def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
plugin.killAllWorkers()
if EDVerbose.isVerboseDebug():
plugin.cleanDispMat(plugin.getWorkingDirectory())
else:
plugin.cleanDispMat()
# Checking obtained results
xsDataResultSPD = plugin.getDataOutput()
outputData = EDF(
xsDataResultSPD.getCakedFile().getPath().getValue()).GetData(0)
referenceData = EDF(
os.path.join(self.getTestsDataImagesHome(),
self.refOutput)).GetData(0)
relError = 100 * (abs(outputData - referenceData).max() -
referenceData.min()) / (referenceData.max() -
referenceData.min())
absError = abs(outputData - referenceData).max()
if relError > 5:
EDAssert.lowerThan(
relError, 5,
"Maximum relative error = %.2f%%, Maximum Absolute Error %.2f"
% (relError, absError))
else:
EDAssert.lowerThan(
absError, 5,
"Maximum relative error = %.2f%%, Maximum Absolute Error %.2f "
% (relError, absError))
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
plugin.killAllWorkers()
# if EDVerbose.isVerboseDebug():
# plugin.cleanDispMat(plugin.getWorkingDirectory())
# else:
# plugin.cleanDispMat()
# Checking obtained results
xsDataResultSPD = plugin.getDataOutput()
outputData = EDF(xsDataResultSPD.getCakedFile().getPath().getValue()).GetData(0)
referenceData = EDF(os.path.join(self.getTestsDataImagesHome(), self.refOutput)).GetData(0)
# print outputData.shape
# print referenceData.shape
relError = 100 * (abs(outputData - referenceData).max() - referenceData.min()) / (referenceData.max() - referenceData.min())
absError = abs(outputData - referenceData).max()
if relError > 5:
EDAssert.lowerThan(relError, 5, "Maximum relative error = %.2f%%, Maximum Absolute Error %.2f" % (relError, absError))
else:
EDAssert.lowerThan(absError, 5, "Maximum relative error = %.2f%%, Maximum Absolute Error %.2f " % (relError, absError))
def edf(self,
x_start=0,
x_end=0,
x_step=1,
y_start=0,
y_end=0,
y_step=1,
z_start=0,
z_end=0,
z_step=1):
"""
Read 3-D tomographic projection data from an EDF (ESRF) file.
Parameters
file_name : str
Input edf file.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
z_start, z_end, z_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
Returns
out : array
Returns the data as a matrix.
"""
# Read data from file.
f = EdfFile(self.file_name, access='r')
dic = f.GetStaticHeader(0)
tmpdata = np.empty((f.NumImages, int(dic['Dim_2']), int(dic['Dim_1'])))
for (i, ar) in enumerate(tmpdata):
tmpdata[i::] = f.GetData(i)
num_z, num_y, num_x = np.shape(tmpdata)
if x_end is 0:
x_end = num_x
if y_end is 0:
y_end = num_y
if z_end is 0:
z_end = num_z
# Construct dataset from desired y.
dataset = tmpdata[z_start:z_end:z_step, y_start:y_end:y_step,
x_start:x_end:x_step]
return dataset
def process(self, _edObject=None):
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginChiToEDFv1_0.process")
# Read the Chi file
pyStrPathToChiFile = self.getDataInput().getChiFile().getPath(
).getValue()
pyNumpyArray = numpy.loadtxt(pyStrPathToChiFile, skiprows=4)
# Prepare the header dictionary
self.m_edDictionaryHeader = {}
for xsDataKeyValuePair in self.getDataInput().getHeader(
).getKeyValuePair():
key = xsDataKeyValuePair.getKey().getValue()
value = xsDataKeyValuePair.getValue().getValue()
self.m_edDictionaryHeader[str(key)] = str(value)
# Save it as an EDF file
if self.getDataInput().getOutputPathEDF() is not None:
strOutputPath = self.getDataInput().getOutputPathEDF().getPath(
).getValue()
else:
strOutputPath = self.getWorkingDirectory()
if strOutputPath is None:
strOutputPath = os.getcwd()
if os.path.exists(strOutputPath):
if os.path.isfile(strOutputPath):
self._strEDFFile = strOutputPath
else: #it is a directory, I guess
self._strEDFFile = os.path.join(
strOutputPath,
os.path.splitext(
os.path.basename(self.getDataInput().getChiFile().
