rework FCS

small changes to g(2) too
small PTU fixes
fix timetrace if historySize is set before numBins

demos/GetCorrelationFCS.py

@@ -11,10 +11,13 @@
     sn.getDeviceIDs()
     sn.getDevice()
     #sn.getFileDevice(r"E:\Data\PicoQuant\CW_Shelved.ptu")
-    sn.initDevice(MeasMode.T2)
+    #sn.getFileDevice(r"e:\Data\PicoQuant\cell01_55pct_1.ptu")
+    #sn.getFileDevice(r"e:\Data\PicoQuant\Correaltion_T3.ptu")
+    #sn.getFileDevice(r"e:\Data\PicoQuant\OpenCLTest\Atto655+Cy5_diff_FCS+FLCS_Conv.ptu")
+    sn.initDevice(MeasMode.T3)
     #sn.device.setInputDeadTime(-1,1000)
-    sn.correlation.setFCSparameters(1, 2, 20, 8)
-    sn.correlation.measure(100000)
+    sn.correlation.setFCSparameters(1, 2, 1e4, 5)
+    sn.correlation.measure(10000,savePTU=True)
 
     while True:
         finished = sn.correlation.isFinished()
@@ -32,7 +35,7 @@
         plt.title("FCS")
         plt.pause(0.1)
 
-        sn.correlation.clearMeasure()
+        #sn.correlation.clearMeasure()
 
         if finished:
             break

demos/GetCorrelationG2.py

@@ -8,19 +8,22 @@
 if(__name__ == "__main__"):
 
     sn = snAPI()
-    sn.getDevice()
-    #sn.getFileDevice(r"E:\Data\PicoQuant\CW_Shelved.ptu")
-    #sn.getFileDevice(r"E:\Data\PicoQuant\PMT-cw-1MHz.ptu")
-    #sn.getFileDevice(r"E:\Data\PicoQuant\HH400-PMT-cw-1MHz.ptu")
+    #sn.getDevice()
+    sn.getFileDevice(r"E:\Data\PicoQuant\CW_Shelved.ptu")
+    #sn.getFileDevice(r"e:\Data\PicoQuant\cell01_55pct_1.ptu")
+    #sn.getFileDevice(r"e:\Data\PicoQuant\Correaltion_T3.ptu")
+    #sn.getFileDevice(r"e:\Data\PicoQuant\Datasets Metrologia 56 025004\Metrologia_g2_SPS1550_INRIM-PTB-NPL\20171023_INRIM-NPL\acq_NPL\g2_1550nm_NPL\acq002_001.ptu")
     sn.initDevice(MeasMode.T2)
     #sn.device.setInputDeadTime(-1,1000)
 
     # set filter window to 1ns
-    sn.filter.setRowParams(0, 1000, 1, False, [0,1], [])
-    sn.filter.enableRow(0,True)
+    #sn.filter.setRowParams(0, 1000, 1, False, [0,1], [])
+    #sn.filter.enableRow(0,True)
+    #sn.manipulators.coincidence([1,2], 200000)
 
-    sn.correlation.setG2parameters(1, 2, 1000, 5)
-    sn.correlation.measure(100000)
+    #sn.setPTUFilePath("test.ptu")
+    sn.correlation.setG2parameters(1, 2, 200000, 200)
+    sn.correlation.measure(10000,savePTU=True)
 
     plt.ion()
     while True:
@@ -36,9 +39,9 @@
         plt.legend()
         plt.title("g(2)")
         plt.pause(0.1)
-        sn.correlation.clearMeasure()
+        #sn.correlation.clearMeasure()
 
         if sn.correlation.isFinished():
             break
 
-    plt.show(block=True)
+    plt.show(block=True)

