def graph(*data,**kwargs):
''' Creates a simple time series graph. Takes the output from getData (a list of Facts).
Alternately, you can pass the same set of parameters that are passed to getData().
Takes an optional elements argument which expresses which elements to show. Also
takes an optional showMissing argument which determines whether missing values (-9999.0)
should be displayed. Also takes an optional lineWidth argument which lets you set lines
heavier or lighter. Example: graph(data,elements=("temp","precip"),showMissing=False).
Returns the plot object in case you want to customize the graph in some way.
'''
from org.jfree.chart import ChartFactory,ChartFrame
from org.jfree.data.time import TimeSeries,TimeSeriesCollection, Minute
from java.awt import BasicStroke
# Were we passed a dataset or parameters for obtaining a dataset?
if len(data) == 3:
station,date,element = data
graph(getData(station,date,element))
return
else:
data = data[0] # unwrap from tuple
showMissing = kwargs.get('showMissing',True)
lineWidth = kwargs.get('lineWidth',2.0)
title = kwargs.get('title',"Time series graph")
elementsToShow = [e.name for e in findElements(kwargs.get('elements',""))]
datasets = {}
for fact in sorted(data):
if fact.value in missingValues and not showMissing: continue
station = str(fact.station.name)
element = fact.element.name
if elementsToShow and element not in elementsToShow: continue
series = station+":"+element
date = fact.datetime
hour = date.getHour()
if fact.subhourlyTime is not None:
subhourlyTime = int(fact.subhourlyTime)
else:
subhourlyTime = 0
if subhourlyTime == 60: # JFreeChart can't handle the 1-60 representation of minute in CRN
subhourlyTime = 0
minute = Minute(subhourlyTime,hour,date.getDay(),date.getMonth()+1,date.getYear()) # JFreeChart's representation of time
if series not in datasets:
datasets[series] = TimeSeries(series)
datasets[series].add(minute,float(fact.value))
timeSeriesCollection = TimeSeriesCollection()
for dataset in datasets.values():
timeSeriesCollection.addSeries(dataset)
chart = ChartFactory.createTimeSeriesChart("", "UTC Date", "Value", timeSeriesCollection, True, True, False)
plot = chart.getPlot()
r = plot.getRenderer()
r.setStroke(BasicStroke(lineWidth))
frame = ChartFrame(title, chart)
frame.pack()
frame.setVisible(True)
return plot
def plot(title, x_label, y_label, *curves):
dataset = XYSeriesCollection()
for legend, curve in curves:
series = XYSeries(legend)
for x, y in curve:
series.add(x, y)
dataset.addSeries(series)
chart = ChartFactory.createXYLineChart(title, x_label, y_label, dataset,
PlotOrientation.VERTICAL, True,
True, False)
frame = ChartFrame(title, chart)
frame.setVisible(True)
frame.setSize(400, 300)
def createHistogram(data):
''' Creates a histogram from a list of arbitrary numerical data in range from 0..1'''
from org.jfree.data.category import DefaultCategoryDataset
from org.jfree.chart import ChartFactory,ChartFrame
from org.jfree.chart.plot import PlotOrientation
from java.lang import Float
numBins=20
datamin = min(data)
datamax = max(data)
#binsize = 1.01 / numBins
bins = {}
for d in data:
binkey = round(d,1)
bin = bins.setdefault(binkey,0)
bins[binkey] = bin + 1
# Create dataset from bins
dataset = DefaultCategoryDataset()
# Ensure that bins exist even if they're empty
i = datamin
while i <= 1.0:
bins.setdefault(round(float(i),1),0)
i += .1
#print "Number of bins:",len(bins)
for bin in sorted(bins):
#print "bin:",bin,type(bin)
dataset.addValue(bins[bin],"","%05.2f"%(bin))
# Create chart from dataset
chart = ChartFactory.createBarChart(
"", # chart title
"Bin", # domain axis label
"Number of occurrences", # range axis label
dataset, # data
PlotOrientation.VERTICAL, # orientation
True, # include legend
True, # tooltips?
False # URLs?
