def loadImageIntoSFH(path, iFileLoader=None):
if iFileLoader is None:
iFileLoader = FILELOADERS[path.split('.')[-1].upper()]
# print "loadIntoSfh loading: %s using %s" % (path, str(iFileLoader))
sfh = ScanFileHolder()
sfh.load(iFileLoader(path))
return sfh
def __init__(self, panelName="Data Vector", iFileLoader=None): self.panel = panelName; self.iFileLoader = iFileLoader; self.filename= None; self.data = ScanFileHolder(); self.dataset = None;
def __init__(self, name, panelName, detector):
self.setName(name);
self.setInputNames([name]);
self.setExtraNames([]);
# self.Units=[strUnit];
self.setLevel(7);
self.panel = panelName;
self.detector = detector;
self.scanNumberTracker = NumTracker("tmp");
self.fileName=None;
self.data = ScanFileHolder()
self.exposureTime = 0
self.logScale = False;
self.alive=True;
# To setup the image folder according to I06 requirement
self.scanImageDirectory();
self.fastMode=False;
self.protection=True;
# self.protectCamera();
self.verbose = False
def saveImage(self, filename):
path = self.filepath + filename
if self.ds is None:
raise Exception("Epics GigE Camera %s has not acquired an image" % self.name)
else:
sfh = ScanFileHolder()
sfh.addDataSet("Image",self.ds)
sfh.save(PNGSaver(path))
class ImageUtility(object):
def __init__(self, panelName="Data Vector", iFileLoader=None):
self.panel = panelName;
self.iFileLoader = iFileLoader;
self.filename= None;
self.data = ScanFileHolder();
self.dataset = None;
def loadDataFromFile(self, fileName, fileLoader):
if fileLoader is None:
import os
fileLoader = GDA_FILELOADERS[os.path.splitext(fileName)[-1].upper()];
print fileName
self.data.load(fileLoader(fileName));
return self.data;
def loadDataset(self, fileName = None, fileLoader = None):
self.dataset = None;
if fileLoader == None:
fileLoader = self.iFileLoader;
if fileName != None:#Get data from file directly
self.data = self.loadDataFromFile(fileName, fileLoader);
if self.data is not None:
self.filename = fileName;
# self.dataset = self.data[0];
self.dataset = self.data.getAxis(0);
else:
print "Please give a full file name"
return;
return self.dataset;
def loadFile(self, fileName = None, fileLoader = None):
return self.loadDataset(fileName, fileLoader);
def open(self, fileName):
self.display(fileName);
def display(self, fileName):
if fileName is None:
print "Please give a full file name to display";
return;
else:
dataset = self.loadDataset(fileName)
if self.panel:
SDAPlotter.imagePlot(self.panel, dataset);
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
def loadPNGFile(self, fileName):
#To check file exist:
if not self.fileExists(fileName, 5):
print "File '" + fileName + "' does not exist!"
raise Exception("No File Found Error")
dataset = None
sfh = ScanFileHolder()
sfh.load(PNGLoader(fileName))
dataset = sfh.getAxis(0)
return dataset
def getScanFileHolderXY(xName,xDataRaw,yName, yDataRaw):
if len(xDataRaw) != len(yDataRaw):
raise ValueError("len(xDataRaw) != len(yDataRaw)")
#convert to list from array
xData = []
yData = []
for i in range(len(yDataRaw)):
xData.append(xDataRaw[i])
yData.append(yDataRaw[i])
scanFileHolder = ScanFileHolder()
scanFileHolder.load(XYDataLoader(xName,xData,yName, yData))
return scanFileHolder
def getScanFileHolderXY(xName, xDataRaw, yName, yDataRaw):
if len(xDataRaw) != len(yDataRaw):
raise "len(xDataRaw) != len(yDataRaw)"
#convert to list from array
xData = []
yData = []
for i in range(len(yDataRaw)):
xData.append(xDataRaw[i])
yData.append(yDataRaw[i])
scanFileHolder = ScanFileHolder()
scanFileHolder.load(XYDataLoader(xName, xData, yName, yData))
return scanFileHolder
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 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 __init__(self, name, panelName, zippedImageSource, fileImageExtension):
self.setName(name)
# self.setInputNames([]);
self.setLevel(7)
self.panel = panelName
self.data = ScanFileHolder()
self.triggerTime = 0
self.filePath = None
self.filePrefix = None
self.logScale = False
self.alive = True
# self.imageProducer=ZipImageProducerClass('/scratch/Dev/gdaDev/gda-config/i07/scripts/Diamond/Pilatus/images100K.zip', 'tif');
self.imageProducer = ZipImageProducerClass(zippedImageSource,
fileImageExtension)
self.fullImageFileName = None
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 __init__(self,
name,
detector,
processors=[],
panelName="Area Detector",
iFileLoader=None):
self.detector = detector
self.processors = processors
self.panel = panelName
self.iFileLoader = iFileLoader
self.filename = None
self.data = ScanFileHolder()
self.dataset = None
self.mask = None
self.result = None
self.passive = False
self.alive = False
self.scannableSetup(name)
