class PrintWindowPopup(BasePopup):
"""
**Print Window to Output File**
The purpose of this dialog is to allow the saving of the drawing of
one of the spectrum windows to a file, in one of the following formats:
PostScript (PS), Encapsulated PostScript (EPS) or Portable Document
Format (PDF).
The one window that is being printed out is specified at the top.
There are four tabs. The first one, Options, is the most important.
In particular, it is used to specify the File name. At its simplest
to print out a window you just need to specify the File name, and
then click "Save Print File". But it is likely you will at the very
least want to change some of the settings in the Options tab.
You can specify a Title and a label for the X axis and/or Y axis.
This tab is also used to specify the Paper size (default A4), the
Orientation of the paper (default Portrait), whether the printout
is Color or Black and white (the Style, default Color), and what
the Format is (PS, EPS or PDF, default PS).
The ticks for the rulers can be chosen to be Inside or Outside the
main frame and can be in any combination of the Top, Bottom, Left
or Right side of the main frame. The Tick Font includes the option
of not printing the tick labels at all. The Tick spacing between
the major and minor ticks can be set automatically (so the program
determines it) or manually. For the latter the user has to specify
the Major and Minor spacings in terms of the unit of the display
(normally ppm), and also the number of decimal places for the Tick
labels.
How the main frame fits into the paper is determined by the Scaling
option. The Percentage option just means that the main frame is
scaled by that amount relative to the biggest size it could be and
still fit on the paper. The remaining options are if you want to
specify the cms or inches per unit (normally ppm), or the inverse
of these. In this case it could be the case that the main frame
actually exceeds the size of the paper.
You can also include the Time and Date and/or the File Name in the
printout, and you can specify the font used for this. The same
font is used for the Title and X and Y axis labels, except that
the Title font is 6 pts bigger.
Finally, you can also set the linewidth, in points (the default is 0.1).
The other three tabs provide fine tuning of what is output. In many
cases they can be ignored.
The Spectra tab lets you choose settings for which of the window's
spectra are drawn, in terms of both the positive and negative contours.
This is independent of what is actually drawn on the screen. But you
need to check the "Use below settings when printing" checkbutton if you
want the values specified here to be used rather than the screen settings.
The values in the table are initially set to be the screen values but
afterwards can only be changed manually. Clicking on the "Reset Selected"
button changes the values in the table to the current screen ones.
The Peak Lists tab is similar, except it applies to the peak lists in
the window rather than the spectra. Again, if you want the values in
the table to be used then you need to check the "Use below settings
when printing" checkbutton.
The Region tab is for specifying the region for the x, y and orthogonal
axes, if you do not want to use the regions as seen in the window on the
screen. Again, you have to check "Use override region when printing"
checkbutton to actually have the values in the table be used in the
printout. By default, the override region is set to the current
window region if it is not set already, otherwise it is left to the
previous value unless you click the "Set Region from Window" or the
"Set Width from Window" or the "Set Center from Window" buttons.
And the override region can be specified either using the min and max
values of the region, or the center and width.
"""
def __init__(self, parent, *args, **kw):
self.waiting = False
title='Window : Print Window'
BasePopup.__init__(self, parent=parent, title=title, **kw)
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 administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setOverrideRegion'):
notifyFunc(self.updateAfter, 'ccpnmr.Analysis.AxisRegion', func)
notifyFunc(self.updateAfter, 'ccpnmr.Analysis.SpectrumWindow', 'setUseOverrideRegion')
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindow', func)
notifyFunc(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindowPane', func)
