"""

The main method of PyHammer which executes the overarching procedure.

Description:

This is the main part of the code that executes the

actual pyhammer algorithms. This is arrived at either

by pyhammerStartCmd or PyHammerStartGui, both of which

get all the necessary options from the user and pass

them to this function. The general process of this

function should be to:

- Define a Spectrum object to be used in reading files.

- Load each spectrum sequentially.

- Guess the spectral type.

- Use the best guess for the spectral type and find the radial

velocity shift. Shift the spectrum to rest.

- Guess the spectral type again.

- Repeat for all spectra

- Bring up eyecheck GUI.

Input:

options: A dict containing the options the user has specified.

Output:

This program outputs two files, an outfile and a rejectfile.

The outfile contains all results of the spectral type guess

as well as the user's eyecheck guess and the rejectfile contains

the list of spectra which could not be classified for some reason.

"""

# Create a Spectrum object

spec = Spectrum()

# If the user has decided to not skip to the eyecheck, let's

# do some processing

if not options['eyecheck']:

# Open the input file

try:

infile = open(options['infile'], 'r')

except IOError as e:

notifyUser(options['useGUI'], str(e))

return

# Open and setup the output files

outfile = open(options['outfile'], 'w')

rejectfile = open(options['rejectfile'], 'w')

if options['lineOutfile']: lineOutfile = open('spectralIndices.csv', 'w')

outfile.write('#Filename,File Type,Radial Velocity (km/s),Guessed Spectral Type,Guessed [Fe/H],User Spectral Type,User [Fe/H]\n')

rejectfile.write('#Filename,File Type,Spectra S/N\n')

if options['lineOutfile']: lineOutfile.write('#Filename,CaK,CaK_var,Cadel,Cadel_var,CaI4217,CaI4217_var,Gband,Gband_var,Hgam,Hgam_var,FeI4383,FeI4383_var,FeI4404,FeI4404_var,Hbeta,Hbeta_var,MgI,MgI_var,NaD,NaD_var,CaI6162,CaI6162_var,Halpha,Halpha_var,CaH2,CaH2_var,CaH3,CaH3_var,TiO5,TiO5_var,VO7434,VO7434_var,VO7445,VO7445_var,VO-B,VO-B_var,VO7912,VO7912_var,Rb-B,Rb-B_var,NaI,NaI_var,TiO8,TiO8_var,TiO8440,TiO8440_var,Cs-A,Cs-A_var,CaII8498,CaII8498_var,CrH-A,CrH-A_var,CaII8662,CaII8662_var,FeI8689,FeI8689_var,FeH,FeH_var,C2-4382,C2-4382_var,C2-4737,C2-4737_var,C2-5165,C2-5165_var,C2-5636,C2-5636_var,CN-6959,CN-6959_var,CN-7088,CN-7088_var,CN-7259,CN-7259_var,CN-7820,CN-7820_var,CN-8067,CN-8067_var,CN-8270,CN-8270_var,WD-Halpha,WD-Halpha_var,WD-Hbeta,WD-Hbeta_var,WD-Hgamma,WD-Hgamma_var\n')

# Define the string to contain all failure messages. These will be compiled

# and printed once at the end, if anything is put into it.

rejectMessage = ''

infile_init = open(options['infile'], 'r')

for i, line in enumerate(infile_init):

num_spec = i + 1

infile_init.close()

#progress = ProgressBar(num_spec, fmt=ProgressBar.FULL)

with warnings.catch_warnings():

warnings.simplefilter("ignore", category=RuntimeWarning)

for i, line in enumerate(tqdm(infile, total=num_spec)):

# Remove extra whitespace and other unwanted characters and split

line = line.strip()

if ',' in line: line = line.replace(',',' ')

if ' ' in line:

fname, ftype = ' '.join(line.split()).rsplit(' ',1)

else:

fname = line

ftype = None

# Print statement of progress for user

#print(i+1, ') Processing ', os.path.basename(fname), sep = '')

# progress.current += 1

# progress()

# Now read in the current file (this process reads in the file, converts air to

# vac when necessary and interpolates onto the template grid)

message, ftype = spec.readFile(options['spectraPath']+fname, ftype)

