def testSingleArrayExport(self):
from PyMca5.PyMcaCore import StackBase
from PyMca5.PyMcaCore import McaStackExport
tmpDir = tempfile.gettempdir()
self._h5File = os.path.join(tmpDir, "Array.h5")
data = numpy.arange(3 * 1024).reshape(3, 1024)
McaStackExport.exportStackList([data], self._h5File)
# read back the stack
from PyMca5.PyMcaIO import HDF5Stack1D
stackRead = HDF5Stack1D.HDF5Stack1D([self._h5File],
{"y": "/measurement/detector_00"})
# let's play
sb = StackBase.StackBase()
sb.setStack(stackRead)
# check the data
self.assertTrue(numpy.allclose(data, stackRead.data),
"Incorrect data readout")
def testStackBaseStack1DDataHandling(self):
from PyMca5.PyMcaCore import StackBase
nrows = 50
ncolumns = 100
nchannels = 500
a = numpy.ones((nrows, ncolumns), numpy.float)
referenceData = numpy.zeros((nrows, ncolumns, nchannels), numpy.float)
for i in range(nchannels):
referenceData[:, :, i] = a * i
a = None
mask = numpy.zeros((nrows, ncolumns), numpy.uint8)
mask[20:30, 15:50] = 1
dummyArray = DummyArray(referenceData)
defaultMca = referenceData.sum(axis=0, dtype=numpy.float64).sum(axis=0)
maskedMca = referenceData[mask > 0, :].sum(axis=0)
for fileindex in [0, 1]:
#usually only one file index case is used but
#we test both to have a better coverage
j = 0
for data in [referenceData, dummyArray]:
if j == 0:
dynamic = ""
j = 1
else:
dynamic = "dynamic "
stackBase = StackBase.StackBase()
stackBase.setStack(data, mcaindex=2, fileindex=fileindex)
channels, counts = stackBase.getActiveCurve()[0:2]
self.assertTrue(numpy.allclose(defaultMca, counts),
"Incorrect %sdefault mca" % dynamic)
# set mask
stackBase.setSelectionMask(mask)
self.assertTrue(
numpy.allclose(stackBase.getSelectionMask(), mask),
"Incorrect mask set and get")
# get mca from mask
mcaDataObject = stackBase.calculateMcaDataObject()
self.assertTrue(
numpy.allclose(mcaDataObject.y[0], maskedMca),
"Incorrect %smca from mask calculation" % dynamic)
#get image from roi
i0 = 100
imiddle = 200
i1 = 400
# calculate
imageDict = stackBase.calculateROIImages(i0,
i1,
imiddle=imiddle)
self.assertTrue(
numpy.allclose(imageDict['ROI'], data[:, :,
i0:i1].sum(axis=-1)),
"Incorrect ROI image from %sROI calculation" % dynamic)
self.assertTrue(
numpy.allclose(imageDict['Left'], data[:, :, i0]),
"Incorrect Left image from %sROI calculation" % dynamic)
self.assertTrue(
numpy.allclose(imageDict['Right'], data[:, :, i1 - 1]),
"Incorrect Right image from %sROI calculation" % dynamic)
self.assertTrue(
numpy.allclose(imageDict['Middle'], data[:, :, imiddle]),
"Incorrect Middle image from %sROI calculation" % dynamic)
stackBase = None
data = None
dummyArray = None
referenceData = None
def testStackBaseAverageAndSum(self):
from PyMca5.PyMcaIO import specfilewrapper as specfile
from PyMca5.PyMcaIO import ConfigDict
from PyMca5.PyMcaCore import DataObject
from PyMca5.PyMcaCore import StackBase
from PyMca5.PyMcaPhysics.xrf import FastXRFLinearFit
spe = os.path.join(self.dataDir, "Steel.spe")
cfg = os.path.join(self.dataDir, "Steel.cfg")
sf = specfile.Specfile(spe)
self.assertTrue(len(sf) == 1, "File %s cannot be read" % spe)
self.assertTrue(sf[0].nbmca() == 1, "Spe file should contain MCA data")
y = counts = sf[0].mca(1)
x = channels = numpy.arange(y.size).astype(numpy.float)
sf = None
configuration = ConfigDict.ConfigDict()
configuration.read(cfg)
calibration = configuration["detector"]["zero"], \
configuration["detector"]["gain"], 0.0
initialTime = configuration["concentrations"]["time"]
# create the data
nRows = 5
nColumns = 10
nTimes = 3
data = numpy.zeros((nRows, nColumns, counts.size), dtype=numpy.float)
live_time = numpy.zeros((nRows * nColumns), dtype=numpy.float)
mcaIndex = 0
for i in range(nRows):
for j in range(nColumns):
data[i, j] = counts
live_time[i * nColumns + j] = initialTime * \
(1 + mcaIndex % nTimes)
mcaIndex += 1
# create the stack data object
stack = DataObject.DataObject()
stack.data = data
stack.info = {}
stack.info["McaCalib"] = calibration
stack.info["McaLiveTime"] = live_time
stack.x = [channels]
# let's play
sb = StackBase.StackBase()
sb.setStack(stack)
x, y, legend, info = sb.getStackOriginalCurve()
readCalib = info["McaCalib"]
readLiveTime = info["McaLiveTime"]
self.assertTrue(abs(readCalib[0] - calibration[0]) < 1.0e-10,