for func in ('addSpectrumWindow', 'removeSpectrumWindow'):
notifyFunc(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindowGroup', func)
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
def changedUseEntry(self, entry):
self.use_entry = entry
self.updateRegionTable()
def resetSpectrum(self):
spectrumWindowViews = self.spectrumTable.currentObjects
analysisSpectra = set()
for spectrumWindowView in spectrumWindowViews:
PrintBasic.setPrintOption(spectrumWindowView, 'PositiveOn', spectrumWindowView.isPosVisible)
PrintBasic.setPrintOption(spectrumWindowView, 'NegativeOn', spectrumWindowView.isNegVisible)
analysisSpectra.add(spectrumWindowView.analysisSpectrum)
for analysisSpectrum in analysisSpectra:
PrintBasic.setPrintOption(analysisSpectrum, 'PositiveColors', analysisSpectrum.posColors)
PrintBasic.setPrintOption(analysisSpectrum, 'NegativeColors', analysisSpectrum.negColors)
self.updateAfter()
def resetPeakList(self):
windowPeakLists = self.peakListTable.currentObjects
analysisPeakLists = set()
for windowPeakList in windowPeakLists:
PrintBasic.setPrintOption(windowPeakList, 'PeaksOn', windowPeakList.isSymbolDrawn)
PrintBasic.setPrintOption(windowPeakList, 'PeakFont', windowPeakList.spectrumWindowView.analysisSpectrum.font)
analysisPeakLists.add(windowPeakList.analysisPeakList)
for analysisPeakList in analysisPeakLists:
PrintBasic.setPrintOption(analysisPeakList, 'PeakColor', analysisPeakList.symbolColor)
self.updateAfter()
def resetSelected(self):
n = self.tabbedFrame.selected
if n == 0:
self.resetSpectrum()
elif n == 1:
self.resetPeakList()
def togglePos(self, spectrumWindowView):
PrintBasic.setPrintOption(spectrumWindowView, 'PositiveOn',
not PrintBasic.getPrintOption(spectrumWindowView, 'PositiveOn', defaultValue=spectrumWindowView.isPosVisible))
self.updateAfter()
def toggleNeg(self, spectrumWindowView):
PrintBasic.setPrintOption(spectrumWindowView, 'NegativeOn',
not PrintBasic.getPrintOption(spectrumWindowView, 'NegativeOn', defaultValue=spectrumWindowView.isNegVisible))
self.updateAfter()
def getPosColor(self, spectrumWindowView):
schemes = getHueSortedColorSchemes(self.analysisProfile)
names = [s.name for s in schemes]
colors = [list(s.colors) for s in schemes]
index = 0
analysisSpec = spectrumWindowView.analysisSpectrum
posColors = list(PrintBasic.getPrintOption(analysisSpec, 'PositiveColors', defaultValue=analysisSpec.posColors))
if posColors in colors:
index = colors.index(posColors)
self.posColorPulldown.setup(names, schemes, index, colors)
def setPosColor(self, *extra):
spectrumWindowView = self.spectrumTable.currentObject
if spectrumWindowView:
analysisSpec = spectrumWindowView.analysisSpectrum
PrintBasic.setPrintOption(analysisSpec, 'PositiveColors', self.posColorPulldown.getObject().colors)
self.updateSpectrumTable()
def getNegColor(self, spectrumWindowView):
schemes = getHueSortedColorSchemes(self.analysisProfile)
names = [s.name for s in schemes]
colors = [list(s.colors) for s in schemes]
index = 0
analysisSpec = spectrumWindowView.analysisSpectrum
negColors = list(PrintBasic.getPrintOption(analysisSpec, 'NegativeColors', defaultValue=analysisSpec.negColors))
if negColors in colors:
index = colors.index(negColors)
self.negColorPulldown.setup(names, schemes, index, colors)
def setNegColor(self, *extra):
spectrumWindowView = self.spectrumTable.currentObject
if spectrumWindowView:
analysisSpec = spectrumWindowView.analysisSpectrum
PrintBasic.setPrintOption(analysisSpec, 'NegativeColors', self.negColorPulldown.getObject().colors)
self.updateSpectrumTable()
def getPeakColor(self, windowPeakList):
color = windowPeakList.analysisPeakList.symbolColor
self.peakColorPulldown.set(color)
def setPeakColor(self, *extra):
windowPeakList = self.peakListTable.currentObject
if windowPeakList:
color = self.peakColorPulldown.getObject()
scheme = self.analysisProfile.findFirstColorScheme(colors=(color,))
if scheme:
color = scheme.name
analysisPeakList = windowPeakList.analysisPeakList
PrintBasic.setPrintOption(analysisPeakList, 'PeakColor', color)
self.updatePeakListTable()
def togglePeaks(self, windowPeakList):
PrintBasic.setPrintOption(windowPeakList, 'PeaksOn',
not PrintBasic.getPrintOption(windowPeakList, 'PeaksOn', defaultValue=windowPeakList.isSymbolDrawn))
self.updateAfter()
def getPeakFont(self, windowPeakList):
if windowPeakList.isAnnotationDrawn:
default = windowPeakList.analysisPeakList.analysisSpectrum.font