getPath().getValue()))[0] + ".edf")
else: #strOutputPath does not exist
if strOutputPath.endswith("/"):
try:
os.makedirs(strOutputPath, int("777", 8))
except IOError:
raise IOError, "Unable to create directory named %s, please chech the rights or the input parameters." % strOutputPath
self._strEDFFile = os.path.join(
strOutputPath,
os.path.splitext(
os.path.basename(self.getDataInput().getChiFile().
getPath().getValue()))[0] + ".edf")
else: #it will be a file, the create the upper directory if needed
upperDir = os.path.dirname(strOutputPath)
if not os.path.isdir(upperDir):
try:
os.makedirs(upperDir, int("777", 8))
except IOError:
raise IOError, "Unable to create directory named %s, please chech the rights or the input parameters." % upperDir
self._strEDFFile = strOutputPath
print self._strEDFFile
edfFile = EdfFile(self._strEDFFile)
edfFile.WriteImage(self.m_edDictionaryHeader, pyNumpyArray)
def newFile(self, filename="test", size=(0, 0), metadata={}):
"""this is a method to create a new empty file
@param filename: name of the file to create, the size and the extension will be added.
@type filename: string
@type size: 2-tuple of integers
@param size: the size of the image to create
"""
if len(size) != 2:
EDVerbose.error("Error in the size of the size-tuple")
raise Exception("Error in the size of the size-tuple")
if size[0] < 0:
EDVerbose.error("Error in the X part of the size tuple")
raise Exception("Error in the X part of the size tuple")
if size[1] < 0:
EDVerbose.error("Error in the Y part of the size tuple")
raise Exception("Error in the Y part of the size tuple")
emptyNParray = numpy.zeros(size, dtype="float32")
self.data[filename] = emptyNParray
self.headers[filename] = metadata
self.size[filename] = size
fullFilename = "%sSize%ix%i.edf" % ((filename, ) + size)
if os.path.isfile(fullFilename):
EDVerbose.warning("Warning, I am going to overwrite the file %s " %
fullFilename)
self.synchronizeOn()
try:
self.edf[filename] = EdfFile(fullFilename)
self.data[filename] = self.edf[filename].GetData(0)
self.headers[filename] = self.edf[filename].GetHeader(0)
except Exception:
EDVerbose.error("[ERROR] in reading file %s" % filename)
self.synchronizeOff()
if self.data[filename].shape != size:
self.data[filename] = emptyNParray
self.headers[filename] = metadata
else:
self.synchronizeOn()
try:
self.edf[filename] = EdfFile(fullFilename)
self.edf[filename].WriteImage(self.headers[filename],
self.data[filename],
Append=0)
except Exception:
EDVerbose.error("[ERROR] in opening and creating file %s" %
filename)
self.synchronizeOff()
def edf2(self, x_start=0, x_end=0, x_step=1, y_start=0, y_end=0, y_step=1):
"""
Read 2-D tomographic projection data from an EDF (ESRF) file.
Parameters
file_name : str
Input edf file.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
Returns
out : array
Output 2-D matrix as numpy array.
"""
try:
# Read data from file.
f = EdfFile(self.file_name, access='r')
dic = f.GetStaticHeader(0)
tmpdata = np.empty((int(dic['Dim_2']), int(dic['Dim_1'])))
tmpdata[::] = f.GetData(0)
num_y, num_x = np.shape(tmpdata)
if x_end is 0:
x_end = num_x
if y_end is 0:
y_end = num_y
array = tmpdata[y_start:y_end:y_step, x_start:x_end:x_step]
except KeyError:
self.logger.error(
"FILE DOES NOT CONTAIN A VALID TOMOGRAPHY DATA SET")
array = None
return array
def process(self, _edObject=None):
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginEDFReadHeaderv1_0.process")
# Read the header contents and put it into an dictionary
edStringPathToInputFile = self.getDataInput().getEdfFile().getPath(
).getValue()
pyFileDescriptor = open(edStringPathToInputFile, "r")
edfFile = EdfFile(pyFileDescriptor)
pyFileDescriptor.close()
iNumberOfImages = edfFile.GetNumImages()
if (iNumberOfImages == 0):
edStringErrorMessage = EDMessage.ERROR_UNEXPECTED_01 % (
self.getPluginName() + ".preProcess: No images in file " +
edStringPathToInputFile)
EDVerbose.error(edStringErrorMessage)
self.addErrorMessage(edStringErrorMessage)
raise RuntimeError, edStringErrorMessage
#if ( iNumberOfImages > 1 ):
# pass
#EDVerbose.warning( "Warning! More than one image in file " + edStringPathToInputFile ", reading header from first image" )
self.m_edDictionaryHeader = edfFile.GetHeader(0)
def edf2(self, x_start=0, x_end=0, x_step=1, y_start=0, y_end=0, y_step=1):
"""
Read 2-D tomographic projection data from an EDF (ESRF) file.
