class EditFitGraphPopup(BasePopup):
"""
**Analyse Function Curve Fitting to Peak Series Data**
This popup is used to display the fit of a curve, of the displayed equation
type, to data that has been extracted for a group of spectrum peaks from an
NMR series. Precisely which kind of data is being fitted depends on the parent
tool that this popup window was launched from. For example, for the `Follow
Intensity Changes`_ tool the displayed graph is of a time or frequency value
on the "X" axis (e.g. T1) verses peak intensity. For the `Follow Shift
Changes`_ system the plot is for the parameters of the experiment titration on
the "X" axis (e.g concentration) verses chemical shift distance.
The upper graph shows the peak data that was used; the blue points, and the
points of the fitted theoretical curve; red points. The lower table lists the
data points for all of the peaks in the group, to which the data relates.
There will be one peak for each row of the table, and hence point on the "X"
axis. For each data point in the table the corresponding peak from which the
data was extracted may be located with the "Follow in window" option, using
the stated spectrum window and making marker lines as desired. Alternatively,
the peak may be viewed in a table with [Show Peak]
In general operation this system is used to check how well the selected
function curve fits the peak data. The data that is displayed comes from the
analysis tool that launched this popup. Any outliers may be removed using
[Remove Point] (only with good reason) or the peaks themselves may be
corrected if something has gone awry. Given that the display is launched from
the selection of a specific group of peaks from a popup like `Follow Shift
Changes`_ or `Follow Intensity Changes`_ and there are usually several peak
groups that need to be analysed, the [Previous Set] and [Next Set] buttons can
be used to quickly jump to the next peak group and see the next curve in the
analysis results.
.. _`Follow Intensity Changes`: CalcRatesPopup.html
.. _`Follow Shift Changes`: FollowShiftChangesPopup.html
"""
def __init__(self,
parent,
dataFitting,
getXYfunction,
updateFunction,
xLabel,
yLabel,
showObjectFunction=None,
nextSetFunction=None,
prevSetFunction=None,
graphTitle='',
**kw):
self.guiParent = parent
self.getXYfunction = getXYfunction
self.updateFunction = updateFunction
self.nextSetFunction = nextSetFunction
self.prevSetFunction = prevSetFunction
self.dataFitting = dataFitting
self.object = None
self.xLabel = xLabel
self.yLabel = yLabel
self.x = []
self.y = []
self.yFit = []
self.params = ()
self.chiSq = 0
self.method = dataFitting.fitFunction
self.waiting = False
self.noiseLevel = dataFitting.noiseLevel
self.graphTitle = graphTitle
self.windowPane = None
self.mark = None
BasePopup.__init__(self, parent=parent, title='Fit Graph', **kw)
parent.protocol("WM_DELETE_WINDOW", self.close)
def body(self, guiFrame):
guiFrame.grid_columnconfigure(0, weight=1)
row = 0
self.scrolledGraph = ScrolledGraph(guiFrame,
width=400,
height=300,
symbolSize=5,
symbols=['square', 'circle'],
dataColors=['#000080', '#800000'],
lineWidths=[0, 1],
grid=(row, 0))
#self.scrolledGraph.setZoom(0.7)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
label = Label(frame, text='Fitting Function:', grid=(0, 0))
tipText = 'Selects which form of function to fit to the experimental data'
self.methodPulldown = PulldownList(frame,
self.changeMethod,
grid=(0, 1),
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
tipText = 'The effective equation of the final fitted graph, incorporating all parameters'
self.equationLabel = Label(frame,
text='Equation:',
grid=(0, 0),
tipText=tipText)
tipText = 'The error in the fit of the selected parameterised function to the experimental data'
self.errorLabel = Label(frame,
text='Fit Error:',
grid=(0, 1),
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
label = Label(frame, text='Include x origin?:', grid=(0, 0))
tipText = 'Whether to include the x=0 point in the drawing'
self.xOriginSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 1),
selected=False,
tipText=tipText)
label = Label(frame, text='Include y origin?:', grid=(0, 2))
tipText = 'Whether to include the y=0 point in the drawing'