else:
default = no_peak_text
font = PrintBasic.getPrintOption(windowPeakList, 'PeakFont', defaultValue=default)
self.fontMenu.set(font)
def setPeakFont(self, windowPeakList):
PrintBasic.setPrintOption(windowPeakList, 'PeakFont', self.fontMenu.getText())
self.updateAfter()
def updateWindows(self, obj=None):
useAll = (self.whichWindows.get() == ACTIVE_OPTIONS[0])
index = 0
windowPane = self.windowPulldown.getObject()
windowPanes = []
names = []
if not windowPane:
application = self.project.application
name = application.getValue(self.analysisProject, keyword='printWindowWindow')
if useAll:
window = self.analysisProject.findFirstSpectrumWindow(name=name)
if window:
windowPane = window.findFirstSpectrumWindowPane()
else:
for window in self.analysisProject.sortedSpectrumWindows():
if isActiveWindow(window):
windowPane = window.findFirstSpectrumWindowPane()
break
else:
window = None
for window in self.analysisProject.sortedSpectrumWindows():
if useAll or isActiveWindow(window):
for windowPane0 in window.sortedSpectrumWindowPanes():
windowPanes.append(windowPane0)
names.append(getWindowPaneName(windowPane0))
if windowPanes:
if windowPane not in windowPanes:
windowPane = windowPanes[0]
index = windowPanes.index(windowPane)
else:
windowPane = None
self.selectWindow(windowPane)
self.windowPulldown.setup(names, windowPanes, index)
def saveFile(self):
windowPane = self.windowPulldown.getObject()
if not windowPane:
return
axisPanels = windowPane.sortedAxisPanels()
aspectRatio = self.getPrintAspectRatio()
pixelWidth = self.totalSize(axisPanels[0])
pixelHeight = aspectRatio*self.totalSize(axisPanels[1])
unitWidth = self.totalOverrideRegion(axisPanels[0])
unitHeight = self.totalOverrideRegion(axisPanels[1])
printFrame = self.printFrame
isOverrideSpectrumSelected = self.overrideSpectrum.isSelected()
if isOverrideSpectrumSelected:
spectrumWindowViews = self.spectrumTable.objectList
# alternatively, spectrumWindowViews = windowPane.spectrumWindowViews
analysisSpectra = set()
for spectrumWindowView in spectrumWindowViews:
spectrumWindowView.printPositive = PrintBasic.getPrintOption(spectrumWindowView, 'PositiveOn', spectrumWindowView.isPosVisible)
spectrumWindowView.printNegative = PrintBasic.getPrintOption(spectrumWindowView, 'NegativeOn', spectrumWindowView.isNegVisible)
analysisSpectra.add(spectrumWindowView.analysisSpectrum)
for analysisSpectrum in analysisSpectra:
analysisSpectrum.printPositiveColors = PrintBasic.getPrintOption(analysisSpectrum, 'PositiveColors', analysisSpectrum.posColors)
analysisSpectrum.printNegativeColors = PrintBasic.getPrintOption(analysisSpectrum, 'NegativeColors', analysisSpectrum.negColors)
isOverridePeakListSelected = self.overridePeakList.isSelected()
if isOverridePeakListSelected:
windowPeakLists = self.peakListTable.objectList
analysisPeakLists = set()
for windowPeakList in windowPeakLists:
windowPeakList.printPeaks = PrintBasic.getPrintOption(windowPeakList, 'PeaksOn', windowPeakList.isSymbolDrawn)
if windowPeakList.isAnnotationDrawn:
default = windowPeakList.analysisPeakList.analysisSpectrum.font
else:
default = no_peak_text
windowPeakList.printFont = PrintBasic.getPrintOption(windowPeakList, 'PeakFont', default)
analysisPeakLists.add(windowPeakList.analysisPeakList)
for analysisPeakList in analysisPeakLists:
analysisPeakList.printColor = PrintBasic.getPrintOption(analysisPeakList, 'PeakColor', analysisPeakList.symbolColor)
xrr = axisPanels[0].findFirstAxisRegion().region
dxx = abs(xrr[0]-xrr[1])
yrr = axisPanels[1].findFirstAxisRegion().region
dyy = abs(yrr[0]-yrr[1])
try:
outputHandler = printFrame.getOutputHandler(pixelWidth, pixelHeight, unitWidth, unitHeight, fonts=printNames)
if not outputHandler:
return
analysisProject = self.analysisProject
major_minor_dict = {}
spacing_choice = PrintBasic.getPrintOption(analysisProject, 'SpacingChoice', spacing_choices[0])
if spacing_choice != spacing_choices[0]:
for attr in ('XMajor', 'XMinor', 'XDecimal',
'YMajor', 'YMinor', 'YDecimal',):
val = PrintBasic.getPrintOption(analysisProject, attr, None)
if val is not None:
major_minor_dict[attr] = val
tick_length_choice = PrintBasic.getPrintOption(analysisProject, 'TickLengthChoice', tick_length_choices[0])
if tick_length_choice != tick_length_choices[0]:
for attr in ('TickMajor', 'TickMinor'):
val = PrintBasic.getPrintOption(analysisProject, attr, None)
if val is not None:
major_minor_dict[attr] = val
windowDraw = WindowDraw(self.parent, windowPane)
