def testWithWoblyData(self):
sfh = ScanFileHolder()
sfh.addDataSet('i1', DatasetFactory.createFromObject([10.1,10.4,9.6, 20.1,20.2,19.9, 30,30,30]))
sfh.addDataSet('i2', DatasetFactory.createFromObject([1.09,1.99,3, 1.01,2.099,3, 1,2,3]))
sfh.addDataSet('e1', DatasetFactory.createFromObject([0,.1,.2,.3,.4,.5,.6, .7, .8, .9]))
self.sfhi = SFHInterpolatorWithHashAccess(sfh, {'i1':10, 'i2':0.2}, ('i1','i2'))
self.assertEquals(self.sfhi.lookupDict, {10.0: {3.0: 2, 2.0: 1, 1.0: 0}, 20.0: {3.0: 5, 2.0: 4, 1.0: 3}, 30.0: {3.0: 8, 2.0: 7, 1.0: 6}})
def plotAxisToDataVectorPlot(self, plotName, xColumnName, yColumnName):
print "plotAxisToDataVectorPlot", plotName, xColumnName, yColumnName
xdataset = DatasetFactory.createFromObject(self.getColumn(xColumnName))
xdataset.setName(xColumnName)
ydataset = DatasetFactory.createFromObject(self.getColumn(yColumnName))
ydataset.setName(yColumnName)
if plotName is not None:
Plotter.plot(plotName, xdataset, [ydataset])
def setUp(self):
sfh = ScanFileHolder()
sfh.addDataSet('i1', DatasetFactory.createFromObject([10.1,10.4,9.6, 20.1,20.2,19.9, 30,30,30]))
sfh.addDataSet('i2', DatasetFactory.createFromObject([1.09,1.99,3, 1.01,2.099,3, 1,2,3]))
sfh.addDataSet('e1', DatasetFactory.createFromObject([0,.1,.2,.3,.4,.5,.6, .7, .8, .9]))
self.sfhi = SFHInterpolatorWithHashAccess(sfh, {'i1':10, 'i2':0.2}, ('i1','i2'))
self.sfhs = ScanFileHolderScannable('sfhs', sfh, ('i1','i2'), ('e1',), {'i1':10, 'i2':0.2})
def createSFH():
result = ScanFileHolder()
result.addDataSet('i1', DatasetFactory.createFromObject([0,1,2,3,4,5,6,7,8,9]))
result.addDataSet('i2', DatasetFactory.createFromObject([0,10,20,30,40,50,60,70,80,90]))
result.addDataSet('e1', DatasetFactory.createFromObject([0,.1,.2,.3,.4,.5,.3,.2,.1,0]))
# result.addDataSet('e2', DatasetFactory.createFromObject([0,.1,.2,.3,.4,.5,.3,.2,.1,0])+100)
result.addDataSet('e2', DatasetFactory.createFromObject([100.,100.1,100.2,100.3,100.4,100.5,100.3,100.2,100.1,100.]))
return result
def setUp(self):
self.x = DatasetFactory.createFromObject([
10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22.,
23., 24., 25., 26.
])
self.peak = DatasetFactory.createFromObject([
1., 1.1, 1.5, 2., 3., 5., 7., 9., 11., 9., 7., 5., 3., 2., 1.5,
1.1, 1.
])
#self.dip = DatasetFactory.createFromObject([5.,4.,3.,2.,1.,0.,1.,2.,3.,4.])
