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normingApp.py
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#!/usr/bin/python3
# -*- coding: utf-8 -*-
import os
import tkinter
from tkinter import ttk
from tkinter.font import Font
import tkinter.filedialog as filedialog
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg as FigCanvas
from matplotlib.backends.backend_tkagg import NavigationToolbar2Tk as NavigationToolbar
# from matplotlib.backends.backend_tkagg import NavigationToolbar2TkAgg as NavigationToolbar
from matplotlib.backend_bases import key_press_handler
from matplotlib.widgets import SpanSelector
from matplotlib.figure import Figure
from matplotlib.ticker import ScalarFormatter, MaxNLocator
from matplotlib.collections import LineCollection
import matplotlib.pyplot as plt
import numpy as np
import glob
#import matplotlib.pyplot as plt
import normAppLogic
class NormSpectra(tkinter.Tk):
def __initAttributes__(self):
self.appLogic = normAppLogic.normAppLogic()
#control variables
self.ifCreateNewRegion = False
self.ifChooseActiveRegion = False
self.ifAddPoint = False
self.ifAutoUpdateNormalization = False
self.ifApplyRadioVelocityCorrection = False
self.numberOfActiveRegion = 0
self.radVelDialog = None
self.periodicTableDialog = None
self.fileList = []
def __init__(self):
tkinter.Tk.__init__(self)
self.__initAttributes__()
self.createMainWindow()
def createMainWindow(self):
self.WENS = tkinter.W+tkinter.E+tkinter.N+tkinter.S
self.createWindow()
self.createControls()
self.createMenu()
self.createPlottingArea()
def createWindow(self):
self.frame = tkinter.Frame(self)
self.frame.pack(fill=tkinter.BOTH, expand=1)
self.wm_title("HANDY - Handy tool for spectra normalization")
img = tkinter.PhotoImage(file=os.path.join(os.path.dirname(os.path.realpath(__file__)),"handy.gif"))
self.tk.call('wm', 'iconphoto', self._w, img)
def createMenu(self):
menu = tkinter.Menu(self)
self.config(menu=menu)
#------------------------------------
fileMenu1 = tkinter.Menu(menu)
menu.add_cascade(label="Open", underline=0, menu=fileMenu1)
fileMenu1.add_command(label="Open spectrum", command=self.onOpenSpectrum)
fileMenu1.add_command(label="Open continuum file",\
command=self.onLoadContinuum)
fileMenu1.add_command(label="Open theoretical spectrum",\
command=self.onLoadTheoreticalSectrum)
fileMenu1.add_command(label="Exit", underline=0, command=self.onExit)
#------------------------------------
fileMenu2 = tkinter.Menu(menu)
menu.add_cascade(label="Save", underline=0, menu=fileMenu2)
fileMenu2.add_command(label="Save normed spectrum",\
command=self.onSaveNormedSpectrum)
fileMenu2.add_command(label="Save normed spectrum VRAD corrected",\
command=self.onSaveVelocityCorrectedNormedSpectrum)
fileMenu2.add_command(label="Save continuum",\
command=self.onSaveContinuum)
fileMenu2.add_command(label="Save theoretical spectrum",\
command=self.onSaveTheoreticalSpectrum)
fileMenu2.add_command(label="Save notes",\
command=self.onSaveNotes)
fileMenu2.add_separator()
fileMenu2.add_command(label="Save all",\
command=self.onSaveAll)
#------------------------------------
fileMenu3 = tkinter.Menu(menu)
menu.add_cascade(label="Spectrum", underline=0, menu=fileMenu3)
self.vlevel = tkinter.IntVar()
lG = self.appLogic.gridDefinitions.listAvailibleGrids()
self.appLogic.gridDefinitions.setChoosenGrid(lG[0])
self.onChooseGrid() # load default grid
for i, gridName in enumerate(lG):
fileMenu3.add_radiobutton(label = gridName,
var = self.vlevel,
value = i,
command = self.onChooseGrid
)
# self.vlevel.set(0)
fileMenu3.add_separator()
self._syntheNumber = len(lG)
fileMenu3.add_radiobutton(label = "SYNTHE",
var = self.vlevel,
value = len(lG),
command = self.onChooseSYNTHE
)
#------------------------------------
fileMenu4 = tkinter.Menu(menu)
menu.add_cascade(label="Line labels", underline=0, menu=fileMenu4)
self.labelSettings = tkinter.IntVar()
self.labelSettings.set(0)
fileMenu4.add_radiobutton(label="No labels", value=0, variable=self.labelSettings, command = self.onCheckLabelSettings)
fileMenu4.add_separator()