PrintBasic.printWindow(windowDraw,
outputHandler,
printFrame.tick_location,
printFrame.tick_placement,
aspectRatio,
printFrame.tick_font,
major_minor_dict)
msg = 'Saved to file "%s"' % printFrame.file_name
showInfo('Success', msg, parent=self)
except IOError, e:
showError('IO Error', str(e), parent=self)
if isOverrideSpectrumSelected:
analysisSpectra = set()
for spectrumWindowView in spectrumWindowViews:
del spectrumWindowView.printPositive
del spectrumWindowView.printNegative
analysisSpectra.add(spectrumWindowView.analysisSpectrum)
for analysisSpectrum in analysisSpectra:
del analysisSpectrum.printPositiveColors
del analysisSpectrum.printNegativeColors
if isOverridePeakListSelected:
analysisPeakLists = set()
for windowPeakList in windowPeakLists:
del windowPeakList.printPeaks
del windowPeakList.printFont
analysisPeakLists.add(windowPeakList.analysisPeakList)
for analysisPeakList in analysisPeakLists:
del analysisPeakList.printColor
class PeakSeparatorGui(BasePopup):
"""
**Separate Merged Peaks Using Peak Models**
The Peak Separator code uses a Markov Chain Monte Carlo search which, using
idealised peak shapes, attempts to deconvolve overlapped peak regions into
their separate constituent peaks.
This routine is also suitable for accurately fitting model shapes to single
peaks in order to calculate precise intensities.
**Options Peak Separator Parameters**
*Min. Number of peaks* is by default set to one, it is not possible to set
this to a value less than one.
*Max. Number of peaks* is by default set to one, increasing this value allows
the search routine to fit more models. The best fit may be found with fewer than
the maximum number models. Higher numbers slow the routine, and setting this
value to 0 allows the routine to (effectively) fit unlimited peaks.
*Only pick positive peaks*. If you are not interested in negative peaks, removing
the possibility of fitting negative peaks can reduce search time.
*Peak Model* fits the spectra with either a Gaussian peak model or a Lorentzian
peak model.
**Options Region**
*Peak List* choose which peak list newly picked peaks should be added to. Peaks
picked using this method will have their details appended with 'PeakSepartor'
so you know where they came from.
*Region Table* shows which area of the current spectrum is about to be searched.
*Add Region*. Once an area of spectra has been highlighted clicking this button
will pass it's details on to the Peak Separator.
*Reset All* will reset all search parameters.
*Separate Peaks* will run the Peak Separator code with your current settings. This
may take a few minutes to run, depending on the size of the spectral region being
searched, the number of peaks being fitted and the speed of your machine. Please
wait while this completes.
After a successful Peak Separation run, the found peaks will be added to the
selected peak list. These peaks intensties (volume) have been found using the
peak model selected.
**Advanced Settings Tab**
*Rate* affects the speed of the Markov Chain Monte Carlo routine. A smaller value
results in longer execution, but possibly higher quality results. The default
setting is deemed sensible for the majority of runs.
*Line Width* offers a finer degree of control over maximum and minimum peak widths
for each dimension. The default values are *very* stupid and could do with
re-checking for each experiment.
*Re-Pick Entire Peak List* if you would like to use the Peak Separator to repick
*every* peak in your peak list, try this option - but note that this may take
a very long time!
"""
def __init__(self, parent, programName='Peak Separator', **kw):
self.parent = parent
self.programName = programName
self.versionInfo = 'Version 0.2'
self.help_url = 'http://www.ccpn.ac.uk/'
self.window = None
self.waiting = False
self.rootWindow = None
# just used for display - PeakSeparator will not see this
self._minSigmaHz = None
self._maxSigmaHz = None
self.customSigma = False
self.rePickPeakList = False
self._sampleStartPpm = None
self._sampleEndPpm = None
try:
self.project = parent.project
except:
pass
self.params = PeakSeparatorParams()
BasePopup.__init__(self,
parent=parent,
title=programName,
location='+100+100',
**kw)
if not self.analysisProject:
print '&&& init: No analysis project found ...'
try:
if parent.argumentServer:
self.argServer = parent.argumentServer
else:
print '&&& init: No argument server found...'
