def body(self, master):
self.alarm_id = None
self.root_widget = getRoot(self)
row = 0
label = Label(master, text='Widget count:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.count_label = Label(master,
text='',
tipText='Number of Tkinter widget objects')
self.count_label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
ind = 1
label = Label(master, text='Auto count:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.on_off_buttons = RadioButtons(master,
entries=self.on_off_entries,
select_callback=self.applyAuto,
selected_index=ind)
self.on_off_buttons.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text='Auto frequency:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.freq_entry = IntEntry(master,
text=60,
returnCallback=self.applyAuto)
self.freq_entry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text='seconds')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
texts = ['Do Immediate Count']
commands = [self.applyManual]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
self.doCount()
def body(self, guiFrame):
self.geometry('600x350')
project = self.project
analysisProject = self.analysisProject
guiFrame.grid_columnconfigure(1, weight=1)
row = 0
frame = Frame(guiFrame, grid=(0,0))
label = Label(frame, text=' Window:', grid=(0,0))
self.windowPulldown = PulldownList(frame, grid=(0,1),
tipText='The window that will be printed out',
callback=self.selectWindow)
tipTexts = ['For the window pulldown, show all of the spectrum windows in the current project, irrespective of the active group',
'For the window pulldown, show only spectrum windows that are in the currently active window group']
self.whichWindows = RadioButtons(frame, grid=(0,2),
entries=ACTIVE_OPTIONS, tipTexts=tipTexts,
select_callback=self.updateWindows)
texts = [ 'Save Print File' ]
tipTexts = [ 'Save the printout to the specified file' ]
commands = [ self.saveFile ]
buttons = UtilityButtonList(guiFrame, helpUrl=self.help_url, grid=(row,2),
commands=commands, texts=texts, tipTexts=tipTexts)
self.buttons = buttons
buttons.buttons[0].config(bg='#B0FFB0')
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
options = ['Options', 'Spectra', 'Peak Lists', 'Region']
tipTexts = ['Optional settings for spectra', 'Optional settings for peak lists', 'Optional settings for the region']
tabbedFrame = TabbedFrame(guiFrame, options=options, tipTexts=tipTexts)
tabbedFrame.grid(row=row, column=0, columnspan=3, sticky='nsew')
self.tabbedFrame = tabbedFrame
optionFrame, spectrumFrame, peakListFrame, regionFrame = tabbedFrame.frames
optionFrame.expandGrid(0, 0)
getOption = lambda key, defaultValue: PrintBasic.getPrintOption(analysisProject, key, defaultValue)
setOption = lambda key, value: PrintBasic.setPrintOption(analysisProject, key, value)
self.printFrame = PrintFrame(optionFrame, getOption=getOption,
grid=(0,0), gridSpan=(1,1),
setOption=setOption, haveTicks=True,
doOutlineBox=False)
spectrumFrame.expandGrid(0, 0)
frame = Frame(spectrumFrame, grid=(0,0), gridSpan=(1,1))
frame.expandGrid(1,0)
self.overrideSpectrum = CheckButton(frame,
text='Use below settings when printing',
tipText='Use below settings when printing instead of the window values',
grid=(0,0), sticky='w')
tipText = 'Change the settings of the selected spectra back to their window values'
button = Button(frame, text='Reset Selected', tipText=tipText,
command=self.resetSelected, grid=(0,1), sticky='e')
self.posColorPulldown = PulldownList(self, callback=self.setPosColor)
self.negColorPulldown = PulldownList(self, callback=self.setNegColor)
headings = ['Spectrum', 'Pos. Contours\nDrawn', 'Neg. Contours\nDrawn', 'Positive\nColours', 'Negative\nColours']
tipTexts = ['Spectrum in window', 'Whether the positive contours should be drawn', 'Whether the negative contours should be drawn',
'Colour scheme for positive contours (can be a single colour)', 'Colour scheme for negative contours (can be a single colour)']
editWidgets = [ None, None, None, self.posColorPulldown, self.negColorPulldown]
editGetCallbacks = [ None, self.togglePos, self.toggleNeg, self.getPosColor, self.getNegColor]
editSetCallbacks = [ None, None, None, self.setPosColor, self.setNegColor]
self.spectrumTable = ScrolledMatrix(frame, headingList=headings,
tipTexts=tipTexts,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(1,0), gridSpan=(1,2))
peakListFrame.expandGrid(0, 0)
frame = Frame(peakListFrame, grid=(0,0), gridSpan=(1,3))
frame.expandGrid(1,0)
self.overridePeakList = CheckButton(frame,
text='Use below settings when printing',
tipText='Use below settings when printing instead of the window values',
grid=(0,0))
tipText = 'Change the settings of the selected peak lists back to their window values'
button = Button(frame, text='Reset Selected', tipText=tipText,
command=self.resetSelected, grid=(0,1), sticky='e')
colors = Color.standardColors
self.peakColorPulldown = PulldownList(self, callback=self.setPeakColor,
texts=[c.name for c in colors],
objects=[c.hex for c in colors],
colors=[c.hex for c in colors])
headings = [ 'Peak List', 'Symbols Drawn', 'Peak Font', 'Peak Colour']
self.fontMenu = FontList(self, mode='Print', extraTexts=[no_peak_text])
editWidgets = [ None, None, self.fontMenu, self.peakColorPulldown]
editGetCallbacks = [ None, self.togglePeaks, self.getPeakFont, self.getPeakColor ]
editSetCallbacks = [ None, None, self.setPeakFont, self.setPeakColor ]
self.peakListTable = ScrolledMatrix(frame, headingList=headings,