)
plot = chart.getPlot()
plot.getRenderer().setShadowVisible(False)
frame = ChartFrame("Histogram", chart);
frame.pack();
frame.setVisible(True);
return plot
def plot2D(points, Ca, Cb): maxIntensity = 255.0 dataset = XYSeriesCollection() seriesNN = XYSeries(channels[Ca+1]+" -ve "+channels[Cb+1]+" -ve") seriesPP = XYSeries(channels[Ca+1]+" +ve "+channels[Cb+1]+" +ve") seriesNP = XYSeries(channels[Ca+1]+" -ve "+channels[Cb+1]+" +ve") seriesPN = XYSeries(channels[Ca+1]+" +ve "+channels[Cb+1]+" -ve") for p in points: posA = channels[Ca+1] in thresholds and p[Ca]>thresholds[ channels[Ca+1] ] posB = channels[Cb+1] in thresholds and p[Cb]>thresholds[ channels[Cb+1] ] if posA and posB: seriesPP.add(p[Cb], p[Ca]) elif posA: seriesPN.add(p[Cb], p[Ca]) elif posB: seriesNP.add(p[Cb], p[Ca]) else: seriesNN.add(p[Cb], p[Ca]) dataset.addSeries(seriesNN) dataset.addSeries(seriesPN) dataset.addSeries(seriesNP) dataset.addSeries(seriesPP) chart = ChartFactory.createScatterPlot( title+" - "+channels[Cb+1]+" vs "+channels[Ca+1], channels[Cb+1], channels[Ca+1], dataset, PlotOrientation.VERTICAL, False,True,False ) plot = chart.getPlot() plot.getDomainAxis().setRange(Range(0.00, maxIntensity), True, False) plot.getRangeAxis().setRange(Range(0.00, maxIntensity), True, False) renderer = chart.getPlot().getRenderer() renderer.setSeriesPaint(0, Color(64,64,64)) #NN renderer.setSeriesPaint(1, Color(0,255,0)) #PN renderer.setSeriesPaint(2, Color(0,0,255)) #NP renderer.setSeriesPaint(3, Color(0,255,255)) #PP shape = Ellipse2D.Float(-1,-1,3,3) renderer.setSeriesShape(0, shape ) renderer.setSeriesShape(1, shape ) renderer.setSeriesShape(2, shape ) renderer.setSeriesShape(3, shape ) frame = ChartFrame(title+" - "+channels[Cb+1]+" vs "+channels[Ca+1], chart) frame.setSize(800, 800) frame.setLocationRelativeTo(None) frame.setVisible(True)
def graphArbitraryData(data,title=""):
''' Creates a line graph of arbitrary data (as opposed to the rather specific format used by graph()). Pass in a
list of datapoints, each consisting of a 3-part tuple: (x,y,category). If you're only graphing one sort of
data (ie you want a graph with one line), you can pass in any constant for category.
Example (one category):
data = []
for i in range(10):
data.append((i,i*i,0))
graphArbitraryData(data)
Example (multiple categories):
data = []
for i in range(30):
data.append((i,i*i,"squared"))
data.append((i,i*i*i,"cubed"))
graphArbitraryData(data)
'''
from org.jfree.data.category import DefaultCategoryDataset
from org.jfree.chart import ChartFactory, ChartFrame, ChartPanel
from org.jfree.chart.plot import PlotOrientation
from org.jfree.data.xy import XYSeriesCollection, XYSeries
datasets = {} # dict of all series
# First, create the individual series from the data
for item in data:
seriesname = str(item[2])
if seriesname not in datasets:
datasets[seriesname] = XYSeries(seriesname)
datasets[seriesname].add(float(item[0]), float(item[1]));
# Second, add those series to a collection
datasetcollection = XYSeriesCollection()
for key in datasets:
datasetcollection.addSeries(datasets[key])
chart = ChartFactory.createXYLineChart("","","",datasetcollection,PlotOrientation.VERTICAL,True,True,False)
frame = ChartFrame(title, chart);