demos/GetHistogramHerald.py

@@ -0,0 +1,44 @@
+# -*- coding: utf-8 -*-
+"""
+Spyder Editor
+
+"""
+
+
+
+
+import time
+import numpy as np
+import matplotlib.pyplot as plt
+from snAPI.Main import snAPI, MeasMode
+
+sn = snAPI()
+sn.getDevice()
+sn.initDevice(MeasMode.T3)
+
+# Time Gating
+GateStart = 36300
+GateWidth = 3450
+ch = sn.manipulators.herald(0, [1,2], GateStart, GateWidth, True)
+
+# Measure
+tic = time.time()
+sn.histogram.measure(2000, waitFinished=True, savePTU=False)
+print(time.time()-tic)
+
+# Plot
+data, bins = sn.histogram.getData()
+print(data.shape, bins.shape)
+
+plt.figure()
+plt.plot(bins*1e-3, data[0])
+plt.plot(bins*1e-3, data[1])
+plt.plot(bins*1e-3, data[2])
+plt.plot(bins*1e-3, data[ch[0]])
+plt.plot(bins*1e-3, data[ch[1]])
+plt.show()
+
+
+
+
+

demos/RecordViewerRaw.py

@@ -4,12 +4,12 @@
 
     sn = snAPI()
     sn.getDevice()
-    #sn.getFileDevice(r"E:\Data\PicoQuant\HH400-PMT-cw-1MHz.ptu")
+    sn.getFileDevice(r"E:\Data\PicoQuant\cell01_55pct_1.ptu")
     sn.initDevice(MeasMode.T2)
-    sn.raw.measure(1000,1024*1024*1024, True, True)
+    sn.raw.measure(100,1024*1024*1024, True, False)
     data = sn.raw.getData(25)
     sn.logPrint("from raw data")
-    sn.logPrint("channel |   timetag")
+    sn.logPrint("channel  |  timetag")
     sn.logPrint("-------------------")
     for i in range(25):
         time = sn.raw.timeTag_T2(data[i])

demos/RecordViewerUF.py

@@ -4,12 +4,13 @@
 
     sn = snAPI()
     sn.getDevice()
-    sn.getFileDevice(r"E:\Data\PicoQuant\11_1.ptu")
+    sn.getFileDevice(r"E:\Data\PicoQuant\MH160_Sun.ptu")
     sn.initDevice(MeasMode.T2)
-    sn.unfold.measure(1000,1024*1024*1024, True, True)
+
+    sn.unfold.measure(1000,1024*1024*1024, True, False)
     times, channels  = sn.unfold.getData()
     sn.logPrint("from unfold data")
-    sn.logPrint("channel |   timetag") 
+    sn.logPrint("channel   | timetag") 
     sn.logPrint("-------------------")
-    for i in range(1000):
+    for i in range(100):
         sn.logPrint(f"{channels[i]:9} | {times[i]:7}")