self.p = None
def reindet(self, thing):
""" read in detector data you want to view per frame """
try:
#print "opening x"+thing["filename"]+"x"
file = open(thing["filename"], 'rb')
size = thing["x"] * thing["y"]
if (thing["endian"] == 0):
# default big endian/motorola
endstr = ">"
else:
# little endian/intel
endstr = "<"
for i in range(thing["frames"]):
list = unpack(endstr + size.__str__() + 'f',
file.read(size * 4))
ds = DatasetFactory.createFromObject(list)
if thing["x"] > 1 and thing["y"] > 1:
ds.setShape(thing["x"], thing["y"])
ds.setName(
os.path.basename(thing["filename"]) + " frame " +
i.__str__())
self.result.addDataSet(thing["name"] + i.__str__(), ds)
file.close()
self.detectors[thing["name"]] = thing["frames"]
except IOError, message:
print "Warning: Could not read (all of) the " + thing[
"name"] + " data: " + message.__str__()
def readout(self):
if self.ds is None:
if self.verbose:
print "%s.readout() getting..." % self.name
t = time.time()
rawdata = self.pvs['DATA'].cagetArray()
if self.verbose:
dt, t = time.time()-t, time.time()
print "%s.readout() (%fs) sign correction..." % (self.name, dt)
data = map(unsign2, rawdata )
if self.verbose:
dt, t = time.time()-t, time.time()
print "%s.readout() (%fs) creating DataSet..." % (self.name, dt)
self.ds = DatasetFactory.createFromObject(data, [int(float(self.pvs['HEIGHT'].caget())), int(float(self.pvs['WIDTH'].caget()))])
if self.verbose:
dt, t = time.time()-t, time.time()
print "%s.readout() (%fs) saving..." % (self.name, dt)
if self.filepath is not None:
self.saveImage(time.strftime("%Y%m%d%H%M%S.png", time.localtime()))
if self.verbose:
dt, t = time.time()-t, time.time()
print "%s.readout() (%fs) ended" % (self.name, dt)
return self.ds
def asynchronousMoveTo(self, newPos):
'''
Moving the scanner to the newPos,
Moving the flipper to position 0, then read out all detectors: [d00, d01, ... , d0n]
Moving the flipper to position 1, then read out all detectors: [d10, d11, ... , d1n]
...
Moving the flipper to position m, then read out all detectors: [dm0, dm1, ... , dmn]
Create a DataSet that represents the about matirx for analysis
'''
print 'move scanning device...'
self.scanner.moveTo(newPos)
self.readouts = []
self.flipPositionsReadback = []
for flipPos in self.flipPositions:
print 'move ' + self.flipper.getName() + ' to ' + str(flipPos)
self.flipper.moveTo(flipPos)
self.flipPositionsReadback.append(self.flipper.getPosition())
print 'counting'
readoutp = self.countOnce()
self.readouts.append(readoutp)
self.dataset = DatasetFactory.createFromObject(
self.readouts
) #ds is a new DataSet with dimension [numberOfFlipPositions, NumberOfDetectors];
return
def test_process(self):
y = DatasetFactory.createFromObject(
[0, 0, 1, 1.000000001, 1, 1, 0, 1, 0, 0])
cen, height, width = self.p._process(self.x, y)
self.assertAlmostEqual(cen, 14)
self.assertAlmostEqual(height, 1.000000001)
self.assertAlmostEqual(width, 5)
def test_process_ones_max_at_right_edge(self):
y = DatasetFactory.createFromObject(
[0, 0, 0, 0, 0, 0, 0, 1, 1, 1.000000001])
cen, height, width = self.p._process(self.x, y)
self.assertAlmostEqual(cen, 18)
self.assertAlmostEqual(height, 1.000000001)
self.assertAlmostEqual(width, 3)
def getNewEpicsData(self, offset, size):
#To check the head
head = self.getHead()
if offset > head:
# print " No new data available. Offset exceeds Head(" + str(head) + ").";
return False
# print "New data available, Offset does not exceed Head(" + str(head) + ").";
la = []
#To get the waveform data from EPICS
# print "---> Debug: get waveform: start at: " + ctime();
for i in range(self.numberOfDetectors):
# self.data[i]=self.chData[i].cagetArrayDouble();
#TODO: make sure that the self.data[i] is a list
# self.data[i]=self.chData[i].cagetArrayDouble();
self.data[i] = self.chData[i].getController().cagetDoubleArray(
