def openFileFromButton(self):
global inputFilename
inputFilename = askopenfilename(parent=root)
print ("Filename = ", inputFilename)
self.e1.delete(0,END)
stuffs= inputFilename.split('/')
shortName = stuffs[len(stuffs)-1]
print(shortName)
self.e1.insert(0,shortName)
self.checkBox1.deselect() #Checkbox 1 is FFT Done
self.checkBox2.deselect() #Checkbox 2 is ARtifacts Removed
self.checkBox3.deselect() #Checkbox 3 is Contanimants
self.checkBox10.deselect() #Checkbox 10 is Molecules
ClearSpectrum2.clearVariables()
def removeContaminants(self, event):
global inputFilename
print (" Removing contaminants ")
print('inputFilename=', inputFilename)
splitName = inputFilename.split('.')
baseNameThatCameIn = splitName[0]
fileType = splitName[1]
if(fileType != 'sp'):
print("looks like we're going to use the exported file name")
print(PeakFinder_BlackChirp2.exportedFileName)
splitName = PeakFinder_BlackChirp2.exportedFileName.split('.')
print(splitName)
baseNameThatCameIn = splitName[0]
fileType = splitName[1]
if(fileType != 'sp'):
print("Sorry - that is not a spectrum file type")
ClearSpectrum2.spectrum_name = baseNameThatCameIn + '.sp'
ClearSpectrum2.file_name = baseNameThatCameIn
ClearSpectrum2.clearVariables()
for i in range(0,3):
# print('index = ' + str(i))
if ((i==0) and (self.checkBoxOCS.get() == 1)): ClearSpectrum2.known_freq_name = 'Contaminants/ocs.cat'
elif((i==1) and (self.checkBoxH2O2.get() == 1)): ClearSpectrum2.known_freq_name = 'Contaminants/h2o_dimer.list'
elif((i==2) and (self.checkBoxSO2.get() == 1)): ClearSpectrum2.known_freq_name = 'Contaminants/so2.cat'
else: ClearSpectrum2.known_freq_name = 'none'
# print(' iteration - file name = ', ClearSpectrum2.known_freq_name)
if (ClearSpectrum2.known_freq_name != 'none'):
ClearSpectrum2.clearVariables()
ClearSpectrum2.readKnownFile()
# the argument True means "doNotPlot"
ClearSpectrum2.peakAssignment(True)
ClearSpectrum2.createListsOfPeaks()
# ClearSpectrum2.clearSpectrum()
# ClearSpectrum2.exportTheClearedFiles()
# ClearSpectrum2.renamedPlot()
# time.sleep(2)
self.commonVariable1 = 4
self.checkBox3.select()
print("Uncontaminated bucket" + str(ClearSpectrum2.bucket))
def removeArtifacts(self, event):
print( ' removing Artifacts - now you know it is real ')
self.commonVariable1 = 3
self.checkBox2.select()
shutil.copy('test.parameters', 'test.par') # copy the parameters file to test.par
subprocess.call(["spfit", 'test']) # run spfit
CallScriptTest.working()
CallScriptTest.fib(100)
# subprocess.call(['helloWithchanges.py'])
#import helloWithchanges.py
ClearSpectrum2.readInputFiles()
ClearSpectrum2.peakAssignment()
ClearSpectrum2.createListsOfPeaks()
ClearSpectrum2.clearSpectrum()
ClearSpectrum2.exportTheClearedGraph()
ClearSpectrum2.doNotCallItPlot()
def removeMolecularLines(self, event):
global inputFilename
listOfMoleculesPresent = []
print ('removing molecular lines')
self.commonVariable1 = 5
self.checkBox10.select()
print('inputFilename=', inputFilename)
splitName = inputFilename.split('.')