Parameters
file_name : str
Input edf file.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole array.
Returns
out : array
Output 2-D matrix as numpy array.
"""
# Read data from file.
f = EdfFile(self.file_name, access='r')
dic = f.GetStaticHeader(0)
tmpdata = np.empty((int(dic['Dim_2']), int(dic['Dim_1'])))
tmpdata[::] = f.GetData(0)
num_y, num_x = np.shape(tmpdata)
if x_end is 0:
x_end = num_x
if y_end is 0:
y_end = num_y
return tmpdata[y_start:y_end:y_step, x_start:x_end:x_step]
def writeData(self):
if self.fileName.endswith('.edf'):
fileEdf = EdfFile(self.fileName, access='wb')
fileEdf.WriteImage({}, self.data)
if self.fileName.endswith('.mat'):
NameFile = self.fileName.split('/')[-1]
NameFile = NameFile.split('.')[0]
sio.savemat(self.fileName, {NameFile: self.data})
if self.fileName.endswith('.tiff'):
tifImage = TiffIO.TiffIO(self.fileName, 'wb+')
tifImage.writeImage(self.data)
if self.fileName.endswith('.png'):
scipy.misc.imsave(self.fileName, self.data)
if self.fileName.endswith('.dcm'):
write_dicom(self.data, self.fileName)
if self.fileName.endswith('.npy'):
np.save(self.fileName, self.data)
def getData(self):
if (self.fileName.endswith('.raw') or self.fileName.endswith('.RAW')
or self.fileName.endswith('.img')):
File = open(str(self.fileName), "rb")
size = os.path.getsize(str(self.fileName)) / 4.
self.width = int(size**.5)
self.height = self.width
self.currentSlice = np.fromfile(File, dtype='<f4')
self.currentSlice.resize(self.height, self.width)
elif (self.fileName.endswith('.edf')
or self.fileName.endswith('.EDF')):
fileEdf = EdfFile(str(self.fileName), access='rb')
self.currentSlice = fileEdf.GetData(0)
elif (self.fileName.endswith('.DOWN')
or self.fileName.endswith('.UP')):
fileEdf = EdfFile(str(self.fileName), access='rb')
self.currentSlice = fileEdf.GetData(0)
elif (self.fileName.endswith('.tif') or self.fileName.endswith('.TIF')
or self.fileName.endswith('.TIFF')
or self.fileName.endswith('.tiff')):
fileTif = TiffIO(str(self.fileName), mode='rb')
self.currentSlice = fileTif.getImage(0)
elif (self.fileName.endswith('.png')
or self.fileName.endswith('.PNG')):
filePng = mpimg.imread(self.fileName)
self.currentSlice = filePng
elif (self.fileName.endswith('.dcm')
or self.fileName.endswith('.DCM')):
image = dicom.read_file(str(self.fileName), force=True)
self.currentSlice = image.pixel_array
elif (self.fileName.endswith('.mat')
or self.fileName.endswith('.MAT')):
image = sio.loadmat(self.fileName)
self.currentSlice = image[image.keys()[0].keys()[0]]
else:
image = dicom.read_file(str(self.fileName), force=True)
self.currentSlice = image
return self.currentSlice
# Synthetic data
l = 256
x = generate_synthetic_data(l)
# Projection operator and projections data, with noise
H = build_projection_operator(l, l/5)
y = H * x.ravel()[:, np.newaxis]
y += 2*np.random.randn(*y.shape)
y[y<0] = 0
y = y.reshape((l/5, l))
y = y.astype(np.float32)
# Write EdfFile with float32 data
phantom = EdfFile("phantom_float.edf")
for line in y:
lines = np.tile(line, (3, 1))
print "writing", lines.shape
phantom._WriteImage({}, lines, DataType="FloatValue", Append=1)
#phantom.WriteImage({}, lines)
phantom._EdfFile__makeSureFileIsClosed()
y *= 2**15 / y.max()
y = y.astype(np.uint16)
# Write EdfFile with uint16 data
phantom = EdfFile("phantom.edf")
def saveDiffractionImage(self,
filename,
colorMaps,
colorMapName,
maskedPixelInfo,
pixel1X=None,
pixel1Y=None,
pixel2X=None,
pixel2Y=None,
lowerBound=0,
upperBound=1,
logScale=None,
invert=None,
drawQLines=None,
drawdQLines=None,
QData=None,
calibrationData=None,
drawPeaks=None,
peakList=None,
qLinesColor=None,
dQLinesColor=None,
peakLinesColor=None):
# save EDF data specially
if getextension(filename) == ".edf":
edf = EdfFile(filename)
#You can write any relevant information in the dictionnary.
