class Plot:
WIDTH = 800
HEIGHT = 600
def __init__(self, logger, id, path, compound):
self.logger = logger
self.logger.info("Parsing experiment data")
self.dic, _ = ng.bruker.read(path)
_, self.pdata = ng.bruker.read_pdata("{}/pdata/1/".format(path))
self.logger.info("Experiment data parsed successfully")
self.compound = compound
self.id = SpectrumDB.Create(
id
) # SpectrumDB.Create(hashlib.sha256(self.pdata.tostring()).hexdigest())
def createReferenceLayout(self):
return column(
row(column(self.reference.old), column(self.reference.new)),
row(self.reference.button))
def createPeakPickingLayout(self):
return column(
CustomRow(column(self.peakPicking.manual),
column(self.peakPicking.peak),
hide=True), row(self.peakPicking.dataTable),
row(column(self.peakPicking.deselectButton),
column(self.peakPicking.deleteButton)),
row(self.peakPicking.chemicalShiftReportTitle),
row(self.peakPicking.chemicalShiftReport))
def createIntegrationLayout(self):
return column(
CustomRow(column(self.integration.manual), hide=True),
row(self.integration.dataTable),
row(column(self.integration.deselectButton),
column(self.integration.deleteButton)))
def createMultipletManagerLayout(self):
return column(
CustomRow(column(self.multipletAnalysis.manual), hide=True),
row(self.multipletAnalysis.dataTable),
row(self.multipletAnalysis.title),
row(column(self.multipletAnalysis.classes),
column(self.multipletAnalysis.integral),
column(self.multipletAnalysis.j)),
row(self.multipletAnalysis.delete),
row(self.multipletAnalysis.reportTitle),
row(self.multipletAnalysis.report))
def createTabs(self, tabs):
callback = CustomJS(args=dict(
referenceTool=self.reference.tool,
peakPickingManualTool=self.peakPicking.manualTool,
peakByPeakTool=self.peakPicking.peakTool,
integrationTool=self.integration.tool,
multipletAnalysisTool=self.multipletAnalysis.tool),
code="""
switch(this.active) {
case 0:
referenceTool.active = true;
break;
case 1:
if (!peakByPeakTool.active) {
peakPickingManualTool.active = true;
}
break;
case 2:
integrationTool.active = true;
break;
case 3:
multipletAnalysisTool.active = true;
break;
}
""")
return Tabs(tabs=tabs, width=500, callback=callback, id="tabs")
def draw(self):
try:
referenceLayout = self.createReferenceLayout()
peakPickingLayout = self.createPeakPickingLayout()
integrationLayout = self.createIntegrationLayout()
multipletManagerLayout = self.createMultipletManagerLayout()
referenceTab = Panel(child=referenceLayout, title="Reference")
peakPickingTab = Panel(child=peakPickingLayout,
title="Peak Picking")
integrationTab = Panel(child=integrationLayout,
title="Integration")
multipletAnalysisTab = Panel(child=multipletManagerLayout,
title="Multiplet Analysis")
tabs = self.createTabs([
referenceTab, peakPickingTab, integrationTab,
multipletAnalysisTab
])
curdoc().add_root(
row(
column(
row(self.plot),
row(Div(text=self.compound, id="compoundContainer"))),
column(row(tabs))))
curdoc().title = "NMR Analysis Tool - " + str(self.id)
except NameError:
print("Please create plot first")
def create(self):
self.makePPMScale()
self.newPlot()
self.dataSource = ColumnDataSource(
data=dict(ppm=self.ppmScale, data=self.pdata))
self.reference = Reference(self.logger, self.dataSource)
self.reference.create()
self.reference.draw(self.plot)
self.peakPicking = PeakPicking(self.logger, self.id, self.dic,
self.udic, self.pdata, self.dataSource,
self.reference)
self.peakPicking.create()
self.peakPicking.draw(self.plot)
self.integration = Integration(self.logger, self.id, self.pdata,
self.dataSource, self.reference)
self.integration.create()
self.integration.draw(self.plot)
self.multipletAnalysis = MultipletAnalysis(self.logger, self.id,
self.dic, self.udic,
self.pdata, self.dataSource,
self.peakPicking,
self.integration,
self.reference)
self.multipletAnalysis.create()
self.multipletAnalysis.draw(self.plot)
self.createMeasureJTool()
self.plot.line('ppm', 'data', source=self.dataSource, line_width=2)
# make ppm scale
def makePPMScale(self):
self.udic = ng.bruker.guess_udic(self.dic, self.pdata)
uc = ng.fileiobase.uc_from_udic(self.udic)
self.ppmScale = uc.ppm_scale()
# create a new plot with a title and axis labels
def newPlot(self):
#Constants
xr = Range1d(start=int(max(self.ppmScale) + 1),
end=int(min(self.ppmScale) - 1))
self.plot = figure(x_axis_label='ppm',
x_range=xr,
toolbar=CustomToolbar(),
tools="pan,save,reset",
plot_width=self.WIDTH,
plot_height=self.HEIGHT)
# Remove grid from plot
self.plot.xgrid.grid_line_color = None
self.plot.ygrid.grid_line_color = None
horizontalBoxZoomTool = HorizontalBoxZoomTool()
self.plot.add_tools(horizontalBoxZoomTool)
self.plot.toolbar.active_drag = horizontalBoxZoomTool
fixedWheelZoomTool = FixedWheelZoomTool(dimensions="height")
self.plot.add_tools(fixedWheelZoomTool)
self.plot.toolbar.active_scroll = fixedWheelZoomTool
fixedZoomOutTool = FixedZoomOutTool(factor=0.4)
self.plot.add_tools(fixedZoomOutTool)
hoverTool = HoverTool(tooltips="($x, $y)")
self.plot.add_tools(hoverTool)
def createMeasureJTool(self):
source = ColumnDataSource(data=dict(x=[], y=[]))
label = Label(x=0,
y=0,
text="",
text_color="#000000",
render_mode="css")
self.plot.add_layout(label)
measureJTool = MeasureJTool(label=label,
frequency=getFrequency(self.udic),
id="measureJTool")
self.plot.add_tools(measureJTool)