baseNameThatCameIn = splitName[0]
fileType = splitName[1]
ClearSpectrum2.spectrum_name = baseNameThatCameIn + '.sp'
ClearSpectrum2.file_name = baseNameThatCameIn
atoms = []; atoms.append("Atoms:")
if(self.checkBoxH.get() == 1): atoms.append("H")
if(self.checkBoxC.get() == 1): atoms.append("C")
if(self.checkBoxN.get() == 1): atoms.append("N")
if(self.checkBoxO.get() == 1): atoms.append("O")
if(self.checkBoxSi.get() == 1): atoms.append("Si")
if(self.checkBoxS.get() == 1): atoms.append("S")
atoms.extend(additionalElementsAdded)
print (atoms)
listOfMolecluesToTry = createListOfPossibleMolecules(atoms)
toMakeTheFTBFileFreq = []
toMakeTheFTBFileIntensity = []
#del toMakeTheFTBFileFreq[:]
#del toMakeTheFTBFileIntensity[:]
del reportFile[:]
path = "MoleculeCatFiles"
for molecule in listOfMolecluesToTry:
print("\nmolecule " + str(molecule))
self.text1.insert(END,molecule[0])
print(molecule[2])
if '.lines' in molecule[2]:
localCatFileName = molecule[2]
else:
localCatFileName = molecule[2] + ".cat"
print(localCatFileName)
ClearSpectrum2.known_freq_name = 'MoleculeCatFiles/' + localCatFileName
ClearSpectrum2.clearVariables()
ClearSpectrum2.readKnownFile()
numberOfMatchedPeaks = ClearSpectrum2.peakAssignment(True) # True means doNotPlot
print("Number of Matched Peaks = ", numberOfMatchedPeaks)
if(numberOfMatchedPeaks >0):
listOfMoleculesPresent.append(molecule[0])
self.text2.insert(END, molecule[0])
ClearSpectrum2.createListsOfPeaks()
print(str(ClearSpectrum2.match_freq))
print("\n Molecule: "+str(molecule)+" \npeaks: ")
reportFile.append("\n Molecule: "+str(molecule)+" \npeaks: "+str(ClearSpectrum2.match_freq))
## ClearSpectrum2.clearSpectrum()
## ClearSpectrum2.exportTheClearedFiles()
## ClearSpectrum2.renamedPlot()
print("\n\nList Of Molecules Present: ", listOfMoleculesPresent)
print("\nNumber of molecules present = ", str(len(listOfMoleculesPresent)))
print("Lines in spectrum: "+ str(ClearSpectrum2.freq_list_end))
for index in range(len(reportFile)):
print(reportFile[index])
print("Final List of removed molecular lines (the Bucket)")
for index in range (len(ClearSpectrum2.bucket)):
print(ClearSpectrum2.bucket[index])
print("\nUnassigned Lines:")
print("Frequency, Intensity")
for index in range (len(ClearSpectrum2.peak_freq_ini)):
if index in ClearSpectrum2.bucketedLines:
print("Cleared: " + str(ClearSpectrum2.peak_freq_ini[index]), str(ClearSpectrum2.peak_int_ini[index]))
else:
print(str(ClearSpectrum2.peak_freq_ini[index]),"\t" , str(ClearSpectrum2.peak_int_ini[index]))
toMakeTheFTBFileFreq.append(ClearSpectrum2.peak_freq_ini[index])
toMakeTheFTBFileIntensity.append(ClearSpectrum2.peak_int_ini[index])
# Create FTB file
FTBFilePeakArray = np.array( [toMakeTheFTBFileFreq, toMakeTheFTBFileIntensity] ).transpose()
FTBFilePeakArray = FTBFilePeakArray[FTBFilePeakArray[:, 1].argsort()[::-1]]
with open(baseNameThatCameIn + '.ftb', 'w') as out_file:
for i in range(len(FTBFilePeakArray)):
# define the number of shots as a function of the intensity
n_shots = ceil(2 / (5 * FTBFilePeakArray[i,1]))
if (n_shots < 10):
n_shots = 10
out_file.write('ftm:%5.3f shots:%1s dipole:1.0 drpower:-20 drfreq:1000.000\n' %(FTBFilePeakArray[i,0], n_shots))
out_file.close()
# Create Report file
filename = baseNameThatCameIn + 'report.txt'
outf = open(filename, 'w')
outf.write("Report File for " + baseNameThatCameIn + '\n\n Lines assigned to molecules:\n')
for index in range (len(ClearSpectrum2.bucket)):
lineToWrite = str(ClearSpectrum2.bucket[index]) + '\n'
outf.write(lineToWrite)
outf.write('\nList of un-assigned lines in Intensity order\n\n')
outf.write('\nFrequency: \tIntensity:\n')
for index in range (len(FTBFilePeakArray)):