"Calibration zero. Expected %f got %f" % \
(calibration[0], readCalib[0]))
self.assertTrue(abs(readCalib[1] - calibration[1]) < 1.0e-10,
"Calibration gain. Expected %f got %f" % \
(calibration[1], readCalib[0]))
self.assertTrue(abs(readCalib[2] - calibration[2]) < 1.0e-10,
"Calibration 2nd order. Expected %f got %f" % \
(calibration[2], readCalib[2]))
self.assertTrue(
abs(live_time.sum() - readLiveTime) < 1.0e-5,
"Incorrect sum of live time data")
mask = sb.getSelectionMask()
if mask is None:
mask = numpy.zeros((nRows, nColumns), dtype=numpy.uint8)
mask[2, :] = 1
mask[0, 0:2] = 1
live_time.shape = mask.shape
sb.setSelectionMask(mask)
mcaObject = sb.calculateMcaDataObject(normalize=False)
live_time.shape = mask.shape
readLiveTime = mcaObject.info["McaLiveTime"]
self.assertTrue(
abs(live_time[mask > 0].sum() - readLiveTime) < 1.0e-5,
"Incorrect sum of masked live time data")
mcaObject = sb.calculateMcaDataObject(normalize=True)
live_time.shape = mask.shape
tmpBuffer = numpy.zeros(mask.shape, dtype=numpy.int32)
tmpBuffer[mask > 0] = 1
nSelectedPixels = float(tmpBuffer.sum())
readLiveTime = mcaObject.info["McaLiveTime"]
self.assertTrue( \
abs((live_time[mask > 0].sum() / nSelectedPixels) - readLiveTime) < 1.0e-5,
"Incorrect average of masked live time data")
def testSingleStackExport(self):
from PyMca5 import PyMcaDataDir
from PyMca5.PyMcaIO import specfilewrapper as specfile
from PyMca5.PyMcaIO import ConfigDict
from PyMca5.PyMcaCore import DataObject
from PyMca5.PyMcaCore import StackBase
from PyMca5.PyMcaCore import McaStackExport
spe = os.path.join(self.dataDir, "Steel.spe")
cfg = os.path.join(self.dataDir, "Steel.cfg")
sf = specfile.Specfile(spe)
self.assertTrue(len(sf) == 1, "File %s cannot be read" % spe)
self.assertTrue(sf[0].nbmca() == 1, "Spe file should contain MCA data")
y = counts = sf[0].mca(1)
x = channels = numpy.arange(y.size).astype(numpy.float)
sf = None
configuration = ConfigDict.ConfigDict()
configuration.read(cfg)
calibration = configuration["detector"]["zero"], \
configuration["detector"]["gain"], 0.0
initialTime = configuration["concentrations"]["time"]
# create the data
nRows = 5
nColumns = 10
nTimes = 3
data = numpy.zeros((nRows, nColumns, counts.size), dtype=numpy.float)
live_time = numpy.zeros((nRows * nColumns), dtype=numpy.float)
xpos = 10 + numpy.zeros((nRows * nColumns), dtype=numpy.float)
ypos = 100 + numpy.zeros((nRows * nColumns), dtype=numpy.float)
mcaIndex = 0
for i in range(nRows):
for j in range(nColumns):
data[i, j] = counts
live_time[i * nColumns + j] = initialTime * \
(1 + mcaIndex % nTimes)
xpos[mcaIndex] += j
ypos[mcaIndex] += i
mcaIndex += 1
# create the stack data object
stack = DataObject.DataObject()
stack.data = data
stack.info = {}
stack.info["McaCalib"] = calibration
stack.info["McaLiveTime"] = live_time
stack.x = [channels]
stack.info["positioners"] = {"x": xpos, "y": ypos}
tmpDir = tempfile.gettempdir()
self._h5File = os.path.join(tmpDir, "SteelStack.h5")
if os.path.exists(self._h5File):
os.remove(self._h5File)
McaStackExport.exportStackList(stack, self._h5File)
# read back the stack
from PyMca5.PyMcaIO import HDF5Stack1D
stackRead = HDF5Stack1D.HDF5Stack1D([self._h5File],
{"y": "/measurement/detector_00"})
# let's play
sb = StackBase.StackBase()
sb.setStack(stackRead)
# positioners
data = stackRead.info["positioners"]["x"]
self.assertTrue(numpy.allclose(data, xpos),
"Incorrect readout of x positions")
data = stackRead.info["positioners"]["y"]
self.assertTrue(numpy.allclose(data, ypos),
"Incorrect readout of y positions")
# calibration and live time
x, y, legend, info = sb.getStackOriginalCurve()
readCalib = info["McaCalib"]
readLiveTime = info["McaLiveTime"]
self.assertTrue(abs(readCalib[0] - calibration[0]) < 1.0e-10,
"Calibration zero. Expected %f got %f" % \
(calibration[0], readCalib[0]))
self.assertTrue(abs(readCalib[1] - calibration[1]) < 1.0e-10,
"Calibration gain. Expected %f got %f" % \
(calibration[1], readCalib[0]))
self.assertTrue(abs(readCalib[2] - calibration[2]) < 1.0e-10,
"Calibration 2nd order. Expected %f got %f" % \
(calibration[2], readCalib[2]))
self.assertTrue(
abs(live_time.sum() - readLiveTime) < 1.0e-5,
"Incorrect sum of live time data")