# If the attempt at reading the file did not succeed, then we

# should just continue

if message is not None:

rejectfile.write(fname + ',' + ('N/A' if ftype is None else ftype) + ',N/A\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: ' + message.replace('\n','') + '\n\n'

continue

# Now that we have the necessary data in the spec object, let's

# begin processing.

# --- 1 ---

# Calculate the signal to noise of the spectrum to potentially reject

snVal = spec.calcSN()

if options['sncut'] is not None:

if snVal < options['sncut']:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: S/N = ' + str(snVal) + ' < ' + str(options['sncut']) + '\n\n'

continue

# --- 2 ---

# Normalize the input spectrum to the same place where the templates are normalized (8000A)

try:

spec.normalizeFlux()

except:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: Could not normalize\n\n'

continue

# --- 3 ---

# Call guessSpecType function for the initial guess

# this function measures the lines then makes a guess of all parameters

try:

spec.guessSpecType()

except Exception as e:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: Could not guess spectral type. Error Message: {}\n\n'.format(e)

continue

# --- 4 ---

# Call findRadialVelocity function using the initial guess

try:

shift = spec.findRadialVelocity()

except Exception as e:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: Could not find radial velocity. Error Message: {}\n\n'.format(e)

continue

# --- 5 ---

# Call shiftToRest that shifts the spectrum to rest wavelengths,

# then interp back onto the grid

try:

spec.shiftToRest(shift)

spec.interpOntoGrid()

except Exception as e:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: Could not shift to rest. Error Message: {}\n\n'.format(e)

continue

# --- 6 ---

# Repeat guessSpecType function to get a better guess of the spectral

# type and metallicity

try:

spec.guessSpecType()

except Exception as e:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: Could not guess spectral type. Error Message: {}\n\n'.format(e)

continue

# If the user wants the calculated spectral indices, write them to a file

if options['lineOutfile']:

for key, value in spec.lines.items():

if key == 'CaK':

lineOutfile.write(fname + ',' + str(value[0]) + ',' + str(value[1])+',')

elif key == 'WD-Hgamma':

lineOutfile.write(str(value[0]) + ',' + str(value[1])+'\n')

elif key in ['region1', 'region2', 'region3', 'region4', 'region5']:

continue

else:

lineOutfile.write(str(value[0]) + ',' + str(value[1])+',')

# End of the automatic guessing. We should have:

# 1. Spectrum object with observed wavelength, flux, var,

# 2. rest wavelength,

# 3. spectral type (guessed),

# 4. radial velocity and uncertainty,

# 5. metallicity estimate,

# 6. and line indice measurements

# --- 7 ---

if spec.guess['specType'] == -1:

rejectfile.write(fname + ',' + ftype + ',' + str(snVal) + '\n')

rejectMessage += 'FILE: ' + fname + '\nREASON: No good spectral type. Error Message: Spectrum might be all nans or 0s.\n\n'

continue

# Translate the numbered spectral types into letters

if spec._isSB2:

# Write the file

outfile.write(options['spectraPath']+fname + ',' + # The spectra path and filename

ftype + ',' + # The filetype

str(shift) + ',' + # The RV shift

spec._SB2_filenameList[spec.guess['specType'] - 10][:-5] + ',' + # The auto-guessed spectral type

'{:+2.1f}'.format(spec.guess['metal']) + # The auto-guessed metallicity

',nan,nan\n') # The to-be-determined user classifications

else:

letterSpt = ['O', 'B', 'A', 'F', 'G', 'K', 'M', 'L', 'dC', 'DA'][spec.guess['specType']]

# Write the file

outfile.write(options['spectraPath']+fname + ',' + # The spectra path and filename

ftype + ',' + # The filetype

str(shift) + ',' + # The RV shift

letterSpt + str(spec.guess['subType']) + ',' + # The auto-guessed spectral type

'{:+2.1f}'.format(spec.guess['metal']) + # The auto-guessed metallicity

',nan,nan\n') # The to-be-determined user classifications

#progress.done()

# We're done so let's close all the files

infile.close()

outfile.close()

rejectfile.close()

# Only close lineOutfile if it was created

if options['lineOutfile']:

lineOutfile.close()

# Check that we processed every spectrum in the infile. If not, print out

# the reject method.

if rejectMessage != '':

# Prepend to the reject message

message = 'At least one spectra was rejected. See the details for more information.'

notifyUser(options['useGUI'], message, details = rejectMessage)

# Check if all spectra were skipped by seeing if the number of

# lines in the reject message is equal to the number of processed

# times 3 (since each reject message has three newlines). If they

# were all skipped, theres nothing to eyecheck so return.

if rejectMessage.count('\n') == 3*(i+1):

notifyUser(options['useGUI'], 'All spectra were bad. Exiting PyHammer.')

# Clean up any temporary input files created

if os.path.basename(options['infile'])[:11] == 'temp_input_':

os.remove(options['infile'])

return

# At this point, we should call up the GUI to do the eyechecking.

Eyecheck(spec, options)

# Finally, clean up any temporary input files created

if os.path.basename(options['infile'])[:11] == 'temp_input_':

"""

Description:

A method for handling sending messages to the

user during the execution of the main function.

The reason for making this a separate function

is to handle where we need to send the message.

If the user started using a GUI, we want to

use a GUI to notify them, otherwise, if they

were using the command line, print to the command

line.