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 loadSRSData(filename):
'''Load SRS data file into a ScanFileHolder object,
supporting relative loading with respect to the current collected data (0)'''
sfh = ScanFileHolder()
try:
if filename == None:
#current file
sfh.load(SRSLoader(_getCurrentFileName(0)))
elif representsInt(filename):
#past file - relative path
sfh.load(SRSLoader(_getCurrentFileName(int(filename))))
elif not filename.startswith(File.separator):
#filename with extension
sfh.load(SRSLoader(os.path.join(PathConstructor.createFromDefaultProperty(),filename)))
else:
#absolute file path
sfh.load(SRSLoader(filename))
except ScanFileHolderException, err:
print "File loader failed. " + err
def saveImage(self, filename):
path = self.filepath + filename
if self.ds is None:
raise Exception("Epics GigE Camera %s has not acquired an image" %
self.name)
else:
sfh = ScanFileHolder()
sfh.addDataSet("Image", self.ds)
sfh.save(PNGSaver(path))
def __init__(self, name, panelName, detectorName, shutterName=None):
self.setName(name)
self.setInputNames(['exposure'])
self.setExtraNames([])
# self.setOutputFormat(['%.2f']);
self.setLevel(7)
self.panel = panelName
self.detector = vars(gdamain)[detectorName]
self.detectorInfo = None
self.data = ScanFileHolder()
self.exposureTime = 0
self.sum = 0
self.maxpix = 0
# self.filePath = None;
# self.filePrefix = None;
# self.fileFormat = "%s%s%4.4d.tif";
# self.fileNumber = self.detector.getFileNumber();
self.logScale = False
self.alive = True
ShutterDeviceClass.__init__(self, shutterName)
def __init__(self, name, detector, processors=[], panelName="Area Detector", iFileLoader=None): self.detector = detector; self.processors = processors; self.panel = panelName; self.iFileLoader = iFileLoader; self.filename= None; self.data = ScanFileHolder(); self.dataset = None; self.mask = None; self.result = None; self.alive = False; self.scannableSetup(name);
def savePNGFile(self, fileName, dataset):
if os.path.exists(fileName) and os.path.isfile(fileName):
print "File " + fileName + " already exist. Choose another name."
return False
#PNG file writer from GDA Analysis package
sfh = ScanFileHolder()
sfh.setAxis("PeemImage", dataset)
sfh.save(PNGSaver(fileName))
return True
def loadMacData(filename):
'''Load MAC data file into a ScanFileHolder object, supporting relative loading with respect to the current collected data (0)'''
sfh = ScanFileHolder()
try:
if filename == None:
#current file
sfh.load(MACLoader(0))
elif representsInt(filename):
#past file - relative path
sfh.load(MACLoader(int(filename)))
else:
#absolute file path
sfh.load(MACLoader(filename))
except ScanFileHolderException, err:
print "File loader failed. " + err
def __init__(self, name, panelName, zippedImageSource, fileImageExtension):
self.setName(name);
# self.setInputNames([]);
self.setLevel(7);
self.panel = panelName;
self.data = ScanFileHolder();
self.triggerTime = 0;
self.filePath = None;
self.filePrefix = None;
self.logScale = False;
self.alive=True;
# self.imageProducer=ZipImageProducerClass('/scratch/Dev/gdaDev/gda-config/i07/scripts/Diamond/Pilatus/images100K.zip', 'tif');
self.imageProducer=ZipImageProducerClass(zippedImageSource, fileImageExtension);
self.fullImageFileName = None;
def ncdredconf(self, detector, **kwords):
"""
if default None passed in no change is made
default is everything off
"""
if detector.lower() == "Waxs".lower():
detector = "Waxs"
else:
detector = "Saxs"
if not detector in self.settings:
self.settings[detector] = {}
for i in self.options:
if not i in self.settings[detector]:
self.settings[detector][i] = False
if i in kwords:
if kwords[i] == None:
self.settings[detector][i] = False
else:
self.settings[detector][i] = kwords[i]
realdet = ncdutils.getDetectorByType(self.detsystem, detector.upper())
realdetname = realdet.getName()
ncdutils.removeDetectorByName(self.detsystem, detector + " chain")
saxsrc = ReductionChain(detector + " chain", realdetname)
saxsrclist = saxsrc.getChain()
panel = detector + " Plot"
beanbag = SDAPlotter.getGuiBean(panel)
if beanbag == None:
beanbag = {}
sroi = None
if self.is2D(realdet):
if GuiParameters.ROIDATA in beanbag:
roi = beanbag[GuiParameters.ROIDATA]
if isinstance(roi, SectorROI):
sroi = roi
radii = sroi.getRadii()
self.settings[detector]["length"] = int(
math.ceil(radii[1] - radii[0]))
self.settings[detector]["disttobeamstop"] = radii[0]
length = self.settings[detector]["length"]
slope = self.settings[detector]["slope"]
intercept = self.settings[detector]["intercept"]
if slope == 0 or slope == False:
axisds = None
else:
axis = []
pis = realdet.getPixelSize() * 1000
d2b = self.settings[detector]["disttobeamstop"]