fileMenu4.add_radiobutton(label="Show all", value=1, variable=self.labelSettings, command = self.onCheckLabelSettings)
fileMenu4.add_radiobutton(label="On hower", value=2, variable=self.labelSettings, command = self.onCheckLabelSettings)
def onChooseGrid(self):
lG = self.appLogic.gridDefinitions.listAvailibleGrids()
numOfGrid = self.vlevel.get()
self.appLogic.gridDefinitions.setChoosenGrid(lG[numOfGrid])
print("Set {} grid".format(lG[numOfGrid]))
# print(d)
paramsList, folder, refWave, paramsNum, paramsMult, fluxFilesFilter, skipRows, waveColumn, fluxColumn, comments = self.appLogic.gridDefinitions.setGridParams()
self.appLogic.specSynthesizer.setGrid(
folder = folder,
refWave = refWave,
paramsList = paramsList,
paramsNum = paramsNum,
paramsMult = paramsMult,
fluxFilesFilter = fluxFilesFilter,
skipRows = skipRows,
waveColumn = waveColumn,
fluxColumn = fluxColumn,
comments = comments,
)
d = self.appLogic.gridDefinitions.getDefinedVariables()
setVal = {True: 'normal', False: 'disabled'}
self.vmacScale['state'] = setVal[True]
self.vsiniScale['state'] = setVal[True]
self.teffScale['state'] = setVal[d["teff"]]
self.loggScale['state'] = setVal[d["logg"]]
self.vmicScale['state'] = setVal[d["vmic"]]
self.meScale['state'] = setVal[d["me"]]
if d["teff"]:
self.teffScale['from_'],self.teffScale['to'] = self.appLogic.specSynthesizer.getRangesOfParameter("teff")
if d["logg"]:
self.loggScale['from_'], self.loggScale['to'] = self.appLogic.specSynthesizer.getRangesOfParameter("logg")
if d["vmic"]:
self.vmicScale['from_'] ,self.vmicScale['to'] = self.appLogic.specSynthesizer.getRangesOfParameter("vmic")
if d["me"]:
minim, maxim = self.appLogic.specSynthesizer.getRangesOfParameter("me")
if minim == 0: #TODO conversion of units should be done better
minim = -2
else:
minim = np.round(np.log10(minim),2)
maxim = np.round(np.log10(maxim),2)
self.meScale['from_'] ,self.meScale['to'] = minim, maxim
def onChooseSYNTHE(self):
setVal = {True: 'normal', False: 'disabled'}
self.vmacScale['state'] = setVal[False] # missing in vidmapy!
self.vsiniScale['state'] = setVal[True]
self.teffScale['state'] = setVal[True]
self.loggScale['state'] = setVal[True]
self.vmicScale['state'] = setVal[True]
self.meScale['state'] = setVal[True]
self.teffScale['from_'], self.teffScale['to'] = 4000, 35000
self.loggScale['from_'], self.loggScale['to'] = 0.5, 6.0
self.vmicScale['from_'], self.vmicScale['to'] = 0.0, 15.0
self.meScale['from_'], self.meScale['to'] = -3.0, 3.0
def onCheckLabelSettings(self):
self.updateLinesAnnotations()
self.canvas.draw()
def onOpenSpectrum(self):
dirname = os.getcwd()
ftypes = [('All files', '*'),('FITS files', '*fits'),('Plain text', '*.txt *.dat')]
answer = filedialog.askopenfilenames(title="Open spectrum...", initialdir=dirname, filetypes=ftypes)
if answer:
self.fileList = answer
fileName = self.fileList[0]
skipRows=1
colWave=0
colFlux=1
self.appLogic.readSpectrum(fileName,\
colWave=colWave,\
colFlux=colFlux,\
skipRows=skipRows)
self.appLogic.continuumRegionsLogic.updateRegionsAndPoints(self.appLogic.spectrum)
self.appLogic.continuum.wave = []
self.appLogic.continuum.flux = []
if self.ifAutoUpdateNormalization:
self.appLogic.normSpectrum()
self.onAlreadyNormed(reprint = False)
self.updateNotesOnNewSpectrum()
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux,ifAutoscale=True)
def onLoadContinuum(self):
dirname = os.getcwd()
ftypes = [('Plain text', '*.cont'),('All files', '*')]
answer = filedialog.askopenfilenames(title="Open ranges file...", initialdir=dirname, filetypes=ftypes)
if answer:
fileName = answer[0]
self.appLogic.continuumRegionsLogic.readRegionsFile(self.appLogic.spectrum,\
fileName)
self.appLogic.continuumRegionsLogic.updateRegionsAndPoints(self.appLogic.spectrum)
order = str(self.appLogic.continuumRegionsLogic.getOrderOfActiveRegion())
self.currentOrder.set(order)
if self.ifAutoUpdateNormalization:
self.appLogic.normSpectrum()
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux)
def onLoadTheoreticalSectrum(self):
dirname = os.getcwd()
ftypes = [('Plain text', '*.txt *.dat *.syn'),('All files', '*')]
