awgsigd(object):
             raise ValueError
             
         def setfunc(Channel):
-            if load_waves_in_memory:
-                self.load_waves_in_AWG_memory()
             
             self.__check_channel_number(Channel)
             tmp = self.channel(Channel)
@@ -1121,7 +1126,7 @@ class Awgsigd(object):
             pars = pars['PORT'],pars['EDGE'],pars['Sync']
             port_sn = tmp.ext_port_list.index(pars[0])
             if port_sn>0:
-                port_sn= int(port_sn+3999)
+                port_sn= int(port_sn+3999) #flags for ext port
             self.__check_command(self._awg.AWGtriggerExternalConfig(Channel,port_sn,tmp.trigger_edge_list.index(pars[1]),int(pars[2])))
 
             

CircleFit/circuit.py

@@ -212,9 +212,6 @@ class circuit(object):
             display_tables((df, df_kappa),
                            names=['Main Results', 'Linewidths'])
 
-        # Plot of data, raw data and (successfully) fitted data if wanted
-        if plt_res:
-            cp.plot_cfit(self)
 
     def plot_steps(self):
         """
@@ -425,14 +422,14 @@ class Reflection(circuit):
             self.phi0 = np.arcsin(self.yc_norm / self.r_norm)
 
         # Fit final circle #####################################################
-        ftol = kwargs['ftol']
+        maxfev = kwargs['maxfev']
         if not kwargs['final_mag']:
             self._cir_fit_pars = ft.fit_model_refl(self.freq,
                                                    self.circle_norm,
                                                    Ql_est, absQc_est, fr_est,
                                                    self.phi0,
                                                    self._weights,
-                                                   ftol=ftol)
+                                                   max_nfev=maxfev)
             # Calculate quality factors
             self.Ql, self.absQc, self.fr, self.phi1 = \
                 np.abs(self._cir_fit_pars[0])

CircleFit/fit_toolbox.py

@@ -97,7 +97,7 @@ def get_delay(data, comb_slopes=True, f_range=.1):
         mean = np.mean(data.phase.y)
         SS_tot = np.sum((data.phase.y - mean)**2)
         R_sq = 1 - res/SS_tot
-        
+
     else:
         lin_fit_first = np.polyfit(data.x[0:fit_range],
                                    data.phase.y[0:fit_range], 1)
@@ -196,7 +196,7 @@ def fit_model_notch(freq, data, Ql, absQc, fr, phi0, weights, max_nfev=1000):
         z1d = np.zeros(data.size * 2, dtype=np.float64)
         z1d[0:z1d.size:2] = diff.real ** 2 * weights
         z1d[1:z1d.size:2] = diff.imag ** 2 * weights
-        return z1d.sum()
+        return z1d
 
     f = spopt.least_squares(res, [np.abs(Ql), np.abs(absQc), fr, phi0],
                             args=(freq, data),
@@ -233,8 +233,28 @@ def reflection_model_mag(x, Ql, Qc, x0, c):
     return c - (2 * Ql / Qc) ** 2 / (1. + 4 * Ql ** 2 * ((x - x0) / x0) ** 2)
 
 
-def fit_model_refl(freq, data, Ql, Qc, fr, phi0, weights, ftol=1e-16):
-    """Final circle fit of the model to get information about Ql, Qc, fr, phi0
+def fit_model_refl(freq, data, Ql, Qc, fr, phi0, weights, max_nfev=1000):
+    """Final fit of the model for reflection to get information about Ql,
+    Qc and fr.
+
+    Parameters
+    -----------
+    freq : np.array, list
+    List of frequencies
+    data : np.array, list
+        List of complex data points
+    Ql : float
+        Guess value for Ql
+    absQc : float
+        Guess value for Qc
+    fr : float
+        Guess value for resonance frequency
+    phi0 : float
+        Guess value for impedance mismatch
+    weights : np.array, list
+        Weights for fit.
+    max_nfev : int
+        Maximum number of iterations. Increase for increased precision.
     """
 
     def res(params, f, data):
@@ -245,18 +265,14 @@ def fit_model_refl(freq, data, Ql, Qc, fr, phi0, weights, ftol=1e-16):
         z1d[1:z1d.size:2] = diff.imag ** 2 * weights
         return z1d
 
