add plot window

README.md

@@ -25,5 +25,10 @@ python -m unittest tests.utilitiesTest
 python example.py
 ```
 
-## Documentation
-Please refer to `documentation/documentation.pdf`.
\ No newline at end of file
+## Project Structure
+- `example.py`: Main file. Execute this to process the data.
+- `config.py`: Initialize gloable variables, including mapping (input) and spectra (output).
+- `utilities.py`: Custom data tyeps. For mapping, calibration coefficient of each SiPM channel is required as an input.
+- `setupParser.py`: Set up the binaray file parser.
+- `coincidenceSelection.py`: Responsible for data processing, including energy calibration and coincidence selection.
+- `plotSpectra.py`: Plot the final results.
\ No newline at end of file

example.py

 '''
 Description: 
 Author: Ming Fang
-Date: 2022-09-04 03:41:17
+Date: 2022-09-20 19:29:43
 LastEditors: Ming Fang
-LastEditTime: 2022-09-20 17:35:30
+LastEditTime: 2022-09-20 22:41:16
 '''
-from matplotlib import pyplot as plt
+import tkinter
+
 # import the parser to use it
 from sources.py_BinFileParser import CITIROCEvent, DT5550WBinFile
 from sources.utilities import Histogram, ImagerSetup, SiPMEvent, CrystalEvent, CoincidenceEvent
-from sources.coincidenceSelection import processPackets
-from typing import List
+from sources.selectCoincidence import processCITIROCEventChunk
+from sources.plotSpectra import plotSpectra
 import config
 
-def processChunk(chunk: List[CITIROCEvent]):
-    timewindow = 50  # ns
-    packets2Process = []
-    lastTimeStamp = 0
-    for newEvent in chunk:
-        currentTimeStamp = newEvent.RunEventTimecode * 0.5  # ns
-        if len(packets2Process) > 0 and abs(currentTimeStamp -
-                                            lastTimeStamp) >= timewindow:
-            processPackets(packets2Process)
-            packets2Process.clear()
-        lastTimeStamp = currentTimeStamp
-        packets2Process.append(newEvent)
-
 
-########### Example 1
+########### Data processing
 # Read the file in chunks of 100k events until end of file (EOF)
 # Depending on available memory size, chunkSize can be made smaller/larger
 fileHandle = DT5550WBinFile(b'test_data/test.data', True)
 chunkSize = 100000
+# Max number of events to process
 maxN = 1000000
 numberOfPulsesRead = 0
 
@@ -39,40 +28,9 @@ while numberOfPulsesRead < maxN and fileHandle.isGood():
     newChunk = fileHandle.readNextNEvents(chunkSize)
     numberOfPulsesRead += len(newChunk)
     print("Read {} events.".format(len(newChunk)))
-    processChunk(newChunk)
-
-
-# for i in range(config.imagerSetup.NSiPMs):
-#     fig, ax = plt.subplots(1, 1, figsize=(6, 6))
-#     asicID, channelID = config.imagerSetup.getAsicChannelID(i)
-#     x = config.singleSiPMSpectra[i].binCenters
-#     y = config.singleSiPMSpectra[i].binCounts
-#     w = config.singleSiPMSpectra[i].binWidth
-#     n = config.singleSiPMSpectra[i].getTotalCounts()
-#     ax.step(x, y, where='mid')
