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 loadFile(self):
dataHolder = DataHolder()
xDataSet = DatasetFactory.zeros(1,len(self.xData),self.xData)
xDataSet.setName(self.xName)
dataHolder.addDataSet(xDataSet.getName(), xDataSet);
yDataSet = DatasetFactory.zeros(1,len(self.yData),self.yData)
yDataSet.setName(self.yName)
dataHolder.addDataSet(yDataSet.getName(), yDataSet);
return dataHolder
def loadFile(self):
dataHolder = DataHolder()
xDataSet = DatasetFactory.zeros(1, len(self.xData), self.xData)
xDataSet.setName(self.xName)
dataHolder.addDataSet(xDataSet.getName(), xDataSet)
yDataSet = DatasetFactory.zeros(1, len(self.yData), self.yData)
yDataSet.setName(self.yName)
dataHolder.addDataSet(yDataSet.getName(), yDataSet)
return dataHolder
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 _process(self, ds, xoffset=0, yoffset=0):###dsxaxis, dsyaxis): ## assert(dsyaxis is None) # STUB ## assert(dsxaxis is None) # STUB integrator = Integrate2D() dsy, dsx = integrator.value(ds) dsyaxis = DatasetFactory.createRange(dsy.shape[0]) dsxaxis = DatasetFactory.createRange(dsx.shape[0]) gaussian = Gaussian(dsyaxis.min(), dsyaxis.max(), dsyaxis.max()-dsyaxis.min(), (dsyaxis.max()-dsyaxis.min())*(dsy.max()-dsy.min()) ) gaussian.getParameter(2).setLowerLimit(0) if self.maxwidth is not None: gaussian.getParameter(1).setUpperLimit(self.maxwidth) ansy = Fitter.fit(dsyaxis, dsy, GeneticAlg(0.001), [ gaussian, Offset( dsy.min(),dsy.max() ) ] ) # ansy = DataSetFunctionFitter().fit( dsyaxis, dsy, GeneticAlg(.001), [ gaussian, Offset( dsy.min(),dsy.max() ) ] ) # ansy = ansy.functionOutput gaussian = Gaussian(dsxaxis.min(), dsxaxis.max(), dsxaxis.max()-dsxaxis.min(), (dsxaxis.max()-dsxaxis.min())*(dsx.max()-dsx.min()) ) gaussian.getParameter(2).setLowerLimit(0) if self.maxwidth is not None: gaussian.getParameter(1).setUpperLimit(self.maxwidth) try: ansx = fitplot( dsxaxis, dsx, GeneticAlg(.001), [ gaussian, Offset( dsx.min(),dsx.max() ) ] ) except java.lang.Exception: # Probably cannot find Plot_Manager on the finder ansx = Fitter.fit(dsxaxis, dsx, GeneticAlg(0.001), [ gaussian, Offset( dsx.min(),dsx.max() ) ] ) #dsyaxis = dsyaxis.subSampleMean(dsy.dimensions[0]/2) #dsy = dsy.subSampleMean(dsy.dimensions[0]/2) #dsxaxis = dsxaxis.subSampleMean(dsx.dimensions[0]/2) #dsx = dsx.subSampleMean(dsx.dimensions[0]/2) peaky = ansy.getParameters()[0].getValue() fwhmy = ansy.getParameters()[1].getValue() areay = ansy.getParameters()[2].getValue() offsety = ansy.getParameters()[3].getValue() / dsx.shape[0] peakx = ansx.getParameters()[0].getValue() fwhmx = ansx.getParameters()[1].getValue() areax = ansx.getParameters()[2].getValue() offsetx = ansx.getParameters()[3].getValue() / dsy.shape[0] background = (offsetx+offsety)/2. fwhmarea = fwhmy*fwhmx*pi/4 topy = areay / fwhmy topx = areax / fwhmx if xoffset==None: xoffset=0 if yoffset==None: yoffset=0 return background, peakx+xoffset, peaky+yoffset, topx, topy, fwhmx, fwhmy, fwhmarea
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 testPainter(self): line = LinePainter(0, 0 , 0, 1) ds = line.paint(DatasetFactory.zeros(2, 3)) expected = [ [1., 1., 0.], [0., 0., 0.]] self.assertEquals(ds2lofl(ds), expected)
def testRenderShapes(self):
self.testAddShape()
ds = DatasetFactory.zeros(4, 5)
result = self.renderer.renderShapes(ds)
expected = [[1., 1., 0., 0., 0.], [0., 1., 1., 1., 1.],
[0., 1., 0., 0., 1.], [0., 1., 1., 1., 1.]]