-    f = spopt.leastsq(res, [Ql, Qc, fr, phi0], args=(freq, data),
-                      full_output=True, xtol=ftol, ftol=ftol)
-    # f = spopt.least_squares(res, [Ql, Qc, fr, phi0], args=(freq, data),
-    #                        bounds=([Ql-.5*Ql, Qc-.5*Qc, fr-10*fr/Ql,
-    #                                 -np.pi],
-    #                                [Ql+0.5*Ql, Qc+0.5*Qc, fr+10*fr/Ql,
-    #                                 np.pi]),
-    #                        xtol=2.3e-16, ftol=2.5e-16, gtol=2.5e-16,
-    #                        loss='huber',
-    #                        verbose=2)
+    f = spopt.least_squares(res, [np.abs(Ql), np.abs(Qc), fr, phi0],
+                            args=(freq, data),
+                            verbose=0, max_nfev=max_nfev, xtol=2.3e-16,
+                            ftol=2.3e-16,
+                            bounds=([0, 0, 0, -np.pi],
+                                    [10e9, 10e9, 20e9, np.pi]))
 
-    return f[0], f[1]
+    return f.x, f
 
 
 def fit_mag_refl(freq, data, Ql, Qc, fr, phi0, weights, ftol=1e-16):
@@ -286,13 +302,21 @@ def subtract_linear_bg(freq, data, fit_range=0.1):
 
 def get_weights(freq, Ql, fr, weight_width):
     """Weighting of the function. In range of FWHM, determined by
-    (Ql/fr)*weight_width. Outer values are weighted prop. to 1/abs(f-fr)
+    (Ql/fr)*weight_width. Outer values are weighted prop. to 1/abs(f-fr)^r
     """
 
     width = fr / Ql
     weights = np.ones(len(freq))
     outer_idx = np.abs(freq - fr) > width * weight_width
-    weights[outer_idx] = (width * weight_width) / (np.abs(freq[outer_idx] - fr))
+
+    left_idx = np.argwhere(outer_idx == 0)[0][0]
+    right_idx = np.argwhere(outer_idx == 0)[-1][0]
+
+    r = 2
+    weights[right_idx:] = 1 / ((freq[right_idx:] - freq[right_idx]) / (
+                freq[right_idx] - fr) + 1) ** r
+    weights[:left_idx] = 1 / ((freq[:left_idx] - freq[left_idx]) / (
+                freq[left_idx] - fr) + 1) ** r
     return weights
 
 

DataModule/data_complex.py

@@ -7,6 +7,7 @@ from CircleFit.plotting import plot_rawdata
 import CircleFit.plotting as cp
 from CircleFit.circuit import Notch, Reflection
 from CircleFit.fit_toolbox import get_delay
+from bokeh.plotting import show
 
 
 class data_complex(data_table):
@@ -235,11 +236,6 @@ class data_complex(data_table):
                                       f_range=f_range)
             self._delayOffset = offset
 
-        else:
-            _, offset = get_delay(self, comb_slopes=comb_slopes,
-                                  f_range=f_range)
-            self._delayOffset = offset
-
         # Save set delay
         self.delay = delay
 
@@ -254,16 +250,43 @@ class data_complex(data_table):
         engine : str
             Chose the plot engine between 'bokeh' (default) and 'pyplot'
         """
-        # TODO Rewrite without try and except
-        try:
+        if self.circuit is not None:
             self.plot_fitted_data(engine=engine, **kwargs)
 
-        except:
+        else:
             self.plot_rawdata(engine=engine, **kwargs)
 
-    def plot_rawdata(self, **kwargs):
+    def plot_rawdata(self, engine='b', **kwargs):
         """Plots plain data"""
-        plot_rawdata(self.x, self.value, **kwargs)
+        plot_rawdata(self, engine=engine, **kwargs)
+
+    def plot_single(self, type='dB', engine='b', fit=True, **kwargs):
+        """Plot a single figure. Choose between 'dB', 'phase', 'ReIm',
+        'Circle'
+
+        Parameters
+        -----------
+        type : 'dB', 'phase', 'ReIm', 'Circle'
+            Choose type of plot.
+        engine : 'b', 'p'
+            Bokeh or pyplot
+        fit : bool
+            Try to plot fit if possible?
+        **kwargs
+            Additional keywords for plot.
+        """
+        if type[0].lower() == 'd':
+            p = cp.plot_MagFreq(self, engine, fit, **kwargs)
+        elif type[0].lower() == 'p':
+            p = cp.plot_PhaseFreq(self, engine, fit, **kwargs)
+        elif type[0].lower() == 'c':
+            p = cp.plot_NormCircle(self, engine, fit, **kwargs)
+        else:
+            p = cp.plot_ReIm(self, engine, fit, **kwargs)
+
+        if engine[0].lower() == 'b':
+            show(p)
+
 