for i in range(length):
axis.append(float((i + d2b) * pis * slope + intercept))
axisds = DataSet("qaxis", axis)
mask = self.settings[detector]["mask"]
sect = self.settings[detector]["sect"]
if sroi != None:
if sect or isinstance(axisds, DataSet):
start = sroi.getPoint()
realdet.setAttribute("beam_center_x", start[0])
realdet.setAttribute("beam_center_y", start[1])
else:
realdet.setAttribute("beam_center_x", None)
realdet.setAttribute("beam_center_y", None)
cameralength = self.settings[detector]["cameralength"]
if cameralength != False:
realdet.setAttribute("distance", cameralength)
else:
realdet.setAttribute("distance", None)
norm = self.settings[detector]["norm"]
if (norm != False):
saxsnorm = Normalisation(detector + "norm", "ignored")
saxsnorm.setCalibChannel(1)
saxsnorm.setCalibName(
ncdutils.getDetectorByType(self.detsystem, "CALIB").getName())
saxsrclist.add(saxsnorm)
bg = self.settings[detector]["bg"]
if bg != False:
if os.path.isfile(bg):
saxsbgs = BackgroundSubtraction(detector + "bg", "ignored")
sfh = ScanFileHolder()
if (norm >= 0):
upstream = detector + "norm.data"
else:
upstream = realdetname + ".data"
sfh.load(NexusLoader(bg, [upstream]))
ds = sfh.getAxis(upstream)
saxsbgs.setBackground(ds)
saxsrclist.add(saxsbgs)
else:
print "background file \"%s\" does not exist." % bg
if (sect):
if sroi != None:
saxssect = SectorIntegration(detector + "sect", "ignored")
saxssect.setROI(sroi)
if isinstance(axisds, DataSet):
saxssect.setqAxis(axisds)
if (mask):
if not GuiParameters.MASKING in beanbag:
print "no mask defined for %s" % panel
else:
mb = beanbag[GuiParameters.MASKING]
if not isinstance(mb, MaskingBean):
print "no mask defined for %s" % panel
else:
saxssect.setMask(mb.getMask())
saxsrclist.add(saxssect)
else:
print "sector integration requested but no ROI found"
inv = self.settings[detector]["inv"]
if (inv):
saxsinvariant = Invariant(detector + "invariant", "ignored")
saxsrclist.add(saxsinvariant)
aver = self.settings[detector]["aver"]
if (aver):
saxsaver = Average(detector + "average", "ignored")
saxsrclist.add(saxsaver)
self.detsystem.addDetector(saxsrc)
class UViewDetectorClass(DetectorBase):
DETECTOR_STATUS_IDLE, DETECTOR_STATUS_BUSY, DETECTOR_STATUS_PAUSED, DETECTOR_STATUS_STANDBY, DETECTOR_STATUS_FAULT, DETECTOR_STATUS_MONITORING = range(6);
ImageFileLoaders={ 'TIF' : TIFFImageLoader,
'TIFF': TIFFImageLoader,
'JPG' : JPEGLoader,
'JPEG': JPEGLoader,
'PNG' : PNGLoader };
def __init__(self, name, panelName, detector):
self.setName(name);
self.setInputNames([name]);
self.setExtraNames([]);
# self.Units=[strUnit];
self.setLevel(7);
self.panel = panelName;
self.detector = detector;
self.scanNumberTracker = NumTracker("tmp");
self.fileName=None;
self.data = ScanFileHolder()
self.exposureTime = 0
self.logScale = False;
self.alive=True;
# To setup the image folder according to I06 requirement
self.scanImageDirectory();
self.fastMode=False;
self.protection=True;
# self.protectCamera();
self.verbose = False
#DetectorBase Implementation
def getPosition(self):
return self.readout();
def asynchronousMoveTo(self,newPos):
self.setCollectionTime(newPos);
self.collectData();
def getCollectionTime(self):
self.exposureTime=self.detector.getCollectionTime();
return self.exposureTime;
def setCollectionTime(self, newExpos):
self.exposureTime = newExpos;
self.detector.setCollectionTime(self.exposureTime);
def collectData(self):
#self.detector.setCollectionTime(self.exposureTime)
self.detector.collectData();
return;
def prepareForCollection(self):
#To put camera in the "camera mode"
self.detector.setCameraInProgress(False);
self.detector.prepareForCollection();
def endCollection(self):
# self.detector.endCollection();
if self.protection:
self.protectCamera();
return;
def readout(self):
self.fileName = self.detector.readout();
if self.alive:
self.display();
return self.fileName;
def getStatus(self):
return self.detector.getStatus();
def createsOwnFiles(self):
return True;
def toString(self):
self.getPosition();
return "Latest image file: " + self.getFullFileName();
def isBusy(self):
return self.detector.getStatus() == Detector.BUSY
## Extra Implementation
def setFileFormat(self, fileExt, contents=2):
'''
fileExtension: dat: Raw data uncompressed
png: PNG compressed
tiff: TIFF compressed
bmp: BMP uncompressed
jpg: JPG compressed
tif: TIFF uncompressed
imagecontents: 0: RGB 8+8+8 bits x,y,z, as seen on screen
1: RGB 8+8+8 bits,x,y raw, z as seen on screen
2: RAW 16 bits graylevel x, y, z raw data
'''
self.detector.setFileFormat(fileExt, contents);
def setImageAverage(self, averageParameter):
'''
averageParameter: -1: Sliding average. Current does NOT work!