answer = filedialog.askopenfilenames(title="Open spectrum...", initialdir=dirname, filetypes=ftypes)
if answer:
fileName = answer[0]
skipRows=1
colWave=0
colFlux=1
self.appLogic.readTheoreticalSpectrum(fileName,\
colWave=colWave,\
colFlux=colFlux,\
skipRows=skipRows)
self.line23.set_data(self.appLogic.theoreticalSpectrum.wave,\
self.appLogic.theoreticalSpectrum.flux)
if self.appLogic.theoreticalSpectrum.wave is not None and len(self.appLogic.theoreticalSpectrum.wave)!=0:
self.updateErrorPlot()
self.canvas.draw()
def onExit(self):
self.quit()
def onSaveNormedSpectrum(self, verbose=True):
initialName = "out.norm"
if self.appLogic.spectrum.name is not None:
fileName = os.path.splitext(self.appLogic.spectrum.name)[0] + ".norm"
if verbose:
initialName = os.path.basename(fileName)
fileName = filedialog.asksaveasfilename(initialfile=initialName)
if fileName and self.appLogic.spectrum.wave is not None and len(self.appLogic.spectrum.wave) != 0:
# self.appLogic.saveNormedSpectrum(fileName,self.ifSaveCorrectedvrad.get())
self.appLogic.saveNormedSpectrum(fileName,False)
def onSaveVelocityCorrectedNormedSpectrum(self, verbose=True):
initialName = "out_rv.norm"
if self.appLogic.spectrum.name is not None:
fileName = os.path.splitext(self.appLogic.spectrum.name)[0] + "_rv.norm"
if verbose:
initialName = os.path.basename(fileName)
fileName = filedialog.asksaveasfilename(initialfile=initialName)
if fileName and self.appLogic.spectrum.wave is not None and len(self.appLogic.spectrum.wave) != 0:
self.appLogic.saveNormedSpectrum(fileName,True)
# self.appLogic.saveSpectrum(fileName)
def onSaveContinuum(self, verbose=True):
initialName = "out.cont"
if self.appLogic.spectrum.name is not None:
fileName = os.path.splitext(self.appLogic.spectrum.name)[0] + ".cont"
if verbose:
initialName = os.path.basename(fileName)
fileName = filedialog.asksaveasfilename(initialfile=initialName)
if fileName and self.appLogic.spectrum.wave is not None and len(self.appLogic.spectrum.wave) != 0:
self.appLogic.continuumRegionsLogic.saveRegionsFile(self.appLogic.spectrum,\
fileName)
def onSaveTheoreticalSpectrum(self, verbose=True):
initialName = "out.syn"
if self.appLogic.spectrum.name is not None:
fileName = os.path.splitext(self.appLogic.spectrum.name)[0] + ".syn"
if verbose:
initialName = os.path.basename(fileName)
fileName = filedialog.asksaveasfilename(initialfile=initialName)
print(fileName)
if fileName and self.appLogic.theoreticalSpectrum.wave is not None and len(self.appLogic.theoreticalSpectrum.wave) != 0:
self.appLogic.saveTheoreticalSpectrum(fileName)
def onSaveAll(self):
self.onSaveNormedSpectrum(verbose=False)
self.onSaveVelocityCorrectedNormedSpectrum(verbose=False)
self.onSaveContinuum(verbose=False)
self.onSaveTheoreticalSpectrum(verbose=False)
self.onSaveNotes()
def createControls(self):
# Create several frames for grouping buttons
self.controlNote = ttk.Notebook(self.frame)
self.controlFrameA=tkinter.Frame(self.controlNote)
self.controlFrameB=tkinter.Frame(self.controlNote)
self.controlFrameC=tkinter.Frame(self.controlNote)
self.controlFrameD=tkinter.Frame(self.controlNote)
self.controlFrameE=tkinter.Frame(self.controlNote)
self.createNormalizationControls()
self.createModellingControls()
self.createOutputPlotControls()
self.createLabelControls()
self.createSpectrumNotes()
self.controlFrameA.pack()
self.controlFrameB.pack()
self.controlFrameC.pack()
self.controlFrameD.pack()
self.controlFrameE.pack()
self.controlNote.add(self.controlFrameA, text = "Controls")
self.controlNote.add(self.controlFrameB, text = "Model")
self.controlNote.add(self.controlFrameD, text = "Labels")
self.controlNote.add(self.controlFrameE, text = "Notes")
self.controlNote.add(self.controlFrameC, text = "Plot")
self.controlNote.pack(fill=tkinter.BOTH, expand=0)
def createNormalizationControls(self):
#=======================================================================
self.bttn11 = tkinter.Button(self.controlFrameA,\
text = "Back",\
command = self.onBack)
self.bttn11.grid(row = 0, column = 0, sticky = self.WENS)
self.bttn21 = tkinter.Button(self.controlFrameA,\