edf.WriteImage(
{
'Title':
"Edf file converted by the Area Diffraction Machine"
},
Numeric.transpose(self.theDiffractionData.data),
DataType="SignedInteger",
Append=0)
del edf # to force file close
return
# otherwise, try to save it using the PIL
image = self.getDiffractionImage(colorMaps, colorMapName,
maskedPixelInfo, None, None, None,
None, None, None, lowerBound,
upperBound, logScale, invert)
if drawQLines or drawdQLines:
if QData == None:
raise Exception(
"Cannot save the diffraction data until a q list is given."
)
if calibrationData == None:
raise Exception(
"Cannot save the diffraction data until the calibration Data is given."
)
if drawQLines:
if qLinesColor == None:
raise Exception(
'Cannot add q lines to the saved image until the q line color is set.'
)
for Q, dQ in QData.getAllQPairs():
MakeDiffractionImage.addConstantQLineDiffractionImage(
image, Q, calibrationData, qLinesColor)
if drawdQLines:
if dQLinesColor == None:
raise Exception(
'Cannot add delta q lines to the saved image until the delta q line color is set.'
)
for Q, dQ in QData.getAllQPairs():
MakeDiffractionImage.addConstantQLineDiffractionImage(
image, Q - dQ, calibrationData, dQLinesColor)
MakeDiffractionImage.addConstantQLineDiffractionImage(
image, Q + dQ, calibrationData, dQLinesColor)
if drawPeaks and peakList != None:
if peakLinesColor == None:
raise Exception(
"Cannot add peaks to the saved iamge until the peak color is set."
)
MakeDiffractionImage.addPeaksDiffractionImage(
image, peakList, peakLinesColor)
# by default, return entire image
if pixel1X != None and pixel1Y != None and pixel2X != None and pixel2Y != None:
image = image.crop(
(min(int(pixel1X),
int(pixel2X)), min(int(pixel1Y), int(pixel2Y)),
max(int(pixel1X),
int(pixel2X)), max(int(pixel1Y), int(pixel2Y))))
try:
image.save(filename)
except Exception, e:
raise UserInputException(
"Cannot save image: %s has an unknown file extension" %
filename)
# Synthetic data
l = 256
x = generate_synthetic_data(l)
# Projection operator and projections data, with noise
H = build_projection_operator(l, l / 5)
y = H * x.ravel()[:, np.newaxis]
y += 2 * np.random.randn(*y.shape)
y[y < 0] = 0
y = y.reshape((l / 5, l))
y = y.astype(np.float32)
# Write EdfFile with float32 data
phantom = EdfFile("phantom_float.edf")
for line in y:
lines = np.tile(line, (3, 1))
print "writing", lines.shape
phantom._WriteImage({}, lines, DataType="FloatValue", Append=1)
#phantom.WriteImage({}, lines)
phantom._EdfFile__makeSureFileIsClosed()
y *= 2**15 / y.max()
y = y.astype(np.uint16)
# Write EdfFile with uint16 data
phantom = EdfFile("phantom.edf")
def set(self, value=0, filename="test.edf", position=(0, 0)):
"""
This is the set method that will first ensure that the data are available
#then set a lock on it and finally #No more
write the data
#before unlocking. #No more
@param: value value of the pixel to set
@type value: probably float but can be any figure
@param filename: name of the file to be processed
@type filename: string
@param position: the position of the pixel to modify
@type position: 2-tuple of integers
"""
if not isinstance(value, float):
EDVerbose.error("ERROR The value %s is not a float" % value)
raise Exception("ERROR The value %s is not a float" % value)
if not (isinstance(filename, str) or isinstance(filename, unicode)):
EDVerbose.error("ERROR The filename variable %s is not a string " %
filename)
raise Exception("ERROR The filename variable %s is not a string " %
filename)
if not isinstance(position, tuple):
