def addRoi(self, x=None, y=None, width=None, height=None, angle=0):
#To get the current GUI situation
guibean = SDAPlotter.getGuiBean(self.panel)
#roi=gbean.get(GuiParameters.ROIDATA)
roi = guibean[GuiParameters.ROIDATA]
roiList = guibean[GuiParameters.ROIDATALIST]
if None in [x, y, width, height, angle]: #No ROI parameter defined.
print "Not enough ROI info defined in the command. Use GUI ROI box selection"
if roi is None: # No ROI selection on the gui
print "Can not add ROI. Please either give ROI five parameters or draw a box in the GUI"
return
else:
roi = RectangularROI(x, y, width, height, angle)
if roiList is None: #No ROI Table on the gui
roiList = RectangularROIList()
roiList.add(roi)
#Update the view with new ROI table
# guibean=GuiBean();
guibean[GuiParameters.ROIDATALIST] = roiList
SDAPlotter.setGuiBean(self.panel, guibean)
self.getRoiTable()
def call(self):
# 1. Register file
if self.pathToRegister:
self.fileRegistrar.registerFile(self.pathToRegister)
# 2. generate position
position = [self.collectionTime]
if self.filepathToReport:
position.append(self.filepathToReport)
processorResults = []
for processor in self.processors:
processorResults += list(
processor.getPosition(self.datasetProvider.getDataset()))
# 3. display image
if self.panelName:
#print "Plotter.plotImage(%r, ...)" % self.panelName
Plotter.plotImage(
self.panelName,
self.renderer.renderShapesOntoDataset(
self.datasetProvider.getDataset()))
if self.panelNameRCP:
#print "RCPPlotter.imagePlot(%r, ...)" % self.panelNameRCP
SDAPlotter.imagePlot(
self.panelNameRCP,
self.renderer.renderShapesOntoDataset(
self.datasetProvider.getDataset()))
metricsResults = [time.time() - self.time_created
] if self.return_performance_metrics else []
return position + metricsResults + processorResults
def plot_viewnexustree(name, tree):
if not isinstance(tree, _h5mgr):
import sys #@Reimport
print >> sys.stderr, "Only tree from loadnexus works for now"
return
# import jyhdf5io._tojavatree as _tojtree
# tree = _tojtree(tree)
_plotter.viewHDF5Tree(name, tree.gettree())
def plot_viewtree(name, tree):
if not isinstance(tree, _h5mgr):
import sys #@Reimport
print >> sys.stderr, "Only tree from loadnexus works for now"
return
# import jyhdf5io._tojavatree as _tojtree
# tree = _tojtree(tree)
_plotter.viewTree(name, tree.gettree())
def imagePlot(self, panel=None):
if panel is None:
panel=self.panel;
da=self.chData.cagetArrayUnsigned();
ds = IntegerDataset.createFromObject(da);
newds=ds.reshape([self.height, self.width]);
SDAPlotter.imagePlot(panel, newds);
def imagePlot0(self, panel=None):
if panel is None:
panel=self.panel;
da=self.chData.cagetArrayByte()
ds = ByteDataset.createFromObject(da);
newds=ds.reshape([self.height, self.width]);
SDAPlotter.imagePlot(panel, newds);
def clearRois(self):
guibean = SDAPlotter.getGuiBean(self.panel)
if GuiParameters.ROIDATALIST in guibean:
#guibean[GuiParameters.ROIDATALIST]=None;
guibean.clear()
SDAPlotter.setGuiBean(self.panel, guibean)
self.roiList = []
self.updateRoiList()
def display(self, fileName):
if fileName is None:
print "Please give a full file name to display";
return;
else:
dataset = self.loadDataset(fileName)
if self.panel:
SDAPlotter.imagePlot(self.panel, dataset);
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
def display(self,file=None):
if file==None:
file = self.getFullFileName()
# self.data.loadPilatusData(file)
self.data.load(PilatusTiffLoader(file));
dataset = self.data.getAxis(0);
if self.panel:
if self.logScale:
SDAPlotter.imagePlot(self.panel, DatasetUtils.lognorm(dataset)); #For RCP GUI
else:
SDAPlotter.imagePlot(self.panel, dataset); #For RCP GUI
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
def display(self, fileName=None):
if fileName is None:
fileName = self.fileName;