text = "Choose region",\
command = self.onChooseActiveRegion)
self.bttn21.grid(row = 1, column = 0, sticky = self.WENS)
self.bttn31 = tkinter.Button(self.controlFrameA,\
text = "Create region",\
command = self.onCreateNewActiveRegion)
self.bttn31.grid(row = 2, column = 0, sticky = self.WENS)
#-----------------------------------------------------------------------
self.bttn12 = tkinter.Button(self.controlFrameA,\
text = "Next spectrum",\
command = self.onNextSpectrum)
self.bttn12.grid(row = 0, column = 1, sticky = self.WENS)
self.bttn22 = tkinter.Button(self.controlFrameA,\
text = "Add special point",\
command = self.onAddSpecialPoint)
self.bttn22.grid(row = 1, column = 1, sticky = self.WENS)
self.bttn32 = tkinter.Button(self.controlFrameA,\
text = "Auto fit special points",\
command = self.onAutoFitSpecialPoints)
self.bttn32.grid(row = 2, column = 1, sticky = self.WENS)
# self.bttn42 = tkinter.Label(self.controlFrameA, text=" <--- Adjust order")
# self.bttn42.grid(row = 3, column = 1, sticky = self.WENS)
#-----------------------------------------------------------------------
self.bttn13 = tkinter.Button(self.controlFrameA,\
text = "Normalize",\
command = self.onNormalize)
self.bttn13.grid(row = 0, column = 2, sticky = self.WENS)
self.bttn23 = tkinter.Button(self.controlFrameA,\
text = "Auto update",\
command = self.onSetAutoUpdateNormalization)
self.bttn23.grid(row = 1, column = 2, sticky = self.WENS)
self.bttn33 = tkinter.Button(self.controlFrameA,\
text = "Radial velocity",\
command = self.onRadialVelocity)
self.bttn33.grid(row = 2, column = 2, sticky = self.WENS)
#=======================================================================
self.currentOrder = tkinter.StringVar()
self.bttn14 = tkinter.Spinbox(self.controlFrameA,\
from_=1,\
to=10,\
width=2,\
command=self.onUpdateOrder,\
textvariable=self.currentOrder,\
state = "readonly",\
font = Font(size=12)
)
# text = "Create new active region",\
# command = self.onCreateNewActiveRegion)
self.bttn14.grid(row = 0, column = 3, rowspan = 3, sticky = self.WENS)
self.backgroundColor = self.bttn11.cget("bg")
self.activeBackground = self.bttn11.cget("activebackground")
def createModellingControls(self):
self.teffVar = tkinter.DoubleVar(value = 22000)
self.loggVar = tkinter.DoubleVar(value = 3.8)
self.vmicVar = tkinter.DoubleVar(value = 2)
self.meVar = tkinter.DoubleVar(value = 0.0)
self.vsiniVar = tkinter.DoubleVar(value = 0)
self.vmacVar = tkinter.DoubleVar(value = 0)
self.resolution = tkinter.DoubleVar() # set value when initializing window
# https://stackoverflow.com/questions/41225071/python-tkinter-spinbox-seems-to-reset-the-variable-value
hor = tkinter.HORIZONTAL
self.teffScale = tkinter.Scale(self.controlFrameB,
variable = self.teffVar,
orient = hor,
label = "Teff",
from_ = 15000,
to = 30000,
resolution = 50,
# sliderlength = 30,
# length = 400,
)
self.teffScale.grid(row = 0, column = 0, columnspan = 2, sticky = self.WENS)
self.loggScale = tkinter.Scale(self.controlFrameB,
variable = self.loggVar,
orient = hor,
label = "logg",
from_ = 3.0,
to = 4.5,
resolution = 0.05,
length = 250,
)
self.loggScale.grid(row = 1, column = 0, sticky = self.WENS)
self.vmicScale = tkinter.Scale(self.controlFrameB,
variable = self.vmicVar,
orient = hor,
label = 'vmic',
from_ = 0,
to = 15,
resolution = 1,
length = 250,
)
self.vmicScale.grid(row = 1, column = 1, sticky = self.WENS)
self.vmacScale = tkinter.Scale(self.controlFrameB,
variable = self.vmacVar,
orient = hor,
label = "vmac",
from_ = 0,
to = 50,
resolution = 1,
length = 250,
)
self.vmacScale.grid(row = 0, column = 2, sticky = self.WENS)
self.vsiniScale = tkinter.Scale(self.controlFrameB,
variable = self.vsiniVar,
orient = hor,
label = "vsini",
from_ = 0,
to = 200,
resolution = 1,
length = 150,
)
self.vsiniScale.grid(row = 1, column = 2, sticky = self.WENS)
self.meScale = tkinter.Scale(self.controlFrameB,
variable = self.meVar,
orient = hor,
label = "[M/H]",
from_ = -1, #TODO work around low metallicity bug
to = 0.3,
resolution = 0.1,
length = 250,
)
self.meScale.grid(row = 0, column = 3, columnspan = 2, sticky = self.WENS)