self.yOriginSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 3),
selected=False,
tipText=tipText)
label = Label(frame, text='Include y error?:', grid=(0, 4))
tipText = 'Whether to include the y error bars in the drawing (if these exist)'
self.yErrorSelect = CheckButton(frame,
callback=self.draw,
grid=(0, 5),
selected=False,
tipText=tipText)
row += 1
frame = Frame(guiFrame, grid=(row, 0), sticky='ew')
label = Label(frame, text='Navigation Window:', grid=(0, 0))
tipText = 'Selects which spectrum window will be used for navigating to peak positions'
self.windowPanePulldown = PulldownList(frame,
self.changeWindow,
grid=(0, 1),
tipText=tipText)
label = Label(frame, text='Follow in window?:', grid=(0, 2))
tipText = 'Whether to navigate to the position of the reference peak (for the group), in the selected window'
self.followSelect = CheckButton(frame,
callback=self.windowPaneNavigate,
grid=(0, 3),
selected=False,
tipText=tipText)
label = Label(frame, text='Mark Ref Peak?:', grid=(0, 4))
tipText = 'Whether to put a multi-dimensional cross-mark through the reference peak position, so it can be identified in spectra'
self.markSelect = CheckButton(frame,
callback=None,
tipText=tipText,
grid=(0, 5),
selected=False)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
tipTexts = [
'The number of the data point, in order of increasing X-axis value',
'For each point, the value of the parameter which is varied in the NMR series, e.g. T1, temperature, concentration etc.',
'For each point, the experimental value being fitted, e.g. peak intensity of chemical shift distance',
'The value of the best-fit function at the X-axis location',
'The difference between the experimental (Y-axis) value and the fitted value',
'The error in the experimental (Y-axis) value'
]
headingList = ['Point', 'x', 'y', 'Fitted y', u'\u0394', 'y error']
self.scrolledMatrix = ScrolledMatrix(guiFrame,
headingList=headingList,
callback=self.selectObject,
tipTexts=tipTexts,
grid=(row, 0))
row += 1
tipTexts = [
'Remove the selected data point, optionally removing the underlying peak',
'Show a table of spectrum peaks that correspond to the selected data point'
]
texts = ['Remove Point', 'Show Peak']
commands = [self.removePoint, self.showObject]
if self.prevSetFunction:
texts.append('Previous Set')
tipTexts.append(
'Move to the previous set of fitted values; the next group of peaks, often corresponding to a different residue or resonance'
)
commands.append(self.prevSet)
if self.nextSetFunction:
tipTexts.append(
'Move to the next set of fitted values; the next group of peaks, often corresponding to a different residue or resonance'
)
texts.append('Next Set')
commands.append(self.nextSet)
bottomButtons = UtilityButtonList(guiFrame,
texts=texts,
commands=commands,
helpUrl=self.help_url,
tipTexts=tipTexts,
grid=(row, 0),
doClone=False)
self.removeButton = bottomButtons.buttons[0]
for func in ('__init__', 'delete', 'setName'):
self.registerNotify(self.updateWindows,
'ccpnmr.Analysis.SpectrumWindow', func)
self.update()
def destroy(self):
for func in ('__init__', 'delete', 'setName'):
self.unregisterNotify(self.updateWindows,
'ccpnmr.Analysis.SpectrumWindow', func)
BasePopup.destroy(self)
def nextSet(self):
if self.nextSetFunction:
self.nextSetFunction()
self.windowPaneNavigate()
def prevSet(self):
if self.prevSetFunction:
self.prevSetFunction()
self.windowPaneNavigate()
def windowPaneNavigate(self, event=None):
if self.followSelect.get() and self.dataFitting:
peaks = self.dataFitting.objects
if self.windowPane and peaks:
peak = peaks[int(len(peaks) / 2)]
windowFrame = self.windowPane.getWindowFrame()
windowFrame.gotoPeak(peak)
if self.markSelect.get():
if self.mark and not self.mark.isDeleted:
self.mark.delete()
self.mark = createPeakMark(self.dataFitting.refObject)
def getWindows(self):
peaks = self.scrolledMatrix.objectList
windowPanes = []
if peaks:
peak = peaks[0]
project = peak.root
spectrum = peak.peakList.dataSource
tryWindows = getActiveWindows(project)
for window in tryWindows:
for windowPane in window.sortedSpectrumWindowPanes():
if isSpectrumInWindowPane(windowPane, spectrum):
windowPanes.append(windowPane)
return windowPanes
def changeWindow(self, windowPane):
if windowPane is not self.windowPane:
self.windowPane = windowPane
self.windowPaneNavigate()
def updateWindows(self, window=None):
windowPanes = self.getWindows()
index = -1
names = [getWindowPaneName(wp) for wp in windowPanes]
windowPane = self.windowPane
if windowPanes:
if windowPane not in windowPanes:
windowPane = windowPanes[0]
index = windowPanes.index(windowPane)
if windowPane is not self.windowPane:
self.windowPane = windowPane
self.windowPaneNavigate()
self.windowPanePulldown.setup(names, windowPanes, index)
def showObject(self):
if self.object and (self.object.className == 'Peak'):
peaks = [self.object]
self.guiParent.guiParent.viewPeaks(peaks)
def close(self):
BasePopup.close(self)
def changeMethod(self, index):
if self.dataFitting:
self.method = index
self.dataFitting.fitFunction = self.method
self.updateAfter()
def updateMethods(self, *opt):
n = len(METHOD_NAMES)
if self.method >= n:
self.method = 1
self.methodPulldown.setup(METHOD_NAMES, range(n), self.method)
def selectObject(self, object, row, col):
if object:
self.object = object
self.updateButtons()
def removePoint(self):
if self.object and (len(self.dataFitting.objects) > 2):
self.dataFitting.objects.remove(self.object)
if showYesNo('Query',
'Delete the corresponding %s?' %
(self.object.className),
parent=self):
self.object.delete()
self.updateAfter()
def draw(self, *junk):
title = '%s Function fit %s' % (self.graphTitle,
METHOD_NAMES[self.method])
dataSet1 = []
dataSet2 = []
useErr = self.yErrorSelect.isSelected()
if not useErr:
useErr = None
for i in range(len(self.scrolledMatrix.textMatrix)):
row = self.scrolledMatrix.textMatrix[i]
x = row[1]
y = row[2]
y2 = row[3]
err = useErr and row[5]
dataSet1.append([x, y, err])
dataSet2.append([x, y2])
dataSet1.sort()
dataSet2.sort()
if dataSet1 and dataSet2:
drawOriginX = self.xOriginSelect.isSelected()
drawOriginY = self.yOriginSelect.isSelected()
self.scrolledGraph.update(dataSets=[dataSet1, dataSet2],
xLabel=self.xLabel,
yLabel=self.yLabel,
title=title,
drawOriginX=drawOriginX,
drawOriginY=drawOriginY)
self.scrolledGraph.draw()
def updateAfter(self, *object):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.update)
def update(self,
dataFitting=None,
xLabel=None,
yLabel=None,
graphTitle=None,
force=False):
if (not force) and dataFitting and (self.dataFitting is dataFitting):
if (self.method, self.xLabel, self.yLabel, self.noiseLevel) == \
(self.dataFitting.fitFunction, xLabel, yLabel, self.dataFitting.noiseLevel):
self.waiting = False
return
if dataFitting:
self.dataFitting = dataFitting
self.xLabel = xLabel or self.xLabel
self.yLabel = yLabel or self.yLabel
self.graphTitle = graphTitle or self.graphTitle
if not self.dataFitting:
self.waiting = False
return
else:
dataFitting = self.dataFitting
dataFitting = self.getXYfunction(dataFitting)
if dataFitting.fitFunction is not None:
self.method = dataFitting.fitFunction
self.noiseLevel = dataFitting.noiseLevel or self.noiseLevel
self.updateMethods()
isFitted = dataFitting.fit()
textMatrix = []
objectList = []
if isFitted and self.method:
methodInfo = getFitMethodInfo()[self.method - 1]
textFormat, indices = methodInfo[2]
textParams = [dataFitting.parameters[i] or 0 for i in indices]
equationText = textFormat % tuple(textParams)
errorText = '%4f' % dataFitting.fitError
x = dataFitting.dataX
y = dataFitting.dataY
yFit = dataFitting.fittedY
N = len(x)
err = hasattr(dataFitting, 'dataErr') and dataFitting.dataErr
if not err:
err = None
# wb104: 10 Mar 2014: not sure why the below was here, it isn't needed
#if self.method == 10:
# x = [sqrt(v) for v in x]
data = [(x[i], y[i], yFit[i], y[i] - yFit[i],
dataFitting.objects[i], err and err[i]) for i in range(N)]
data.sort()
for i in range(N):
xi, yi, yFiti, deltai, object, erri = data[i]
textMatrix.append([i + 1, xi, yi, yFiti, deltai, erri])
objectList.append(object)
else:
equationText = 'Equation: <No Fit>'
errorText = '<None>'
x = dataFitting.dataX
y = dataFitting.dataY
for i, x in enumerate(x):
textMatrix.append([i + 1, x, y[i], None, None, None])
objectList.append(dataFitting.objects[i])
self.equationLabel.set('Equation: %s' % equationText)
self.errorLabel.set('Fit Error: %s' % errorText)
self.scrolledMatrix.update(textMatrix=textMatrix,
objectList=objectList)