docs/snAPI.Main.html

@@ -3351,7 +3351,7 @@ <h2>Info<a class="headerlink" href="#info" title="Permalink to this heading">#</
 <p>sample of a g(2) <cite>Correlation</cite> measurement drawn with matplotlib</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="snAPI_Main_Correlation_setG2parameters">
-<span class="sig-name descname"><span class="pre">setG2parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">startChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clickChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numBins</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binWidth</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snAPI_Main_Correlation_setG2parameters" title="Permalink to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">setG2parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">startChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clickChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">windowSize</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">binWidth</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snAPI_Main_Correlation_setG2parameters" title="Permalink to this definition">#</a></dt>
 <dd><p>This function sets the the parameters for the g(2) correlation. If the startChannel is the same as the
 clickChannel an autocorrelation is calculated and if the channels are different a
 cross calculation is calculated.</p>
@@ -3369,7 +3369,7 @@ <h2>Info<a class="headerlink" href="#info" title="Permalink to this heading">#</
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>startChannel</strong> (<em>int</em><em> (</em><em>0 is sync channel</em><em>)</em>) – start channel</p></li>
 <li><p><strong>clickChannel</strong> (<em>int</em><em> (</em><em>0 is sync channel</em><em>)</em>) – click channel</p></li>
-<li><p><strong>numBins</strong> (<em>int</em><em> (</em><em>default: 10000</em><em>)</em>) – number of bins</p></li>
+<li><p><strong>windowSize</strong> (<em>int</em><em> [</em><em>ps</em><em>]</em>) – size of the correlation window</p></li>
 <li><p><strong>binWidth</strong> (<em>int</em><em> [</em><em>ps</em><em>]</em>) – width of bins</p></li>
 </ul>
 </dd>
@@ -3378,15 +3378,15 @@ <h2>Info<a class="headerlink" href="#info" title="Permalink to this heading">#</
 </dd>
 </dl>
 <p class="rubric">Example</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># sets thew number of bins to 10000</span>
-<span class="n">sn</span><span class="o">.</span><span class="n">correlation</span><span class="o">.</span><span class="n">setG2parameters</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span> <span class="p">,</span><span class="mi">1000</span><span class="p">,</span> <span class="mi">200</span><span class="p">)</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># sets the window size to 5000ps with a bin width of 5ps (that means 1000 bins will be calculated)</span>
+<span class="n">sn</span><span class="o">.</span><span class="n">correlation</span><span class="o">.</span><span class="n">setG2parameters</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span> <span class="p">,</span> <span class="mi">5000</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
 </pre></div>
 </div>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="snAPI_Main_Correlation_setFCSparameters">
-<span class="sig-name descname"><span class="pre">setFCSparameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">startChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clickChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numIntervals</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intervalLength</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snAPI_Main_Correlation_setFCSparameters" title="Permalink to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">setFCSparameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">startChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clickChannel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">windowSize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000000000000.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">startTime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#snAPI_Main_Correlation_setFCSparameters" title="Permalink to this definition">#</a></dt>
 <dd><p>This function sets the the parameters for the FCS correlation. If the startChannel is the same as the
 clickChannel an autocorrelation is calculated and if the channels are different a
 cross calculation is calculated.</p>
@@ -3409,17 +3409,17 @@ <h2>Info<a class="headerlink" href="#info" title="Permalink to this heading">#</
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>startChannel</strong> (<em>int</em><em> (</em><em>0 is sync channel</em><em>)</em>) – start channel</p></li>
 <li><p><strong>clickChannel</strong> (<em>int</em><em> (</em><em>0 is sync channel</em><em>)</em>) – click channel</p></li>
-<li><p><strong>numIntervals</strong> (<em>int</em><em> (</em><em>default: 10</em><em>)</em>) – number of intervals</p></li>
-<li><p><strong>intervalLength</strong> (<em>int</em><em> (</em><em>default: 8</em><em>)</em>) – num of bins</p></li>
+<li><p><strong>windowSize</strong> (<em>int</em><em> [</em><em>ps</em><em>]</em>) – size of the correlation window</p></li>
+<li><p><strong>startTime</strong> (<em>int</em><em> [</em><em>ps</em><em>]</em>) – width of bins None: T2: BaseResolution, T3: Resolution</p></li>
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
 <dd class="field-even"><p>none</p>
 </dd>
 </dl>
 <p class="rubric">Example</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># sets thew number of bins to 10000</span>
-<span class="n">sn</span><span class="o">.</span><span class="n">correlation</span><span class="o">.</span><span class="n">setG2parameters</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span> <span class="p">,</span><span class="mi">1000</span><span class="p">,</span> <span class="mi">200</span><span class="p">)</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># sets the window size to 1s with a startTime of 50000ps</span>
+<span class="n">sn</span><span class="o">.</span><span class="n">correlation</span><span class="o">.</span><span class="n">setG2parameters</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span> <span class="p">,</span> <span class="mf">1e12</span><span class="p">,</span> <span class="mf">5e4</span><span class="p">)</span>
 </pre></div>
 </div>
 </dd></dl>

snAPI/Main.py

@@ -3459,7 +3459,7 @@ def __init__(self, parent):
         self.finished = ct.pointer(ct.c_bool(False))
 
 
-    def setG2parameters(self, startChannel: int, clickChannel: int, numBins: int, binWidth: int):
+    def setG2parameters(self, startChannel: int, clickChannel: int, windowSize: float, binWidth: float):
         """
 This function sets the the parameters for the g(2) correlation. If the startChannel is the same as the
 clickChannel an autocorrelation is calculated and if the channels are different a
@@ -3484,8 +3484,8 @@ def setG2parameters(self, startChannel: int, clickChannel: int, numBins: int, bi
         start channel
     clickChannel: int (0 is sync channel)
         click channel
-    numBins: int (default: 10000)
-        number of bins
+    windowSize: int [ps]
+        size of the correlation window
     binWidth: int [ps]
         width of bins 
 
@@ -3497,21 +3497,22 @@ def setG2parameters(self, startChannel: int, clickChannel: int, numBins: int, bi
 -------
 ::
 