# self.resolutionScale = tkinter.Scale(self.controlFrameB,
# variable = self.resolution,
# orient = hor,
# label = 'resolution',
# from_ = 1000,
# to = 100000,
# resolution = 1000,
# length = 150,
# )
# self.resolutionScale = tkinter.Entry(self.controlFrameB,
# textvariable = self.resolution,
# )
self.resolutionLabel = tkinter.Label(self.controlFrameB,
text = "resolution",
)
self.resolutionLabel.grid(row = 1, column = 3, sticky = self.WENS)
self.resolutionScale = tkinter.Spinbox(self.controlFrameB,
textvariable = self.resolution,
values = (1000,2000,5000,10000,20000,50000,100000,np.inf),
state = 'readonly',
width = 7,
)
self.resolution.set(np.inf) # Must be like that :(
self.resolutionScale.grid(row = 1, column = 4, sticky = self.WENS)
self.bttnClearTheorSpec = tkinter.Button(self.controlFrameB,\
text = "Clear\ntheoretical\nspectrum",\
command = self.onClearTheoreticalSpectrum)
self.bttnClearTheorSpec.grid(row = 0, column = 5, rowspan = 1, sticky = self.WENS)
self.bttnLoadTheorSpec = tkinter.Button(self.controlFrameB,\
text = "Compute\ntheoretical\nspectrum",\
command = self.onComputeTheoreticalSpectrum)
self.bttnLoadTheorSpec.grid(row = 1, column = 5, rowspan = 1, sticky = self.WENS)
self.ifAlreadyNormed = tkinter.IntVar()
self.workWithNormedSpectrum = tkinter.Checkbutton(self.controlFrameB,
text = "Already\nnormalised\nspectrum?",
variable = self.ifAlreadyNormed,
command = self.onAlreadyNormed,
)
self.workWithNormedSpectrum.grid(row = 0, column = 6,rowspan=1, sticky = self.WENS)
self.workWithNormedSpectrum = tkinter.Button(self.controlFrameB,
text = "Periodic table",
# variable = self.ifAlreadyNormed,
command = self.onPeriodicTableDialog,
state = tkinter.DISABLED,
)
self.workWithNormedSpectrum.grid(row = 1, column = 6,rowspan=1, sticky = self.WENS)
def createOutputPlotControls(self):
self.bttnOpenSaveWindow = tkinter.Button(self.controlFrameC,\
text = "Plot fitted spectrum",\
command = self.onOpenSavePlot)
self.bttnOpenSaveWindow.pack(side=tkinter.TOP, fill=tkinter.Y)
def createLabelControls(self):
self._visibility_depth = tkinter.DoubleVar(value = 0.95)
self.appLogic.setLabelsThreshold(self._visibility_depth.get())
self.labelScale = tkinter.Scale(self.controlFrameD,
variable = self._visibility_depth,
orient = tkinter.HORIZONTAL,
label = "Line depth",
from_ = 0,
to = 1,
resolution = 0.01,
command = self.onUpdateLabelDepth,
length = 200,
)
self.labelScale.pack(side=tkinter.TOP, fill=tkinter.Y)
def createSpectrumNotes(self):
topframe = tkinter.Frame(self.controlFrameE)
topframe.pack(side=tkinter.TOP)
self.spectrumBasenameVar = tkinter.StringVar()
tkinter.Label(topframe, textvariable=self.spectrumBasenameVar).pack(side=tkinter.LEFT)
self.spectrumBasenameVar.set("Spectrum name: " + self.appLogic.getSpectrumBaseName())
note_data = self.appLogic.getNoteData()
bottomframe = tkinter.Frame(self.controlFrameE)
bottomframe.pack(side=tkinter.BOTTOM, expand=0)
leftbottomframe = tkinter.Frame(bottomframe)
leftbottomframe.pack(side=tkinter.LEFT, expand=0)
rightbottomframe = tkinter.Frame(bottomframe)
rightbottomframe.pack(side=tkinter.LEFT, expand=0)
#-------------------------------------- TEFF
self.noteTeff = tkinter.StringVar()
self.noteTeffLabel = tkinter.Label(leftbottomframe,
text = "teff",
)
self.noteTeffEntry = tkinter.Entry(leftbottomframe,
textvariable = self.noteTeff,
)
self.noteTeff.set(note_data['teff'])
self.noteTeffLabel.grid(row = 1, column = 1, sticky = self.WENS)
self.noteTeffEntry.grid(row = 1, column = 2, sticky = self.WENS)
#-------------------------------------- LOGG
self.noteLogg = tkinter.StringVar()
self.noteLoggLabel = tkinter.Label(leftbottomframe,
text = "logg",
)
self.noteLoggEntry = tkinter.Entry(leftbottomframe,
textvariable = self.noteLogg,
)
self.noteLogg.set(note_data['logg'])
self.noteLoggLabel.grid(row = 2, column = 1, sticky = self.WENS)
self.noteLoggEntry.grid(row = 2, column = 2, sticky = self.WENS)
#-------------------------------------- ME
self.noteMe = tkinter.StringVar()
self.noteMeLabel = tkinter.Label(leftbottomframe,