self.dataHolder=dnp.io.load(fileName);
dataset = self.dataHolder[0];
if self.panel:
if self.logScale:
SDAPlotter.imagePlot(self.panel, DatasetUtils.lognorm(dataset)); #For RCP GUI
else:
SDAPlotter.imagePlot(self.panel, dataset); #For RCP GUI
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
def display(self, dataset=None):
if dataset is None:
if self.dataset is None:
print "No dataset to display"
return
else:
dataset = self.dataset
if self.panel:
SDAPlotter.imagePlot(self.panel, dataset)
else:
print "No panel set to display"
raise Exception(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
def plot_getdatabean(name):
jdb = _plotter.getDataBean(name)
if jdb is not None:
jgb = jdb.getGuiParameters()
if jgb is not None:
_wrap_gui_bean(jgb, jgb)
return jdb
def display(self, dataset=None):
if dataset is None:
dataset = self.dataset
if dataset is None:
print("No dataset to display")
return
if self.panel:
from uk.ac.diamond.scisoft.analysis import SDAPlotter
SDAPlotter.imagePlot(self.panel, dataset)
else:
print("No panel set to display")
raise ValueError(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
def plot_getdatabean(name):
jdb = _plotter.getDataBean(name)
if jdb is not None:
jgb = jdb.getGuiParameters()
if jgb is not None:
_wrap_gui_bean(jgb, jgb)
return jdb
def imagePlot2(self, panel=None):
if panel is None:
panel=self.panel;
da=self.chData.cagetArrayByte();
#To convert from singed to unsigned
#method 2
da=[x&0xff for x in da]
#method 3
# ds1=array.array('B' [x&0xff for x in ds1] )
ds = IntegerDataset.createFromObject(da);
newds=ds.reshape([self.height, self.width]);
SDAPlotter.imagePlot(panel, newds);
def display(self, retryUntilTimeout=True):
if self.panel_name == None and self.panel_name_rcp == None:
raise Exception("No panel_name or panel_name_rcp set in %s. " +
"Set this or set %s.display_image=False" %
(self.name, self.name))
if self.panel_name:
#print "Plotter.plotImage(%r, ...)" % self.panel_name
Plotter.plotImage(
self.panel_name,
self.renderer.renderShapesOntoDataset(
self.getDataset(retryUntilTimeout)))
if self.panel_name_rcp:
#print "RCPPlotter.imagePlot(%r, ...)" % self.panel_name_rcp
SDAPlotter.imagePlot(
self.panel_name_rcp,
self.renderer.renderShapesOntoDataset(
self.getDataset(retryUntilTimeout)))
def getRoiSelectionBox(self):
#Get current ROI info from the View
guibean = SDAPlotter.getGuiBean(self.panel)
#roi=gbean.get(GuiParameters.ROIDATA)
roi = guibean[GuiParameters.ROIDATA]
if roi is None:
print None
else:
print self.getRoiParameters(roi)
return roi
def display(self, file=None):
if file == None:
file = self.getFullFileName()
# self.data.loadPilatusData(file)
self.data.load(PilatusTiffLoader(file))
dataset = self.data.getAxis(0)
if self.panel:
if self.logScale:
SDAPlotter.imagePlot(self.panel, DatasetUtils.lognorm(dataset))
#For RCP GUI
else:
SDAPlotter.imagePlot(self.panel, dataset)
#For RCP GUI
else:
print "No panel set to display"
raise Exception(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
def display(self, file=None):
if file is None:
file = self.fileName
# self.dataHolder.loadPilatusData(file)
# self.dataHolder.load(PilatusTiffLoader(file));
# dataset = self.dataHolder.getAxis(0);
self.dataHolder = dnp.io.load(file)
dataset = self.dataHolder[0]
if self.panel:
if self.logScale:
SDAPlotter.imagePlot(self.panel, DatasetMaths.lognorm(dataset))
#For RCP GUI
else:
SDAPlotter.imagePlot(self.panel, dataset)
#For RCP GUI
else:
print "No panel set to display"
raise Exception(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
def updateRoiList(self):
guibean = SDAPlotter.getGuiBean(self.panel)
roiList = guibean[GuiParameters.ROIDATALIST]
tempRoiList = []
if not isinstance(
roiList,
RectangularROIList): #No rectangular roi list defined.