except:
print '&&& init: Test'
###########################################################################
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 administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete'):
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.Experiment', 'setName')
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.DataSource', 'setName')
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
###########################################################################
# update parameters from PS Region
def updateFromRegion(self):
if not self.params.peakList:
print '&&& update from region: Need a peak list'
return
if (self.argServer.parent.currentRegion) == None:
showError('No Region',
'Please select a peak region to be separated')
return
self.rePickPeakList = False
getRegionParams(self.params, argServer=self.argServer)
if not self.customSigma: self.initSigmaParams()
self.setWidgetEntries()
###########################################################################
# update parameters from PS PeakList
def updateFromPeakList(self):
if not self.params.peakList:
print '&&& update from peakList: Need a peak list'
return
getPeakListParams(self.params)
if not self.customSigma: self.initSigmaParams()
self.setWidgetEntries()
###########################################################################
# Run the C library!
def runPeakSeparator(self):
""" run the peak separator """
# hack for Macs - focus isn't always lost on mouse move
# so bind event not always called. Shouldn't affect other OS.
self.applyChange()
if not self.params.peakList:
print '&&& Peak list not yet set'
else:
# SeparatePeakRoutine(self.params, self.params.peakList, routine='pymc' )
SeparatePeakRoutine(self.params,
self.params.peakList,
routine='bayesys')
def runRepickPeaks(self):
""" Run the Peak Separator on entire chosen peak list """
# hack for Macs - focus isn't always lost on mouse move
# so bind event not always called. Shouldn't affect other OS.
self.applyChange()
if not self.params.peakList:
print '&&& Peak list not yet set'
else:
SeparatePeaksInPeakList(self.params)
###########################################################################
def setWidgetEntries(self):
### Page One widgets
self.minPeaksEntry.set(self.params.minAtoms)
self.maxPeaksEntry.set(self.params.maxAtoms)
if self.params.positivePeaks == 1:
self.posPeaksButtons.set('True') # only pick pos peaks
else:
self.posPeaksButtons.set('False')
# do something fancy if different shapes for each dim!
n = self.params.peakShape - 3 # shape is only 3, 4, (5)
self.shapeButtons.setIndex(n)
if self.project is not None:
self.updatePeakListList()
self.updateSpectrumWindow()
if self.params.sampleStart and self.params.peakList:
if not self.rePickPeakList:
objectList = []
textMatrix = []
if len(self.params.samplePpmStart) != self.params.Ndim: return
for i in range(self.params.Ndim):
dim_entry = []
dim_entry.append('%2d' % (i + 1))
dim_entry.append('%7.3f' % self.params.samplePpmStart[i])
dim_entry.append('%7.3f' % self.params.samplePpmEnd[i])
dim_entry.append('%3d' % self.params.sampleSize[i])
textMatrix.append(dim_entry)
self.regionTable.update(textMatrix=textMatrix,
objectList=objectList)
### Page Two widgets
self.rateEntry.set(self.params.rate)
if self.params.peakList and self.params.Ndim:
textMatrix = []
objectList = []
for i in range(self.params.Ndim):
if self.params.isFreqDim[i]:
dim_entry = []
objectList.append(i)
dim_entry.append('%2d' % (i + 1))
dim_entry.append('%7.3f' % self._minSigmaHz[i])
dim_entry.append('%7.3f' % self._maxSigmaHz[i])
textMatrix.append(dim_entry)
self.lineWidthTable.update(textMatrix=textMatrix,
objectList=objectList)
def applyChange(self, *event):
""" Upon change, add settings to params """
# Page One apply changes
self.params.minAtoms = self.minPeaksEntry.get()
self.params.maxAtoms = self.maxPeaksEntry.get()
if self.posPeaksButtons.get() == 'True': # asked only pick pos peaks
self.params.positivePeaks = 1
else:
self.params.positivePeaks = 0
# do something fancy if different shapes for each dim!
n = self.shapeButtons.getIndex() # shape is only 3, 4, (5)
self.params.peakShape = n + 3
# Page Two apply changes
self.params.rate = float(self.rateEntry.get())
self.updateSigmaParams()
###########################################################################
# Peak list functions provide PeakSeparator some inherited params
def getPeakListList(self):
""" given a spectrum, get list of peak lists """
project = self.project
peakLists = []
for experiment in self.nmrProject.experiments:
for spectrum in experiment.dataSources:
for peakList in spectrum.peakLists:
peakLists.append([
'%s:%s:%d' %
(experiment.name, spectrum.name, peakList.serial),
peakList
])
peakLists.sort()
return peakLists
def updatePeakListList(self):
""" set the peaklist list in the pulldown menu """
peakListData = self.getPeakListList()
index = -1
names = []
peakList = self.params.peakList
if peakListData:
names = [x[0] for x in peakListData]
peakLists = [x[1] for x in peakListData]
if peakList not in peakLists:
peakList = peakLists[0]
index = peakLists.index(peakList)
else:
peakList = None
peakLists = []
if peakList is not self.params.peakList:
self.params.peakList = peakList
self.peakListPulldown.setup(names, peakLists, index)
self.repickListPulldown.setup(names, peakLists, index)
def setRePickPeakList(self, peakList):
""" Set the peak list to be repicked (and hit a Flag) """
self.rePickPeakList = True
self.setPeakList(peakList)
def setManuallyPickPeakList(self, peakList):
""" Set the peak list to add new peaks to (and hit a Flag) """
self.rePickPeakList = False
self.setPeakList(peakList)
def setPeakList(self, peakList):
""" Sets the Peak List """
if peakList is not self.params.peakList:
self.params.peakList = peakList
# # interrogate the peak list and get all the usefull parameters out
self.updateFromPeakList()
self.updateSpectrumWindow()
self.setWidgetEntries()
###########################################################################
# TBD I suspect this is for matching region with peak list, but may be obsolete now
def getSpectrumWindowList(self):
""" get list of windows which spectrum could be in """
windows = {}
if self.params.peakList:
views = getSpectrumViews(self.params.peakList.dataSource)
for view in views:
windows[view.spectrumWindowPane.spectrumWindow] = None
return [[w.name, w] for w in windows.keys()]
def updateSpectrumWindow(self):
""" update the spectrum window """
windowData = self.getSpectrumWindowList()
index = -1
names = []
window = self.rootWindow
if windowData:
names = [x[0] for x in windowData]
windows = [x[1] for x in windowData]
if window not in windows:
window = windows[0]
index = windows.index(window)
else:
window = None
windows = []
if window is not self.rootWindow:
self.rootWindow = window
###########################################################################
# get and set sigma stuff
def setSigmaMin(self, dim):
value = self.editMinSigmaEntry.get()
self._minSigmaHz[dim] = value
# dont go and re-write users settings
self.customSigma = True
# make sure changes are in params object
self.updateSigmaParams(dim)
self.setWidgetEntries()
def getSigmaMin(self, dim):
if dim is not None:
self.editMinSigmaEntry.set(self._minSigmaHz[dim])
def setSigmaMax(self, dim):
value = self.editMaxSigmaEntry.get()
self._maxSigmaHz[dim] = value
# dont go and re-write users settings
self.customSigma = True
# make sure changes are in params object
self.updateSigmaParams(dim)
self.setWidgetEntries()
def getSigmaMax(self, dim):
if dim is not None:
self.editMaxSigmaEntry.set(self._maxSigmaHz[dim])
def updateSigmaParams(self, dim=None):
""" updateSigmaParams Just updates the parameters (params obj) for sigma values.
If dim is None, do this for each dim
"""
dataDimRefs = self.params.dataDimRefs
if not dataDimRefs: return
if not self.params.minSigma or len(
self.params.minSigma) != self.params.Ndim:
self.params.minSigma = [0.] * self.params.Ndim
if not self.params.maxSigma or len(
self.params.maxSigma) != self.params.Ndim:
self.params.maxSigma = [0.] * self.params.Ndim
def updateSigmaParam(dim, dataDimRefs):
""" Convert and update sigma for dim """
if self.params.isFreqDim[dim]:
# note factor of two!
self.params.minSigma[dim] = self.rHz2pnt(
self._minSigmaHz[dim], dataDimRefs[dim]) / 2.
self.params.maxSigma[dim] = self.rHz2pnt(
self._maxSigmaHz[dim], dataDimRefs[dim]) / 2.
else:
self.params.minSigma[dim] = 1.0
self.params.maxSigma[dim] = 1.0
if dim:
updateSigmaParam(dim, dataDimRefs)
else:
for dim in range(self.params.Ndim):
updateSigmaParam(dim, dataDimRefs)
# utility functions for sigma values
def pnt2rHz(self, point, dataDimRef):
""" Point to relative Hz frequency relative to frequency at Zeroeth point
Necessary when (for example) looking for width of peak in Hz
"""
assert point, dataDimRef
sigmaBase = pnt2hz(0, dataDimRef)
sigmaHz = pnt2hz(point, dataDimRef)
return abs(sigmaHz - sigmaBase)
def rHz2pnt(self, freq, dataDimRef):
""" Relative Hz to point frequency relative to frequency at Zeroeth point
Necessary when (for example) looking for width of peak in Hz
"""
assert freq, dataDimRef
sigmaBase = hz2pnt(0, dataDimRef)
sigmaPoint = hz2pnt(freq, dataDimRef)
return abs(sigmaPoint - sigmaBase)
def initSigmaParams(self):
""" Set some initial default values for sigma """
self._minSigmaHz = []
self._maxSigmaHz = []
if self.params.Ndim:
for dim in range(self.params.Ndim):
self._minSigmaHz.append(6.)
self._maxSigmaHz.append(28.)