lineToWrite = str(FTBFilePeakArray[index,0]) +' \t' + str(FTBFilePeakArray[index,1]) + '\n'
outf.write(lineToWrite)
outf.write('\nList of un-assigned lines in Frequency order\n\n')
outf.write('\nFrequency: \tIntensity\n')
FTBFilePeakArray = FTBFilePeakArray[FTBFilePeakArray[:, 0].argsort()]
for index in range (len(FTBFilePeakArray)):
lineToWrite = str(FTBFilePeakArray[index,0]) + ' \t'+ str(FTBFilePeakArray[index,1]) + '\n'
outf.write(lineToWrite)
outf.close()
# Now create graph
xCoord = []
yCoord = []
for index in range(len(ClearSpectrum2.bucket)):
xCoord.append (ClearSpectrum2.bucket[index][0])
yCoord.append (ClearSpectrum2.bucket[index][1])
# print ("X coord " + str(xCoord[index]))
# print ("Y coord " + str(yCoord[index]))
plt.figure(3) # creation of a figure
#
# Known frequencies
plt.subplot(211) #
plt.title ('Peaks removed ')
plt.ion() #interactive mode
#xlim([freq_list_ini[0], freq_list_ini[-1]])
plt.vlines(xCoord, 0, yCoord, colors='red')
# Initial spectrum in the background, Cleared spectrum in the front
plt.subplot(212, sharex=plt.subplot(211))
plt.title ('Initial spectrum (blue), Matched lines (red)')
#, color='red')
plt.plot(ClearSpectrum2.freq_list_ini,ClearSpectrum2.int_list_ini)
newY = max(ClearSpectrum2.int_list_ini) * 1.1
plt.vlines(xCoord, 0, newY, colors='red')
#vlines(match_peak_array, 1e-6, match_int, colors='gray', linestyle = '--')
plt.show(block=True)
def removeArtifacts(self, event):
global inputFilename # The input file might have been a spectrum file or a FID file.
print( ' removing Artifacts - ')
self.commonVariable1 = 3
self.checkBox2.select()
print('inputFilename=', inputFilename)
splitName = inputFilename.split('.')
baseNameThatCameIn = splitName[0]
fileType = splitName[1]
if(fileType != 'sp'): # IF the input file was FID, then use the file created by 'createFT', above
print("Getting the spectrum file created by the routine createFT,")
print(PeakFinder_BlackChirp2.exportedFileName)
splitName = PeakFinder_BlackChirp2.exportedFileName.split('.')
print(splitName)
baseNameThatCameIn = splitName[0]
fileType = splitName[1]
if(fileType != 'sp'):
print("Sorry - that is not a spectrum file type")
ClearSpectrum2.clearVariables()
ClearSpectrum2.spectrum_name = baseNameThatCameIn + '.sp'
ClearSpectrum2.file_name = baseNameThatCameIn
ClearSpectrum2.known_freq_name = 'ArtifactFiles/artifacts_18950MHz.cat'
# ClearSpectrum2.known_name = 'artifacts' - now calculated in ClearSpectrum2.py praa Feb 10 2016
ClearSpectrum2.readSpectrumAndLineFiles()
ClearSpectrum2.readKnownFile()
ClearSpectrum2.peakAssignment(False) # False means it's not necessary to supress the plot
ClearSpectrum2.createListsOfPeaks()
ClearSpectrum2.clearSpectrum()
ClearSpectrum2.exportTheClearedFiles()
print("Original bucket" + str(ClearSpectrum2.bucket))
# now re-load in the cleared spectrum and line file PRAA April 11 2016
ClearSpectrum2.spectrum_name = baseNameThatCameIn + '_clear_artifacts_18950MHz.sp'
ClearSpectrum2.file_name = baseNameThatCameIn + '_clear_artifacts_18950MHz'
ClearSpectrum2.readSpectrumAndLineFiles()
print("Un - Original bucket" + str(ClearSpectrum2.bucket))
ClearSpectrum2.renamedPlot()
def removeArtifacts(self, event):
print(' removing Artifacts - now you know it is real ')
self.commonVariable1 = 3
self.checkBox2.select()
shutil.copy('test.parameters',
'test.par') # copy the parameters file to test.par
subprocess.call(["spfit", 'test']) # run spfit
CallScriptTest.working()
CallScriptTest.fib(100)
# subprocess.call(['helloWithchanges.py'])
#import helloWithchanges.py
ClearSpectrum2.readInputFiles()
ClearSpectrum2.peakAssignment()
ClearSpectrum2.createListsOfPeaks()
ClearSpectrum2.clearSpectrum()
ClearSpectrum2.exportTheClearedGraph()
ClearSpectrum2.doNotCallItPlot()