-#     ax.set_title('ASIC {0}, Channel {1}, Total counts {2}'.format(asicID, channelID, n))
-#     ax.set_xlabel('Energy (keV)')
-#     ax.set_ylabel('Counts')
-#     plt.show()
-#     ax.clear()
-
-# for i in range(config.imagerSetup.NCrystals):
-#     fig, ax = plt.subplots(1, 1, figsize=(6, 6))
-#     x = config.SiPMPairSpectra[i].binCenters
-#     y = config.SiPMPairSpectra[i].binCounts
-#     w = config.SiPMPairSpectra[i].binWidth
-#     n = config.SiPMPairSpectra[i].getTotalCounts()
-#     ax.step(x, y, where='mid')
-#     ax.set_title('Crystal {0}, Total counts {1}'.format(i, n))
-#     ax.set_xlabel('Energy (keV)')
-#     ax.set_ylabel('Counts')
-#     plt.show()
-#     ax.clear()
-
+    processCITIROCEventChunk(newChunk)
 
-fig, ax = plt.subplots(1, 1, figsize=(6, 6))
-ax.step(config.coincidenceSpectra.binCenters, config.coincidenceSpectra.binCounts, where='mid')
-ax.set_title('Coincidence spctrum. Total counts {}'.format(config.coincidenceSpectra.getTotalCounts()))
-ax.set_xlabel('Energy (keV)')
-ax.set_ylabel('Counts')
-plt.show()
+########## Plot spectra
+root = tkinter.Tk()
+plotSpectra(root)
+root.mainloop()

sources/plotSpectra.py

+'''
+Description: Plot spectra
+Author: Ming Fang
+Date: 2022-09-20 21:06:52
+LastEditors: Ming Fang mingf2@illinois.edu
+LastEditTime: 2022-09-20 22:25:00
+'''
+import tkinter
+from tkinter import ttk
+from matplotlib.backends.backend_tkagg import (
+    FigureCanvasTkAgg, NavigationToolbar2Tk)
+# Implement the default Matplotlib key bindings.
+from matplotlib.backend_bases import key_press_handler
+from matplotlib.figure import Figure
+import config
+
+
+def plotSpectra(root):
+    def SiPMID_changed(event):
+        AsicID = int(selectedAsicID.get())
+        channelID = int(selectedChannelID.get())
+        SiPMID = config.imagerSetup.getChannelID((AsicID, channelID))
+        # print(AsicID, channelID, SiPMID)
+        # update datas
+        line1.set_data(config.singleSiPMSpectra[SiPMID].binCenters, config.singleSiPMSpectra[SiPMID].binCounts)
+        ax1.set_title('ASIC {0:d}, Channel {1:d}. Total counts {2:d}'.format(AsicID, channelID, config.singleSiPMSpectra[SiPMID].getTotalCounts()))
+        # rescale
+        # recompute the ax.dataLim
+        ax1.relim()
+        # update ax.viewLim using the new dataLim
+        ax1.autoscale_view()
+        # required to update canvas and attached toolbar!
+        canvas.draw()
+    
+    def crystalID_changed(event):
+        crystalID = int(selectedCrystalID.get())
+        # print(crystalID)    
+        # update datas
+        line2.set_data(config.SiPMPairSpectra[crystalID].binCenters, config.SiPMPairSpectra[crystalID].binCounts)
+        ax2.set_title('Crystal {0:d}. Total counts {1:d}'.format(crystalID, config.SiPMPairSpectra[crystalID].getTotalCounts()))
+        # rescale
+        # recompute the ax.dataLim
+        ax2.relim()
+        # update ax.viewLim using the new dataLim
+        ax2.autoscale_view()
+        # required to update canvas and attached toolbar!