self.updateWindows()
self.updateButtons()
self.draw()
if self.updateFunction:
self.updateFunction(dataFitting)
self.waiting = False
def updateButtons(self):
if self.object:
self.removeButton.enable()
else:
self.removeButton.disable()
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 CreateShiftListPopup(BasePopup):
help_url = joinPath(getHelpUrlDir(), 'CreateShiftList.html')
def __init__(self, parent, project):
self.project = project
self.peakLists = []
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Create shift list from peak lists',
modal=False,
transient=True)
def body(self, master):
#
# Peaklist setup
#
self.peakListDict = {}
for experiment in self.project.currentNmrProject.sortedExperiments():
for dataSource in experiment.sortedDataSources():
for peakList in dataSource.sortedPeakLists():
peakListLabel = "%s:%s:%d:%s" % (
experiment.name, dataSource.name, peakList.serial,
peakList.name)
self.peakListDict[peakListLabel] = peakList
peakListLabels = self.peakListDict.keys()
peakListLabels.sort()
#
# chemical shift list setup
#
self.shiftListDict = {}
self.shiftListDict['None'] = None
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
shiftListLabel = "%d:%s" % (shiftList.serial, shiftList.name)
self.shiftListDict[shiftListLabel] = shiftList
shiftListLabels = self.shiftListDict.keys()
shiftListLabels.sort()
row = 0
label = Label(master, text="Generation of chemical shift list")
label.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
row += 1
label = Label(master, text="Peak lists:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.peakListBox = ScrolledListbox(master,
width=50,
height=5,
selectmode=Tkinter.MULTIPLE,
initial_list=peakListLabels)
self.peakListBox.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use existing shift list:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.shiftListSelect = PulldownMenu(master, entries=shiftListLabels)
self.shiftListSelect.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(master, text="Use multiple assignments:")
label.grid(row=row, column=0, sticky=Tkinter.W)
self.useAllContribs = CheckButton(master)
self.useAllContribs.grid(row=row, column=1, sticky=Tkinter.W)
#
# Setup the default shift error per nucleus
#
self.defaultShiftError = {}
for (nucl, text, defValue) in [('1H', 'proton', '0.002'),
('13C', 'carbon', '0.1'),
('15N', 'nitrogen', '0.1')]:
row += 1
label = Label(master, text="Default %s shift error:" % text)
label.grid(row=row, column=0, sticky=Tkinter.W)
self.defaultShiftError[nucl] = Entry(master, text=defValue)
self.defaultShiftError[nucl].grid(row=row,
column=1,
sticky=Tkinter.W)
row += 1
texts = ['Create shift list']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, columnspan=2, column=0)
def apply(self):
selectedPeakLists = self.peakListBox.getSelectedItems()
for peakListLabel in selectedPeakLists:
self.peakLists.append(self.peakListDict[peakListLabel])
chemShiftList = self.shiftListDict[self.shiftListSelect.getSelected()]
if not chemShiftList:
chemShiftListName = askString("Enter chemical shift list name",
"New chemical shift list name", '',
self)
else:
chemShiftListName = chemShiftList.name
useAllContribs = self.useAllContribs.isSelected()
defaultShiftError = {}
for nucl in self.defaultShiftError.keys():
defaultShiftError[nucl] = returnFloat(
self.defaultShiftError[nucl].get())
listCreated = createChemShifts(self.peakLists,
guiParent=self.parent,
multiDialog=self.parent.multiDialog,
shiftList=chemShiftList,
useAllContribs=useAllContribs,
defaultShiftError=defaultShiftError,
shiftListName=chemShiftListName)
if listCreated:
showInfo(
"Success",
"Succesfully created a chemical shift list from peaklist(s)")
return True
class ArchiveProjectPopup(BasePopup):
"""
**Archive the Project**
This popup window enables the user to archive the CCPN Project into a gzipped
tar file. By default it only includes the *.xml files which reside in the
project directory. If the "Include *.xml.bak files" check button is checked
then it will also include the *.xml.bak files which reside in the project
directory. If the "Include data files which are in the project directory"
check button is checked then it will also include the binary data files
which reside in the project directory.