multiSelect=True,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(1,0), gridSpan=(1,2))
regionFrame.expandGrid(0, 0)
frame = Frame(regionFrame, grid=(0,0), gridSpan=(1,3))
frame.expandGrid(3,0)
tipText = 'Use the specified override region when printing rather than the window values'
self.overrideButton = CheckButton(frame, text='Use override region when printing',
tipText=tipText,
callback=self.toggledOverride, grid=(0,0))
tipTexts = ('Use min and max to specify override region', 'Use center and width to specify override region')
self.use_entry = USE_ENTRIES[0]
self.useButtons = RadioButtons(frame, entries=USE_ENTRIES,
tipTexts=tipTexts,
select_callback=self.changedUseEntry,
grid=(1,0))
texts = ('Set Region from Window', 'Set Center from Window', 'Set Width from Window')
tipTexts = ('Set the override region to be the current window region',
'Set the center of the override region to be the center of the current window region',
'Set the width of the override region to be the width of the current window region')
commands = (self.setRegionFromWindow, self.setCenterFromWindow, self.setWidthFromWindow)
self.setRegionButton = ButtonList(frame, texts=texts,
tipTexts=tipTexts,
commands=commands, grid=(2,0))
self.minRegionWidget = FloatEntry(self, returnCallback=self.setMinRegion, width=10)
self.maxRegionWidget = FloatEntry(self, returnCallback=self.setMaxRegion, width=10)
headings = MIN_MAX_HEADINGS
editWidgets = [ None, None, self.minRegionWidget, self.maxRegionWidget ]
editGetCallbacks = [ None, None, self.getMinRegion, self.getMaxRegion ]
editSetCallbacks = [ None, None, self.setMinRegion, self.setMaxRegion ]
self.regionTable = RegionScrolledMatrix(frame, headingList=headings,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(3,0))
self.updateWindows()
self.updateAfter()
self.administerNotifiers(self.registerNotify)
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
def __init__(self, guiParent, basePopup):
self.guiParent = guiParent
self.basePopup = basePopup
# selection hash. This needs to be stored so that we can
# refresh with the same criteria
self.select = None
# should the screen autorefresh
self.autoRefresh = False
# add this to shortcuts to ease navigation
self.basePopup.frameShortcuts['Tasks'] = self
#self.registerNotify=basePopup.registerNotify
#self.unregisterNotify=basePopup.unregisterNotify
#self.frames = []
# FIXME JMCI
# This frame is specific for a single repository so we need a
# method for identifying one from the whole set (or could have
# subtabs)
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=1, minsize=30)
self.grid_columnconfigure(2, weight=0, minsize=40)
self.grid_rowconfigure(0, weight=0, minsize=20)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=0)
self.grid_rowconfigure(3, weight=0, minsize=0)
self.grid_rowconfigure(4, weight=0, minsize=0)
self.grid_rowconfigure(5, weight=1, minsize=0)
self.grid_rowconfigure(6, weight=0, minsize=10)
self.grid_rowconfigure(7, weight=0, minsize=10)
initial_cols = ['ID','Task','User','Status']
self.task_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=15,
doubleCallback=self.goto_task_tab)
# Filters for narrowing down tasks. should probably code this
# specifically inside this package
#self.filter = FilterFrame(self, self.basePopup, text='Filter')
self.filter = TaskFilterFrame(self, self.basePopup, text='Filter')
# Frame for controlling the main client side daemon
# seems to be a problem. add a simple button for now
opts = ['Client','Server']
self.daemonFrame = TabbedFrame(self, options=opts,
toggleOff=False, selected=0)
self.daemonSwitchLabel = Label(self, text= 'Task Daemon')
self.daemonSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_daemon, selected_index = 1)
sel = 1
if self.autoRefresh:
sel = 0
self.autoRefreshSwitchLabel = Label(self, text= 'Auto Refresh')
self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_refresh, selected_index = sel)
self.label_rep = Label(self, text='', font='Helvetica16')
# set up a loop
self.refresh()
def body(self, guiFrame):
self.geometry('600x350')
guiFrame.expandGrid(0, 0)
tipTexts = ['', '', '', '']
options = [
'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions',
'Region Peak Find'
]
tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0))
frameA, frameB, frameC, frameD = tabbedFrame.frames
self.tabbedFrame = tabbedFrame
# Find Params
frameA.expandGrid(2, 0)
row = 0
label = LabelFrame(frameA,
text='Extrema to search for:',
grid=(row, 0),
gridSpan=(1, 2))
label.expandGrid(0, 1)
entries = ['positive and negative', 'positive only', 'negative only']
tipTexts = [
'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima',
]
self.extrema_buttons = RadioButtons(label,
entries=entries,
select_callback=self.apply,
direction='horizontal',
grid=(0, 0),
tipTexts=tipTexts)
row += 1
label = LabelFrame(frameA,
text='Nearby points to check:',
grid=(row, 0),
gridSpan=(1, 2))
label.expandGrid(None, 1)
entries = ['+-1 in at most one dim', '+-1 allowed in any dim']
tipTexts = [
'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region',
]
self.adjacent_buttons = RadioButtons(label,
entries=entries,
select_callback=self.apply,
direction='horizontal',
grid=(0, 0),
tipTexts=tipTexts)
row += 1
labelFrame = LabelFrame(frameA,
text='Other parameters:',
grid=(row, 0),
gridSpan=(1, 2))
labelFrame.expandGrid(5, 2)
frow = 0
label = Label(labelFrame,
text='Scale relative to contour levels:',
grid=(frow, 0),
sticky='e')
tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible'