0: No average
1 ~ 99: Number of frames to be averaged
'''
self.detector.setImageAverageNumber(averageParameter);
def getImageAverage(self):
iv=self.detector.getImageAverageNumber();
return iv;
def protectCamera(self):
#self.detector.setCollectionTime(0.1);
self.detector.setCameraInProgress(True);
if self.verbose:
print "Camera is set to 'Recorder Mode' for protection.";
return;
def setAlive(self, newAlive=True):
self.alive = newAlive;
def setLogScale(self, newLogScale=True):
self.logScale = newLogScale;
def setPanel(self, newPanelName):
self.panel = newPanelName;
def getDetectorInfo(self):
return self.detectorInfo;
def singleFastShot(self, newExpos=None):
if newExpos is not None: # New exposure time given
self.exposureTime = newExpos;
self.setCollectionTime(newExpos);
return self.detector.shotSingleImage();
def singleShot(self, newExpos=None):
"""Shot single image with given exposure time""";
#To put camera in the "camera mode"
self.detector.setCameraInProgress(False);
if self.getStatus() != Detector.IDLE:
print 'Camera not available, please try later';
return;
if newExpos is not None: # New exposure time given
self.exposureTime = newExpos;
self.setCollectionTime(self.exposureTime);
self.detector.setCameraSequentialMode(True);
#self.setNumOfImages(1);
self.collectData();
sleep(self.exposureTime);
while self.getStatus() != Detector.IDLE:
sleep(self.exposureTime/10.0);
if self.protection:
self.protectCamera();
return self.readout();
def multiShot(self, numberOfImages, newExpos=None, newDir=True):
"""Shot multiple images with given exposure time""";
#To put camera in the "camera mode"
self.detector.setCameraInProgress(False);
if self.getStatus() != Detector.IDLE:
print 'Camera not available, please try later';
return;
if newExpos is not None: # New exposure time given
self.exposureTime = newExpos;
self.setCollectionTime(self.exposureTime);
if newDir:
self.newImageDirectory();
self.scanImageDirectory();
else:
self.detector.setCameraSequentialMode(True);
temp=self.alive;
self.alive=False;#To turn off the display
if self.fastMode:
fn=self.multiFastShot(numberOfImages);
else:
fn=self.multiSafeShot(numberOfImages);
self.alive=temp; #To restoru the display setting
if self.protection:
self.protectCamera();
return fn;
def multiSafeShot(self, numberOfImages):
fn=[];
#self.setNumOfImages(numberOfImages);
for n in range(numberOfImages):
self.collectData();
sleep(self.exposureTime);
while self.getStatus() != Detector.IDLE:
sleep(self.exposureTime/10.0);
fn.append( self.readout() );
return fn;
def multiFastShot(self, numberOfImages):
fn=[];
#To take the first image
self.collectData()
sleep(self.exposureTime + 0.15);
i=0;
while i<numberOfImages-1:
self.collectData();#To trigger a new acquisition
t0=time.time();
fn.append( self.readout() );#To save the previous picture
t1=time.time();
td=t1-t0;
if td < self.exposureTime+0.15:#To wait the exposure time, plus a 150ms delay?
sleep(self.exposureTime+0.15-td);
i+=1;
fn.append( self.readout() );#To save the last previous triggered picture
return fn;
def display(self,file=None):
if file==None:
file = self.getFullFileName()
fileLoader = UViewDetectorClass.ImageFileLoaders[os.path.splitext(file)[-1].split('.')[-1].upper()];
self.data.load( fileLoader(file) );
dataset = self.data.getAxis(0);
if self.panel:
if self.logScale:
RCPPlotter.imagePlot(self.panel, DatasetUtils.lognorm(dataset)); #For RCP GUI
else:
RCPPlotter.imagePlot(self.panel, dataset); #For RCP GUI
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
def setNumOfImages(self, number):
# self.detector.setNumOfImages(number);
return;
def getNumOfImages(self):