**Caveats & Tips**
The archive excludes the reference data *.xml files (quite sensibly).
"""
def __init__(self,
parent,
project,
title='Project : Archive',
callback=None,
help_msg='',
help_url='',
dismiss_text='',
*args,
**kw):
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
BasePopup.__init__(self,
parent=parent,
project=project,
title=title,
*args,
**kw)
def body(self, guiParent):
now = datetime.date.today().strftime('%y%m%d')
filePrefix = '%s_%s' % (self.project.name, now)
projDir = getUserDataPath(self.project)
directory = os.path.dirname(projDir)
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Archive File:')
label.grid(row=row, column=0, sticky=Tkinter.E)
tipText = 'File name (excluding .tgz ending) for archive'
self.fileEntry = Entry(guiParent, text=filePrefix, tipText=tipText)
self.fileEntry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(guiParent, text='.tgz (automatically appended)')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
self.backupCheck = CheckButton(
guiParent,
text='Include *.xml.bak files',
tipText='If checked include *.xml.bak files')
self.backupCheck.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
self.dataCheck = CheckButton(
guiParent,
text='Include data files which are in project directory',
tipText=
'If checked include data files if they are located in project directory'
)
self.dataCheck.grid(row=row, column=1, columnspan=2, sticky=Tkinter.W)
row = row + 1
labelFrame = LabelFrame(guiParent, text='Archive Location')
labelFrame.grid(row=row, column=0, columnspan=3, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
self.dirSelect = FileSelect(labelFrame,
directory=directory,
show_file=False)
self.dirSelect.grid(row=0, column=0, sticky=Tkinter.NSEW)
guiParent.grid_rowconfigure(row, weight=1)
row = row + 1
texts = ['Save']
tipTexts = ['Create archive file']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
def save(self):
filePrefix = self.fileEntry.get()
directory = self.dirSelect.getDirectory()
filePrefix = joinPath(directory, filePrefix)
fileName = filePrefix + '.tgz'
if os.path.exists(fileName):
if not showYesNo('File exists',
'File "%s" exists, overwrite?' % fileName,
parent=self):
return
includeBackups = self.backupCheck.isSelected()
includeData = self.dataCheck.isSelected()
packageProject(self.project, filePrefix, includeBackups, includeData)
class SaveProjectFrame(Frame):
def __init__(self,
guiParent,
project,
callback=None,
help_msg='',
help_url='',
dismiss_text='',
modal=False,
*args,
**kw):
self.project = project
self.callback = callback
self.help_msg = help_msg
self.help_url = help_url
self.dismiss_text = dismiss_text
self.modal = modal
self.did_save = False
Frame.__init__(self, guiParent, *args, **kw)
projDir = Io.getUserDataPath(self.project)
guiParent.grid_columnconfigure(1, weight=1)
row = 0
label = Label(guiParent, text='Project Name:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.proj_name_entry = Entry(
guiParent,
text=self.project.name,
returnCallback=self.updateInfo,
leaveCallback=self.updateInfo,
tipText='The name used for the project save directory')
self.proj_name_entry.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(guiParent, text='Project Directory:')
label.grid(row=row, column=0, sticky=Tkinter.E)
label = self.proj_dir_label = Label(guiParent, text=projDir)
label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
guiParent,
text='Note: Project Directory = Save Location + Project Name')
label.grid(row=row, column=1, sticky=Tkinter.W)
text = 'Save binary data with project'
tipText = 'Copy data files (e.g. for spectra) into new project directory if not already in current project directory: careful, this can take some time'
row = row + 1
self.dataCheckButton = CheckButton(guiParent,
text=text,
tipText=tipText)
self.dataCheckButton.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
guiParent.grid_rowconfigure(row, weight=1)
labelFrame = LabelFrame(guiParent, text='Save Location')
labelFrame.grid(row=row, column=0, columnspan=2, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(0, weight=1)
directory = os.path.dirname(projDir)
self.proj_dir_select = FileSelect(
labelFrame,
directory=directory,
select_dir_callback=self.selectDir,
change_dir_callback=self.updateInfo,
should_change_dir_callback=self.shouldChangeDir,
getRowColor=self.getEntryColor,
show_file=False)
self.proj_dir_select.grid(row=0, column=0, sticky=Tkinter.NSEW)
row = row + 1
