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Improvements to plotting of pulse moment calculation.

tags/1.6.1
Trevor Irons 5 years ago
parent
commit
719b0ba530
2 changed files with 78 additions and 20 deletions
  1. 54
    9
      akvo/terminal/plotyaml.py
  2. 24
    11
      akvo/tressel/mrsurvey.py

+ 54
- 9
akvo/terminal/plotyaml.py View File

@@ -1,7 +1,15 @@
1
-import yaml
1
+from ruamel import yaml
2 2
 import os, sys
3 3
 import numpy as np
4 4
 
5
+import matplotlib.pyplot as plt
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+import seaborn as sns
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+sns.set(style="ticks")
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+import cmocean 
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+from SEGPlot import *
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+from matplotlib.ticker import FormatStrFormatter
11
+import matplotlib.ticker as plticker
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+
5 13
 def slicedict(d, s):
6 14
     return {k:v for k,v in d.items() if k.startswith(s)}
7 15
 
@@ -31,34 +39,71 @@ class AkvoData(yaml.YAMLObject):
31 39
         # Converts to a dictionary with Eigen vectors represented as Numpy arrays 
32 40
         return self
33 41
 
34
-def loadAkvoData(fnamein, chan):
42
+def loadAkvoData(fnamein):
35 43
     """ Loads data from an Akvo YAML file. The 0.02 is hard coded as the pulse length. This needs to be 
36 44
         corrected in future kernel calculations. The current was reported but not the pulse length. 
37 45
     """
38 46
     fname = (os.path.splitext(fnamein)[0])
39 47
     with open(fnamein, 'r') as stream:
40 48
         try:
41
-            AKVO = (yaml.load(stream))
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+            AKVO = (yaml.load(stream, Loader=yaml.Loader))
42 50
         except yaml.YAMLError as exc:
43 51
             print(exc)
44 52
     return AKVO 
45 53
 
46 54
 def plotQt( akvo ):
47
-    import matplotlib.pyplot as plt
55
+ 
48 56
     plt.style.use('ggplot')
57
+    #plt.style.use('seaborn-white')
49 58
     for pulse in akvo.Gated:
50 59
         if pulse[0:5] == "Pulse":
51 60
             #print(akvo.GATED[pulse].keys())
52 61
             nq = akvo.Pulses[pulse]["current"].size
53 62
             for chan in slicedict(akvo.Gated[pulse], "Chan."):
54 63
                 # accumulate pulse moments
55
-                X = np.zeros( (nq, len( akvo.Gated[pulse]["abscissa"].data )) )
64
+                CA = np.zeros( (nq, len( akvo.Gated[pulse]["abscissa"].data )) )
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+                RE = np.zeros( (nq, len( akvo.Gated[pulse]["abscissa"].data )) )
66
+                IM = np.zeros( (nq, len( akvo.Gated[pulse]["abscissa"].data )) )
56 67
                 for q in range(nq):
57
-                    plt.plot(  akvo.Gated[pulse]["abscissa"].data,  akvo.Gated[pulse][chan]["Q-" + str(q)+" CA"].data ) 
58
-                    X[q] = akvo.Gated[pulse][chan]["Q-" + str(q)+" CA"].data
59
-    plt.matshow(X)
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+                    #plt.plot(  akvo.Gated[pulse]["abscissa"].data,  akvo.Gated[pulse][chan]["Q-" + str(q)+" CA"].data ) 
69
+                    CA[q] = akvo.Gated[pulse][chan]["Q-" + str(q)+" CA"].data
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+                    RE[q] = akvo.Gated[pulse][chan]["Q-" + str(q)+" RE"].data
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+                    IM[q] = akvo.Gated[pulse][chan]["Q-" + str(q)+" IM"].data
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+                    #X[q] = akvo.Gated[pulse][chan]["Q-" + str(q)+" RE"].data
73
+            Windows = akvo.Gated[pulse]["windows"].data
74
+            Q = np.array(akvo.Pulses[pulse]["current"].data)
75
+            print("pulse length ", akvo.pulseLength[0])
76
+            Q *= akvo.pulseLength[0]
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+       
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+            fig = plt.figure( figsize=( pc2in(20), pc2in(26) ) ) 
79
+            ax1 = fig.add_axes([.25,.05,.6,.9])
80
+            im = ax1.pcolormesh(Windows,Q,CA, cmap=cmocean.cm.curl_r, vmin=-np.max(np.abs(CA)), vmax=(np.max(np.abs(CA))))
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+            cb = plt.colorbar( im, orientation='horizontal', pad=.175,  )
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+            cb.set_label("FID (nV)", fontsize=10)
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+            cb.ax.tick_params(labelsize=10) 
84
+            ax1.set_yscale('log')
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+            ax1.set_ylabel("Q (A$\cdot$s)", fontsize=10)
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+            ax1.set_xscale('log')
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+            ax1.set_xlabel("time (s)", fontsize=10)
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+
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+            #loc = plticker.MultipleLocator(25) #base=50.0) # this locator puts ticks at regular intervals
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+            #loc = plticker.MaxNLocator(5, steps=[1,2]) #base=50.0) # this locator puts ticks at regular intervals
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+            #ax1.xaxis.set_major_locator(loc)
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+
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+            #ax1.xaxis.set_minor_locator(plticker.NullLocator())
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+            ax1.xaxis.set_major_formatter(FormatStrFormatter('%2.0f'))
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+            ax1.yaxis.set_major_formatter(FormatStrFormatter('%2.1f'))
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+
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+            #plt.figure()
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+            #sns.kdeplot(Windows, Q, CA) #, kind="hex", color="#4CB391")
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+            #sns.heatmap(CA, annot=False, center=0)
100
+
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+    #plt.matshow(RE)
102
+    #plt.matshow(IM)
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+
104
+
60 105
 