EDVerbose.error("ERROR The position variable %s is not a tuple " %
position)
raise Exception("ERROR The position variable %s is not a tuple " %
position)
if len(position) != 2:
EDVerbose.error("ERROR in the size of the position-tuple")
raise Exception("ERROR in the size of the position-tuple")
if position[0] < 0:
EDVerbose.error("ERROR in the X part of the position-tuple")
raise Exception("ERROR in the X part of the position-tuple")
if position[1] < 0:
EDVerbose.error("ERROR in the Y part of the position-tuple")
raise Exception("ERROR in the Y part of the position-tuple")
if not self.data.has_key(filename):
EDVerbose.warning(
"ERROR, the destination image %s is not in the list of images tracked : %s"
% (filename, self.data.keys()))
pystrDirname, pystrFilename = os.path.split(filename)
fileInDir = []
for onefile in os.listdir(pystrDirname):
if onefile.find("%sSize" % pystrFilename) == 0:
if onefile[-4:].lower() == ".edf":
XxY = onefile.split("Size")[-1][:-4]
try:
size = tuple(
[int(i) for i in tuple(XxY.split("x"))])
except Exception:
size = None
if size:
fileInDir.append(onefile)
if len(fileInDir) > 1:
EDVerbose.warning(
"ERROR, for %s, I found too many images corresponding to what you are looking for : %s"
% (filename, fileInDir))
raise Exception(
"ERROR, I found too many images corresponding to what you are looking for : %s"
% (filename, fileInDir))
elif len(fileInDir) == 1:
EDVerbose.warning(
"WARNING, As The file %s exists, I will try to read it. The expected size is %s"
% (filename, size))
self.size[filename] = size
fullFilename = "%sSize%ix%i.edf" % ((filename, ) + size)
self.headers[filename] = {}
self.data[filename] = numpy.zeros(size, dtype="float32")
self.synchronizeOn()
try:
self.edf[filename] = EdfFile(fullFilename)
self.headers[filename] = self.edf[filename].GetHeader(0)
self.data[filename] = self.edf[filename].GetData(0)
except Exception:
EDVerbose.warning(
"ERROR in reading file %s: Reintializing it" %
filename)
self.edf[filename] = EdfFile(fullFilename)
self.data[filename] = numpy.zeros(size, dtype="float32")
self.headers[filename] = {}
self.synchronizeOff()
if self.data[filename].shape != size:
self.data[filename] = numpy.zeros(size, dtype="float32")
self.headers[filename] = {}
else:
EDVerbose.error(
"ERROR, the destination image %s is not in the list of images tracked : %s"
% (filename, self.data.keys()))
raise Exception(
"ERROR, the destination image %s is not in the list of images tracked : %s"
% (filename, self.data.keys()))
if position[0] > self.data[filename].shape[0]:
EDVerbose.error(
"ERROR in the X part of the position-tuple: too large %i > %i"
% (position[0], npArray.shape[0]))
raise Exception(
"ERROR in the X part of the position-tuple: too large %i > %i"
% (position[0], npArray.shape[0]))
if position[1] > self.data[filename].shape[1]:
EDVerbose.error(
"ERROR in the Y part of the position-tuple: too large %i > %i"
% (position[1], npArray.shape[1]))
raise Exception(
"ERROR in the Y part of the position-tuple: too large %i > %i"
% (position[1], npArray.shape[1]))
self.data[filename][position[0], position[1]] = value
self.synchronizeOn()
try:
self.edf[filename].WriteImage(self.headers[filename],
self.data[filename],
Append=0)
except Exception:
EDVerbose.error("ERROR in writing image %s at position %s" %
(filename, position))
self.synchronizeOff()
def process(self, _edObject=None):
EDPluginControl.process(self)
EDVerbose.DEBUG("EDPluginBioSaxsMetadatav1_0.process")
if not os.path.isfile(self.strInputImage):
EDVerbose.WARNING("The given input file does not exist !!!")
