Update README

README.md

@@ -10,7 +10,7 @@ The recommended install for SPSPy dependencies is via pip.
 To create a virtual environment with pip in the terminal for MacOS or Linux use `python3 -m venv env` to create a local virtual environment named `env` (or whatever name you'd like), or on Windows use `py -m venv env` to do the same. To activate your new environment run `source env/bin/activate` in MacOS or Linux, or `.\env\Scripts\activate`. Now you can run the above `pip` command to install all dependencies to the virtual environment. To leave the virtual environment use the command `deactivate` in your terminal.
 
 ## SPSPlot
-This tool is intended to be used for guiding the settings of the SPS to show specific states on the focal plane detector. The user gives the program reaction information, and the program runs through the kinematics to calculate the energies of ejecta into the the SESPS. To evaluate different states, the program scrapes a list of levels from [NNDC](https://www.nndc.bnl.gov/), and these levels are then passed on to the reaction handler. These levels are then shown on the screen with labels. The labels can be modified to show either the excitation energy of the state, the kinetic energy of the ejectile, or the focal plane z-offset for a state. Note that since levels are obtained from NNDC, SPSPlot requires an internet connection.
+This tool is intended to be used for guiding the settings of the SPS to show specific states on the focal plane detector. The user gives the program reaction information, and the program runs through the kinematics to calculate the energies of ejecta into the the SESPS. To evaluate different states, the program scrapes a list of levels from [NNDC](https://www.nndc.bnl.gov/), and these levels are then passed on to the reaction handler. These levels are then shown on the screen with labels. The labels can be modified to show either the excitation energy of the state, the kinetic energy of the ejectile, or the focal plane z-offset for a state. Note that since levels are obtained from NNDC, SPSPlot requires an internet connection. SPSPlot can also export the calculated reaction information to a csv file.
 
 ## SPANC
 SPANC is the program used to calibrate SESPS focal plane spectra. It works by the user specifying a target, reaction, calibration peaks, and output peaks. The target is a description of the physical target foil used in the SPS, which is used to calculate energy loss effects. The target must contain the isotope used as the target in the reaction description. The reaction indicates to the program what type of ejecta are expected, as well as the settings of the spectrograph. Calibration data is given as centroids from a spectrum with correspoding excitation energies, as well as associated uncertainties. The calibration peaks are then fit using the scipy ODR package (see scipy ODR for more documentation). The fit is plotted, and the results are shown in a table. Additionally, residuals are plotted and shown in a table. The user can then feed the program an output peak, or a peak for which the user would like to calculate the excitation energy of a state using the calibration fit. The peak excitation energy will then be reported, with uncertainty. The user can also give a FWHM to be converted from focal plane position to energy. 

spspy/SPSPlotUI.py

@@ -19,6 +19,9 @@ import matplotlib as mpl
 import sys
 import pickle
 
+DEFAULT_RHO_MIN: float = 69.0
+DEFAULT_RHO_MAX: float = 87.0
+
 class PlotType(Enum):
     PLOT_EX = auto()
     PLOT_KE = auto()
@@ -49,11 +52,12 @@ class SPSPlotGUI(QMainWindow):
         self.create_canvas()
         self.create_inputs()
         self.create_target_table()
+        self.update_plot()
         self.show()
 
     def create_canvas(self) -> None:
         self.canvas = MPLCanvas(self.plotTab, width=14, height=5, dpi=100)
-        self.plotLayout.addWidget(self.canvas, 5)
+        self.plotLayout.addWidget(self.canvas, 4)
 
     def create_menus(self) -> None:
         self.fileMenu = self.menuBar().addMenu("&File")
@@ -82,58 +86,67 @@ class SPSPlotGUI(QMainWindow):
         exportLevels.triggered.connect(self.handle_export_levels)
 