frame.pack();
frame.setVisible(True);
panel = ChartPanel(chart)
return chart.getPlot()
def histogram(title, values):
dataset = HistogramDataset()
dataset.setType(HistogramType.RELATIVE_FREQUENCY)
#NBINS = int(maths.sqrt(len(values)))
#NBINS = int( (max(values)-min(values))/binW )
NBINS = 64
dataset.addSeries(title, values, NBINS)
chart = ChartFactory.createHistogram(title, "Distance (nm)",
"Relative Frequency", dataset,
PlotOrientation.VERTICAL, False, True,
False)
plot = chart.getXYPlot()
renderer = plot.getRenderer()
renderer.setSeriesPaint(0, Colour.BLUE)
painter = StandardXYBarPainter()
renderer.setBarPainter(painter)
frame = ChartFrame(title, chart)
frame.setSize(1200, 800)
frame.setLocationRelativeTo(None)
frame.setVisible(True)
def measure(stack, cells, nuclei):
time = [ (t-1)*cal.frameInterval for t in range(T+1) ]
cellValues0 = [ 0.0 for t in range(T+1) ]
cellValues1 = [ 0.0 for t in range(T+1) ]
cellAreas0 = [ 0.0 for t in range(T+1) ]
cellAreas1 = [ 0.0 for t in range(T+1) ]
nucleusValues0 = [ 0.0 for t in range(T+1) ]
nucleusValues1 = [ 0.0 for t in range(T+1) ]
nucleusAreas0 = [ 0.0 for t in range(T+1) ]
nucleusAreas1 = [ 0.0 for t in range(T+1) ]
nonNucleusValues0 = [ 0.0 for t in range(T+1) ]
nonNucleusValues1 = [ 0.0 for t in range(T+1) ]
for t in range(1,T+1):
ip = stack.getProcessor(t)
if cells[t] is None:
continue
#subtract background Z from all intensity Z measurements
if cells [t] is None:
print("Nocellsfound" + str(t))
bothCells = ShapeRoi(cells[t][0]).or(ShapeRoi(cells[t][1]))
backRoi = ShapeRoi(Rectangle(0,0,imp.getWidth(),imp.getHeight())).not( bothCells )
ip.setRoi(backRoi)
backMean = ip.getStatistics().mean
ip.setRoi( cells[t][0] )
stats0 = ip.getStatistics()
cellValues0[t] = stats0.mean - backMean
cellAreas0[t] = stats0.area * cal.pixelWidth * cal.pixelHeight
nuc0 = None
for nuc in nuclei[t]:
rect = nuc.getBounds()
nx = int(rect.x+(rect.width/2.0))
ny = int(rect.y+(rect.height/2.0))
if cells[t][0].contains(nx,ny):
nuc0 = nuc
break
if nuc0 is not None:
ip.setRoi( nuc0 )
nucStats0 = ip.getStatistics()
nucleusValues0[t] = nucStats0.mean - backMean
nucleusAreas0[t] = nucStats0.area * cal.pixelWidth * cal.pixelHeight
nuc0.setPosition(0,0,t)
nuc0.setStrokeColor(Color.CYAN)
ol.add(nuc0)
nonnucRoi0 = ShapeRoi(cells[t][0]).not( ShapeRoi(nuc0) )
ip.setRoi( nonnucRoi0 )
nonNucleusValues0[t] = ip.getStatistics().mean - backMean
ip.setRoi( cells[t][1] )
stats1 = ip.getStatistics()
cellValues1[t] = stats1.mean - backMean
cellAreas1[t] = stats1.area * cal.pixelWidth * cal.pixelHeight
nuc1 = None
for nuc in nuclei[t]:
rect = nuc.getBounds()
nx = int(rect.x+(rect.width/2.0))
ny = int(rect.y+(rect.height/2.0))
if cells[t][1].contains(nx,ny):
nuc1 = nuc
break
if nuc1 is not None:
ip.setRoi( nuc1 )
nucStats1 = ip.getStatistics()
nucleusValues1[t] = nucStats1.mean - backMean
nucleusAreas1[t] = nucStats1.area * cal.pixelWidth * cal.pixelHeight
nuc1.setPosition(0,0,t)
nuc1.setStrokeColor(Color.CYAN)
ol.add(nuc1)
nonnucRoi1 = ShapeRoi(cells[t][1]).not( ShapeRoi(nuc1) )
ip.setRoi( nonnucRoi1 )
nonNucleusValues1[t] = ip.getStatistics().mean - backMean
rt = ResultsTable()
rt.showRowNumbers(False)
for t in range(1,T+1):
rt.setValue("Time ("+cal.getTimeUnit()+")", t-1, IJ.d2s(time[t],1))