self.scale_entry = FloatEntry(labelFrame,
grid=(frow, 1),
tipText=tipText,
returnCallback=self.apply,
width=10)
self.scale_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Exclusion buffer around peaks (in points):',
grid=(frow, 0),
sticky='e')
tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking'
self.buffer_entry = IntEntry(labelFrame,
returnCallback=self.apply,
grid=(frow, 1),
width=10,
tipText=tipText)
self.buffer_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Extra thickness in orthogonal dims (in points):',
grid=(frow, 0),
sticky='e')
tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals'
self.thickness_entry = IntEntry(labelFrame,
returnCallback=self.apply,
width=10,
grid=(frow, 1),
tipText=tipText)
self.thickness_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Minimum drop factor (0.0-1.0):',
grid=(frow, 0),
sticky='e')
tipText = ''
self.drop_entry = FloatEntry(labelFrame,
returnCallback=self.apply,
width=10,
grid=(frow, 1),
tipText=tipText)
self.drop_entry.bind('<Leave>', self.apply, '+')
frow += 1
label = Label(labelFrame,
text='Volume method:',
grid=(frow, 0),
sticky='e')
tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"'
self.method_menu = PulldownList(labelFrame,
texts=PeakBasic.PEAK_VOLUME_METHODS,
grid=(frow, 1),
callback=self.apply,
tipText=tipText)
# Spectrum widths
frameB.expandGrid(1, 1)
label = Label(frameB, text='Spectrum: ')
label.grid(row=0, column=0, sticky='e')
tipText = 'The spectrum which determines the widths being shown'
self.expt_spectrum = PulldownList(frameB,
tipText=tipText,
callback=self.setSpectrumProperties)
self.expt_spectrum.grid(row=0, column=1, sticky='w')
self.editLinewidthEntry = FloatEntry(self,
text='',
returnCallback=self.setLinewidth,
width=10)
self.editBoxwidthEntry = FloatEntry(self,
text='',
returnCallback=self.setBoxwidth,
width=10)
tipTexts = [
'The number of the spectrum dimension to which the settings apply',
'The nuclear isotope measures in the spectrum dimension',
'The smallest value for the linewidth of a peak for it to be picked',
'The size of the spectrum region to perform the volume integral over'
]
headingList = [
'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth'
]
editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth]
editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth]
editWidgets = [
None, None, self.editLinewidthEntry, self.editBoxwidthEntry
]
self.spectrumMatrix = ScrolledMatrix(frameB,
initialRows=6,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
callback=self.selectCell,
tipTexts=tipTexts)
self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew')
# Diagonal Exclusions
frameC.expandGrid(0, 0)
tipTexts = [
'The isotope as measures on the axis of a spectrum window',
'The distance from the homonuclear diagonal line within which no peak picking can occur'
]
self.exclusionEntry = FloatEntry(self,
text='',
returnCallback=self.setExclusion,
width=10)
headingList = ['Isotope', 'Diagonal Exclusion (ppm)']
editSetCallbacks = [None, self.setExclusion]
editGetCallbacks = [None, self.getExclusion]
editWidgets = [None, self.exclusionEntry]
self.isotopeMatrix = ScrolledMatrix(frameC,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
headingList=headingList,
grid=(0, 0),
tipTexts=tipTexts)
# Region peak find
self.regionFindPeakList = None
self.regionCondition = None
self.regionConditions = []
self.regionCol = 1
row = 0
label = Label(frameD, text='Peak List: ', grid=(0, 0))
tipText = 'Selects which peak list to perform region-wide peak picking for'
self.regionPeakListPulldown = PulldownList(
frameD,
callback=self.changeRegionPeakList,
grid=(0, 1),
tipText=tipText)
row += 1
frameD.expandGrid(row, 1)
self.regionEntry = FloatEntry(self,
text='',
returnCallback=self.setRegion,
width=10)
self.conditionMenu = PulldownList(self,
texts=('include', 'exclude'),
callback=self.setCondition)
tipTexts = [
'Whether to include or exclude the states region from region-wide peak picking',
]
headingList = ['Condition']
editSetCallbacks = [None]
editGetCallbacks = [None]
editWidgets = [self.conditionMenu]
self.regionFindMatrix = ScrolledMatrix(
frameD,
headingList=headingList,
callback=self.selectRegionCell,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
grid=(row, 0),
gridSpan=(1, 2))
row += 1
tipTexts = [
'Sets the currently selected region row to cover the whole spectrum',
'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas',
'Remove the selected region specification',
'Go to the panel for setting the parameters that control how peaks extrema are picked',
'Using the stated regions and parameters, perform region-wide peak picking'
]
texts = [
'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params',
'Find Peaks!'
]
commands = [
self.wholeRegion, self.addCondition, self.deleteCondition,
self.adjustParams, self.regionFindPeaks
]
buttons = ButtonList(frameD,
texts=texts,
commands=commands,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
buttons.buttons[4].config(bg='#B0FFB0')
utilButtons = UtilityButtonList(tabbedFrame.sideFrame,
grid=(0, 0),
helpUrl=self.help_url,
sticky='e')
self.dataDim = None
self.setParamsEntries()
self.updateSpectrum()
self.setIsotopeProperties()
self.updateRegionPeakLists()
self.administerNotifiers(self.registerNotify)
def body(self):
'''Describes the body of this tab. It consists
out of a number of radio buttons, check buttons
and number entries that allow the user to
indicate which assignments should be transferred.