Input:

useGUI: A boolean indicating whether or not to

use a GUI to notify the user. This is set

in the options dict.

message: The message to present to the user.

"""

if not useGUI:

# Simple case, just print the message.

print(message, flush=True)

print(details, flush=True)

else:

# More involved case, create a base pyqt window

# derive a message box from it to display the

# message, then close the base window and move on.

win = QMainWindow()

win.setWindowIcon(QIcon(os.path.join(os.path.split(__file__)[0],'resources','sun.ico')))

MessageBox(win, message, 'PyHammer Notification', details = details)

"""

Description:

This class provies the user with a GUI for providing

settings. These settings will define everything the

rest of the PyHammer program needs to run including

the input files, output files, and settings to use

when running the auto-classify process. When the user

is ready, they can hit the "Start PyHammer" button.

A check will be performed to make sure the settings

are good and if so, this window will close itself

and call the main method in this file, passing along

the settings that it pulls from the GUI.

Inputs:

options: A dict containing the options the

user can specify. These may already

have default values if they were

provided when the program was launched.

Example:

This class inherits from the PyQt QMainWindow class.

As such, it needs to be run with the following commands

app = QApplication([])

PyHammerSettingsGui(options) # Pass in options dict

app.exec_()

"""

def __init__(self, options):

super().__init__() # Call the parent class init method

self.options = options # Store the options

# Create and show the GUI

self.defineHelpText() # Define text to be display when user hits help buttons

self.createGui() # Define all the variables used to create the GUI

self.layoutGui() # Set the layout of the GUI components in the window

self.configureGui() # Configure the GUI component settings

self.updateGui() # Perform some updates to the display of the GUI

self.show() # Finally, show the GUI to the user

def defineHelpText(self):

self.infileHelpText = (

'Here you can provide an input file of spectra to process. '

'Browse for an already created file, or else choose to create '

'the file within the GUI. If you supply a path to an already '

'defined file, you should include the full path, or else a '

'path relative to the PyHammer directory. The input file can '

'be any ascii file including txt and csv.\n\n'

'To create the input file, list all your spectra in one column '

'and the corresponding spectra type in the second column. '

'You should ideally supply the full path for each spectra, '

"but if they're all in the same directory, a later setting "

'allows for prepending the same path to all spectra.')

self.outfileHelpText = (

'You should include the full path to the output file '

'which will contain the results of PyHammer. However, '

'if no path is supplied, the file will be saved to the '

'the pyhammer folder. The output file is, by default, '

'set to PyHammerResults.csv unless specified otherwise. '

'The output filetype should be a csv file.')

self.rejectfileHelpText = (

'You should include the full path to the reject file '

'which will contain the list of any spectra unable to '

'be classified. However, if no path is supplied, the '

'file will be saved to the the pyhammer folder. The '

'reject file is, by default, set to RejectSpectra.csv '

'unless specified otherwise. The reject filetype should '

'be a csv file.')

self.fullPathHelpText = (

'Choose whether or not the spectra listed in your input '

'file have a full path specified. If you choose no, you '

'will need to specify the full path to the spectra. ')

self.spectraPathHelpText = (

'If your spectra list does not contain the full path '

'to the files in the name, provide a path to prepend '

'to each spectra filename.')

self.eyecheckHelpText = (

'If you have already classified your spectra you can '

'choose to skip directly to checking them by eye, rather '

'than re-running the classification algorithm again. Note '

'that you cannot skip to eye checking without first '

'classifying your spectra and creating an output file.')

self.sncutHelpText = (

'If you would like to only classify spectra with a S/N '

'above a threshold, provide that value here. If you do not '

'want to provide a cutoff, leave this field blank. This '

'option does not apply if you choose to skip to the eyecheck.')

self.lineHelpText = (

'If you would like the spectral lines used in classifying '

'the spectra to be printed out to a .CSV file, select yes '

'for this option. Otherwise select no. Note that this file '

'is only output if the classification algorithm is run and '

'you choose to NOT skip directly to the eye check.')

def createGui(self):

# Define the basic, top-level GUI components

self.widget = QWidget() # The central widget in the main window

self.grid = QVBoxLayout() # The layout manager of the central widget

self.icon = QIcon(os.path.join(os.path.split(__file__)[0],'resources','sun.ico')) # The window icon

# Input Field

# Define Input Widgets

self.infileFrame = QFrame()

self.infileLabel = QLabel('Provide an existing input file or create a new input file', alignment = Qt.AlignCenter)

self.infileEntry = QLineEdit(placeholderText = 'Input File...')

self.infileBrowseButton = QPushButton('Browse')

self.infileCreateButton = QPushButton('Create')

self.createPressed = False

self.infileHelpButton = QPushButton('?')