text = "me",
)
self.noteMeEntry = tkinter.Entry(leftbottomframe,
textvariable = self.noteMe,
)
self.noteMe.set(note_data['me'])
self.noteMeLabel.grid(row = 3, column = 1, sticky = self.WENS)
self.noteMeEntry.grid(row = 3, column = 2, sticky = self.WENS)
#========================================
#-------------------------------------- VMIC
self.noteVmic = tkinter.StringVar()
self.noteVmicLabel = tkinter.Label(leftbottomframe,
text = "vmic",
)
self.noteVmicEntry = tkinter.Entry(leftbottomframe,
textvariable = self.noteVmic,
)
self.noteVmic.set(note_data['vmic'])
self.noteVmicLabel.grid(row = 1, column = 3, sticky = self.WENS)
self.noteVmicEntry.grid(row = 1, column = 4, sticky = self.WENS)
#-------------------------------------- VSINI
self.noteVsini = tkinter.StringVar()
self.noteVsiniLabel = tkinter.Label(leftbottomframe,
text = "vsini",
)
self.noteVsiniEntry = tkinter.Entry(leftbottomframe,
textvariable = self.noteVsini,
)
self.noteVsini.set(note_data['vsini'])
self.noteVsiniLabel.grid(row = 2, column = 3, sticky = self.WENS)
self.noteVsiniEntry.grid(row = 2, column = 4, sticky = self.WENS)
#-------------------------------------- VMAC
self.noteVmac = tkinter.StringVar()
self.noteVmacLabel = tkinter.Label(leftbottomframe,
text = "vmac",
)
self.noteVmacEntry = tkinter.Entry(leftbottomframe,
textvariable = self.noteVmac,
)
self.noteVmac.set(note_data['vmac'])
self.noteVmacLabel.grid(row = 3, column = 3, sticky = self.WENS)
self.noteVmacEntry.grid(row = 3, column = 4, sticky = self.WENS)
#======================================= Notes
self.noteText = tkinter.StringVar()
self.noteTextDisplay = tkinter.Text(rightbottomframe,height=5)
self.noteText.set(note_data['text_notes'])
self.noteTextDisplay.insert(tkinter.INSERT, self.noteText.get())
self.noteTextDisplay.pack(side=tkinter.LEFT, expand=True, fill=tkinter.Y)
#======================================= SAVE NOTES BUTTON
self.noteSaveBttn = tkinter.Button(rightbottomframe,\
text = "Save notes",\
command = self.onSaveNotes)
self.noteSaveBttn.pack(side=tkinter.LEFT, expand=True, fill=tkinter.Y)
self.noteGetParamsBttn = tkinter.Button(rightbottomframe,\
text = "Get paramters\nfrom model",\
command = self.onGetParamsFromModel)
self.noteGetParamsBttn.pack(side=tkinter.LEFT, expand=True, fill=tkinter.Y)
self.noteSetParamsBttn = tkinter.Button(rightbottomframe,\
text = "Set model\nfrom notes",\
command = self.onSetModelFromNotes)
self.noteSetParamsBttn.pack(side=tkinter.LEFT, expand=True, fill=tkinter.Y)
def onSaveNotes(self):
note_data = {
"text_notes": self.noteTextDisplay.get("1.0",tkinter.END),
"teff": self.noteTeff.get(),
"logg": self.noteLogg.get(),
"me": self.noteMe.get(),
"vmic": self.noteVmic.get(),
"vsini": self.noteVsini.get(),
"vmac": self.noteVmac.get(),
}
self.appLogic.setNoteData(note_data)
def updateNotesOnNewSpectrum(self):
self.spectrumBasenameVar.set("Spectrum name: " + self.appLogic.getSpectrumBaseName())
note_data = self.appLogic.getNoteData()
self.noteTeff.set(note_data['teff'])
self.noteLogg.set(note_data['logg'])
self.noteMe.set(note_data['me'])
self.noteVmic.set(note_data['vmic'])
self.noteVsini.set(note_data['vsini'])
self.noteVmac.set(note_data['vmac'])
self.noteText.set(note_data['text_notes'])
self.noteTextDisplay.delete("1.0", tkinter.END)
self.noteTextDisplay.insert(tkinter.INSERT, self.noteText.get())
def onGetParamsFromModel(self):
self.noteTeff.set(self.teffVar.get())
self.noteLogg.set(self.loggVar.get())
self.noteMe.set(self.meVar.get())
self.noteVmic.set(self.vmicVar.get())
self.noteVsini.set(self.vsiniVar.get())
self.noteVmac.set(self.vmacVar.get())
def onSetModelFromNotes(self):
self.teffVar.set(self.noteTeff.get())
self.loggVar.set(self.noteLogg.get())
self.meVar.set(self.noteMe.get())
self.vmicVar.set(self.noteVmic.get())
self.vsiniVar.set(self.noteVsini.get())
self.vmacVar.set(self.noteVmac.get())
def onUpdateLabelDepth(self, value):
self.appLogic.setLabelsThreshold(self._visibility_depth.get())
self.updateLinesAnnotations()
self.canvas.draw()
def onAlreadyNormed(self,reprint = True):
if self.ifAlreadyNormed.get() == 1:
# print("Spectrum is already normed!!!")
self.appLogic.ifOnNormedSpectrum(True)
self.bttn11['state'] = 'disabled'
self.bttn21['state'] = 'disabled'
self.bttn31['state'] = 'disabled'
self.bttn12['state'] = 'disabled'
self.bttn22['state'] = 'disabled'
self.bttn32['state'] = 'disabled'
self.bttn13['state'] = 'disabled'
self.bttn23['state'] = 'disabled'
else:
self.appLogic.ifOnNormedSpectrum(False)
self.bttn11['state'] = 'normal'
self.bttn21['state'] = 'normal'
self.bttn31['state'] = 'normal'
self.bttn12['state'] = 'normal'
self.bttn22['state'] = 'normal'
self.bttn32['state'] = 'normal'
self.bttn13['state'] = 'normal'
self.bttn23['state'] = 'normal'
self.numberOfActiveRegion = self.appLogic.continuumRegionsLogic.activeRegionNumber
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux)
def onUpdateOrder(self):
order = int(self.currentOrder.get())
self.appLogic.updateOrderOfActiveRegion(order)
if self.ifAutoUpdateNormalization:
self.appLogic.normSpectrum()
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux)
def onBack(self):
self.appLogic.continuumRegionsLogic.restoreLast()
self.numberOfActiveRegion = self.appLogic.continuumRegionsLogic.activeRegionNumber
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux)
if self.ifAutoUpdateNormalization:
self.onNormalize()
def onChooseActiveRegion(self):
self.ifCreateNewRegion = False
self.ifChooseActiveRegion = not self.ifChooseActiveRegion
self.ifAddPoint = False
self.setButtons(self.bttn21,self.ifChooseActiveRegion)
def onCreateNewActiveRegion(self):
self.ifCreateNewRegion = not self.ifCreateNewRegion
self.ifChooseActiveRegion = False
self.ifAddPoint = False
self.setButtons(self.bttn31,self.ifCreateNewRegion)
def onAddSpecialPoint(self):
self.ifCreateNewRegion = False
self.ifChooseActiveRegion = False
self.ifAddPoint = not self.ifAddPoint
self.setButtons(self.bttn22,self.ifAddPoint)
def setButtons(self,button,boolKeyVar):
self.bttn21.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
self.bttn31.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
self.bttn22.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
if self.ifAddPoint:
self.spanNormalization.set_visible(False)
if self.ifChooseActiveRegion:
self.spanNormalization.set_visible(False)
if boolKeyVar:
button.configure(bg = "#567",activebackground="#678")
else:
self.spanNormalization.set_visible(True)
button.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
def resetButtons(self):
self.bttn21.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
self.bttn31.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
self.bttn22.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
self.spanNormalization.set_visible(True)
def onNextSpectrum(self):
if self.appLogic.spectrum.name is not None:
fit = os.path.join(os.path.dirname(self.appLogic.spectrum.name), "*fits")
# print(self.appLogic.spectrum.name)
# print(fit)
filesInFolder=glob.glob(fit)
filesInFolder.sort()
n = filesInFolder.index(self.appLogic.spectrum.name) + 1
if n < len(filesInFolder):
fileName = filesInFolder[n]
skipRows=1
colWave=0
colFlux=1
self.appLogic.readSpectrum(fileName,\
colWave=colWave,\
colFlux=colFlux,\
skipRows=skipRows)
self.appLogic.continuumRegionsLogic.updateRegionsAndPoints(self.appLogic.spectrum)
if self.ifAutoUpdateNormalization:
self.appLogic.normSpectrum()
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux,ifAutoscale=True)
else:
print("Last spectrum in choosen folder!")
def onAutoFitSpecialPoints(self):
self.appLogic.continuumRegionsLogic.autoFitPoints(self.appLogic.theoreticalSpectrum)
if self.ifAutoUpdateNormalization:
self.appLogic.normSpectrum()
contRegionsWaveAndFlux = self.appLogic.getContinuumRangesForPlot()
self.replotUpdatedRanges(contRegionsWaveAndFlux)
def onNormalize(self):
self.appLogic.normSpectrum()
if self.appLogic.spectrum.wave is not None:
self.updateNormedPlot()
self.canvas.draw()
def onSetAutoUpdateNormalization(self):
self.ifAutoUpdateNormalization = not self.ifAutoUpdateNormalization
if self.ifAutoUpdateNormalization:
self.onNormalize()
self.bttn23.configure(bg = "#567",activebackground="#678")
else:
self.bttn23.configure(bg = self.backgroundColor,activebackground=self.activeBackground)
def onRadialVelocity(self):
if np.any(self.appLogic.theoreticalSpectrum.wave)\
and self.appLogic.spectrum is not None:
if self.radVelDialog is None:
self.radVelDialog = radialVelocityDialog(self.appLogic,self.onCloseRadialVelocityDialog)
self.radVelDialog.wm_protocol('WM_DELETE_WINDOW', lambda: self.onCloseRadialVelocityDialog())
else:
print("WARNING:NormSpectra.onRadialVelocity\n"\
+"Load theoretical spectra first!")