self.chData[i].getChannel(), head + 1)
# print "The type of subarray data from caget is: ", type(self.data[i]);
# print "The subarray data from caget is: ", self.data[i];
la.append(self.data[i])
# print "---> Debug: get waveform: end at: " + ctime();
ds = DatasetFactory.createFromObject(
la) #ds is a new DataSet with dimension [numberOfDetectors, size];
self.dataset = ds
return True
def getCameraData(self): # self.rawData = self.frameData.getController().cagetByteArray(self.frameData.getChannel()); self.width = int(float(self.frameWidth.caget())); self.height = int(float(self.frameHeight.caget())); self.rawData = self.frameData.cagetArrayByte(); #cast the byte array to double array for dataset tempDoubleList = [float(x) for x in self.rawData]; # self.dataset=DataSet.array(self.frameData.cagetArrayDouble()); self.dataset = DatasetFactory.createFromObject(tempDoubleList) self.dataset.shape = [self.height, self.width] # self.data = ScanFileHolder(); # self.data.addDataSet(self.getName(), self.dataset); self.data.setDataSet(self.getName(), self.dataset); return self.dataset;
def _configureNewDatasetProvider(self, wait_for_exposure_callable=None):
def createDatasetProvider(path):
if path == '':
raise IOError(
"Could no load dataset: %s does not have a record of the last file saved"
% self.name)
path = self.replacePartOfPath(path)
if path[0] != '/':
#if relative path then we have to assume it's from the data directory
path = gda.data.PathConstructor.createFromDefaultProperty(
) + "/" + path
self.datasetProvider = LazyDataSetProvider(
path, self.iFileLoader, self.fileLoadTimout,
self.printNfsTimes, wait_for_exposure_callable)
self.logger.debug("datasetProvider is {}", self.datasetProvider)
if self.det.createsOwnFiles():
path = self.getFilepath()
createDatasetProvider(path)
else:
# if not isinstance(dataset, DataSet, gda.device.detector.NXDetectorData):
# raise Exception("If a detector does not write its own files, ProcessingDetectorWrapper %s only works with detectors that readout DataSets.")
dataset = self._readout()
if isinstance(
dataset,
gda.device.detector.NXDetectorDataWithFilepathForSrs):
path = dataset.getFilepath()
self.logger.debug(
"dataset is NXDetectorDataWithFilepathForSrs: {}", dataset)
createDatasetProvider(path)
return
elif isinstance(dataset, gda.device.detector.NXDetectorData):
data = dataset.getNexusTree().getChildNode(1).getChildNode(
1).getData()
dataset = DatasetFactory.createFromObject(data.getBuffer())
dataset.setShape(data.dimensions)
dataset.squeeze()
self.logger.debug("dataset is NXDetectorData: {}", dataset)
else:
self.logger.debug("dataset is neither: {}", dataset)
self.datasetProvider = BasicDataSetProvider(dataset)
self.logger.debug("datasetProvider is {}", self.datasetProvider)
def reincal(self, thing): """ read in calibration data you want to view per channel for all frames """ try: #print "opening x"+thing["filename"]+"x" file=open(thing["filename"],'rb') size=thing["x"]*thing["frames"] if (thing["endian"]==0): # default big endian/motorola endstr=">" else: # little endian/intel endstr="<" list=unpack(endstr+size.__str__()+'f', file.read(size*4)) ds = DatasetFactory.createFromObject(list) if thing["x"] > 1 and thing["frames"] > 1: ds.setShape(thing["x"], thing["frames"]) ds.setName(os.path.basename(thing["filename"])+" all frames") self.result.addDataSet(thing["name"], ds) file.close() self.detectors[thing["name"]]=thing["frames"] except IOError, message: print "Warning: Could not read (all of) the "+thing["name"]+" data: "+message.__str__()
def readout(self):
if self.ds is None:
if self.verbose:
print "%s.readout() getting..." % self.name
t = time.time()
rawdata = self.pvs['DATA'].cagetArray()
if self.verbose:
dt, t = time.time() - t, time.time()