# Define Create Widgets

self.createFrame = QFrame()

self.textArea = QTextEdit()

self.selectSpectraButton = QPushButton('Select Spectra')

self.dataTypeList = QComboBox()

self.applyType = QPushButton('Apply Data Type')

# Output Field

self.outfileFrame = QFrame()

self.outfileLabel = QLabel('Provide an output file', alignment = Qt.AlignCenter)

self.outfileEntry = QLineEdit(placeholderText = 'Output File...')

self.outfileBrowseButton = QPushButton('Browse')

self.outfileHelpButton = QPushButton('?')

# Reject Field

self.rejectFrame = QFrame()

self.rejectLabel = QLabel('Provide a reject file', alignment = Qt.AlignCenter)

self.rejectEntry = QLineEdit(placeholderText = 'Reject File...')

self.rejectBrowseButton = QPushButton('Browse')

self.rejectHelpButton = QPushButton('?')

# Full Path Field

self.fullPathFrame = QFrame()

self.fullPathLabel = QLabel('Do the spectra in the input file contain full paths?', alignment = Qt.AlignCenter)

self.fullPathChoice = QButtonGroup()

self.fullPathYes = QRadioButton('Yes', checked = True)

self.fullPathNo = QRadioButton('No', checked = False)

self.fullPathChoice.addButton(self.fullPathYes, 0)

self.fullPathChoice.addButton(self.fullPathNo, 1)

self.fullPathHelpButton = QPushButton('?')

# Spectra Path Field

self.spectraPathFrame = QFrame()

self.spectraPathLabel = QLabel('Provide a path to the spectra files', alignment = Qt.AlignCenter)

self.spectraPathEntry = QLineEdit(placeholderText = 'Path to spectra files...')

self.spectraPathBrowseButton = QPushButton('Browse')

self.spectraPathHelpButton = QPushButton('?')

# Eyecheck Field

self.eyecheckFrame = QFrame()

self.eyecheckLabel = QLabel('Do you want to skip to classifying by eye?', alignment = Qt.AlignCenter)

self.eyecheckChoice = QButtonGroup()

self.eyecheckYes = QRadioButton('Yes', checked = True)

self.eyecheckNo = QRadioButton('No', checked = False)

self.eyecheckChoice.addButton(self.fullPathYes, 0)

self.eyecheckChoice.addButton(self.fullPathNo, 1)

self.eyecheckHelpButton = QPushButton('?')

# S/N Cut Field

self.sncutFrame = QFrame()

self.sncutLabel = QLabel('Enter a signal to noise cutoff', alignment = Qt.AlignCenter)

self.sncutEntry = QLineEdit(placeholderText = 'S/N cutoff...')

self.sncutHelpButton = QPushButton('?')

# Spectral Line Output File Field

self.lineFrame = QFrame()

self.lineLabel = QLabel('Do you print the spectral classification lines to a file?', alignment = Qt.AlignCenter)

self.lineChoice = QButtonGroup()

self.lineYes = QRadioButton('Yes', checked = True)

self.lineNo = QRadioButton('No', checked = False)

self.lineChoice.addButton(self.fullPathYes, 0)

self.lineChoice.addButton(self.fullPathNo, 1)

self.lineHelpButton = QPushButton('?')

# Start Button

self.startButton = QPushButton('Start PyHammer')

# Separators

self.sep = []

for i in range(8):

line = QFrame(frameShape = QFrame.HLine, frameShadow = QFrame.Sunken, lineWidth = 1)

line.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Fixed)

self.sep.append(line)

def layoutGui(self):

# Input Field

# Setup Input Widgets

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.infileLabel, 0, 0, 1, 4)

frameGrid.addWidget(self.infileEntry, 1, 0)

frameGrid.addWidget(self.infileBrowseButton, 1, 1)

frameGrid.addWidget(self.infileCreateButton, 1, 2)

frameGrid.addWidget(self.infileHelpButton, 1, 3)

self.infileFrame.setLayout(frameGrid)

self.grid.addWidget(self.infileFrame)

# Setup Create Widgets

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.textArea, 0, 0, 1, 5)

frameGrid.addWidget(self.selectSpectraButton, 1, 0)

frameGrid.addWidget(QFrame(frameShape = QFrame.VLine, frameShadow = QFrame.Sunken, lineWidth = 1), 1, 1)

frameGrid.addWidget(self.dataTypeList, 1, 2)

frameGrid.addWidget(self.applyType, 1, 3)

frameGrid.setColumnStretch(4, 1)

self.createFrame.setLayout(frameGrid)

self.grid.addWidget(self.createFrame)

self.grid.addWidget(self.sep[0])