def onPeriodicTableDialog(self):
if self.periodicTableDialog is None:
print("xxx")
self.periodicTableDialog = PeriodicTableDialog(self.appLogic, self.onClosePeriodicTableDialog)
print("xxx")
self.periodicTableDialog.wm_protocol('WM_DELETE_WINDOW', lambda: self.onClosePeriodicTableDialog())
def onComputeTheoreticalSpectrum(self):
if self.vlevel.get() == self._syntheNumber:
self.getTheoreticalSpectrumUsingSynthe()
else:
self.getTheoreticalSpectrumFromGrid()
self.updateTheoreticalSpectrumPlot()
self.updateLinesAnnotations()
if self.appLogic.theoreticalSpectrum.wave is not None and len(self.appLogic.theoreticalSpectrum.wave)!=0:
self.updateErrorPlot()
self.canvas.draw()
def updateTheoreticalSpectrumPlot(self):
wave = self.appLogic.theoreticalSpectrum.wave if self.appLogic.theoreticalSpectrum.wave is not None else []
flux = self.appLogic.theoreticalSpectrum.flux if self.appLogic.theoreticalSpectrum.flux is not None else []
self.line23.set_data(wave,flux)
def updateLinesAnnotations(self):
for i in range(len(self.lines_annotations)): # Remove existing texts from axis and empty list
self.lines_annotations[-1].remove()
self.lines_annotations.pop()
self.lines_indicators.set_segments([])
if self.appLogic.theoreticalSpectrum.lines_identification is not None:
segments = self.appLogic.getLinesIdentification(shape=self.labelSettings.get())
self.lines_indicators.set_segments(segments)
if self.labelSettings.get() == 1:
texts, positions = self.appLogic.getLabelsAndPositions()
for text, (x,y) in zip(texts, positions):
self.lines_annotations.append(self.ax2.text(x, y, text, rotation=90, ha='right', va='bottom'))
def onHover(self, event):
if event.inaxes == self.ax2 and self.labelSettings.get() == 2:
cont, ind = self.lines_indicators.contains(event)
if cont :
self.upateAnnotation(ind, event)
self.line_annotation.set_visible(True)
self.canvas.draw()
else:
if self.line_annotation.get_visible():
self.line_annotation.set_visible(False)
self.canvas.draw()
def upateAnnotation(self, ind, event):
pos = (event.xdata, event.ydata)
self.line_annotation.xy = pos
text = "{}".format("; ".join([self.appLogic.getLineLabelText(n) for n in ind["ind"]]))
self.line_annotation.set_text(text)
self.line_annotation.get_bbox_patch().set_facecolor('w')
self.line_annotation.get_bbox_patch().set_alpha(0.9)
def getTheoreticalSpectrumUsingSynthe(self):
minWave, maxWave = self.ax1.get_xlim()
self.appLogic.computeSpectrumUsingSYNTHE(self.teffVar.get(),
self.loggVar.get(),
self.vmicVar.get(),
self.meVar.get(),
self.vsiniVar.get(),
self.vmacVar.get(),
float(self.resolution.get()),
minWave,
maxWave
)
def getTheoreticalSpectrumFromGrid(self):
self.appLogic.computeTheoreticalSpectrum(self.teffVar.get(),
self.loggVar.get(),
self.vmicVar.get(),
self.meVar.get(),
self.vsiniVar.get(),
self.vmacVar.get(),
float(self.resolution.get()),
)
def onClearTheoreticalSpectrum(self):
self.appLogic.theoreticalSpectrum.wave = None
self.appLogic.theoreticalSpectrum.flux = None
self.appLogic.theoreticalSpectrum.lines_identification = None
self.line23.set_data([],[])
self.updateLinesAnnotations()
self.updateErrorPlot()
self.canvas.draw()
def onOpenSavePlot(self):
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
w = self.appLogic.normedSpectrum.wave if self.appLogic.normedSpectrum.wave is not None else []
f = self.appLogic.normedSpectrum.flux if self.appLogic.normedSpectrum.flux is not None else []
wt = self.appLogic.theoreticalSpectrum.wave if self.appLogic.theoreticalSpectrum.wave is not None else []
ft = self.appLogic.theoreticalSpectrum.flux if self.appLogic.theoreticalSpectrum.flux is not None else []
line11,line12, = ax.plot(w,f,'b-',
wt,ft,'k--',
)
ax.set_ylim([0.0,1.1])
ax.set_xlim(self.ax1.get_xlim())
ax.set_xlabel('Wavelength $[\AA]$')
ax.set_ylabel('Flux')
plt.show()
def createPlottingArea(self):
self.plotFrame = tkinter.Frame(self.frame)
self.dpi = 100
self.fig = Figure((5.0, 5.0), dpi=self.dpi)
# self.fig = Figure((5.0, 5.0), dpi=self.dpi,tight_layout=True)
# self.fig.tight_layout(w_pad = 0.0)
self.fig.subplots_adjust(wspace=0.0, hspace=0.0, top=0.95, bottom=0.05, left=0.05, right=0.95)
from matplotlib.gridspec import GridSpec
gs = GridSpec(5, 1)
self.canvas = FigCanvas(self.fig, master=self.plotFrame)
self.canvas.draw()
# self.ax1 = self.fig.add_subplot(311)
self.ax1 = self.fig.add_subplot(gs[:2])
self.ax1.grid(True)
self.line11,self.line12,self.line13,=self.ax1.plot([],[],'k-',\
[],[],'ro',\
[],[],'b-')
# self.ax2 = self.fig.add_subplot(312,sharex=self.ax1)
self.ax2 = self.fig.add_subplot(gs[2:4],sharex=self.ax1)
self.ax2.grid(True)
self.line21,self.line22,self.line23 = self.ax2.plot([],[],'k',\
[],[],'b--',\
[],[],'b')
self.lines_indicators = self.ax2.add_collection(LineCollection([], colors='#FF8800'))
self.lines_annotations = []
self.line_annotation = self.ax2.annotate("", xy=(0,0),
xytext=(20,20),
# rotation=90,
textcoords="offset points",
bbox=dict(boxstyle="round", fc="w"),
arrowprops=dict(arrowstyle="->"),
zorder=40)
self.line_annotation.set_visible(False)
# self.ax3 = self.fig.add_subplot(313,sharex=self.ax1)
self.ax3 = self.fig.add_subplot(gs[-1],sharex=self.ax1)