return 1
# return self.detector.getNumOfImages();
# To use the directory with scan number to save image, like what scan command does.
def scanImageDirectory(self):
#increase the scan number for one
self.scanNumberTracker.incrementNumber();
self.prepareForCollection();
# To create a new directory following the PEEM image directory rules
def newImageDirectory(self, newDir=None):
if newDir is not None:
self.detector.setImageDir(newDir);
self.detector.prepare();
def getFullFileName(self):
"""Returns file path of the LAST CREATED image"""
return self.fileName;
class DummyAreaDetectorClass(DetectorBase):
def __init__(self, name, panelName, zippedImageSource, fileImageExtension):
self.setName(name);
# self.setInputNames([]);
self.setLevel(7);
self.panel = panelName;
self.data = ScanFileHolder();
self.triggerTime = 0;
self.filePath = None;
self.filePrefix = None;
self.logScale = False;
self.alive=True;
# self.imageProducer=ZipImageProducerClass('/scratch/Dev/gdaDev/gda-config/i07/scripts/Diamond/Pilatus/images100K.zip', 'tif');
self.imageProducer=ZipImageProducerClass(zippedImageSource, fileImageExtension);
self.fullImageFileName = None;
# DetectorBase Implementation
def collectData(self):
self.triggerTime = time.time();
self.fullImageFileName = self.imageProducer.getNextImage();
return;
def readout(self):
if self.alive:
self.display();
return self.fullImageFileName;
def getStatus(self):
currenttime = time.time();
if currenttime<self.triggerTime + self.getCollectionTime():
return Detector.BUSY
else:
return Detector.IDLE;
def createsOwnFiles(self):
return True;
def toString(self):
self.getPosition();
return "Latest image file: " + self.getFullFileName();
## Extra Implementation
def setAlive(self, newAlive=True):
self.alive = newAlive;
def setLogScale(self, newLogScale=True):
self.logScale = newLogScale;
def setPanel(self, newPanelName):
self.panel = newPanelName;
def singleShot(self, newExpos):
"""Shot single image with given exposure time""";
if self.getStatus() != Detector.IDLE:
print 'Area Detector not available, please try later';
return;
self.setCollectionTime(newExpos);
self.collectData();
while self.getStatus() != Detector.IDLE:
time.sleep(self.getCollectionTime()/2.0);
return self.readout();
def multiShot(self, numberOfImages, newExpos=None):
"""Shot multiple images with given exposure time""";
if self.getStatus() != Detector.IDLE:
print 'Camera not available, please try later';
return;
if newExpos is not None: # New exposure time given
exposureTime=newExpos;
self.setCollectionTime(exposureTime);
exposureTime=self.getCollectionTime();
fn=[];
#self.setNumOfImages(numberOfImages);
for n in range(numberOfImages):
self.collectData();
time.sleep(exposureTime);
while self.getStatus() != Detector.IDLE:
time.sleep(exposureTime/10.0);
fn.append( self.readout() );
return fn;
def display(self,file=None):
if file==None:
file = self.getFullFileName()
# self.data.loadPilatusData(file)
self.data.load(PilatusTiffLoader(file));
dataset = self.data.getAxis(0);
if self.panel:
if self.logScale:
SDAPlotter.imagePlot(self.panel, DatasetUtils.lognorm(dataset)); #For RCP GUI
else:
SDAPlotter.imagePlot(self.panel, dataset); #For RCP GUI
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
## Area Detector Implementation
def setFile(self, subDir, newFilePrefix):
"""Set file path and name"""
# imagePath = PathConstructor.createFromProperty("gda.data.scan.datawriter.datadir");
imagePath=PathConstructor.createFromDefaultProperty() + File.separator;
fullPath = os.path.join(imagePath, subDir);
print "Note: Current Pilatus image path: " + fullPath;
self.imageProducer.setFilePath(fullPath);
self.imageProducer.setFilePrefix(newFilePrefix);
#a.setFilePath("/scratch/temp")
#a.setFilePrefix("p100k")
def getFilePath(self):
return self.imageProducer.getFilePath();
def getFilePrefix(self):
return self.imageProducer.getFilePrefix();
def getFileNumber(self):
"""Get filenumber"""
self.fileNumber = self.imageProducer.getFileNumber();
return self.fileNumber
def getFullFileName(self):
return self.fullImageFileName;
class DummyAreaDetectorClass(DetectorBase):
def __init__(self, name, panelName, zippedImageSource, fileImageExtension):
self.setName(name)
# self.setInputNames([]);
self.setLevel(7)
self.panel = panelName
self.data = ScanFileHolder()
self.triggerTime = 0
self.filePath = None
self.filePrefix = None
self.logScale = False
self.alive = True
# self.imageProducer=ZipImageProducerClass('/scratch/Dev/gdaDev/gda-config/i07/scripts/Diamond/Pilatus/images100K.zip', 'tif');
self.imageProducer = ZipImageProducerClass(zippedImageSource,
fileImageExtension)
self.fullImageFileName = None
# DetectorBase Implementation
def collectData(self):
self.triggerTime = time.time()
