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 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 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)
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()
]:
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 = []
if cif.exists("_pd_sum_2theta_range_min"):
pylRegionsOfInterest.append([
float(cif["_pd_sum_2theta_range_min"]),
float(cif["_pd_sum_2theta_range_max"])
])
else:
for oneloop in cif["loop_"]:
if "_pd_sum_2theta_range_min" in oneloop[0]:
for i in oneloop[1]:
pylRegionsOfInterest.append([
float(i["_pd_sum_2theta_range_min"]),
float(i["_pd_sum_2theta_range_max"])
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)