# Output Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.outfileLabel, 0, 0, 1, 3)

frameGrid.addWidget(self.outfileEntry, 1, 0)

frameGrid.addWidget(self.outfileBrowseButton, 1, 1)

frameGrid.addWidget(self.outfileHelpButton, 1, 2)

self.outfileFrame.setLayout(frameGrid)

self.grid.addWidget(self.outfileFrame)

self.grid.addWidget(self.sep[1])

# Reject Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.rejectLabel, 0, 0, 1, 3)

frameGrid.addWidget(self.rejectEntry, 1, 0)

frameGrid.addWidget(self.rejectBrowseButton, 1, 1)

frameGrid.addWidget(self.rejectHelpButton, 1, 2)

self.rejectFrame.setLayout(frameGrid)

self.grid.addWidget(self.rejectFrame)

self.grid.addWidget(self.sep[2])

# Full Path Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.fullPathLabel, 0, 0, 1, 3)

frameGrid.addWidget(self.fullPathYes, 1, 0, alignment = Qt.AlignRight)

frameGrid.addWidget(self.fullPathNo, 1, 1)

frameGrid.addWidget(self.fullPathHelpButton, 1, 2)

self.fullPathFrame.setLayout(frameGrid)

self.grid.addWidget(self.fullPathFrame)

self.grid.addWidget(self.sep[3])

# Spectra Path Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.spectraPathLabel, 0, 0, 1, 2)

frameGrid.addWidget(self.spectraPathEntry, 1, 0)

frameGrid.addWidget(self.spectraPathBrowseButton, 1, 1)

frameGrid.addWidget(self.spectraPathHelpButton, 1, 2)

self.spectraPathFrame.setLayout(frameGrid)

self.grid.addWidget(self.spectraPathFrame)

self.grid.addWidget(self.sep[4])

# Eyecheck Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.eyecheckLabel, 0, 0, 1, 3)

frameGrid.addWidget(self.eyecheckYes, 1, 0, alignment = Qt.AlignRight)

frameGrid.addWidget(self.eyecheckNo, 1, 1)

frameGrid.addWidget(self.eyecheckHelpButton, 1, 2)

self.eyecheckFrame.setLayout(frameGrid)

self.grid.addWidget(self.eyecheckFrame)

self.grid.addWidget(self.sep[5])

# S/N Cut Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.sncutLabel, 0, 0, 1, 2)

frameGrid.addWidget(self.sncutEntry, 1, 0)

frameGrid.addWidget(self.sncutHelpButton, 1, 2)

self.sncutFrame.setLayout(frameGrid)

self.grid.addWidget(self.sncutFrame)

self.grid.addWidget(self.sep[6])

# Spectral Line Output File Field

frameGrid = QGridLayout(spacing = 2, margin = 0)

frameGrid.addWidget(self.lineLabel, 0, 0, 1, 3)

frameGrid.addWidget(self.lineYes, 1, 0, alignment = Qt.AlignRight)

frameGrid.addWidget(self.lineNo, 1, 1)

frameGrid.addWidget(self.lineHelpButton, 1, 2)

self.lineFrame.setLayout(frameGrid)

self.grid.addWidget(self.lineFrame)

self.grid.addWidget(self.sep[7])

# Start Button

self.grid.addWidget(self.startButton)

def configureGui(self):

# Input Field

# Configure Input Widgets

self.infileEntry.setText(self.options['infile'])

self.infileEntry.setMinimumWidth(300)

self.infileBrowseButton.clicked.connect(lambda: self.browse(self.infileEntry))

self.infileBrowseButton.setToolTip('Browse for an existing input file')

self.infileCreateButton.clicked.connect(self.createButtonClicked)

self.infileCreateButton.setToolTip('Create a new input file')

self.infileHelpButton.setMaximumWidth(25)

self.infileHelpButton.clicked.connect(lambda: MessageBox(self, self.infileHelpText, 'PyHammer Help'))

self.infileHelpButton.setToolTip('Help')

# Configure Create Widgets

self.textArea.setMinimumSize(600,300)

self.textArea.setLineWrapMode(QTextEdit.NoWrap)

font = self.textArea.currentFont()

font.setPointSize(10)

font.setFamily('courier')

self.textArea.setFont(font)

self.selectSpectraButton.clicked.connect(self.selectSpectraButtonClicked)

self.selectSpectraButton.setToolTip('Select a set of spectrum files\nto add to the input file')

self.dataTypeList.addItems(['SDSSdr12', 'SDSSdr7', 'fits', 'txt', 'csv','tempfits'])

self.applyType.clicked.connect(self.applyTypeClicked)

self.applyType.setToolTip('<b>Optional:</b> Append the selected data\ntype to every file in the list to give a\nhint to PyHammer about the file type')

self.createFrame.hide()