'''
# self.frame.expandColumn(0)
self.frame.expandGrid(8, 0)
self.frame.expandGrid(8, 1)
typeOfAssignmentFrame = LabelFrame(self.frame,
text='type of assignment')
typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw')
# typeOfAssignmentFrame.expandGrid(0,5)
peakSelectionFrame = LabelFrame(self.frame,
text='which peaks to assign')
peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2)
spinSystemSelectionFrame = LabelFrame(self.frame,
text='Which spin-systems to use')
spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw')
tipText = 'What to do when a residue has already a spin system assigned to it.'
assignedResidueFrame = LabelFrame(
self.frame,
text='if residue already has spin-system',
tipText=tipText)
assignedResidueFrame.grid(row=2, column=1, sticky='nesw')
spectrumSelectionFrame = LabelFrame(self.frame, text='spectra')
spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw')
row = 0
Label(typeOfAssignmentFrame,
text='Resonances to Peak Dimensions',
grid=(row, 0))
self.peaksCheckButton = CheckButton(typeOfAssignmentFrame,
selected=True,
grid=(row, 1))
row += 1
Label(typeOfAssignmentFrame,
text='SpinSystems to Residues',
grid=(row, 0))
self.residuesCheckButton = CheckButton(typeOfAssignmentFrame,
selected=True,
grid=(row, 1))
row = 0
Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0))
self.intraCheckButton = CheckButton(peakSelectionFrame,
selected=True,
grid=(row, 1))
row += 1
Label(peakSelectionFrame, text='Sequential', grid=(row, 0))
self.sequentialCheckButton = CheckButton(peakSelectionFrame,
selected=True,
grid=(row, 1))
row += 1
Label(peakSelectionFrame,
text='Do not assign diagonal peaks',
grid=(row, 0))
self.noDiagonalCheckButton = CheckButton(peakSelectionFrame,
selected=True,
grid=(row, 1))
entries = [
'Only assigned spin systems',
'All that have a score of at least: ', 'User Defined',
'Solution number:'
]
tipTexts = [
'Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.',
'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.',
"As defined in the lower row of buttons in the 'results' tab.",
'One of the single solutions of the annealing.'
]
self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(4, 1),
tipTexts=tipTexts)
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minScoreEntry = FloatEntry(spinSystemSelectionFrame,
grid=(1, 1),
width=7,
text=str(self.minScore),
returnCallback=self.changeMinScore,
tipText=tipText)
self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+')
self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame,
grid=(3, 1),
width=7,
text=1,
returnCallback=self.solutionUpdate,
tipText=tipText)
self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+')
#self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w')
entries = ['all spectra', 'only:']
tipTexts = [
'Assign peaks in all the spectra that where selected before the annealing ran.',
'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.'
]
self.spectrumSelect = RadioButtons(spectrumSelectionFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(2, 1),
tipTexts=tipTexts)
self.spectraPullDown = PulldownList(spectrumSelectionFrame,
self.changeSpectrum,
grid=(1, 1),
sticky='w')
entries = [
'skip this residue', 'de-assign old spin system from residue',
'assign, but never merge', 'warn to merge'
]
tipTexts = [
"Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances",
"De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.",
"Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.",
"Ask to merge individually for each spin system, this might result in clicking on a lot of popups."
]
self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame,
entries=entries,
grid=(0, 0),
select_callback=None,
direction=VERTICAL,
gridSpan=(2, 1),
tipTexts=tipTexts)
texts = ['Transfer Assignments']
commands = [self.transferAssignments]
self.transferButton = ButtonList(self.frame,
commands=commands,
texts=texts)
self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
def body(self, guiFrame):
self.geometry('450x500')
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(0, weight=1)
options = ['Peak Separator', 'Advanced Settings']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
buttons = UtilityButtonList(tabbedFrame.sideFrame,
helpUrl=self.help_url)
buttons.grid(row=0, column=0, sticky='e')
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
#
# FrameA : Main Settings
#
frameA.grid_columnconfigure(1, weight=1)
row = 0 # Label row
row += 1
div = LabelDivider(frameA, text='Peak Separator Parameters')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Min. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Minimum number of peaks to find (must be > 0)')
self.minPeaksEntry.grid(row=row, column=1, sticky='n')
self.minPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Max. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Maximum number of peaks to find (0 is unlimited - not recommended)')
self.maxPeaksEntry.grid(row=row, column=1, sticky='n')
self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Only pick positive peaks:')
label.grid(row=row, column=0, sticky='w')
entries = ['False', 'True']
self.posPeaksButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Search for both positive and negative intensity peaks',
'Limit search to only positive peaks'
])
self.posPeaksButtons.grid(row=row, column=1, sticky='n')
row += 1
label = Label(frameA, text='Peak Model:')
label.grid(row=row, column=0, sticky='w')
### G/L Mixture works, but volume calculation involves Gamma function
# entries = ['Gaussian', 'Lorentzian', 'G/L Mixture']
entries = ['Gaussian', 'Lorentzian']
self.shapeButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Choose a Gaussian model peak shape to fit to peaks',
'Choose a Lorentzian model peak shape to fit to peaks'
])
self.shapeButtons.grid(row=row, column=1, sticky='n')
row += 1
div = LabelDivider(frameA,
text='Region',
tipText='Region that search will limit itself to')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Peak List:')
label.grid(row=row, column=0, sticky='nw')
self.peakListPulldown = PulldownList(
frameA,
callback=self.setManuallyPickPeakList,
tipText='Select which peak list new peaks are to be added to')
self.peakListPulldown.grid(row=row, column=1, sticky='nw')
# tricky scrolled matrix
row += 1
self.regionTable = None
frameA.grid_rowconfigure(row, weight=1)
headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size')
self.editDimEntry = IntEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Dimension number')
self.editStartEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area lower bound')
self.editEndEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area upper bound')
editWidgets = [
self.editDimEntry, self.editStartEntry, self.editEndEntry, None
]
editGetCallbacks = [None, None, None, None]
editSetCallbacks = [None, None, None, None]
self.regionTable = ScrolledMatrix(frameA,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=5)
self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew')
# Run Button
row += 1
texts = ['Add Region']
commands = [self.updateFromRegion]
self.addResetButtons = ButtonList(
frameA,
texts=texts,
commands=commands,
tipTexts=['Add selected specrtral region'])
self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameA,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
#
# FrameB : Further Settings
#
frameB.grid_columnconfigure(0, weight=1)
row = 0
div = LabelDivider(frameB, text='Rate:')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text='Rate of MCMC step size change')
label.grid(row=row, column=0, columnspan=1, sticky='w')
self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \
tipText='Rate effects speed of run, smaller values take longer but may produce better results')
self.rateEntry.grid(row=row, column=1, sticky='n')
self.rateEntry.bind('<Leave>', self.applyChange, '+')
self.rateEntry.set(self.params.rate)
# tricky scrolled matrix for line width
row += 2
div = LabelDivider(frameB, text='Line Width (Hz):')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text="Descr.")