areaRatio = cellAreas0[t] / cellAreas1[t] if cellAreas0[t]>0 and cellAreas1[t]>0 else 0.0
rt.setValue("Cell 0:Cell 1 Area Ratio", t-1, areaRatio)
nucleusRatio = nucleusValues0[t] / nucleusValues1[t] if nucleusValues0[t]>0 and nucleusValues1[t]>0 else 0.0
rt.setValue("Cell 0:Cell 1 Nucleus Ratio", t-1, nucleusRatio)
nonNucleusRatio = nonNucleusValues0[t] / nonNucleusValues1[t] if nonNucleusValues0[t]>0 and nonNucleusValues1[t]>0 else 0.0
rt.setValue("Cell 0:Cell 1 Non-Nucleus Ratio", t-1, nonNucleusRatio)
nnnRatio0 = nucleusValues0[t] / nonNucleusValues0[t] if nucleusValues0[t]>0 and nonNucleusValues0[t]>0 else 0.0
rt.setValue("Cell 0 Nucleus:Non-Nucleus Ratio", t-1, nnnRatio0)
nnnRatio1 = nucleusValues1[t] / nonNucleusValues1[t] if nucleusValues1[t]>0 and nonNucleusValues1[t]>0 else 0.0
rt.setValue("Cell 1 Nucleus:Non-Nucleus Ratio", t-1, nnnRatio1)
rt.setValue("Cell 0 (red) Area ("+cal.getUnit()+u"\u00b2"+")", t-1, cellAreas0[t])
rt.setValue("Cell 0 Nucleus Area ("+cal.getUnit()+u"\u00b2"+")", t-1, nucleusAreas0[t])
rt.setValue("Cell 0 All", t-1, cellValues0[t])
rt.setValue("Cell 0 Nucleus", t-1, nucleusValues0[t])
rt.setValue("Cell 0 Non-Nucleus", t-1, nonNucleusValues0[t])
rt.setValue("Cell 1 (green) Area ("+cal.getUnit()+u"\u00b2"+")", t-1, cellAreas1[t])
rt.setValue("Cell 1 Nucleus Area ("+cal.getUnit()+u"\u00b2"+")", t-1, nucleusAreas1[t])
rt.setValue("Cell 1 All", t-1, cellValues1[t])
rt.setValue("Cell 1 Nucleus", t-1, nucleusValues1[t])
rt.setValue("Cell 1 Non-Nucleus", t-1, nonNucleusValues1[t])
rt.show(imp.getTitle()+"-Results")
dataset = DefaultXYDataset()
dataset.addSeries( "Cell 0", [time[1:], cellValues0[1:]] )
dataset.addSeries( "Cell 1", [time[1:], cellValues1[1:]] )
dataset.addSeries( "Nucleus 0", [time[1:], nucleusValues0[1:]] )
dataset.addSeries( "Nucleus 1", [time[1:], nucleusValues1[1:]] )
dataset.addSeries( "Non-Nucleus 0", [time[1:], nonNucleusValues0[1:]] )
dataset.addSeries( "Non-Nucleus 1", [time[1:], nonNucleusValues1[1:]] )
chart = ChartFactory.createScatterPlot( imp.getTitle(), "Time ("+cal.getTimeUnit()+")", "Intensity Z", dataset, PlotOrientation.VERTICAL, True,True,False )
plot = chart.getPlot()
plot.setBackgroundPaint(Color(64, 128, 255))
plot.setDomainGridlinePaint(Color.BLACK)
plot.setRangeGridlinePaint(Color.BLACK)
renderer = plot.getRenderer()
legend = LegendItemCollection()
shapeR = 2.0
nucShape = Ellipse2D.Float(-shapeR,-shapeR,shapeR*2,shapeR*2)
nonNucShape = Path2D.Float()
nonNucShape.moveTo(-shapeR,-shapeR)
nonNucShape.lineTo(shapeR,shapeR)
nonNucShape.moveTo(shapeR,-shapeR)
nonNucShape.lineTo(-shapeR,shapeR)
for s in range(dataset.getSeriesCount()):
if s == 0:
renderer.setSeriesLinesVisible(s, True)
renderer.setSeriesShapesVisible(s, False)
renderer.setSeriesStroke(s, BasicStroke(1))
renderer.setSeriesPaint(s, Color.RED)
legend.add( LegendItem("Cell 0", Color.RED) )
elif s == 1:
renderer.setSeriesLinesVisible(s, True)
renderer.setSeriesShapesVisible(s, False)
renderer.setSeriesStroke(s, BasicStroke(1))
renderer.setSeriesPaint(s, Color.GREEN)
legend.add( LegendItem("Cell 1", Color.GREEN) )
elif s == 2:
renderer.setSeriesLinesVisible(s, False)
renderer.setSeriesShapesVisible(s, True)
renderer.setSeriesShape(s, nucShape)