self.fullImageFileName = self.imageProducer.getNextImage()
return
def readout(self):
if self.alive:
self.display()
return self.fullImageFileName
def getStatus(self):
currenttime = time.time()
if currenttime < self.triggerTime + self.getCollectionTime():
return Detector.BUSY
else:
return Detector.IDLE
def createsOwnFiles(self):
return True
def toString(self):
self.getPosition()
return "Latest image file: " + self.getFullFileName()
## Extra Implementation
def setAlive(self, newAlive=True):
self.alive = newAlive
def setLogScale(self, newLogScale=True):
self.logScale = newLogScale
def setPanel(self, newPanelName):
self.panel = newPanelName
def singleShot(self, newExpos):
"""Shot single image with given exposure time"""
if self.getStatus() != Detector.IDLE:
print 'Area Detector not available, please try later'
return
self.setCollectionTime(newExpos)
self.collectData()
while self.getStatus() != Detector.IDLE:
time.sleep(self.getCollectionTime() / 2.0)
return self.readout()
def multiShot(self, numberOfImages, newExpos=None):
"""Shot multiple images with given exposure time"""
if self.getStatus() != Detector.IDLE:
print 'Camera not available, please try later'
return
if newExpos is not None: # New exposure time given
exposureTime = newExpos
self.setCollectionTime(exposureTime)
exposureTime = self.getCollectionTime()
fn = []
#self.setNumOfImages(numberOfImages);
for n in range(numberOfImages):
self.collectData()
time.sleep(exposureTime)
while self.getStatus() != Detector.IDLE:
time.sleep(exposureTime / 10.0)
fn.append(self.readout())
return fn
def display(self, file=None):
if file == None:
file = self.getFullFileName()
# self.data.loadPilatusData(file)
self.data.load(PilatusTiffLoader(file))
dataset = self.data.getAxis(0)
if self.panel:
if self.logScale:
SDAPlotter.imagePlot(self.panel, DatasetUtils.lognorm(dataset))
#For RCP GUI
else:
SDAPlotter.imagePlot(self.panel, dataset)
#For RCP GUI
else:
print "No panel set to display"
raise Exception(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
## Area Detector Implementation
def setFile(self, subDir, newFilePrefix):
"""Set file path and name"""
# imagePath = PathConstructor.createFromProperty("gda.data.scan.datawriter.datadir");
imagePath = PathConstructor.createFromDefaultProperty(
) + File.separator
fullPath = os.path.join(imagePath, subDir)
print "Note: Current Pilatus image path: " + fullPath
self.imageProducer.setFilePath(fullPath)
self.imageProducer.setFilePrefix(newFilePrefix)
#a.setFilePath("/scratch/temp")
#a.setFilePrefix("p100k")
def getFilePath(self):
return self.imageProducer.getFilePath()
def getFilePrefix(self):
return self.imageProducer.getFilePrefix()
def getFileNumber(self):
"""Get filenumber"""
self.fileNumber = self.imageProducer.getFileNumber()
return self.fileNumber
def getFullFileName(self):
return self.fullImageFileName
class AnalyserDetectorClass(DetectorBase):
def __init__(self, name, detector, processors=[], panelName="Area Detector", iFileLoader=None):
self.detector = detector;
self.processors = processors;
self.panel = panelName;
self.iFileLoader = iFileLoader;
self.filename= None;
self.data = ScanFileHolder();
self.dataset = None;
self.mask = None;
self.result = None;
self.alive = False;
self.scannableSetup(name);
def scannableSetup(self, name):
self.setName(name);
self.setInputNames([]);
extraNames = ['ExposureTime', 'file'];
# extraNames = ['file'];
# extraNames = [];
outputFormat = ['%f','%s'];
if self.processors != None:
for processor in self.processors:
for label in processor.labelList:
extraNames.append(self.name + '_' + label)
outputFormat.append( '%f' );
# self.extraNames = extraNames;
# self.outputFormat = outputFormat;
self.setExtraNames(extraNames);
self.setOutputFormat(outputFormat);
self.level = self.detector.getLevel() + 1;
def setAlive(self, newAlive=True):
self.alive = newAlive;
def loadDataFromFile(self, fileName, fileLoader=None):
if fileLoader is None:
fileLoader = ImageFileLoaders[os.path.splitext(fileName)[-1].split('.')[-1].upper()];
try:
self.data.load(fileLoader(fileName));
except IllegalArgumentException:
raise IOError("Oh Dear. How to load this image file?");
return self.data;
def loadDataset(self, fileName = None, fileLoader = None):
self.dataset = None;
if fileLoader == None:
fileLoader = self.iFileLoader;
if fileName != None:#Get data from file directly
self.data = self.loadDataFromFile(fileName, fileLoader);
if self.data is not None:
self.filename = fileName;
# self.dataset = self.data[0];
self.dataset = self.data.getAxis(0);
else: #Get data from detector
if self.detector.createsOwnFiles():
fn=self.detector.readout();
self.data = self.loadDataFromFile(fn, fileLoader);
if self.data is not None:
self.filename = fn;
# self.dataset = self.data[0];
self.dataset = self.data.getAxis(0);
else:
self.filename = None;
ds = self.detector.readout();
if isinstance(ds, DataSet):
self.dataset = ds;
else:
self.dataset = None;
raise Exception('For none file generating detector, a DataSet is needed for analysis.');
#Apply mask if available:
self.dataset = self.applyMask(self.mask, self.dataset);
return self.dataset;
def loadFile(self, fileName = None, fileLoader = None):
return self.loadDataset(fileName, fileLoader);
def getResult(self, processor, dataset):
result = [];
if dataset is None:
print "Warning: None dataset";
return result;
twodDataSetResult = processor.process(dataset, 0, 0);
d = twodDataSetResult.resultsDict
for key in processor.labelList:
result.append(d[key])
return result
def setResult(self, pos):
self.result = {}
for key, val in zip(list(self.getInputNames()) + list(self.getExtraNames()), pos):
self.result[key] = val
def getMask(self):
return self.mask;
def removeMask(self):
self.mask = None;
def createMask(self, low, high, dataset=None):
if dataset is None:
if self.dataset is None:
print "No reference dataset to mask";
return;
else:
dataset = self.dataset;
maskMaker=MakeMask(low, high);
# arrayListDataset = ArrayList(dataset.exec(maskMaker));
# self.mask=DataSet(arrayListDataset.get(0));
self.mask = ArrayList(dataset.exec(maskMaker)).get(0).cast(Dataset.FLOAT64);
return self.mask;
def applyMask(self, mask=None, dataset=None):
if dataset is None:
if self.dataset is None:
print "No dataset to mask";
return;
else:
dataset = self.dataset;
if mask is None:
if self.mask is None:
# print "No mask provided, please create new mask";
return dataset;
else:
mask = self.mask;
maskedDataet = dataset * mask
# if self.alive:
# self.display(maskedDataet);
return maskedDataet;
def display(self, dataset=None):
if dataset is None:
if self.dataset is None:
print "No dataset to display";
return;
else:
dataset = self.dataset;
if self.panel:
RCPPlotter.imagePlot(self.panel, dataset);
else:
print "No panel set to display"
raise Exception("No panel_name set in %s. Set this or set %s.setAlive(False)" % (self.name,self.name));
### DetectorBase implementations:
def createsOwnFiles(self):
return False;
def getCollectionTime(self):
return self.detector.getCollectionTime();
def setCollectionTime(self, newExpos):
self.detector.setCollectionTime(newExpos);
def collectData(self):
self.dataset = None;
self.result = None;
self.detector.collectData();
def readout(self):
self.loadDataset();
result = [self.detector.getCollectionTime(), self.filename];
if self.processors != None:
for processor in self.processors:
result += list(self.getResult(processor, self.dataset));
self.setResult(result);
if self.alive:
self.display();
return result;
def getStatus(self):
return self.detector.getStatus();
def getDescription(self):
return "An Detector based analyser";
def getDetectorID(self):
return "dumbdumb-1";
def getDetectorType(self):
return "AnalyserDetectorClass";
def ncdredconf(self, detector, **kwords):
"""
if default None passed in no change is made
default is everything off
"""
if detector.lower() == "Waxs".lower():
detector="Waxs"
else:
detector="Saxs"
if not detector in self.settings:
self.settings[detector] = {}
for i in self.options:
if not i in self.settings[detector]:
self.settings[detector][i] = False
if i in kwords:
if kwords[i] == None:
self.settings[detector][i] = False
else:
self.settings[detector][i] = kwords[i]
realdet=ncdutils.getDetectorByType(self.detsystem, detector.upper())
realdetname = realdet.getName()
ncdutils.removeDetectorByName(self.detsystem, detector+" chain")
saxsrc=ReductionChain(detector+" chain", realdetname)
saxsrclist=saxsrc.getChain()
panel=detector+" Plot"
beanbag=SDAPlotter.getGuiBean(panel)
if beanbag == None:
beanbag = {}
sroi = None
if self.is2D(realdet):
if GuiParameters.ROIDATA in beanbag:
roi = beanbag[GuiParameters.ROIDATA]
if isinstance(roi, SectorROI):
sroi = roi
radii = sroi.getRadii()
self.settings[detector]["length"]=int(math.ceil(radii[1]-radii[0]))
self.settings[detector]["disttobeamstop"]=radii[0]
length = self.settings[detector]["length"]
slope = self.settings[detector]["slope"]
intercept = self.settings[detector]["intercept"]
if slope == 0 or slope == False:
axisds=None
else:
axis=[]
pis = realdet.getPixelSize()*1000
d2b = self.settings[detector]["disttobeamstop"]
for i in range(length):
axis.append(float((i+d2b)*pis*slope+intercept))
axisds=DataSet("qaxis", axis)
mask = self.settings[detector]["mask"]
sect = self.settings[detector]["sect"]
if sroi != None:
if sect or isinstance(axisds, DataSet):
start = sroi.getPoint()
realdet.setAttribute("beam_center_x", start[0])
realdet.setAttribute("beam_center_y", start[1])