-    # sets thew number of bins to 10000
-    sn.correlation.setG2parameters(1, 2 ,1000, 200)
+    # sets the window size to 5000ps with a bin width of 5ps (that means 1000 bins will be calculated)
+    sn.correlation.setG2parameters(1, 2 , 5000, 5)
     
         """
         self.startChannel = startChannel
         self.clickChannel = clickChannel
-        self.numIntervals = 1
-        self.intervalLength = numBins
+        self.windowSize = windowSize
         self.binWidth = binWidth
+        self.intervalLength = int(windowSize / binWidth)
         self.isFcs = False
 
-        self.parent.dll.setCorrelationParams(startChannel, clickChannel, False, 1, numBins, binWidth)
+        self.parent.dll.setG2Params.argtypes = [ct.c_int, ct.c_int, ct.c_double, ct.c_double]
+        self.parent.dll.setG2Params(startChannel, clickChannel, windowSize, binWidth)
 
 
-    def setFCSparameters(self, startChannel: int, clickChannel: int, numIntervals: typing.Optional[int] = 10, intervalLength: typing.Optional[int] = 8):
+    def setFCSparameters(self, startChannel: int, clickChannel: int, windowSize: typing.Optional[float] = 1e12, startTime: typing.Optional[int] = None):
         """
 This function sets the the parameters for the FCS correlation. If the startChannel is the same as the
 clickChannel an autocorrelation is calculated and if the channels are different a
@@ -3541,10 +3542,10 @@ def setFCSparameters(self, startChannel: int, clickChannel: int, numIntervals: t
         start channel
     clickChannel: int (0 is sync channel)
         click channel
-    numIntervals: int (default: 10)
-        number of intervals
-    intervalLength: int (default: 8)
-        num of bins 
+    windowSize: int [ps]
+        size of the correlation window
+    startTime: int [ps]
+        width of bins None: T2: BaseResolution, T3: Resolution
 
 Returns
 -------
@@ -3554,18 +3555,29 @@ def setFCSparameters(self, startChannel: int, clickChannel: int, numIntervals: t
 -------
 ::
 
-    # sets thew number of bins to 10000
-    sn.correlation.setG2parameters(1, 2 ,1000, 200)
+    # sets the window size to 1s with a startTime of 50000ps
+    sn.correlation.setG2parameters(1, 2 , 1e12, 5e4)
     
         """
+        if startTime is None:
+            if self.parent.deviceConfig["MeasMode"] == MeasMode.T2.value:
+                startTime = self.parent.deviceConfig["BaseResolution"]
+            elif self.parent.deviceConfig["MeasMode"] == MeasMode.T3.value:
+                startTime = self.parent.deviceConfig["Resolution"]
+
         self.startChannel = startChannel
         self.clickChannel = clickChannel
-        self.numIntervals = numIntervals
-        self.intervalLength = intervalLength
-        self.isFcs = intervalLength
+        self.windowSize = windowSize
+        self.startTime = startTime
+        self.isFcs = True
+        pNumIntervals = ct.pointer(ct.c_int(0))
+        pIntervalLength = ct.pointer(ct.c_int(0))
+
+        self.parent.dll.setFCSParams.argtypes = [ct.c_int, ct.c_int, ct.POINTER(ct.c_int), ct.POINTER(ct.c_int), ct.c_double, ct.c_double]
+        self.parent.dll.setFCSParams(startChannel, clickChannel, pNumIntervals, pIntervalLength, windowSize, startTime)
+        self.numIntervals = pNumIntervals.contents.value
+        self.intervalLength = pIntervalLength.contents.value
 
-        self.parent.dll.setCorrelationParams(startChannel, clickChannel, True, numIntervals, intervalLength, 0)
-
 
     def measure(self, acqTime: typing.Optional[int] = 1000, waitFinished: typing.Optional[bool] = False, savePTU: typing.Optional[bool] = False):
         """
@@ -3724,7 +3736,7 @@ def getFCSdata(self):
     
         """
         return np.lib.stride_tricks.as_strided(self.data, shape=(2, self.numBins),
-            strides=(ct.sizeof(self.data._type_) * self.numBins, ct.sizeof(self.data._type_))), self.bins
+            strides=(ct.sizeof(self.data._type_) * self.numBins, ct.sizeof(self.data._type_)))[:, 4:], self.bins[4:]
 
 
     def stopMeasure(self):