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
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 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 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 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 = []