# Output Field

self.outfileEntry.setText(self.options['outfile'])

self.outfileBrowseButton.clicked.connect(lambda: self.browse(self.outfileEntry))

self.outfileBrowseButton.setToolTip('Browse for an existing output file or define a new one')

self.outfileHelpButton.setMaximumWidth(25)

self.outfileHelpButton.clicked.connect(lambda: MessageBox(self, self.outfileHelpText, 'PyHammer Help'))

self.outfileHelpButton.setToolTip('Help')

# Reject Field

self.rejectEntry.setText(self.options['rejectfile'])

self.rejectBrowseButton.clicked.connect(lambda: self.browse(self.rejectEntry))

self.rejectBrowseButton.setToolTip('Browse for an existing reject file or define a new one')

self.rejectHelpButton.setMaximumWidth(25)

self.rejectHelpButton.clicked.connect(lambda: MessageBox(self, self.rejectfileHelpText, 'PyHammer Help'))

self.rejectHelpButton.setToolTip('Help')

# Full Path Field

if self.options['fullPath'] is None or not self.options['fullPath']:

self.fullPathNo.setChecked(True)

else:

self.fullPathYes.setChecked(True)

self.fullPathYes.clicked.connect(self.updateGui)

self.fullPathNo.clicked.connect(self.updateGui)

self.fullPathHelpButton.setMaximumWidth(25)

self.fullPathHelpButton.clicked.connect(lambda: MessageBox(self, self.fullPathHelpText, 'PyHammer Help'))

self.fullPathHelpButton.setToolTip('Help')

# Spectra Path Field

self.spectraPathEntry.setText(self.options['spectraPath'])

self.spectraPathBrowseButton.clicked.connect(lambda: self.browse(self.spectraPathEntry, 'directory'))

self.spectraPathBrowseButton.setToolTip('Browse for the directory containing the spectra files')

self.spectraPathHelpButton.setMaximumWidth(25)

self.spectraPathHelpButton.clicked.connect(lambda: MessageBox(self, self.spectraPathHelpText, 'PyHammer Help'))

self.spectraPathHelpButton.setToolTip('Help')

# Eyecheck Field

if self.options['eyecheck'] is None or not self.options['eyecheck']:

self.eyecheckNo.setChecked(True)

else:

self.eyecheckYes.setChecked(True)

self.eyecheckYes.clicked.connect(self.updateGui)

self.eyecheckNo.clicked.connect(self.updateGui)

self.eyecheckHelpButton.setMaximumWidth(25)

self.eyecheckHelpButton.clicked.connect(lambda: MessageBox(self, self.eyecheckHelpText, 'PyHammer Help'))

self.eyecheckHelpButton.setToolTip('Help')

# S/N Cut Field

self.sncutEntry.setText(self.options['sncut'])

self.sncutHelpButton.setMaximumWidth(25)

self.sncutHelpButton.clicked.connect(lambda: MessageBox(self, self.sncutHelpText, 'PyHammer Help'))

self.sncutHelpButton.setToolTip('Help')

# Spectral Line Output File Field

if self.options['lineOutfile'] is None or not self.options['lineOutfile']:

self.lineNo.setChecked(True)

else:

self.lineYes.setChecked(True)

self.lineHelpButton.setMaximumWidth(25)

self.lineHelpButton.clicked.connect(lambda: MessageBox(self, self.lineHelpText, 'PyHammer Help'))

self.lineHelpButton.setToolTip('Help')

# Start Button

self.startButton.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Preferred)

self.startButton.clicked.connect(self.goToMain)

# Top Level Grid

self.grid.setSpacing(4)

self.grid.setContentsMargins(2,2,2,2)

# Set the main window properties

self.widget.setLayout(self.grid)

self.setCentralWidget(self.widget)

self.setWindowTitle('PyHammer Settings')

self.setWindowIcon(self.icon)

def updateGui(self):

if self.fullPathYes.isChecked():

self.spectraPathFrame.hide()

self.sep[4].hide()

elif self.fullPathNo.isChecked():

self.spectraPathFrame.show()

self.sep[4].show()

if self.eyecheckYes.isChecked():

self.sncutFrame.hide()

self.sep[6].hide()

elif self.eyecheckNo.isChecked():

self.sncutFrame.show()

self.sep[6].show()

self.setFixedSize(self.grid.minimumSize())

def browse(self, entry, target = 'file'):

if target == 'file':

if entry is self.infileEntry:

dlg = QFileDialog(directory = __file__, windowTitle = 'Select an input file')

dlg.setFileMode(QFileDialog.ExistingFile)

if dlg.exec_():

entry.setText(dlg.selectedFiles()[0])

elif entry is self.outfileEntry:

dlg = QFileDialog(directory = __file__, windowTitle = 'Select or create an output file')