header = {}
else:
header = EdfFile(self.strInputImage).GetHeader(0)
for key in EDUtilsBioSaxs.TRANSLATION:
if key in dir(self) and self.__getattribute__(key) is None:
if EDUtilsBioSaxs.TRANSLATION[key] in header:
if key in EDUtilsBioSaxs.FLOAT_KEYS:
setattr(
self, key,
float(header[EDUtilsBioSaxs.TRANSLATION[key]]))
else:
setattr(self, key,
header[EDUtilsBioSaxs.TRANSLATION[key]])
if self.strOutputImage is not None:
if os.path.abspath(self.strOutputImage) != os.path.abspath(
self.strInputImage):
shutil.copy(self.strInputImage, self.strOutputImage)
keyToUpgrade = []
for key in EDUtilsBioSaxs.TRANSLATION:
if key in dir(self) and self.__getattribute__(key) is None:
if EDUtilsBioSaxs.TRANSLATION[key] not in header:
keyToUpgrade.append(key)
else:
if key in EDUtilsBioSaxs.FLOAT_KEYS:
oneHeader = float(
header[EDUtilsBioSaxs.TRANSLATION[key]])
else:
oneHeader = header[EDUtilsBioSaxs.TRANSLATION[key]]
oneValue = eval("self.%s" % key)
EDVerbose.DEBUG(
"key: %s value_header=%s(%s) value_extra=%s(%s)" %
(key, oneHeader, oneHeader.__class__,
eval("self.%s" % key), eval(
"self.%s" % key).__class__))
if oneHeader != oneValue:
keyToUpgrade.append(key)
for key in keyToUpgrade:
if not self.__bSaxsMetadataFailed:
xsdi = XSDataInputSaxsAddMetadatav1_0()
xsdi.setInputImage(self.xsdInputData.getOutputImage())
xsdi.setKey(XSDataString(EDUtilsBioSaxs.TRANSLATION[key]))
xsdi.setValue(XSDataString("%s" % eval("self.%s" % key)))
edPlugin = self.loadPlugin(
self.__strControlledPluginMetadata)
edPlugin.setDataInput(xsdi)
edPlugin.connectSUCCESS(self.doSuccessMetadata)
edPlugin.connectFAILURE(self.doFailureMetadata)
edPlugin.executeSynchronous()
if self.__bSaxsMetadataFailed:
EDVerbose.screen(
"EDPluginBioSaxsMetadatav1_0.process: writeMetadata using EdfFile "
)
edf = EdfFile(self.strOutputImage)
headers = [
edf.GetHeader(i) for i in xrange(edf.GetNumImages())
]
data = [edf.GetData(i) for i in xrange(edf.GetNumImages())]
del edf
for key in EDUtilsBioSaxs.TRANSLATION:
if key in dir(self) and self.__getattribute__(key) is None:
header[EDUtilsBioSaxs.TRANSLATION[key]] = eval(
"self.%s" % key)
edf = EdfFile(self.strOutputImage)
if len(data) == 1:
edf.WriteImage(header, data[0], Append=0)
elif len(data) > 1:
edf.WriteImage(header, data[0], Append=0)
for datum in data[1:]:
edf.WriteImage({}, datum, Append=1)
else:
EDVerbose.WARNING("There are not data in %s !!!" %
self.strInputImage)
roi = PowderIntegrator(cif)
pyintXpos, pyintYpos = roi.getSinogramPosition()
strLockFile = lockFile(suffix=os.path.splitext(strPathToCif)[0],
path='.',
basename="lock")
startWriteTime = time.time()
for pystSinogramFilename in [
"sinogramPhotonFlux.edf", "sinogramIntegratedRaw.edf",
"sinogramIntegratedCor.edf"
]:
if os.path.isfile(pystSinogramFilename):
edf = EdfFile(pystSinogramFilename)
npSinogramArray = edf.GetData(0)
else:
npSinogramArray = roi.getEmptySinogramArray()
edf = EdfFile(pystSinogramFilename)
if pystSinogramFilename == "sinogramPhotonFlux.edf":
npSinogramArray[pyintXpos, pyintYpos] = roi.pyfPhotonFlux
elif pystSinogramFilename == "sinogramIntegratedRaw.edf":
npSinogramArray[pyintXpos, pyintYpos] = roi.integrate()
elif pystSinogramFilename == "sinogramIntegratedCor.edf":
npSinogramArray[pyintXpos,
pyintYpos] = roi.integrate() / roi.pyfPhotonFlux
edf.WriteImage(pydMetaDataEDF, npSinogramArray, Append=0)
pylRegionsOfInterest = []
Comm.start()
if DoConfigure:
Comm.Configure()
if not Comm.isAlive():
raise SystemExit
Comm.startAcquisition()
if not Comm.isAlive():
raise SystemExit
while Comm.getCurrentCommand() != Comm.COM_NONE:
time.sleep(0.2)
for i in range(Comm.getNbFramesReady()):
if not Comm.isAlive():
raise SystemExit
arr = Comm.getBuffer(i)
arr.resize(240,566)
f = EDF("%s_%.4d%s" % (filename,i,".edf"))
f.WriteImage({},arr[:,5:565])
del f
Comm.quit()
del Comm
if __name__ == "__main__":
main()