61 106
     plt.show()
62 107
 if __name__ == "__main__":
63
-    akvo = loadAkvoData( sys.argv[1] , "Chan. 1")
108
+    akvo = loadAkvoData( sys.argv[1] ) #, "Chan. 1")
64 109
     plotQt(akvo)

+ 24
- 11
akvo/tressel/mrsurvey.py View File

@@ -363,7 +363,7 @@ class GMRDataProcessor(SNMRDataProcessor):
363 363
                 ax1.set_xlabel(r"time (ms)", fontsize=8)
364 364
 
365 365
                 if ichan == 0:
366
-                    ax1.set_ylabel(r"signal [nV]", fontsize=8)
366
+                    ax1.set_ylabel(r"signal (nV)", fontsize=8)
367 367
                 else:
368 368
                     plt.setp(ax1.get_yticklabels(), visible=False)
369 369
                     plt.setp(ax1.get_yaxis().get_offset_text(), visible=False) 
@@ -499,7 +499,9 @@ class GMRDataProcessor(SNMRDataProcessor):
499 499
                 #im2.append(ax2.matshow( db, aspect='auto', vmin=vvmin, vmax=vvmax))
500 500
                 #im2 = ax2.matshow( db, aspect='auto', cmap=cmocean.cm.ice, vmin=vvmin, vmax=vvmax)
501 501
                 if ichan == 0:
502
-                    ax2.set_ylabel(r"$q$ (A $\cdot$ s)", fontsize=8)
502
+                    #ax2.set_ylabel(r"$q$ (A $\cdot$ s)", fontsize=8)
503
+                    ax2.set_ylabel(r"pulse index", fontsize=8)
504
+                    #ax1.set_ylabel(r"FID (nV)", fontsize=8)
503 505
                 else:
504 506
                     #ax2.yaxis.set_ticklabels([])
505 507
                     plt.setp(ax2.get_yticklabels(), visible=False)
@@ -1084,8 +1086,8 @@ class GMRDataProcessor(SNMRDataProcessor):
1084 1086
                 ax1 = axes[2*ichan  ]
1085 1087
                 ax2 = axes[2*ichan+1] # TODO fix hard coded number
1086 1088
                 if phase == 0: # Re Im 
1087
-                    print("plot dog", np.shape(QQ), np.shape(self.DATADICT["RE"][pulse][chan]))
1088
-                    print("QQ", QQ) 
1089
+                    #print("plot dog", np.shape(QQ), np.shape(self.DATADICT["RE"][pulse][chan]))
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+                    #print("QQ", QQ) 
1089 1091
                     im1 = ax1.pcolormesh( time_sp, QQ[iQ], self.DATADICT["RE"][pulse][chan][iQ], cmap=dcmap, \
1090 1092
                          vmin=-self.DATADICT["REmax"][pulse] , vmax=self.DATADICT["REmax"][pulse] )
1091 1093
                     im2 = ax2.pcolormesh( time_sp, QQ[iQ], self.DATADICT["IM"][pulse][chan][iQ], cmap=dcmap, \
@@ -1575,7 +1577,7 @@ class GMRDataProcessor(SNMRDataProcessor):
1575 1577
         