renderer.setSeriesPaint(s, Color.RED)
elif s == 3:
renderer.setSeriesLinesVisible(s, False)
renderer.setSeriesShapesVisible(s, True)
renderer.setSeriesShape(s, nucShape)
renderer.setSeriesPaint(s, Color.GREEN)
elif s == 4:
renderer.setSeriesLinesVisible(s, False)
renderer.setSeriesShapesVisible(s, True)
renderer.setSeriesShape(s, nonNucShape)
renderer.setSeriesPaint(s, Color.RED)
elif s == 5:
renderer.setSeriesLinesVisible(s, False)
renderer.setSeriesShapesVisible(s, True)
renderer.setSeriesShape(s, nonNucShape)
renderer.setSeriesPaint(s, Color.GREEN)
plot.setFixedLegendItems(legend)
frame = ChartFrame(imp.getTitle()+" Z-Normalised Intensity", chart)
frame.pack()
frame.setSize( Dimension(800, 800) )
frame.setLocationRelativeTo(None)
frame.setVisible(True)
def histogram(*data,**kwargs):
''' Creates a histogram. Takes the output from getData (a list of Facts), or alternately the
same parameters that getData() takes. Takes an optional 'numBins=k' argument, where k
specifies the number of bins. Returns the plot object in case you want to customize the
graph in some way. Takes an optional 'title' argument.
'''
# TODO: offset labels.
from org.jfree.data.category import DefaultCategoryDataset
from org.jfree.chart import ChartFactory,ChartFrame
from org.jfree.chart.plot import PlotOrientation
from java.lang import Float
# Were we passed a dataset or parameters for obtaining a dataset?
if len(data) == 3:
station,date,element = data
histogram(getData(station,date,element),**kwargs)
return
else:
data = data[0] # unwrap from tuple
# Find min and max; decide on number of bins
numBins=kwargs.get('numBins',16)
datamin,datamax = _getminmax(data)
binsize = abs((datamax - datamin) / (Decimal(numBins)*Decimal("0.999"))) # divide by .999; otherwise there's always a final bin with one member, the max
if binsize == 0:
raise Exception("Cannot create histogram; all values are equal to "+str(datamin))
title = kwargs.get('title',"Histogram")
# Create bins based on value.
stations = {}
for d in data:
if d.value in missingValues: continue
binkey = round(float(datamin + binsize * int((d.value - datamin) / binsize)),2)
name = d.station.getNameString()+", "+d.element.name
bin = stations.setdefault(name,{}).setdefault(binkey,0)
stations[name][binkey] = bin + 1
# Create dataset from bins
dataset = DefaultCategoryDataset()
for station in stations:
# Ensure that bins exist even if they're empty
i = datamin
while i < datamax:
stations[station].setdefault(round(float(i),2),0)
i += binsize
#print "Number of bins:",len(stations[station])
for bin in sorted(stations[station]):
#print "bin:",bin,type(bin)
dataset.addValue(stations[station][bin],station,Float(bin))
# Create chart from dataset
chart = ChartFactory.createBarChart(
"", # chart title
"Bin", # domain axis label
"Number of occurrences", # range axis label
dataset, # data
PlotOrientation.VERTICAL, # orientation
True, # include legend
True, # tooltips?
False # URLs?
)
plot = chart.getPlot()
plot.getRenderer().setShadowVisible(False)
frame = ChartFrame(title, chart);
frame.pack();
frame.setVisible(True);
return plot
def scatter(data,x=None,y=None,**kwargs):
''' Creates a scatter plot comparing two elements. At minimum, takes a collection of data.