texts = ['Save']
tipTexts = ['Save project with specified name in specified directory']
commands = [self.save]
buttons = createDismissHelpButtonList(guiParent,
texts=texts,
tipTexts=tipTexts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url,
dismiss_text=self.dismiss_text,
expands=True)
buttons.grid(row=row, column=0, columnspan=2, sticky=Tkinter.EW)
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
except IOError, e:
showError('Save project', str(e))
class LinkResonancesPopup(TemporaryBasePopup):
help_url = joinPath(getHelpUrlDir(), 'LinkResonances.html')
def __init__(self,
parent,
formatNamesList,
formatNamesDict,
title='Link resonances setup'):
self.guiParent = parent
self.formatNamesList = formatNamesList
self.formatNamesDict = formatNamesDict
self.status = False
TemporaryBasePopup.__init__(self,
parent=parent,
title=title,
modal=False,
transient=False)
def body(self, master):
row = 0
label = Label(master, text='File format reference:')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.menu = PulldownMenu(master, entries=self.formatNamesList)
self.menu.grid(row=row, column=1, sticky=Tkinter.E, ipadx=20)
row = row + 1
label = Label(master, text='Try to link unrecognized atom names')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.linkRes = CheckButton(master, selected=True)
self.linkRes.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Try IUPAC names (as backup)')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.iupacNames = CheckButton(master)
self.iupacNames.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Use ambiguous name information')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.useAmb = CheckButton(master)
self.useAmb.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Complete stereospecific assignment')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.allStereo = CheckButton(master)
self.allStereo.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Force shift merges')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.shiftMerge = CheckButton(master)
self.shiftMerge.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master,
text='Status other atom for all single prochiral atoms')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.allSingleProchiral = PulldownMenu(
master, entries=['Unknown', 'Same information', 'Always ignore'])
self.allSingleProchiral.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
master,
text='Status other atom for all possibly equivalent single atoms')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.allSinglePossEquiv = PulldownMenu(
master, entries=['Unknown', 'Always equivalent', 'Always ignore'])
self.allSinglePossEquiv.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
master,
text=
'Automatically connect ambiguous resonances to stereospecific ones'
)
label.grid(row=row, column=0, sticky=Tkinter.E)
self.connStereo = CheckButton(master)
self.connStereo.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Use minimal number of popups')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.minimalPopups = CheckButton(master)
self.minimalPopups.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(master, text='Verbose output')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.verbose = CheckButton(master, selected=True)
self.verbose.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
label = Label(
master,
text=
'Warning: it is recommended you save your project first,\nin case linkResonances is interrupted (this might corrupt the data).',
fg='red')
label.grid(row=row,
column=0,
columnspan=2,
ipady=15,
sticky=Tkinter.EW)
row = row + 1
texts = ['Link resonances to atoms']
commands = [
self.ok
] # This calls 'ok' in BasePopup, this then calls 'apply' in here
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3)
def apply(self):
self.assignFormat = self.formatNamesDict[self.menu.getSelected()]
self.globalStereoAssign = self.allStereo.isSelected()
self.useIupacMatching = self.iupacNames.isSelected()
self.useLinkResonancePopup = self.linkRes.isSelected()
self.minimalPrompts = self.minimalPopups.isSelected()
self.verbose = self.verbose.isSelected()
self.forceShiftMerge = self.shiftMerge.isSelected()
self.useAmbiguity = self.useAmb.isSelected()
self.autoConnectStereo = self.connStereo.isSelected()
self.setSingleProchiral = self.allSingleProchiral.getSelected()
self.setSinglePossEquiv = self.allSinglePossEquiv.getSelected()
self.status = True
return True