label.grid(row=row, rowspan=2, column=0, sticky='w')
row += 1
self.lineWidthTable = None
frameB.grid_rowconfigure(row, weight=1)
lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)')
self.editMinSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Minimum line width (Hz)')
self.editMaxSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Maximum line width (Hz)')
# self.editDimEntry is also from regionTable
initialWidthRows = 4
editLineWidthWidgets = [
None, self.editMinSigmaEntry, self.editMaxSigmaEntry
]
editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax]
editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax]
self.lineWidthTable = ScrolledMatrix(
frameB,
headingList=lineWidthHeadings,
multiSelect=False,
editWidgets=editLineWidthWidgets,
editGetCallbacks=editLineWidthGetCallbacks,
editSetCallbacks=editLineWidthSetCallbacks,
initialRows=initialWidthRows)
self.lineWidthTable.grid(row=row,
column=0,
columnspan=2,
sticky='nsew')
# option to 'repick' exisiting peak list
row += initialWidthRows
div = LabelDivider(frameB, text='(optional - repick entire peak list)')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
self.repickListPulldown = PulldownList(
frameB,
callback=self.setRePickPeakList,
tipText=
'Select which peak list to repick (new peaks will be put into a new peak list)'
)
self.repickListPulldown.grid(row=row, column=0, sticky='nw')
texts = ['Repick Peak List']
commands = [self.runRepickPeaks]
self.runButton = ButtonList(
frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Repick selected peak list into a new peak list.'])
self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew')
row += 1
div = LabelDivider(frameB)
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.setWidgetEntries()
self.administerNotifiers(self.registerNotify)
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
# should the screen autorefresh
self.autoRefresh = False
# add this to shortcuts to ease navigation
self.basePopup.frameShortcuts['Repository'] = self
# get a port proxy instance
# this should probably belong to the repository directly
# or else should belong in a dictionary in the main gui
# layer when it can be picked up easily
# FIXME JMCI
# need to work out how to get a number of these!
loc = SharedBeanServiceLocator()
self.port = loc.getSharedBean()
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=1, minsize=10)
self.grid_columnconfigure(2, weight=0, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=0)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
self.grid_rowconfigure(4, weight=0, minsize=10)
self.grid_rowconfigure(5, weight=1, minsize=10)
self.grid_rowconfigure(6, weight=0, minsize=10)
self.grid_rowconfigure(7, weight=0, minsize=10)
# widgets for view when no data
self.noDataWidgets = []
self.noRepLabel = Label(self, text='No repository currently selected.')
self.noDataWidgets.append(self.noRepLabel)
# widgets for view when current repository set
self.dataWidgets = []
self.repTitle = Label(self, text='Repository:', font='Helvetica16')
self.dataWidgets.append(self.repTitle)
#self.repLabel = Label(self,text='All Projects in Repository')
#self.dataWidgets.append(self.repLabel)
self.repTree = Tree(self, doubleCallback=self.goto_project_tab)
self.dataWidgets.append(self.repTree)
sel = 1
if self.autoRefresh:
sel = 0
self.autoRefreshSwitchLabel = Label(self, text='Auto Refresh')
self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'],
select_callback=self.set_refresh,
selected_index=sel)
# need to decide whether this is static or not
r_button_texts = [
'Add to Basket', ' Import ', ' Export ', ' Refresh ',
'Properties'
]
r_button_cmds = [
self.tmpCall, self.import_project, self.export_project,
self.drawFrame, self.goto_project_tab
]
self.rep_button_list = ButtonList(self, r_button_texts, r_button_cmds)
self.dataWidgets.append(self.rep_button_list)
self.filterFrame = FilterFrame(self, self.basePopup, text='Filter')
self.dataWidgets.append(self.filterFrame)
baskets = ('basket1', 'basket2', 'basket3')
self.basketSelect = PulldownList(self, self.tmpCall, baskets)
self.dataWidgets.append(self.basketSelect)
basketElements = ('1ay3', '1ay7')
self.basketList = ScrolledListbox(self, basketElements, 25, 18)
self.dataWidgets.append(self.basketList)
b_button_texts = ['Remove from Basket', 'New Basket']
b_button_cmds = [self.tmpCall, self.tmpCall]
self.b_button_list = ButtonList(self, b_button_texts, b_button_cmds)
self.dataWidgets.append(self.b_button_list)
# draw if not automatically refreshing
if sel == 1:
self.drawFrame()
# set up a loop
self.refresh()
def body(self, master):
fileName = self.fileName
directory = os.path.dirname(fileName)
if not directory:
directory = os.getcwd()
fileName = os.path.basename(fileName)
m = template_re.match(fileName)
if m:
n = len(m.groups(2))
ss = '%%0%dd' % n
template = re.sub(template_re, r'\1%s\3' % ss, fileName)
else:
template = fileName
master.rowconfigure(0, weight=1)
master.rowconfigure(1, weight=1)
master.columnconfigure(1, weight=1)
tipTexts = [
'The experiment is pseudo-N dimensional, with a sampled axis',
'The experiment is the regular kind with only NMR frequency axes'
]
self.pseudoButton = RadioButtons(
master,
entries=self.pseudoEntries,
select_callback=self.changedPseudoMode,
grid=(0, 0),
sticky='nw',
tipTexts=tipTexts)
frame = self.pseudoFrame = Frame(master)
self.pseudoFrame.grid(row=1, column=0, sticky='nsew')
row = 0
npts = self.params.npts[self.dim]
tipText = 'Number of data points (planes) along sampled axis'
label = Label(frame, text='Number of points: ')
label.grid(row=row, column=0, sticky='e')
self.nptsEntry = IntEntry(frame,
text=npts,
tipText=tipText,
width=8,
grid=(row, 1))
tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values'
Button(frame,
text='Load values from text file',
command=self.loadValues,
tipText=tipText,
grid=(row, 2),
sticky='ew')
row = row + 1
tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis'
label = Label(frame, text='Point values: ')
label.grid(row=row, column=0, sticky='e')
self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText)
self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row = row + 1
tipText = 'Fetch the Point values from the files given by the NMRPipe template'
button = Button(
frame,
text='Fetch values from file(s) specified by template below',
command=self.fetchValues,
tipText=tipText)
button.grid(row=row, column=1, columnspan=2, sticky='w')
row = row + 1
tipText = 'The directory where the data files reside'
button = Button(frame,
text='Data directory: ',
command=self.chooseDirectory)
button.grid(row=row, column=0, sticky='e')
self.directoryEntry = Entry(frame,
text=directory,
width=40,
tipText=tipText)
self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row = row + 1
tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from'
button = Button(frame,
text='NMRPipe template: ',
command=self.chooseFile)
button.grid(row=row, column=0, sticky='e')
self.templateEntry = Entry(frame, text=template, tipText=tipText)
self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
for n in range(row):
frame.rowconfigure(n, weight=1)
frame.columnconfigure(1, weight=1)
buttons = UtilityButtonList(master,
closeText='Ok',
doClone=False,
closeCmd=self.updateParams,
helpUrl=self.help_url)
buttons.grid(row=2, column=0, sticky='ew')
def body(self, guiFrame):
row = 0
col = 0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu(guiFrame)
self.menuBar.grid(row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col = 0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes)
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew')
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = [
'old', 'new from PDB', 'new from CCPN', 'new from CYANA'
]
self.projOptionsSelect = RadioButtons(frame,
selected_index=0,
entries=self.projectOptions,
direction='vertical',
select_callback=self.updateGui)
self.projOptionsSelect.grid(row=srow,
column=0,
rowspan=len(self.projectOptions),
columnspan=2,
sticky='w')
if self.options.name:
text = self.options.name
else:
text = ''
# end if
self.projEntry = Entry(frame,
bd=1,
text=text,
returnCallback=self.updateGui)
self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame,
bd=1,
command=self.chooseOldProjectFile,
text='browse')
projButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow, column=2, sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame,
bd=1,
command=self.choosePdbFile,
text='browse')
pdbButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow, column=2, sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame,
bd=1,
command=self.chooseCcpnFile,
text='browse')
ccpnButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow, column=2, sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame,
bd=1,
command=self.chooseCyanaFile,
text='browse')
cyanaButton.grid(row=srow, column=3, sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow, column=0, sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow, column=2, sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.openProjectButton = Button(frame,
command=self.openProject,
text='Open Project',
**actionButtonAttributes)
self.openProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid(row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame,
height=11,
width=70,
borderwidth=0,
relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.closeProjectButton = Button(frame,
command=self.closeProject,
text='Close Project',
**actionButtonAttributes)
self.closeProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row += 1
col = 0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow, column=0, sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1, sticky='nw')
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow, column=2, sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1, sticky='nw')
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1, sticky='nw')
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1, sticky='nw')
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1, sticky='nw')
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,
column=2,
columnspan=3,
sticky='ew')
scriptButton = Button(frame,
bd=1,
command=self.chooseValidScript,
text='browse')
scriptButton.grid(row=srow, column=5, sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow, column=0, sticky='nw')
self.rangesEntry = Entry(frame, text='')
self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation', 'View Results', 'Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row += 0
col = 1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame,
text='Miscellaneous',
**labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1, minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow, column=0, sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1, sticky='nw')
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1, sticky='nw')
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1, sticky='nw')
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1, sticky='nw')
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1, sticky='nw')
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow, column=3, sticky='ew')
script2Button = Button(frame,
bd=1,
command=self.chooseMiscScript,
text='browse')
script2Button.grid(row=srow, column=4, sticky='ew')
srow += 1
texts = ['Export', 'Run Script']
commands = [None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row += 1
col = 0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
def body(self, guiFrame):
self.geometry('500x130')
guiFrame.grid_columnconfigure(2, weight=1)
guiFrame.grid_rowconfigure(3, weight=1)
self.alarm_id = None
row = 0
tipText = 'Browse for the directory into which project backups will be made'
button = Button(guiFrame,
text='Directory:',
command=self.selectDir,
grid=(row, 0),