+        canvas.draw()
+
+    topFrame = tkinter.Frame(root)
+    bottomFrame = tkinter.Frame(root)
+
+    # create AsicID combobox
+    AsicIDLabel = ttk.Label(text="ASIC ID: ")
+    selectedAsicID = tkinter.StringVar()
+    AsicID_combobox = ttk.Combobox(root, textvariable=selectedAsicID)
+    AsicID_combobox['values'] = ['0', '1', '2', '3']
+    AsicID_combobox['state'] = 'readonly'
+    AsicID_combobox.current(0)
+    AsicID_combobox.bind('<<ComboboxSelected>>', SiPMID_changed)
+
+    # create ChannelID combobox
+    channelIDLabel = ttk.Label(text="Channel ID: ")
+    selectedChannelID = tkinter.StringVar()
+    channelID_combobox = ttk.Combobox(root, textvariable=selectedChannelID)
+    channelID_combobox['values'] = [str(i) for i in range(2, 16)]
+    channelID_combobox['state'] = 'readonly'
+    channelID_combobox.current(0)
+    channelID_combobox.bind('<<ComboboxSelected>>', SiPMID_changed)
+    
+    # create crystalID combobox
+    crystalIDLabel = ttk.Label(text="Crystal ID: ")
+    selectedCrystalID = tkinter.StringVar()
+    crystalID_combobox = ttk.Combobox(root, textvariable=selectedCrystalID)
+    crystalID_combobox['values'] = [str(i) for i in range(28)]
+    crystalID_combobox['state'] = 'readonly'
+    crystalID_combobox.current(0)
+    crystalID_combobox.bind('<<ComboboxSelected>>', crystalID_changed)
+
+    fig = Figure(figsize=(8, 8), dpi=100)
+    ax1 = fig.add_subplot(221)
+    AsicID = int(selectedAsicID.get())
+    channelID = int(selectedChannelID.get())
+    SiPMID = config.imagerSetup.getChannelID((AsicID, channelID))
+    # print(SiPMID)
+    line1, = ax1.step(config.singleSiPMSpectra[SiPMID].binCenters, config.singleSiPMSpectra[SiPMID].binCounts, where='mid')
+    ax1.set_title('ASIC {0:d}, Channel {1:d}. Total counts {2:d}'.format(AsicID, channelID, config.singleSiPMSpectra[SiPMID].getTotalCounts()))
+    ax1.set_xlabel("Energy (keV)")
+    ax1.set_ylabel("Counts")
+
+    ax2 = fig.add_subplot(222)
+    crystalID = int(selectedAsicID.get())
+    # print(crystalID)
+    line2, = ax2.step(config.SiPMPairSpectra[crystalID].binCenters, config.SiPMPairSpectra[crystalID].binCounts, where='mid')
+    ax2.set_title('Crystal {0:d}. Total counts {1:d}'.format(crystalID, config.SiPMPairSpectra[crystalID].getTotalCounts()))
+    ax2.set_xlabel("Energy (keV)")
+    ax2.set_ylabel("Counts")
+
+    ax3 = fig.add_subplot(223)
+    line3, = ax3.step(config.coincidenceSpectra.binCenters, config.coincidenceSpectra.binCounts, where='mid')
+    ax3.set_title('Coincidence spctrum. Total counts {0:d}'.format(config.coincidenceSpectra.getTotalCounts()))
+    ax3.set_xlabel("Energy (keV)")
+    ax3.set_ylabel("Counts")
+
+    canvas = FigureCanvasTkAgg(fig, master=root)  # A tk.DrawingArea.
+    canvas.draw()
+
+    # pack_toolbar=False will make it easier to use a layout manager later on.
+    toolbar = NavigationToolbar2Tk(canvas, root, pack_toolbar=False)
+    toolbar.update()
+
+    canvas.mpl_connect(
+        "key_press_event", lambda event: print(f"you pressed {event.key}"))
+    canvas.mpl_connect("key_press_event", key_press_handler)
+
+    # Packing order is important. Widgets are processed sequentially and if there
+    # is no space left, because the window is too small, they are not displayed.
+    # The canvas is rather flexible in its size, so we pack it last which makes
+    # sure the UI controls are displayed as long as possible.
+    AsicIDLabel.pack(in_=topFrame, side=tkinter.LEFT, fill=tkinter.X)
+    AsicID_combobox.pack(in_=topFrame, side=tkinter.LEFT, fill=tkinter.X)
+    channelIDLabel.pack(in_=topFrame, side=tkinter.LEFT, fill=tkinter.X)
+    channelID_combobox.pack(in_=topFrame, side=tkinter.LEFT, fill=tkinter.X)
+    crystalIDLabel.pack(in_=topFrame, side=tkinter.LEFT, fill=tkinter.X)
+    crystalID_combobox.pack(in_=topFrame, side=tkinter.LEFT, fill=tkinter.X)
+    toolbar.pack(in_=bottomFrame, side=tkinter.TOP, fill=tkinter.X)
+    canvas.get_tk_widget().pack(in_=bottomFrame, side=tkinter.TOP, fill=tkinter.BOTH, expand=True)
+    topFrame.pack(side=tkinter.TOP)
+    bottomFrame.pack(side=tkinter.BOTTOM, fill=tkinter.BOTH, expand=True)

sources/coincidenceSelection.py → sources/selectCoincidence.py

 '''
-Description: Selection coincidences between two SiPM channels on the same crystal, and coincidences between two crystals.