print "%s.readout() (%fs) sign correction..." % (self.name, dt)
data = map(unsign2, rawdata)
if self.verbose:
dt, t = time.time() - t, time.time()
print "%s.readout() (%fs) creating DataSet..." % (self.name,
dt)
self.ds = DatasetFactory.createFromObject(data, [
int(float(self.pvs['HEIGHT'].caget())),
int(float(self.pvs['WIDTH'].caget()))
])
if self.verbose:
dt, t = time.time() - t, time.time()
print "%s.readout() (%fs) saving..." % (self.name, dt)
if self.filepath is not None:
self.saveImage(
time.strftime("%Y%m%d%H%M%S.png", time.localtime()))
if self.verbose:
dt, t = time.time() - t, time.time()
print "%s.readout() (%fs) ended" % (self.name, dt)
return self.ds
def setUp(self): self.p = CenFromSPEC() # -> cen, height, width self.x = DatasetFactory.createFromObject([10.,11.,12.,13.,14.,15.,16.,17.,18.,19.]) self.l = [0, 10, 20, 30, 40]
def setUp(self):
sfh = ScanFileHolder()
sfh.addDataSet('i1', DatasetFactory.createFromObject([10,10,10, 20,20,20, 30,30,30]))
sfh.addDataSet('i2', DatasetFactory.createFromObject([1,2,3, 1,2,3, 1,2,3]))
sfh.addDataSet('e1', DatasetFactory.createFromObject([0,.1,.2,.3,.4,.5,.6, .7, .8, .9]))
self.sfhi = SFHInterpolatorWithHashAccess(sfh, {'i1':1, 'i2':1}, ('i1','i2'))
def test_process_ones_max_at_right_edge(self): y = DatasetFactory.createFromObject([0, 0, 0, 0, 0, 0, 0, 1, 1, 1.000000001]) cen, height, width = self.p._process(self.x, y) self.assertAlmostEqual(cen, 18) self.assertAlmostEqual(height, 1.000000001) self.assertAlmostEqual(width, 3)
def setUp(self):
self.p = CenFromSPEC() # -> cen, height, width
self.x = DatasetFactory.createFromObject(
[10., 11., 12., 13., 14., 15., 16., 17., 18., 19.])
self.l = [0, 10, 20, 30, 40]
def process(self, dataset):
sum = dataset.sum()
return DatasetFactory.createFromObject(sum)
def process(self, dataset):
max = dataset.max(False, False)
return DatasetFactory.createFromObject(max)
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=DatasetFactory.createFromObject(dataset.getCountArray())
channeldata=DatasetFactory.createFromObject(dataset.getChannelArray())
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 setUp(self): self.x = DatasetFactory.createFromObject([10.,11.,12.,13.,14.,15.,16.,17.,18.,19.,20.,21.,22.,23.,24.,25.,26.]) self.peak = DatasetFactory.createFromObject([1.,1.1,1.5,2.,3.,5.,7.,9.,11.,9.,7.,5.,3.,2.,1.5,1.1,1.]) #self.dip = DatasetFactory.createFromObject([5.,4.,3.,2.,1.,0.,1.,2.,3.,4.]) self.p = None
from gda.analysis import RCPPlotter
from uk.ac.diamond.scisoft.analysis.plotserver import GuiBean
from uk.ac.diamond.scisoft.analysis.plotserver import GuiParameters
from org.eclipse.dawnsci.analysis.dataset.roi import RectangularROI, RectangularROIList
from org.eclipse.january.dataset import DatasetFactory
pp = RCPPlotter()
pp.plot("Area Detector", DatasetFactory.createFromObject(range(100)))
#This is used to plot on the PlotView
#d = DataSet.arange(10000)
#d.shape = [100,100]
d = DatasetFactory.createRange(10000)
d.shape = [100, 100]
# or, d = DataSet.arange(10000).reshape((100,100)) in GDA v8.12
pp.imagePlot("Area Detector", d)
#This is used to plot on the ImageExploreView
pp.plotImageToGrid("Image Explorer", DatasetFactory.ones([20, 30]))
pp.plotImageToGrid("Image Explorer", "/home/xr56/temp/p100kImage26455.tif")
#RCPPlotter().plotImageToGrid("Image Explorer","/home/xr56/temp/pilatus100K/p686905.tif")
RCPPlotter().scanForImages("Image Explorer",
"/dls/i06/data/2010/cm1895-1/demoImages")
#ROI
#Get ROI info
def process(self, dataset):
mean = dataset.mean()
return DatasetFactory.createFromObject(mean)
def test_process(self): y = DatasetFactory.createFromObject([0, 0, 1, 1.000000001, 1, 1, 0, 1, 0, 0]) cen, height, width = self.p._process(self.x, y) self.assertAlmostEqual(cen, 14) self.assertAlmostEqual(height, 1.000000001) self.assertAlmostEqual(width, 5)