tipText=tipText,
sticky='ew')
repository = self.project.findFirstRepository(name='backup')
if repository:
text = repository.url.path
else: # this is trouble, but should not happen
text = ''
tipText = 'Enter the name of the directory into which project backups will be made'
self.dir_entry = Entry(guiFrame,
text=text,
tipText=tipText,
width=40,
returnCallback=self.applyAuto,
grid=(row, 1),
gridSpan=(1, 2),
sticky='ew')
row += 1
label = Label(guiFrame, text='Auto-backup:', grid=(row, 0))
if self.analysisProject.doAutoBackup:
ind = 0
else:
ind = 1
tipTexts = [
'Toggle the timed automatic backup on',
'Toggle the timed automatic backup off'
]
self.on_off_buttons = RadioButtons(guiFrame,
entries=self.on_off_entries,
tipTexts=tipTexts,
select_callback=self.applyAuto,
selected_index=ind,
grid=(row, 1))
row += 1
tipText = 'The number of minutes to wait before automatic project backups'
label = Label(guiFrame, text='Auto-backup frequency:', grid=(row, 0))
self.freq_entry = IntEntry(guiFrame,
text=self.analysisProject.autoBackupFreq,
returnCallback=self.applyAuto,
tipText=tipText)
self.freq_entry.grid(row=row, column=1)
label = Label(guiFrame, text=' (minutes)', grid=(row, 2))
row = row + 1
# Blank for expansion
row = row + 1
texts = ['Apply Auto Settings', 'Do Immediate Backup']
commands = [self.applyAuto, self.applyManual]
tipTexts = [
'Commit the specified settings and commence automated CCPN project backup',
'Backup the CCPN project now, into the specified backup directory'
]
buttons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
doClone=False,
helpMsg=self.help_msg,
helpUrl=self.help_url,
tipTexts=tipTexts,
grid=(row, 0),
gridSpan=(1, 3),
sticky='nsew')
def body(self, master):
pseudoExpts = getSampledDimExperiments(self.parent.nmrProject)
master.rowconfigure(0, weight=1)
master.rowconfigure(1, weight=1)
master.columnconfigure(0, weight=1)
tipTexts = ['The experiment is pseudo-N dimensional, with a sampled axis',
'The experiment is the regular kind with only NMR frequency axes']
self.pseudoEntries = [x % len(self.params.npts) for x in PSEUDO_ENTRIES]
self.pseudoButton = RadioButtons(master, entries=self.pseudoEntries,
select_callback=self.changedPseudoMode,
grid=(0,0), sticky='nw', tipTexts=tipTexts)
frame = self.pseudoFrame = Frame(master)
self.pseudoFrame.grid(row=1, column=0, sticky='nsew')
row = 0
if pseudoExpts:
tipText = 'Select from existing pseudo nD experiments to copy sampled axis values from'
texts = [x.name for x in pseudoExpts]
label = Label(frame, text='Existing pseudo expts: ')
label.grid(row=row, column=0, sticky='e')
self.pseudoList = PulldownList(frame, texts=texts, objects=pseudoExpts, tipText=tipText)
self.pseudoList.grid(row=row, column=1, sticky='w')
tipText = 'Transfer the sampled axis values from the existing experiment to the new one'
Button(frame, text='Copy values down', command=self.copyValues,
tipText=tipText, grid=(row,2))
row += 1
npts = self.params.npts[self.dim]
tipText = 'Number of data points (planes) along sampled axis'
label = Label(frame, text='Number of points: ')
label.grid(row=row, column=0, sticky='e')
self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row,1))
tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values'
Button(frame, text='Load File', command=self.loadValues,
tipText=tipText, grid=(row,2), sticky='ew')
row += 1
tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis'
label = Label(frame, text='Point values: ')
label.grid(row=row, column=0, sticky='e')
self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText)
#minRows = self.params.npts[self.dim]
#self.valueEntry = MultiWidget(frame, FloatEntry, callback=None, minRows=minRows, maxRows=None,
# options=None, values=[], useImages=False)
self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row += 1
label = Label(frame, text='(requires comma-separated list, of length number of points)')
label.grid(row=row, column=1, columnspan=2, sticky='w')
row += 1
for n in range(row):
frame.rowconfigure(n, weight=1)
frame.columnconfigure(1, weight=1)
buttons = UtilityButtonList(master, closeText='Ok', closeCmd=self.updateParams,
helpUrl=self.help_url)
buttons.grid(row=row, column=0, sticky='ew')
def body(self, guiFrame):
self.doUpdateForm = True
self.spectrum = None
guiFrame.grid_columnconfigure(1, weight=1)
row = 0
specFrame = LabelFrame(guiFrame, text='Spectrum', grid=(row, 0))
tipText = 'The spectrum for which you are setting the contour levels'
self.expt_spectrum = PulldownList(specFrame,
grid=(0, 0),
tipText=tipText,
callback=self.setSpectrumDetails)
tipText = 'Open the edit spectrum table to view and change other properties associated with the selected spectrum'
button = Button(specFrame,
text='Spectrum Properties',
command=self.editProperties,
borderwidth=1,
grid=(1, 0),
sticky='ew',
tipText=tipText)
globalFrame = LabelFrame(guiFrame, text='Global scale')
globalFrame.grid(row=row, column=1, sticky='nsew')
globalFrame.grid_columnconfigure(0, weight=1)
tipText = 'The value by which all contour levels in all spectra are multiplied; to give the actual contour level in terms of the stored spectrum data'
self.global_entry = FloatEntry(
globalFrame,
width=10,
tipText=tipText,
text=self.analysisProject.globalContourScale,
returnCallback=self.applyAuto,
grid=(0, 0),
gridSpan=(1, 2),
sticky='ew')
tipText = 'Divide the global scaling factor by two; moving all contour for all spectra levels closer to zero'
button = Button(globalFrame,
borderwidth=1,
text='/2',
sticky='ew',
tipText=tipText,
command=lambda: self.changeGlobalScale(0.5),
grid=(0, 2))
tipText = 'Multiple the global scaling factor by two; moving all contour for all spectra levels away from zero'
button = Button(globalFrame,
borderwidth=1,
text='*2',
sticky='ew',
tipText=tipText,
command=lambda: self.changeGlobalScale(2.0),
grid=(0, 3))
tipText = 'Set the global contour scale for all spectra to the default of 100,000'