     def create_inputs(self) -> None:
-        inputLayout = QHBoxLayout()
+        inputLayout = QVBoxLayout()
         self.inputGroupBox = QGroupBox("Adjustable Inputs", self.plotTab)
-        rhoMinLabel = QLabel("Rho Min", self.inputGroupBox)
+
-        self.rhoMinInput = QDoubleSpinBox(self.inputGroupBox)
+        self.spsGroupBox = QGroupBox("SPS Parameters", self.inputGroupBox)
+        spsGroupLayout = QHBoxLayout()
+        rhoMinLabel = QLabel("<p>&rho;<sub>Min<\sub><\p>", self.spsGroupBox)
+        self.rhoMinInput = QDoubleSpinBox(self.spsGroupBox)
         self.rhoMinInput.setRange(0.0, 150.0)
+        self.rhoMinInput.setValue(DEFAULT_RHO_MIN)
+        self.sps.rhoMin = DEFAULT_RHO_MIN
         self.rhoMinInput.setSuffix(" cm")
-        rhoMaxLabel = QLabel("RhoMax", self.inputGroupBox)
+        rhoMaxLabel = QLabel("<p>&rho;<sub>Max<\sub><\p>", self.spsGroupBox)
-        self.rhoMaxInput = QDoubleSpinBox(self.inputGroupBox)
+        self.rhoMaxInput = QDoubleSpinBox(self.spsGroupBox)
         self.rhoMaxInput.setRange(0.0,150.0)
+        self.rhoMaxInput.setValue(DEFAULT_RHO_MAX)
+        self.sps.rhoMax = DEFAULT_RHO_MAX
         self.rhoMaxInput.setSuffix(" cm")
-        bkeLabel = QLabel("Beam KE", self.inputGroupBox)
+        bkeLabel = QLabel("<p>E<sub>beam<\sub><\p>", self.spsGroupBox)
-        self.bkeInput = QDoubleSpinBox(self.inputGroupBox)
+        self.bkeInput = QDoubleSpinBox(self.spsGroupBox)
         self.bkeInput.setRange(0.0, 500.0)
         self.bkeInput.setSuffix(" MeV")
-        bfieldLabel = QLabel("B-field", self.inputGroupBox)
+        bfieldLabel = QLabel("B", self.spsGroupBox)
-        self.bfieldInput = QDoubleSpinBox(self.inputGroupBox)
+        self.bfieldInput = QDoubleSpinBox(self.spsGroupBox)
         self.bfieldInput.setRange(0.0, 17.0)
         self.bfieldInput.setSuffix(" kG")
-        angleLabel = QLabel("Angle", self.inputGroupBox)
+        angleLabel = QLabel("<p>&theta;<sub>SPS<\sub><\p>", self.spsGroupBox)
-        self.angleInput = QDoubleSpinBox(self.inputGroupBox)
+        self.angleInput = QDoubleSpinBox(self.spsGroupBox)
         self.angleInput.setRange(0.0, 180.0)
         self.angleInput.setSuffix(" deg")
-        self.runButton = QPushButton("Set", self.inputGroupBox)
+        self.runButton = QPushButton("Set", self.spsGroupBox)
         self.runButton.clicked.connect(self.handle_run)
+        spsGroupLayout.addWidget(rhoMinLabel, 1)
+        spsGroupLayout.addWidget(self.rhoMinInput, 2)
+        spsGroupLayout.addWidget(rhoMaxLabel,1 )
+        spsGroupLayout.addWidget(self.rhoMaxInput, 2)
+        spsGroupLayout.addWidget(bkeLabel, 1)
+        spsGroupLayout.addWidget(self.bkeInput, 2)
+        spsGroupLayout.addWidget(bfieldLabel, 1)
+        spsGroupLayout.addWidget(self.bfieldInput, 2)
+        spsGroupLayout.addWidget(angleLabel, 1)
+        spsGroupLayout.addWidget(self.angleInput, 2)
+        spsGroupLayout.addWidget(self.runButton, 1)
+        self.spsGroupBox.setLayout(spsGroupLayout)
 
-        self.energyButtonGroup = QGroupBox("Ex/KE switch",self.plotTab)
+        self.energyButtonGroup = QGroupBox("Labels",self.plotTab)
         buttonLayout = QHBoxLayout()
-        self.exButton = QRadioButton("Excitation energy (MeV)", self.energyButtonGroup)
+        self.exButton = QRadioButton("Excitation Energy(MeV)", self.energyButtonGroup)
         self.exButton.toggled.connect(self.handle_ex_switch)
         self.exButton.toggle()
-        self.keButton = QRadioButton("Ejectile Kinetic energy (MeV)", self.energyButtonGroup)
+        self.keButton = QRadioButton("Ejectile KE(MeV)", self.energyButtonGroup)
         self.keButton.toggled.connect(self.handle_ke_switch)
-        self.zButton = QRadioButton("Focal Plane Z Shift (cm)", self.energyButtonGroup)
+        self.zButton = QRadioButton("FocalPlane Z-Shift(cm)", self.energyButtonGroup)
         self.zButton.toggled.connect(self.handle_z_switch)
         buttonLayout.addWidget(self.exButton)
         buttonLayout.addWidget(self.keButton)
         buttonLayout.addWidget(self.zButton)
         self.energyButtonGroup.setLayout(buttonLayout)
 
-        inputLayout.addWidget(rhoMinLabel)
+        inputLayout.addWidget(self.spsGroupBox)
-        inputLayout.addWidget(self.rhoMinInput)
-        inputLayout.addWidget(rhoMaxLabel)
-        inputLayout.addWidget(self.rhoMaxInput)
-        inputLayout.addWidget(bkeLabel)
-        inputLayout.addWidget(self.bkeInput)
-        inputLayout.addWidget(bfieldLabel)
-        inputLayout.addWidget(self.bfieldInput)
-        inputLayout.addWidget(angleLabel)
-        inputLayout.addWidget(self.angleInput)
-        inputLayout.addWidget(self.runButton)
-        self.inputGroupBox.setLayout(inputLayout)
         inputLayout.addWidget(self.energyButtonGroup)
+        self.inputGroupBox.setLayout(inputLayout)
 
         self.plotLayout.addWidget(self.inputGroupBox, 1)
 