return
else:
for roi in roiList:
if isinstance(roi, RectangularROI):
tempRoiList.append(roi)
tempRoiList.sort(key=lambda roi: roi.name)
self.roiList = tempRoiList
def plot_addline(*arg, **kwarg):
_plotter.addPlot(*arg, **kwarg)
def plot_surface(*arg, **kwarg):
_plotter.surfacePlot(*arg, **kwarg)
def plot_updatepoints2d(*arg, **kwarg):
_plotter.scatter2DPlotOver(*arg, **kwarg)
def plot_image(*arg, **kwarg):
_plotter.imagePlot(*arg, **kwarg)
def plot_setupimagegrid(*arg, **kwarg):
_plotter.setupNewImageGrid(*arg, **kwarg)
def plot_updateline(*arg, **kwarg):
_plotter.updatePlot(*arg, **kwarg)
def plot_addstack(*arg, **kwarg):
_plotter.addStackPlot(*arg, **kwarg)
def plot_images(*arg, **kwarg):
_plotter.imagesPlot(*arg, **kwarg)
def plot_setdatabean(name, bean):
gb = bean.getGuiParameters()
_unwrap_gui_bean(gb, gb)
_plotter.setDataBean(name, bean)
def plot_updatestack(*arg, **kwarg):
_plotter.updateStackPlot(*arg, **kwarg)
def plot_image(*arg, **kwarg):
_plotter.imagePlot(*arg, **kwarg)
def plot_addstack(*arg, **kwarg):
_plotter.addStackPlot(*arg, **kwarg)
def plot_stack(*arg, **kwarg):
_plotter.stackPlot(*arg, **kwarg)
def plot_updateline(*arg, **kwarg):
_plotter.updatePlot(*arg, **kwarg)
def plot_line(*arg, **kwarg):
_plotter.plot(*arg, **kwarg)
def plot_setbean(name, bean):
_plotter.setGuiBean(name, _unwrap_gui_bean(bean, _jyguibean()))
def plot_addline(*arg, **kwarg):
_plotter.addPlot(*arg, **kwarg)
def setPlotMode(self, plotmode=GuiPlotMode.TWOD):
# guibean=GuiBean();
guibean = SDAPlotter.getGuiBean(self.panel)
guibean[GuiParameters.PLOTMODE] = plotmode
SDAPlotter.setGuiBean(self.panel, guibean)
def plot_stack(*arg, **kwarg):
_plotter.stackPlot(*arg, **kwarg)
def plot_viewtree(name, tree):
_plotter.viewTree(name, tree._getnative())
def plot_updatestack(*arg, **kwarg):
_plotter.updateStackPlot(*arg, **kwarg)
def plot_getbean(name):
jb = _plotter.getGuiBean(name)
if jb is not None:
return _wrap_gui_bean(jb, _guibean())
return jb
def plot_images(*arg, **kwarg):
_plotter.imagesPlot(*arg, **kwarg)
def plot_scanforimages(*arg, **kwarg):
_plotter.scanForImages(*arg, **kwarg)
def plot_imagetogrid(*arg, **kwarg):
_plotter.plotImageToGrid(*arg, **kwarg)
def plot_points3d(*arg, **kwarg):
_plotter.scatter3DPlot(*arg, **kwarg)
def plot_points2d(*arg, **kwarg):
_plotter.scatter2DPlot(*arg, **kwarg)
def plot_setdatabean(name, bean):
gb = bean.getGuiParameters()
_unwrap_gui_bean(gb, gb)
_plotter.setDataBean(name, bean)
def plot_getdatabean(name):
jdb = _plotter.getDataBean(name)
jgb = jdb.getGuiParameters()
_wrap_gui_bean(jgb)
return jdb
def plot_line(*arg, **kwarg):
_plotter.plot(*arg, **kwarg)
def plot_volume(*arg, **kwarg):
_plotter.volumePlot(*arg, **kwarg)
def plot_points2d(*arg, **kwarg):
_plotter.scatter2DPlot(*arg, **kwarg)
def plot_updatepoints2d(*arg, **kwarg):
_plotter.scatter2DPlotOver(*arg, **kwarg)
def plot_setbean(name, bean):
_plotter.setGuiBean(name, _unwrap_gui_bean(bean, _jyguibean()))
def plot_setupimagegrid(*arg, **kwarg):
_plotter.setupNewImageGrid(*arg, **kwarg)
def ncdredconf(self, detector, **kwords):
"""
if default None passed in no change is made
default is everything off
"""
if detector.lower() == "Waxs".lower():
detector="Waxs"
else:
detector="Saxs"
if not detector in self.settings:
self.settings[detector] = {}
for i in self.options:
if not i in self.settings[detector]:
self.settings[detector][i] = False
if i in kwords:
if kwords[i] == None:
self.settings[detector][i] = False
else:
self.settings[detector][i] = kwords[i]
realdet=ncdutils.getDetectorByType(self.detsystem, detector.upper())
realdetname = realdet.getName()
ncdutils.removeDetectorByName(self.detsystem, detector+" chain")
saxsrc=ReductionChain(detector+" chain", realdetname)
saxsrclist=saxsrc.getChain()
panel=detector+" Plot"
beanbag=SDAPlotter.getGuiBean(panel)
if beanbag == None:
beanbag = {}
sroi = None
if self.is2D(realdet):
if GuiParameters.ROIDATA in beanbag:
roi = beanbag[GuiParameters.ROIDATA]
if isinstance(roi, SectorROI):
sroi = roi
radii = sroi.getRadii()
self.settings[detector]["length"]=int(math.ceil(radii[1]-radii[0]))
self.settings[detector]["disttobeamstop"]=radii[0]
length = self.settings[detector]["length"]
slope = self.settings[detector]["slope"]
intercept = self.settings[detector]["intercept"]
if slope == 0 or slope == False:
axisds=None
else:
axis=[]
pis = realdet.getPixelSize()*1000
d2b = self.settings[detector]["disttobeamstop"]
for i in range(length):
axis.append(float((i+d2b)*pis*slope+intercept))
axisds=DataSet("qaxis", axis)
mask = self.settings[detector]["mask"]
sect = self.settings[detector]["sect"]
if sroi != None:
if sect or isinstance(axisds, DataSet):
start = sroi.getPoint()
realdet.setAttribute("beam_center_x", start[0])
realdet.setAttribute("beam_center_y", start[1])
else:
realdet.setAttribute("beam_center_x", None)
realdet.setAttribute("beam_center_y", None)
cameralength = self.settings[detector]["cameralength"]
if cameralength != False:
realdet.setAttribute("distance", cameralength)
else:
realdet.setAttribute("distance", None)
norm = self.settings[detector]["norm"]
if (norm != False):
saxsnorm=Normalisation(detector+"norm","ignored")
saxsnorm.setCalibChannel(1)
saxsnorm.setCalibName(ncdutils.getDetectorByType(self.detsystem, "CALIB").getName())
saxsrclist.add(saxsnorm)
bg = self.settings[detector]["bg"]
if bg != False:
if os.path.isfile(bg):
saxsbgs=BackgroundSubtraction(detector+"bg","ignored")
sfh=ScanFileHolder()
if (norm>=0):
upstream=detector+"norm.data"
else:
upstream=realdetname+".data"
sfh.load(NexusLoader(bg,[upstream]))
ds=sfh.getAxis(upstream)
saxsbgs.setBackground(ds)
saxsrclist.add(saxsbgs)
else:
print "background file \"%s\" does not exist." % bg
if (sect):
if sroi != None:
saxssect=SectorIntegration(detector+"sect","ignored")
saxssect.setROI(sroi)
if isinstance(axisds, DataSet):
saxssect.setqAxis(axisds)
if (mask):
if not GuiParameters.MASKING in beanbag:
print "no mask defined for %s" % panel
else:
mb=beanbag[GuiParameters.MASKING]
if not isinstance(mb, MaskingBean):
print "no mask defined for %s" % panel
else:
saxssect.setMask(mb.getMask())
saxsrclist.add(saxssect)
else:
print "sector integration requested but no ROI found"
inv = self.settings[detector]["inv"]
if (inv):
saxsinvariant=Invariant(detector+"invariant", "ignored")
saxsrclist.add(saxsinvariant)
aver = self.settings[detector]["aver"]
if (aver):
saxsaver=Average(detector+"average", "ignored")
saxsrclist.add(saxsaver)
self.detsystem.addDetector(saxsrc)
def plot_imagetogrid(*arg, **kwarg):
_plotter.plotImageToGrid(*arg, **kwarg)
def plot_surface(*arg, **kwarg):
_plotter.surfacePlot(*arg, **kwarg)
def plotdata(filename, dataType=MAC, plotPane="DataPlot", Overlay=True):
'''Plot existing data on "MAC, PSD", or "SRS" (if any) Panel, the default is MAC data on DataPlot panel and overlay is True.