button = Button(globalFrame,
borderwidth=1,
text='10^5',
tipText=tipText,
command=self.defaultGlobalScale,
grid=(1, 0))
tipText = 'Click to decrease "-" or increase "+" the global contour scale by small amounts'
frame = ValueRamp(globalFrame,
callback=self.changeGlobalScale,
tipText=tipText)
frame.grid(row=1, column=1, columnspan=3, sticky='e')
row += 1
self.autoFrame = LabelFrame(guiFrame, text='Auto contour levels')
self.autoFrame.grid(row=row, column=0, columnspan=5, sticky='nsew')
self.autoFrame.grid_columnconfigure(1, weight=1)
frow = 0
label = Label(self.autoFrame,
text='Base level:',
grid=(frow, 0),
sticky='e')
tipText = 'The first contour level (closest to zero) for an automated series of levels: the start of a geometric or arithmetic series defining levels'
self.base_entry = FloatEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
command = lambda: self.changeBaseLevel(0.5)
tipText = 'Lower the base contour level so that it is half of the previous value; moving the series of contour levels closer to zero'
button = Button(self.autoFrame,
borderwidth=1,
text='/2',
tipText=tipText,
command=command,
grid=(frow, 2),
sticky='ew')
command = lambda: self.changeBaseLevel(2.0)
tipText = 'Raise the base contour level so that it is double the previous value; moving the series of contour levels further from zero'
button = Button(self.autoFrame,
borderwidth=1,
text='*2',
tipText=tipText,
command=command,
grid=(frow, 3),
sticky='ew')
tipText = 'Click to decrease "-" or increase "+" the base contour level by small amounts'
frame = ValueRamp(self.autoFrame,
callback=self.changeBaseLevel,
tipText=tipText)
frame.grid(row=frow, column=4, columnspan=3, sticky='ew')
frow += 1
label = Label(self.autoFrame,
text='Number of levels:',
grid=(frow, 0),
sticky='e')
#self.numberEntry = IntEntry(guiFrame, text=numberLevels,
# returnCallback=self.applyAuto)
tipText = 'The number of contour levels to make in the automated series'
self.numberEntry = IntEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
command = lambda w=-1: self.changeNumberLevels(w)
tipText = 'Decrease the number of contour levels in the series by one'
button = Button(self.autoFrame,
borderwidth=1,
text='-1',
tipText=tipText,
command=command,
grid=(frow, 2),
sticky='ew')
command = lambda w=1: self.changeNumberLevels(w)
tipText = 'Increase the number of contour levels in the series by one'
button = Button(self.autoFrame,
borderwidth=1,
text='+1',
tipText=tipText,
command=command,
grid=(frow, 3),
sticky='ew')
n = 4
for w in (5, 10, 15, 20):
tipText = 'Set the number of contour levels in the series to %d' % w
command = lambda w=w: self.setNumberLevels(w)
button = Button(self.autoFrame,
borderwidth=1,
text='%d' % w,
command=command,
grid=(frow, n),
sticky='ew',
tipText=tipText)
n += 1
frow += 1
self.change_label = Label(self.autoFrame,
text='%s:' % multiplier_text,
grid=(frow, 0),
sticky='e')
tipText = 'The multiplication factor (or increment if adding levels) to repetitively apply to the base level to generate the series of levels'
self.change_entry = FloatEntry(self.autoFrame,
returnCallback=self.applyAuto,
width=10,
grid=(frow, 1),
sticky='ew',
tipText=tipText)
self.change_level_buttons = []
n = 2
for w in multiplier_changes:
tipText = 'Set the automated series multiplication factor or increment to %f' % w
command = lambda w=w: self.setChange(w)
button = Button(self.autoFrame,
borderwidth=1,
text=str(w),
command=command,
grid=(frow, n),
sticky='ew',
tipText=tipText)
self.change_level_buttons.append(button)
n += 1
frow += 1
frame = Frame(self.autoFrame,
grid=(frow, 0),
gridSpan=(1, 7),
sticky='ew')
tipTexts = [
'Toggles whether positive contour levels from the automated series will be used. Overrides any manual settings',
'Toggles whether negative contour levels from the automated series will be used. Overrides any manual settings'
]
entries = ('Positive', 'Negative')
selected = (True, False)
self.which_buttons = CheckButtons(frame,
entries,
selected=selected,
select_callback=self.applyAuto,
grid=(0, 0),
sticky='w',
tipTexts=tipTexts)
tipTexts = [
'Set the contour level generation to use a geometric series, starting from the base level and using the specified factor',
'Set the contour level generation to use an arithmetic series, starting from the base level and using the specified increment'
]
entries = ('Multiply levels', 'Add levels')
self.change_mode_buttons = RadioButtons(
frame,
entries,
grid=(0, 1),
sticky='ew',
select_callback=self.modeChanged,
tipTexts=tipTexts)
row += 1
manualFrame = LabelFrame(guiFrame,
text='Positive levels',
grid=(row, 0),
gridSpan=(1, 2))
manualFrame.expandGrid(None, 0)
tipText = 'The positive contour levels that will be used for the spectrum; filled in by the automation or set/modified manually'
self.posLevelsEntry = FloatEntry(manualFrame,
isArray=True,
width=60,
returnCallback=self.applyManual,
tipText=tipText,
grid=(0, 0),
sticky='ew')
row += 1
manualFrame = LabelFrame(guiFrame,
text='Negative levels',
grid=(row, 0),
gridSpan=(1, 2))
manualFrame.expandGrid(None, 0)
tipText = 'The negative contour levels that will be used for the spectrum; filled in by the automation or set/modified manually'
self.negLevelsEntry = FloatEntry(manualFrame,
isArray=True,
width=60,
returnCallback=self.applyManual,
tipText=tipText,
grid=(0, 0),
sticky='ew')
row += 1
tipTexts = [
'Set the spectrum contour levels, updating the display, to the automated series, ignoring any manual edits.',
'Set the spectrum contour levels, updating the display, to the values displayed in the level entry fields'
]
texts = ['Apply Auto Levels', 'Apply Manual Edits']
commands = [self.applyAuto, self.applyManual]
self.buttons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
grid=(row, 0),
gridSpan=(1, 2),
tipTexts=tipTexts)
guiFrame.grid_rowconfigure(row, weight=1)
self.curateNotifiers(self.registerNotify)
self.update()