@@ -142,7 +155,9 @@ class SPSPlotGUI(QMainWindow):
         tableLayout = QVBoxLayout()
         self.targetTable = QTableWidget(self.targetGroup)
         self.targetTable.setColumnCount(6)
-        self.targetTable.setHorizontalHeaderLabels(["Layer1 Thickness(ug/cm^2", "Layer1 (Z, A, S)","Layer2 Thickness(ug/cm^2", "Layer2 (Z, A, S)","Layer3 Thickness(ug/cm^2", "Layer3 (Z, A, S)"])
+        self.targetTable.setHorizontalHeaderLabels(["L1 Thickness(ug/cm^2)", "L1 Compound",
+                                                    "L2 Thickness(ug/cm^2)", "L2 Compound",
+                                                    "L3 Thickness(ug/cm^2)", "Layer3 Compound"])
         tableLayout.addWidget(self.targetTable)
         self.targetGroup.setLayout(tableLayout)
         self.targetLayout.addWidget(self.targetGroup)
@@ -257,6 +272,7 @@ class SPSPlotGUI(QMainWindow):
         self.canvas.axes.set_xlim(self.sps.rhoMin, self.sps.rhoMax)
         self.canvas.axes.set_yticks(range(1,len(self.sps.data)+2))
         self.canvas.axes.set_yticklabels(ylabels)
+        self.canvas.axes.set_xlabel(r"$\rho$ (cm)")
         self.canvas.draw()
 
     def update_inputs(self):
@@ -275,6 +291,8 @@ class SPSPlotGUI(QMainWindow):
                 self.targetTable.setCellWidget(row, 1+col*2, QLabel(str(layer)))
         self.targetTable.resizeColumnsToContents()
         self.targetTable.resizeRowsToContents()
+        
+
 
 def run_spsplot_ui():
     mpl.use("Qt5Agg")

spspy/SpancUI.py

@@ -110,7 +110,7 @@ class SpancGUI(QMainWindow):
         targetLayout = QVBoxLayout()
         self.targetTable = QTableWidget(self.targetGroup)
         self.targetTable.setColumnCount(6)
-        self.targetTable.setHorizontalHeaderLabels(["Layer1 Thickness(ug/cm^2", "Layer1 (Z, A, S)","Layer2 Thickness(ug/cm^2", "Layer2 (Z, A, S)","Layer3 Thickness(ug/cm^2", "Layer3 (Z, A, S)"])
+        self.targetTable.setHorizontalHeaderLabels(["L1 Thickness(ug/cm^2)", "L1 Compound","L2 Thickness(ug/cm^2)", "L2 Compound","L3 Thickness(ug/cm^2)", "L3 Compound"])
         targetLayout.addWidget(self.targetTable)
         self.targetGroup.setLayout(targetLayout)
         self.tablelayout.addWidget(self.targetGroup)

spspy/ui/MPLCanvas.py

@@ -11,7 +11,7 @@ matplotlib.rcParams["ytick.color"] = "w"
 matplotlib.rcParams["text.color"] = "w"
 
 class MPLCanvas(FigureCanvasQTAgg):
-	def __init__(self, parent=None, width=5, height=4, dpi=100):
+	def __init__(self, parent=None, width=3, height=4, dpi=100):
 		self.fig = Figure(figsize=(width, height), dpi=dpi, edgecolor="black",linewidth=0.5)
 		self.axes = self.fig.add_subplot(111)
 		self.axes.spines['top'].set_visible(False)

spspy/ui/ReactionDialog.py

@@ -94,9 +94,9 @@ class ReactionDialog(QDialog):
             self.bfieldInput = QDoubleSpinBox(self.parameterGroupBox)
             self.bfieldInput.setRange(MINIMUM_MAG_FIELD, MAXIMUM_MAG_FIELD)
             self.bfieldInput.setDecimals(6)
-            parameterLayout.addRow("Beam KE(Mev)",self.bkeInput)
+            parameterLayout.addRow(QLabel("E<sub>beam</sub>(Mev)"),self.bkeInput)
-            parameterLayout.addRow("Theta(deg)",self.thetaInput)
+            parameterLayout.addRow("<p>&theta;<sub>SPS</sub>(deg)</p>",self.thetaInput)
-            parameterLayout.addRow("Bfield(kG)",self.bfieldInput)
+            parameterLayout.addRow("B(kG)",self.bfieldInput)
             self.parameterGroupBox.setLayout(parameterLayout)
             self.layout.addWidget(self.parameterGroupBox)