1576 1578
         canvas.reAxH(2)
1577 1579
         nstack = len(self.DATADICT["stacks"]) 
1578
-        canvas.ax1.set_yscale('log')
1580
+        #canvas.ax1.set_yscale('log')
1579 1581
 
1580 1582
         for pulse in self.DATADICT["PULSES"]:
1581 1583
             self.DATADICT[pulse]["qeff"] = {}
@@ -1600,17 +1602,28 @@ class GMRDataProcessor(SNMRDataProcessor):
1600 1602
                     v = np.fft.fftfreq(len(x), self.dt)
1601 1603
                     v = v[0:len(X)]
1602 1604
                     v[-1] = np.abs(v[-1])
1605
+
1603 1606
                     # calculate effective current/moment
1604 1607
                     I0 = np.abs(X)/len(X) 
1605
-                    qeff = I0 * (self.DATADICT[pulse]["PULSE_TIMES"][-1]-self.DATADICT[pulse]["PULSE_TIMES"][0])
1606
-                    canvas.ax1.set_title(r"pulse moment index " +str(ipm), fontsize=10)
1607
-                    canvas.ax1.set_xlabel(r"$\nu$ [Hz]", fontsize=8)
1608
-                    canvas.ax1.set_ylabel(r"$q_{eff}$ [A$\cdot$sec]", fontsize=8)
1609
-                    canvas.ax1.plot(v, qeff, color=scolours[iistack] ) # eff current
1608
+                    qeff = I0 #* (self.DATADICT[pulse]["PULSE_TIMES"][-1]-self.DATADICT[pulse]["PULSE_TIMES"][0])
1609
+
1610
+                    # frequency plot
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+                    #canvas.ax1.set_title(r"pulse moment index " +str(ipm), fontsize=10)
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+                    #canvas.ax1.set_xlabel(r"$\nu$ [Hz]", fontsize=8)
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+                    #canvas.ax1.set_ylabel(r"$q_{eff}$ [A$\cdot$sec]", fontsize=8)
1614
+                    #canvas.ax1.plot(v, qeff, color=scolours[iistack] ) # eff current
1615
+                    
1616
+                    # time plot
1617
+                    canvas.ax1.plot(1e2*(self.DATADICT[pulse]["PULSE_TIMES"]-self.DATADICT[pulse]["PULSE_TIMES"][0]), x, color=scolours[iistack])
1618
+
1610 1619
                     self.DATADICT[pulse]["qeff"][ipm][istack] = qeff
1611 1620
                     self.DATADICT[pulse]["q_nu"][ipm][istack] = v
1612 1621
                     iistack += 1
1622
+
1623
+                canvas.ax1.set_xlabel("time (ms)", fontsize=8)
1624
+                canvas.ax1.set_ylabel("current (A)", fontsize=8)
1613 1625
                 canvas.draw()
1626
+
1614 1627
                         
1615 1628
                 percent = int(1e2* (float)((istack)+ipm*self.DATADICT["nPulseMoments"]) / 
1616 1629
                                    (float)(len(self.DATADICT["PULSES"])*self.DATADICT["nPulseMoments"]*nstack))
@@ -1640,7 +1653,7 @@ class GMRDataProcessor(SNMRDataProcessor):
1640 1653
                 istack = 0
1641 1654
                 for stack in self.DATADICT["stacks"]:
1642 1655
                     # find index 
1643
-                    icv = int (round(cv / self.DATADICT[pulse]["q_nu"][ipm][stack][1]))
1656
+                    icv = int(round(cv / self.DATADICT[pulse]["q_nu"][ipm][stack][1]))
1644 1657
                     self.DATADICT[pulse]["Q"][ipm,istack] = self.DATADICT[pulse]["qeff"][ipm][stack][icv]
1645 1658
                     if ilabel:
1646 1659
                         ax.scatter(ipm, self.DATADICT[pulse]["qeff"][ipm][stack][icv], facecolors='none', edgecolors=scolours[istack], label=(str(pulse)))

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