+Description: Select coincidences between two SiPM channels on the same crystal, and coincidences between two crystals.
 Author: Ming Fang
 Date: 2022-09-19 17:50:22
-LastEditors: Ming Fang
-LastEditTime: 2022-09-20 18:01:07
+LastEditors: Ming Fang mingf2@illinois.edu
+LastEditTime: 2022-09-20 22:21:22
 '''
 from sources.utilities import Histogram, ImagerSetup, SiPMEvent, CrystalEvent, CoincidenceEvent
 from sources.py_BinFileParser import CITIROCEvent
@@ -12,11 +12,29 @@ from typing import List
 import config
 
 
-def processPackets(packets: List[CITIROCEvent]) -> None:
-    """Process a chunk of CITIROC events. Update the spectra and the list of coincidence events.
+def processCITIROCEventChunk(chunk: List[CITIROCEvent]):
+    """Process a chunk of events from binary file.
 
     Args:
-        packets (List[CITIROCEvent]): A chunk of CITIROC events.
+        chunk (List[CITIROCEvent]): A list of CITIROC events.
+    """
+    packets2Process = []
+    lastTimeStamp = 0
+    for newEvent in chunk:
+        currentTimeStamp = newEvent.RunEventTimecode * 0.5  # ns
+        if len(packets2Process) > 0 and abs(currentTimeStamp -
+                                            lastTimeStamp) >= config.imagerSetup.timeWindow:
+            processCoincidentCITIROCEvents(packets2Process)
+            packets2Process.clear()
+        lastTimeStamp = currentTimeStamp
+        packets2Process.append(newEvent)
+
+
+def processCoincidentCITIROCEvents(packets: List[CITIROCEvent]) -> None:
+    """Process the CITIROC events that are in coincidence. Update the spectra and the list of coincidence events.
+
+    Args:
+        packets (List[CITIROCEvent]): A list of CITIROC events.
     """
     SiPMEvents = []
     if extractSiPMEvents(packets, SiPMEvents):
@@ -138,4 +156,3 @@ def findZPosition(e1: float, z1: float, e2: float, z2: float) -> float:
         float: z coordainate of the interaction position.
     """
     return (e1 * z1 + e2 * z2) / (e1 + e2)
-

sources/utilities.py

@@ -3,7 +3,7 @@ Description:
 Author: Ming Fang
 Date:  2022-09-19 15:43:38
 LastEditors: Ming Fang
-LastEditTime: 2022-09-20 18:32:46
+LastEditTime: 2022-09-20 19:44:45
 '''
 import json
 import numpy as np
@@ -23,6 +23,8 @@ class ImagerSetup:
         self.NSiPMs = len(self._channelSettings)
         # Number of crystal
         self.NCrystals = self.NSiPMs // 2
+        # Coincidence time window, ns
+        self.timeWindow = 50
     
     def _loadSettingsFromJson(self, fpath) -> None:
         """Load the settings from a json file.
@@ -248,7 +250,7 @@ class Histogram:
         self.binCenters = (self.binEdges[:-1] + self.binEdges[1:]) / 2
         self.nBins = nbins
         # counts in each bin
-        self.binCounts = np.zeros(self.binCenters.shape)
+        self.binCounts = np.zeros(self.binCenters.shape, dtype=int)
     
     def fill(self, x: float) -> None:
         """Find the bin that x falls into and increment the counts in that bin by 1.