###########################################################################
def updateAll(self):
self.updateSpectrumWindow()
self.updatePeakListList()
self.waiting = False
def updateAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.updateAll)
class CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
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)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index-2
format = ['PDB','CCPN','CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get()
if not file:
showWarning('Failure','No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append( ('script',script) )
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [ FileType('CING', ['project.xml']),
FileType('All', ['*'])
]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Select CING project file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy,name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'PDB file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir,name,dummy = nTpath( fileName )
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CCPN project XML file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir,name,dummy = nTpath( fileName )
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CYANA fproject file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self ):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self ):
fName = self.projEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open( name=fName, status='old', verbose=False )
#end def
def initPdb(self ):
fName = self.pdbEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open( self.nameEntry.get(), status='new' )
self.project.initPDB( pdbFile=fName, convention = 'PDB' )
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:',geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:',geometry
sys.exit(0) # remove later
class NmrPipePseudoPopup(BasePopup):
pseudoEntries = ('Is Pseudo Expt', 'Is Not Pseudo Expt')
def __init__(self, parent, params, dim, fileName='', *args, **kw):
self.dim = dim
self.params = params
self.fileName = 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
self.template = template
BasePopup.__init__(self,
parent=parent,
title='NMRPipe Pseudo Data',
modal=True,
**kw)
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 loadValues(self):
directory = self.parent.fileSelect.getDirectory()
fileSelectPopup = FileSelectPopup(self,
title='Select Sampled Data File',
dismiss_text='Cancel',
selected_file_must_exist=True,
multiSelect=False,
directory=directory)
fileName = fileSelectPopup.file_select.getFile()
if not fileName:
return
fileObj = open(fileName, 'rU')
data = ''
line = fileObj.readline()
while line:
data += line
line = fileObj.readline()
fileObj.close()
data = re.sub(',\s+', ',', data)
data = re.sub('\s+', ',', data)
data = re.sub(',,', ',', data)
data = re.sub('[^0-9,.\-+eE]', '', data)
self.valueEntry.set(data)
def chooseDirectory(self):
directory = os.path.dirname(self.fileName)
if not directory:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory, show_file=False)
directory = popup.getDirectory()
popup.destroy()
if directory:
self.directoryEntry.set(directory)
def chooseFile(self):
directory = self.directoryEntry.get()
if not directory:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory)
file = popup.getFile()
popup.destroy()
if file:
template = os.path.basename(file)
self.templateEntry.set(template)
def updateParams(self):
params = self.params
if self.pseudoButton.get() == self.pseudoEntries[0]:
npts = self.nptsEntry.get()
params.npts[self.dim] = npts
values = self.valueEntry.get()
try:
params.setSampledDim(self.dim, values)
except ApiError, e:
showError('Set Sampled Dim', e.error_msg, parent=self)
return
params.fixNullDims(ignoreDim=self.dim)
else:
class CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
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)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index - 2
format = ['PDB', 'CCPN', 'CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry,
self.cyanaEntry][i].get()
if not file:
showWarning('Failure', 'No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append(('script', script))
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [FileType('CING', ['project.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Select CING project file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy, name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='PDB file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
if len(fileName) > 0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir, name, dummy = nTpath(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='CCPN project XML file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
if len(fileName) > 0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir, name, dummy = nTpath(fileName)
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='CYANA fproject file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Script file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Script file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self):
fName = self.projEntry.get()
if not os.path.exists(fName):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open(name=fName,
status='old',
verbose=False)
#end def
def initPdb(self):
fName = self.pdbEntry.get()
if not os.path.exists(fName):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open(self.nameEntry.get(), status='new')
self.project.initPDB(pdbFile=fName, convention='PDB')
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [
self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry,
self.nameEntry
]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(
sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:', geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:', geometry
sys.exit(0) # remove later
class BackupProjectPopup(BasePopup):
"""
**Create Automatic Project Backup**
The purpose of this dialog is to allow the user to create backups
of their project automatically. The XML files for the backup go
into a separate directory from the project itself. If the project
directory is called PROJECTDIR then the default for the backup
directory is PROJECTDIR_backup, although that can be changed to
something else in this dialog.
Other than the backup directory, the user can specify the frequency
of the backup, in minutes.
The "Apply Auto Settings" does not have to be applied if the user
has changed the on/off setting or if the user has changed the
Auto-backup frequency and entered a carriage return.
The "Do Immediate Backup" is in case the user wants to do a backup
then and there.
There is no backup for the backup.