self.assertEquals(ds2lofl(result), expected)
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_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 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 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 arange(start, stop=None, step=1, dtype=None):
'''Create a 1D dataset of given type where values range from specified start up to
but not including stop in given steps
Arguments:
start -- optional starting value, defaults to 0
stop -- exclusive stop value
step -- difference between neighbouring values, defaults to 1
dtype -- defaults to None which means the type is inferred from given start, stop, step values
'''
if stop is None:
stop = start
start = 0
dtype = _translatenativetype(dtype)
if dtype is None:
if type(start) is _types.ComplexType or type(stop) is _types.ComplexType or type(step) is _types.ComplexType:
dtype = complex128
elif type(start) is _types.FloatType or type(stop) is _types.FloatType or type(step) is _types.FloatType:
dtype = float64
elif type(start) is _types.IntType or type(stop) is _types.IntType or type(step) is _types.IntType:
dtype = int32
else:
raise ValueError, "Unknown or invalid type of input value"
if dtype == bool:
return None
return _df.createRange(start, stop, step, dtype.value)
def testSimpleCreation(self):
# file = NexusUtils.createNexusFile(self.abspath)
# g = file.getGroup("/ScanFileHolder:NXentry/datasets:NXdata", True)
# lazy = NexusUtils.createLazyWriteableDataset("heading1", Dataset.FLOAT64, [10, 100000], None, None)
# file.createData(g, lazy)
# dataIn = DatasetFactory.createRange(lazy.getSize(), Dataset.FLOAT64)
# dataIn.shape = lazy.getShape()
# lazy.setSlice(None, dataIn, SliceND.createSlice(lazy, None, None))
# file.close()
# os.remove(self.abspath)
# This cannot work as the saved file is _NOT_ a valid SRS format
# sfh.save(AsciiScanFileHolderSaver(self.abspath+"_srs"));
#
dataIn = DatasetFactory.createRange(1000000, Dataset.FLOAT64)
dataIn.shape = [10, 100000]
sfh = ScanFileHolder()
sfh.addDataSet("heading1", dataIn)
# sfh.load(SRSLoader(self.abspath+"_srs"));#@UndefinedVariable
# os.remove(self.abspath)
sfh.save(SimpleNexusSaver(self.abspath))
file = NexusUtils.openNexusFileReadOnly(self.abspath)
g = file.getGroup("/ScanFileHolder:NXentry/datasets:NXdata", False)
dataOut = file.getData(g, "heading1").getDataset().getSlice()
file.close()
if dataIn != dataOut:
self.fail("dataIn != dataOut")
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 renderShapes(self, targetDataset):
# Make a blank data set
# beware bizarre Jython bug where it cannot call correct method with only a shape argument
image = DatasetFactory.zeros(targetDataset.getShape(), Dataset.FLOAT64)
for shapeDict in self.shapesToPaint.values():
for shape in shapeDict.values():
image = shape.paint(image)
return image
def testPainter(self): rect = RectPainter(1, 1, 3, 4) ds = rect.paint(DatasetFactory.zeros(4, 5)) expected = [ [0., 0., 0., 0., 0.], [0., 1., 1., 1., 1.], [0., 1., 0., 0., 1.], [0., 1., 1., 1., 1.]] self.assertEquals(ds2lofl(ds), expected)
def __init__(self, shape=None, dtype=None, buffer=None, copy=False):
# check what buffer is and convert if necessary
if buffer is not None:
self.__dataset = __cvt_jobj(_jinput(buffer), dtype=dtype, copy=copy, force=True)
if shape is not None:
self.__dataset.setShape(asIterable(shape))
else:
dtype = _translatenativetype(dtype)
self.__dataset = _df.zeros(dtype.elements, asIterable(shape), dtype.value)
def testRenderShapes(self): self.testAddShape() ds = DatasetFactory.zeros(4, 5) result = self.renderer.renderShapes(ds) expected = [ [1., 1., 0., 0., 0.], [0., 1., 1., 1., 1.], [0., 1., 0., 0., 1.], [0., 1., 1., 1., 1.]] self.assertEquals(ds2lofl(result), expected)
def testRenderShapesOntoDataset(self):
self.testAddShape()
ds = DatasetFactory.zeros(4, 5)
ds.set(10, (2, 2))
result = self.renderer.renderShapesOntoDataset(ds)
expected = [[-10.0, -10.0, 0.0, 0.0, 0.0],
[0.0, -10.0, -10.0, -10.0, -10.0],
[0.0, -10.0, 10.0, 0.0, -10.0],
[0.0, -10.0, -10.0, -10.0, -10.0]]
self.assertEquals(ds2lofl(result), expected)