     def circle_fit_notch(self, delay=None, a=None, alpha=None, phi0=None,
                          subtract_bg=True, fr_init=None, Ql_init=None,
@@ -336,18 +359,21 @@ class data_complex(data_table):
         kwargs = {'delay': delay, 'a': a, 'alpha': alpha, 'phi0': phi0,
                   'subtract_bg': subtract_bg, 'fr_init': fr_init,
                   'Ql_init': Ql_init, 'weight_width': weight_width,
-                  'print_res': print_res, 'plt_res': plot_res,
+                  'print_res': print_res, 'plt_res':plot_res,
                   'maxfev': maxfev, 'comb_slopes': comb_slopes,
                   'final_mag': final_mag, 'ftol': ftol,
                   'fit_range': fit_range}
         self.circuit = Notch(self, **kwargs)
 
+        # Plot if wanted
+        if plot_res:
+            cp.plot_cfit(self)
         # Further save fitresults in data_complex class
         self.fitresults = self.circuit.fitresults
 
     def circle_fit_reflection(self,  delay=None, a=None, alpha=None, phi0=0,
                               subtract_bg=True, fr_init=None, Ql_init=None,
-                              weight_width=1, print_res=True, plt_res=True,
+                              weight_width=1, print_res=True, plot_res=True,
                               comb_slopes=False, final_mag=False, maxfev=1e3,
                               ftol=1e-16, fit_range=0.15):
         """Circle fit for reflection configuration.
@@ -418,17 +444,20 @@ class data_complex(data_table):
         kwargs = {'delay': delay, 'a': a, 'alpha': alpha, 'phi0': phi0,
                   'subtract_bg': subtract_bg, 'fr_init': fr_init,
                   'Ql_init': Ql_init, 'weight_width': weight_width,
-                  'print_res': print_res, 'plt_res': plt_res, 'maxfev': maxfev,
+                  'print_res': print_res, 'plt_res': plot_res, 'maxfev': maxfev,
                   'comb_slopes': comb_slopes, 'final_mag': final_mag,
                   'ftol': ftol, 'fit_range': fit_range}
         self.circuit = Reflection(self, **kwargs)
 
+        # Plot if wanted
+        if plot_res:
+            cp.plot_cfit(self)
         # Further save fitresults in data_complex class
         self.fitresults = self.circuit.fitresults
 
-    def plot_fitted_data(self, **kwargs):
+    def plot_fitted_data(self, engine='b', **kwargs):
         """Plot fitted data"""
-        cp.plot_cfit(self.circuit, **kwargs)
+        cp.plot_cfit(self, engine=engine, **kwargs)
 
     def plot_steps(self):
         """Plot each step of the circlefit routine"""

DataModule/data_table.py

@@ -348,9 +348,10 @@ class data_table(data_module_base):
                     kws['x_axis_type'] = 'log'
                 if logy:
                     kws['y_axis_type'] = 'log'
-                fig = bp.figure(plot_width=800, plot_height=400, tools=tools,
-                                toolbar_location='above', title=title,
-                                **kws)
+                fig = bp.figure(tools=tools,
+                                height=300,
+                                sizing_mode='scale_width',
+                                title=title, **kws)
 
             # Empty legend if no legend is given
             if legend is None:

DataModule/functions.py

@@ -12,8 +12,8 @@ import pickle
 import numpy as np
 import pandas as pd
 
-from .downwards_compatibility.data_line import data_line
-from .downwards_compatibility.data_surface import data_surface
+from .downwards_compatibility.data_line import data_line,data_2d
+from .downwards_compatibility.data_surface import data_surface,data_3d
 
 from .data_complex import data_complex
 from .data_grid import data_grid
@@ -170,26 +170,9 @@ def plot_multiple(dm_list, label_list, figure=None, colormap=None,
     kwargs : keywords
         Optional: Keywords for bokeh or pyplot
     """