syntax:
plotdata(filename,[MAC|SRS|PSD],["MAC"|"Mythen"|"DataPlot"],[True|False])
where:
filename: the filename string in quote.
dataType: the input data types or formats available
MAC - plot MAC data on MAC panel
PSD - plot PSD data on Mythen panel
SRS - plot SRS data on SRS panel
plotPane: the graph panel to display the plot
Overlay:
'True': plot over the exist data on the graph (Default)
'False': clear existing plot data from the graph before plotting new data
'''
print("Data plotting to " + plotPane + " panel, please wait ...")
if dataType == MAC:
sfh = loadMacData(filename)
dataset=sfh.getAxis(1)
dataset.setName(filename)
if Overlay:
Plotter.plotOver(plotPane, sfh.getAxis(0), dataset)
else:
Plotter.plot(plotPane, sfh.getAxis(0), dataset)
elif dataType == SRS:
sfh = loadSRSData(filename)
if Overlay:
Plotter.plotOver(plotPane, sfh.getAxis(0), sfh.getAxis(1))
else:
Plotter.plot(plotPane, sfh.getAxis(0), sfh.getAxis(1))
elif dataType == PSD:
if not str(filename).find("mythen") == -1:
# mythen data file
dataset = loadMythenData(filename)
data=dataset.getCountDataSet()
data.setName(filename)
if Overlay:
Plotter.plotOver(plotPane, dataset.getAngleDataSet(), data)
else:
Plotter.plot(plotPane, dataset.getAngleDataSet(), data)
else:
parts = str(filename).split(File.separator)
name=parts[-1]
names=str(name).split(".")
if representsInt(names[0]):
# Mythen SRS file
for each in loadMythenSRSFile(filename):
dataset = loadMythenData(str(each) + ".dat")
data=dataset.getCountDataSet()
data.setName(each)
if Overlay:
Plotter.plotOver(plotPane, dataset.getAngleDataSet(), data)
else:
Plotter.plot(plotPane, dataset.getAngleDataSet(), data)
else:
dataset = loadMythenData(filename)
data=dataset.getCountDataSet()
data.setName(filename)
if Overlay:
Plotter.plotOver(plotPane, dataset.getAngleDataSet(), data)
else:
Plotter.plot(plotPane, dataset.getAngleDataSet(), data)
elif dataType == RAW:
# mythen raw data file
dataset = loadMythenRawData(filename)
data=DoubleDataset(dataset.getCountArray(), dataset.getCountArray().length)
channeldata=DoubleDataset(dataset.getChannelArray(),dataset.getChannelArray().length)
data.setName(filename)
if Overlay:
Plotter.plotOver(plotPane, channeldata, data)
SDAPlotter.addPlot(plotPane, "", channeldata, data, "delta", "counts")
else:
Plotter.plot(plotPane, channeldata, data)
SDAPlotter.plot(plotPane, "", channeldata, data, "delta", "counts")
else:
print "Data Type is not recognised or supported."
print "Plotting completed."
def plot_getbean(name):
jb = _plotter.getGuiBean(name)
_wrap_gui_bean(jb)
return jb