def testRenderShapesOntoDataset(self): self.testAddShape() ds = DatasetFactory.zeros(4, 5) ds.set(10, (2, 2)) result = self.renderer.renderShapesOntoDataset(ds) expected = [ [-10.0, -10.0, 0.0, 0.0, 0.0], [0.0, -10.0, -10.0, -10.0, -10.0], [0.0, -10.0, 10.0, 0.0, -10.0], [0.0, -10.0, -10.0, -10.0, -10.0]] self.assertEquals(ds2lofl(result), expected)
def zeros(shape, dtype=float64, elements=None):
'''Create a dataset filled with 0'''
dtype = _translatenativetype(dtype)
if elements is not None:
if type(dtype) is _types.FunctionType:
dtype = dtype(elements)
else:
dtype.elements = elements
elif type(dtype) is _types.FunctionType:
raise ValueError, "Given data-type is a function and needs elements defining"
return _df.zeros(dtype.elements, asIterable(shape), dtype.value)
def linspace(start, stop, num=50, endpoint=True, retstep=False, dtype=None):
'''Create a 1D dataset from start to stop in given number of steps
Arguments:
start -- starting value
stop -- stopping value
num -- number of steps, defaults to 50
endpoint -- if True (default), include the stop value
retstep -- if False (default), do not include the calculated step value as part of return tuple
'''
if not endpoint:
stop = ((num - 1) * stop + start)/num
dtype = _translatenativetype(dtype)
if dtype is None:
dtype = _getdtypefromobj(((start, stop)))
if dtype.value < float64.value:
dtype = float64
if dtype.value >= complex64.value:
dtype = complex128
if type(start) is _types.IntType:
start = start+0j
if type(stop) is _types.IntType:
stop = stop+0j
rresult = _df.createLinearSpace(start.real, stop.real, num, float64.value)
iresult = _df.createLinearSpace(start.imag, stop.imag, num, float64.value)
result = Sciwrap(_dsutils.createCompoundDataset(complex128.value, (rresult, iresult)))
del rresult, iresult
else:
result = Sciwrap(_df.createLinearSpace(start, stop, num, dtype.value))
if retstep:
step = result[1] - result[0]
return (result, step)
else:
return result
def collectData(self): #rawdata = self.pvs['DATA'].cagetArray() if self.determine_data_pv_based_on_zoom: zoom_ordinal = int(float(self.pvs['ZOOM'].caget())) rawdata = self.pv_data[zoom_ordinal].get() else: rawdata = self.pv_data[0].get() data = map(unsign2, rawdata ) self.ds = DatasetFactory.zeros(int(float(self.pvs['HEIGHT'].caget())), int(float(self.pvs['WIDTH'].caget())), data) self.last_image_number += 1 self.last_filename = self._generateCurrentFilename() if self.filepath is not None: self.saveImage(self.last_filename);
def full(shape, fill_value, dtype=None, elements=None):
'''Create a dataset filled with fill_value'''
dtype = _translatenativetype(dtype)
if dtype is None:
dtype = _getdtypefromobj(fill_value)
if elements is not None:
if type(dtype) is _types.FunctionType:
dtype = dtype(elements)
else:
dtype.elements = elements
elif type(dtype) is _types.FunctionType:
raise ValueError, "Given data-type is a function and needs elements defining"
return _df.zeros(dtype.elements, asIterable(shape), dtype.value).fill(fill_value)
def collectData(self):
#rawdata = self.pvs['DATA'].cagetArray()
if self.determine_data_pv_based_on_zoom:
zoom_ordinal = int(float(self.pvs['ZOOM'].caget()))
rawdata = self.pv_data[zoom_ordinal].get()
else:
rawdata = self.pv_data[0].get()
data = map(unsign2, rawdata)
self.ds = DatasetFactory.zeros(int(float(self.pvs['HEIGHT'].caget())),
int(float(self.pvs['WIDTH'].caget())),
data)
self.last_image_number += 1
self.last_filename = self._generateCurrentFilename()
if self.filepath is not None:
self.saveImage(self.last_filename)
def plotWholeData(self, numberOfPoints):
arrayEnergyPGM = self.energyPGM.cagetArrayDouble()
arrayEnergyIDGAP = self.energyIDGAP.cagetArrayDouble()
arrayChannel01 = self.channel01.cagetArrayDouble()
arrayChannel02 = self.channel02.cagetArrayDouble()
arrayChannel03 = self.channel03.cagetArrayDouble()
arrayChannel04 = self.channel04.cagetArrayDouble()
dataSetPGM = DatasetFactory.zeros(numberOfPoints)
for i in range(numberOfPoints):
dataSetPGM.set(arrayEnergyPGM[i], i)
dvp = Plotter()
dvp.plotOver("Data Vector", dataSetPGM.getIndexDataSet(), dataSetPGM)
def logspace(start, stop, num=50, endpoint=True, base=10.0, dtype=None):