The second and third arguments, if they exist, are treated as the two elements to
compare. If these arguments do not exist, the first two elements in the list are
compared. If an optional regress=True argument is present, superimposes a linear
regression for each series and prints some related info (R-value etc).
Note that scatter plots can be zoomed with the mouse. Returns the plot object in
case you want to customize the graph in some way. Takes an optional showMissing argument
which determines whether missing values (-9999.0) should be displayed.
Examples: scatter(data), scatter(data,"tmin","tmax",regress=True)
'''
from org.jfree.data.xy import XYSeriesCollection,XYSeries
from org.jfree.data import UnknownKeyException
from org.jfree.chart import ChartFactory,ChartFrame
from org.jfree.chart.plot import PlotOrientation,DatasetRenderingOrder
from org.jfree.chart.renderer.xy import XYLineAndShapeRenderer
from java.awt import Color
regress=kwargs.get('regress',False)
showMissing=kwargs.get('showMissing',False)
# Try to be flexible about element parameters
if x is not None: x = findElement(x).name
if y is not None: y = findElement(y).name
# Create a dataset from the data
collection = XYSeriesCollection()
for ob in data.groupedByObservation().items():
key,values = ob
name = str(key[0])
if x==None:
x = values[0].element.name
try:
xFact = (i for i in values if i.element.name == x).next()
except StopIteration: # missing value
continue
xval = xFact.value
if xval in missingValues and not showMissing: continue
if y==None:
try:
y = values[1].element.name
except IndexError:
raise Exception("Error! Your data request returned only 1 value per observation. "
"Must have 2 values to generate a scatter plot.")
try:
yFact = (i for i in values if i.element.name == y).next()
except StopIteration: # missing value
continue
yval = yFact.value
if yval in missingValues and not showMissing: continue
try:
series = collection.getSeries(name)
except UnknownKeyException:
collection.addSeries(XYSeries(name))
series = collection.getSeries(name)
series.add(float(xval),float(yval))
# Create chart from dataset
chart = ChartFactory.createScatterPlot( "", x, y, collection, PlotOrientation.VERTICAL,
True, True, False );
plot = chart.getPlot()
frame = ChartFrame("Scatter Plot", chart);
frame.pack();
frame.setVisible(True);
# Superimpose regression if desired
if regress:
regressioncollection = XYSeriesCollection()
for series in collection.getSeries():
regression = _getregression(series)
x1 = series.getMinX()
y1 = regression.predict(x1)
x2 = series.getMaxX()
y2 = regression.predict(x2)
regressionseries = XYSeries(series.getKey())
regressionseries.add(float(x1),float(y1))
regressionseries.add(float(x2),float(y2))
regressioncollection.addSeries(regressionseries)
print series.getKey(),":"
print " R: %8.4f" % regression.getR()
print " R-squared: %8.4f" % regression.getRSquare()
print " Significance: %8.4f" % regression.getSignificance()
print
plot.setDataset(1,regressioncollection)
regressionRenderer = XYLineAndShapeRenderer(True,False)
plot.setRenderer(1,regressionRenderer)
plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
colors = [0xec0000,0x58b911,0x6886ea,0xedd612,0xa93bb9,0xffb71b,0xe200df,0x1de2b6,0xdc91db,0x383838,0xb09344,0x4ea958,0xd78c9e,0x64008d,0xb0c95b]
mainRenderer = plot.getRenderer(0)
for i in range(collection.getSeriesCount()):
try:
mainRenderer.setSeriesPaint(i,Color(colors[i]))
regressionRenderer.setSeriesPaint(i,Color(colors[i]))
except IndexError: # Finite # of colors in the color array; beyond that let jfreechart pick
break
'''
# Jump through some hoops to ensure regressions are same color as scatters for each series.
# Initially: doesn't work because series are not indexed the same. And I don't see a way
# to get the actual series from the renderer in order to compare names or something.
mainRenderer = plot.getRenderer(0)
print "Renderer is",type(mainRenderer)
index = 0
paint = mainRenderer.lookupSeriesPaint(index)
print "Paint is",type(paint)
while (paint is not None):
print "Setting paint."
regressionRenderer.setSeriesPaint(index,paint)
index += 1
paint = mainRenderer.getSeriesPaint(index)
'''
return plot