"""
on_off_entries = ['on', 'off']
def __init__(self, parent, help_msg='', help_url='', *args, **kw):
self.help_msg = help_msg
self.help_url = help_url
BasePopup.__init__(self, parent=parent, title='Project : Backup', **kw)
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 selectDir(self):
popup = FileSelectPopup(self, show_file=False)
dir = popup.getDirectory()
popup.destroy()
if (dir):
self.dir_entry.set(dir)
self.setDir()
def setDir(self):
directory = self.dir_entry.get()
if not directory:
showWarning('No directory',
'No directory specified, not setting backup directory',
parent=self)
return
if not os.path.abspath(directory):
directory = joinPath(os.getcwd(), directory)
if os.path.exists(directory):
if not os.path.isdir(directory):
showWarning('Path not directory',
'Path "%s" exists but is not a directory' %
directory,
parent=self)
return
else:
if showYesNo(
'Directory does not exist',
'Directory "%s" does not exist, should it be created?' %
directory,
parent=self):
os.mkdir(directory)
else:
showWarning(
'Directory not created',
'Directory "%s" not created so not setting backup directory'
% directory,
parent=self)
return
repository = self.project.findFirstRepository(name='backup')
if not repository:
showWarning(
'No backup repository',
'No backup repository found (something wrong somewhere)',
parent=self)
return
url = repository.url
if url.path != directory:
repository.url = Url(path=normalisePath(directory))
def setFreq(self):
freq = self.freq_entry.get()
if (freq is None):
freq = 0
self.analysisProject.autoBackupFreq = freq
def setInfo(self):
self.setFreq()
self.setDir()
on_off = (self.on_off_buttons.get() == 'on')
self.analysisProject.doAutoBackup = on_off
def applyAuto(self, *event):
self.setInfo()
on_off = self.on_off_buttons.get()
if on_off == 'on':
self.parent.setBackupOn()
else:
self.parent.setBackupOff()
def applyManual(self):
self.setDir()
self.parent.doBackup()
class BrukerPseudoPopup(BasePopup):
def __init__(self, parent, params, dim, *args, **kw):
self.dim = dim
self.params = params
BasePopup.__init__(self, parent=parent, title='Bruker Pseudo Data', modal=True, **kw)
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 loadValues(self):
directory = self.parent.fileSelect.getDirectory()
fileSelectPopup = FileSelectPopup(self, title='Select Sampled Data File',
dismiss_text='Cancel',
selected_file_must_exist=True,
multiSelect=False,
directory=directory)
fileName = fileSelectPopup.file_select.getFile()
fileObj = open(fileName, 'rU')
data = ''
line = fileObj.readline()
while line:
data += line
line = fileObj.readline()
data = re.sub(',\s+', ',', data)
data = re.sub('\s+', ',', data)
data = re.sub(',,', ',', data)
data = re.sub('[^0-9,.\-+eE]', '', data)
self.valueEntry.set(data)
def copyValues(self):
expt = self.pseudoList.getObject()
if expt:
dataDim = getExperimentSampledDim(expt)
values = dataDim.pointValues
self.nptsEntry.set(len(values))
self.valueEntry.set(values)
def updateParams(self):
params = self.params
if self.pseudoButton.get() == self.pseudoEntries[0]:
npts = self.nptsEntry.get()
params.npts[self.dim] = npts
values = self.valueEntry.get()
try:
params.setSampledDim(self.dim, values)
except ApiError, e:
showError('Set Sampled Dim', e.error_msg, parent=self)
return
else:
class WidgetCountPopup(BasePopup):
on_off_entries = ['on', 'off']
def __init__(self, parent, help_msg='', help_url='', *args, **kw):
self.help_msg = help_msg
self.help_url = help_url
BasePopup.__init__(self,
parent=parent,
title='Widget Count',
*args,
**kw)
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 applyAuto(self, *event):
on_off = self.on_off_buttons.get()
if on_off == 'on':
self.setCountOn()
else:
self.setCountOff()
def applyManual(self):
self.doCount()
def setCountOn(self):
self.setCountOff()
freq = self.freq_entry.get()
if freq is not None and freq > 0:
freq *= 1000 # convert from sec to msec
self.alarm_id = self.after(freq, self.doCountAuto)
def setCountOff(self):
if self.alarm_id:
self.after_cancel(self.alarm_id)
self.alarm_id = None
def doCountAuto(self):
if self.on_off_buttons.get() == 'on':
self.doCount()
freq = self.freq_entry.get()
if freq is not None and freq > 0:
freq *= 1000 # convert from sec to msec
self.alarm_id = self.after(freq, self.doCountAuto)
def doCount(self):
count = getWidgetCount(self.root_widget)
self.count_label.set('%d' % count)