'''Create a 1D dataset of values equally spaced on a logarithmic scale'''
if not endpoint:
stop = ((num - 1) * stop + start)/num
dtype = _translatenativetype(dtype)
if complex(start).imag == 0 and complex(stop).imag == 0:
if dtype is None:
dtype = _getdtypefromobj(((start, stop)))
if dtype.value < float64.value:
dtype = float64
return _df.createLogSpace(start, stop, num, base, dtype.value)
else:
result = linspace(start, stop, num, endpoint, False, dtype)
return _maths.power(base, result)
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 plotData(self):
newHead = self.getDataNumbers()
if self.arrayHead >= newHead:
print "No new data added for plotting"
return
self.arrayHead = newHead
#to get new data
arrayEnergyPGM = self.energyPGM.cagetArrayDouble()
arrayEnergyIDGAP = self.energyIDGAP.cagetArrayDouble()
arrayChannel01 = self.channel01.cagetArrayDouble()
arrayChannel02 = self.channel02.cagetArrayDouble()
arrayChannel03 = self.channel03.cagetArrayDouble()
arrayChannel04 = self.channel04.cagetArrayDouble()
dataSetEnergyPGM = DatasetFactory.zeros(newHead)
dataSetEnergyPGM.setName("PGM Energy")
dataSetEnergyIDGAP = DatasetFactory.zeros(newHead)
dataSetEnergyIDGAP.setName("ID Gap Energy")
dataSetChannel01 = DatasetFactory.zeros(newHead)
dataSetChannel01.setName("Channel 1")
dataSetChannel02 = DatasetFactory.zeros(newHead)
dataSetChannel02.setName("Channel 2")
dataSetChannel03 = DatasetFactory.zeros(newHead)
dataSetChannel03.setName("Channel 3")
dataSetChannel04 = DatasetFactory.zeros(newHead)
dataSetChannel04.setName("Channel 4")
for i in range(0, newHead):
#print i, arrayEnergyPGM[i], arrayEnergyIDGAP[i], arrayChannel01[i], arrayChannel02[i], arrayChannel03[i], arrayChannel04[i];
dataSetEnergyPGM[i] = arrayEnergyPGM[i]
dataSetEnergyIDGAP[i] = arrayEnergyIDGAP[i]
dataSetChannel01[i] = arrayChannel01[i]
dataSetChannel02[i] = arrayChannel02[i]
dataSetChannel03[i] = arrayChannel03[i]
dataSetChannel04[i] = arrayChannel04[i]
#print i, arrayEnergyPGM[i], arrayEnergyIDGAP[i], arrayChannel01[i], arrayChannel02[i], arrayChannel03[i], arrayChannel04[i];
dvp = Plotter()
indexDataSet = dataSetEnergyPGM.getIndexDataSet()
#dvp.plot("Data Vector", indexDataSet, [dataSetChannel01, dataSetChannel02, dataSetChannel03, dataSetChannel04]);
dvp.plot("Data Vector", dataSetEnergyPGM, [
dataSetChannel01, dataSetChannel02, dataSetChannel03,
dataSetChannel04
])
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 testSimpleCreation(self):
abspath = os.path.abspath(TestFileFolder + "/1.nxs")
parentPath = os.path.split(abspath)[0]
if not os.path.exists(parentPath):
os.makedirs(parentPath)
file = NexusUtils.createNexusFile(abspath)
g = file.getGroup("/ScanFileHolder:NXentry/datasets:NXdata", True)
lazy = NexusUtils.createLazyWriteableDataset("heading1",
Dataset.FLOAT64,
[10, 100000], None, None)
file.createData(g, lazy)
dataIn = DatasetFactory.createRange(lazy.getSize(), Dataset.FLOAT64)
dataIn.shape = lazy.getShape()
lazy.setSlice(None, dataIn, SliceND.createSlice(lazy, None, None))
file.close()
file = NexusUtils.openNexusFileReadOnly(abspath)
g = file.getGroup("/ScanFileHolder:NXentry/datasets:NXdata", False)
dataOut = file.getData(g, "heading1").getDataset().getSlice()
file.close()
self.assertEqual(dataIn, dataOut)
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 process(self, dataset):
mean = dataset.mean()
return DatasetFactory.createFromObject(mean)
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 zeros_like(a, dtype=None):
z = _df.zeros(a)
if dtype is not None:
dtype = _translatenativetype(dtype)
z = z.cast(dtype.value)
return z
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 ones_like(a, dtype=None):
o = _df.ones(a)
if dtype is not None:
dtype = _translatenativetype(dtype)
o = o.cast(dtype.value)
return o
def ones(shape, dtype=float64):
'''Create a dataset filled with 1'''
dtype = _translatenativetype(dtype)
return _df.ones(dtype.elements, asIterable(shape), dtype.value)
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 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 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."