dlg.setFileMode(QFileDialog.AnyFile)

if dlg.exec_():

entry.setText(dlg.selectedFiles()[0])

elif entry is self.rejectEntry:

dlg = QFileDialog(directory = __file__, windowTitle = 'Select or create a reject file')

dlg.setFileMode(QFileDialog.AnyFile)

if dlg.exec_():

entry.setText(dlg.selectedFiles()[0])

if target == 'directory':

if entry is self.spectraPathEntry:

dlg = QFileDialog(directory = __file__, windowTitle = 'Select a directory')

dlg.setFileMode(QFileDialog.Directory)

dlg.setOption(QFileDialog.ShowDirsOnly, True)

if dlg.exec_():

entry.setText(dlg.selectedFiles()[0])

def createButtonClicked(self):

self.createPressed = not self.createPressed # Invert boolean

self.infileEntry.setEnabled(not self.createPressed)

self.infileBrowseButton.setEnabled(not self.createPressed)

if self.createPressed:

self.createFrame.show()

self.infileLabel.setText('Create your input file in the text field below. '

'Use the buttons to help populate your input file.')

self.fullPathYes.setChecked(True)

self.updateGui()

else:

self.createFrame.hide()

self.infileLabel.setText('Provide an existing input file or choose to create a new input file')

self.updateGui()

def selectSpectraButtonClicked(self):

dlg = QFileDialog(directory = __file__, windowTitle = 'Select your spectra files')

dlg.setFileMode(QFileDialog.ExistingFiles)

if dlg.exec_():

[self.textArea.append(file) for file in dlg.selectedFiles()]

def applyTypeClicked(self):

# Pull out currently selected data type to apply and current

# text in text area

dataType = self.dataTypeList.currentText()

originalText = self.textArea.toPlainText()

# Go through the text line by line, remove any current types

# that already exist, and apply the new type.

newText = []

for line in originalText.split('\n'):

if line == '': continue

comma = line.find(',')

if comma >= 0: line = line[:comma]

newText.append(line + ', ' + dataType)

# Put the new text into the text area

self.textArea.setPlainText('\n'.join(newText))

def goToMain(self):

"""

This will go through all the inputs of the GUI and

first perform a check to make sure the user's input

is valid. If it all inputs are valid, this will then

progress to calling the main function with the options

from the GUI being passed to it. If any of the input

is invalid, a message will be displayed indicating

the problems that need fixing.

"""

message = '' # The output message in case errors are found

# Check each input field for errors

# Input File

if not self.createPressed:

if self.infileEntry.text() == '':

message += '- A spectra list filename was not provided.\n'

else:

if not os.path.isfile(self.infileEntry.text()):

message += '- The input file cannot be found.\n'

else:

if self.textArea.toPlainText() == '':

message += '- The text field for creating an input file is empty.\n'

# Output File

if self.outfileEntry.text() == '':

message += '- An output filename was not provided.\n'

else:

outfileExt = self.outfileEntry.text()[-4:]

if outfileExt[0] == '.' and outfileExt[1:] != 'csv':

message += '- The output file must be a csv file.\n'

# Reject File

if self.rejectEntry.text() == '':

message += '- A reject filename was not provided.\n'

else:

rejectExt = self.rejectEntry.text()[-4:]

if rejectExt[0] == '.' and rejectExt[1:] != 'csv':

message += '- The reject file must be a csv file.\n'

# Spectra Path

if self.fullPathNo.isChecked():

if self.spectraPathEntry.text() == '':

message += '- A path for the spectra was not provided.\n'

else:

if not os.path.isdir(self.spectraPathEntry.text()):

message += '- The spectra path is not a valid directory.\n'

# Eyecheck

if self.eyecheckYes.isChecked() and not os.path.isfile(self.outfileEntry.text()):

message += '- You cannot skip to eyecheck without an existing output file.\n'

# S/N Cut

if self.eyecheckNo.isChecked() and self.sncutEntry.text() != '':

try:

if float(self.sncutEntry.text()) < 0:

message += '- The entered S/N cut must be positive.\n'

except ValueError as e:

message += '- The entered S/N cut is not a valid number.\n'

# If a message was formed to notify the user, print that message and return

if message != '':

message = 'The following issues were found with your input.\n' \

'Please correct them and try again.\n\n' + message

MessageBox(self, message, title = 'PyHammer Settings Error')

return

# If we've made it to this point, the user's inputs are valid. Store them

# in the options dict and move to the main part of the code.

if not self.createPressed:

self.options['infile'] = self.infileEntry.text()

else:

# Create a temporary input file based on what's in the create

# input file text field

fname = 'temp_input_'+str(int(time()))+'.txt'

with open(fname, 'w') as f:

line = self.textArea.toPlainText()

if line != '\n':

f.write(line)

self.options['infile'] = fname

self.options['outfile'] = self.outfileEntry.text() + '.csv'*(self.outfileEntry.text()[-4:] != '.csv')

self.options['rejectfile'] = self.rejectEntry.text() + '.csv'*(self.rejectEntry.text()[-4:] != '.csv')

self.options['fullPath'] = self.fullPathYes.isChecked()

self.options['spectraPath'] = self.spectraPathEntry.text() * (not self.options['fullPath'])

self.options['lineOutfile'] = self.lineYes.isChecked()

# Append a slash to the end of the spectra path if there isn't one

if (self.options['spectraPath'] != '' and self.options['spectraPath'][-1] not in ['\\', '/']):

self.options['spectraPath'] += '/'

self.options['eyecheck'] = self.eyecheckYes.isChecked()

if (self.options['eyecheck'] or self.sncutEntry.text() == ''):

self.options['sncut'] = None

else:

self.options['sncut'] = float(self.sncutEntry.text())

self.close()

"""

Description:

This provides command line inputs for the user

to enter options. It will only ask questions

about options the user has not already specified

at run time. This will then pass the updated

options to the main function.

Inputs:

options: A dict containing the options the

user can specify. These may already

have default values if they were

provided when the program was launched.

"""

##

# If the input options were not provided on the command line at

# execution, we need to ask for them here.

#

# Get the input filename if one was not provided

if options['infile'] is None:

while True:

options['infile'] = input('Please enter the filename which contains the spectra list: ')

if options['infile'].find('.') == -1:

print('Make sure to supply an extension for your input file.', flush = True)

continue

if not os.path.isfile(options['infile']):

print('The input file cannot be found.', flush = True)

continue

break

# Ask user if they want to change the results file and what to use if they do.

if options['outfile'] == 'PyHammerResults.csv':

ans = input('The results file is set to PyHammerResults.csv. Do you want to change it? (y/n): ')

if ans.lower() == 'y':

while True:

options['outfile'] = input('Please enter the filename for the results file: ')

outfileExt[0] = options['outfile'][-4:]

if outfileExt[0] == '.' and outfileExt[1:] != 'csv':

print('The output file must be a csv file.', flush = True)

continue

break

# Append a .csv extension to the filename if none was provided

options['outfile'] += '.csv'*(options['outfile'][-4:] != '.csv')

# Ask user if they want to change the reject file and what to use if they do.

if options['rejectfile'] == 'RejectSpectra.csv':

ans = input('The reject file is set to RejectSpectra.csv. Do you want to change it? (y/n): ')

if ans.lower() == 'y':

while True:

options['rejectfile'] = input('Please enter the filename for the reject file: ')

rejectExt[0] = options['rejectfile'][-4:]

if rejectExt[0] == '.' and rejectExt[1:] != 'csv':

print('The reject file must be a csv file.', flush = True)

continue

break

# Append a .csv extension to the filename if none was provided

options['rejectfile'] += '.csv'*(options['rejectfile'][-4:] != '.csv')

# Check whether the input file list contains the full path if

# the user didn't already specify.

if options['fullPath'] is None:

ans = input('Does your input list give the full path to each spectrum? (y/n): ')

if ans.lower() == 'y':

options['fullPath'] = True

options['spectraPath'] = ''

else:

options['fullPath'] = False

while True:

options['spectraPath'] = input('Enter the necessary path for each file: ')

if not os.path.isdir(options['spectraPath']):

print('The path provided is not a valid directory.', flush = True)

continue

break

# Append a slash to the end of the spectra path, if there isn't one

if options['spectraPath'][-1] not in ['\\', '/']:

options['spectraPath'] += '\\'

# Asks the user if they want to skip the auto-classifying and go straight

# to checking by eye, if they have not already specified.

if (options['eyecheck'] is None):

ans = input('Do you want to skip straight to eye-checking? (y/n): ')

options['eyecheck'] = (ans.lower() == 'y')

# Asks the user if they want to apply a S/N cut when classifying the spectra.

# This only applies if they chose not to skip the auto-classification

if (options['eyecheck'] == False and options['sncut'] is None):

ans = input('Do you want to supply a S/N cut when auto-classifying? (y/n): ')

if ans.lower() == 'y':

while True:

ans = input('Choose a S/N cutoff (~3-5 recommended): ')

try:

options['sncut'] = float(ans)

break

except Error as e:

print(str(e), flush = True)

# Asks the user if they want to have the spectral lines written to a file.

if (options['lineOutfile'] is None):

ans = input('Do you want to have the spectral lines used for classification written to a file? (y/n): ')

options['lineOutfile'] = (ans.lower() == 'y')

# Now that all the options have been set, let's get started