else:
realdet.setAttribute("beam_center_x", None)
realdet.setAttribute("beam_center_y", None)
cameralength = self.settings[detector]["cameralength"]
if cameralength != False:
realdet.setAttribute("distance", cameralength)
else:
realdet.setAttribute("distance", None)
norm = self.settings[detector]["norm"]
if (norm != False):
saxsnorm=Normalisation(detector+"norm","ignored")
saxsnorm.setCalibChannel(1)
saxsnorm.setCalibName(ncdutils.getDetectorByType(self.detsystem, "CALIB").getName())
saxsrclist.add(saxsnorm)
bg = self.settings[detector]["bg"]
if bg != False:
if os.path.isfile(bg):
saxsbgs=BackgroundSubtraction(detector+"bg","ignored")
sfh=ScanFileHolder()
if (norm>=0):
upstream=detector+"norm.data"
else:
upstream=realdetname+".data"
sfh.load(NexusLoader(bg,[upstream]))
ds=sfh.getAxis(upstream)
saxsbgs.setBackground(ds)
saxsrclist.add(saxsbgs)
else:
print "background file \"%s\" does not exist." % bg
if (sect):
if sroi != None:
saxssect=SectorIntegration(detector+"sect","ignored")
saxssect.setROI(sroi)
if isinstance(axisds, DataSet):
saxssect.setqAxis(axisds)
if (mask):
if not GuiParameters.MASKING in beanbag:
print "no mask defined for %s" % panel
else:
mb=beanbag[GuiParameters.MASKING]
if not isinstance(mb, MaskingBean):
print "no mask defined for %s" % panel
else:
saxssect.setMask(mb.getMask())
saxsrclist.add(saxssect)
else:
print "sector integration requested but no ROI found"
inv = self.settings[detector]["inv"]
if (inv):
saxsinvariant=Invariant(detector+"invariant", "ignored")
saxsrclist.add(saxsinvariant)
aver = self.settings[detector]["aver"]
if (aver):
saxsaver=Average(detector+"average", "ignored")
saxsrclist.add(saxsaver)
self.detsystem.addDetector(saxsrc)
class DetectorAnalyserClass(ScannableMotionBase):
def __init__(self,
name,
detector,
processors=[],
panelName="Area Detector",
iFileLoader=None):
self.detector = detector
self.processors = processors
self.panel = panelName
self.iFileLoader = iFileLoader
self.filename = None
self.data = ScanFileHolder()
self.dataset = None
self.mask = None
self.result = None
self.passive = False
self.alive = False
self.scannableSetup(name)
def scannableSetup(self, name):
self.setName(name)
self.inputNames = [self.detector.getName() + 'Wrapper_' + name]
extraNames = ['file']
outputFormat = ['%f', '%s']
if self.processors != None:
for processor in self.processors:
for label in processor.labelList:
extraNames.append(self.name + '_' + label)
outputFormat.append('%f')
self.extraNames = extraNames
self.outputFormat = outputFormat
self.level = self.detector.getLevel() + 1
def setPassive(self, newPassive=True):
"""
Set the detector analyser to be Passive or Active
Device Passive means this analyser will not drive its detector but only works with the latest detector data.
Device NoPassive/Active means this analyser will drive its detector to get new data and then works with the new acquisition.
"""
self.passive = newPassive
def setAlive(self, newAlive=True):
self.alive = newAlive
def loadDataFromFile(self, fileName, fileLoader):
if fileLoader is None:
fileLoader = GDA_FILELOADERS[os.path.splitext(fileName)
[-1].upper()]
# print "loadIntoSfh loading: %s using %s" % (fileName, str(iFileLoader))
print fileName
self.data.load(fileLoader(fileName))
return self.data
def loadDataset(self, fileName=None, fileLoader=None):
self.dataset = None
if fileLoader == None:
fileLoader = self.iFileLoader
if fileName != None: #Get data from file directly
self.data = self.loadDataFromFile(fileName, fileLoader)
if self.data is not None:
self.filename = fileName
# self.dataset = self.data[0];
self.dataset = self.data.getAxis(0)
else: #Get data from detector
if self.detector.createsOwnFiles():
fn = self.detector.readout()
self.data = self.loadDataFromFile(fn, fileLoader)
if self.data is not None:
self.filename = fn
# self.dataset = self.data[0];
self.dataset = self.data.getAxis(0)
else:
self.filename = None
ds = self.detector.readout()
if isinstance(ds, DoubleDataset):
self.dataset = ds
else:
self.dataset = None
raise Exception(
'For none file generating detector, a DataSet is needed for analysis.'
)
#Apply mask if available:
self.dataset = self.applyMask(self.mask, self.dataset)
return self.dataset
def loadFile(self, fileName=None, fileLoader=None):
return self.loadDataset(fileName, fileLoader)
def getResult(self, processor, dataset):
result = []
if dataset is None:
print "Warning: None dataset"
return result
twodDataSetResult = processor.process(dataset, 0, 0)
d = twodDataSetResult.resultsDict
for key in processor.labelList:
result.append(d[key])
return result
def setResult(self, pos):
self.result = {}
for key, val in zip(
list(self.getInputNames()) + list(self.getExtraNames()), pos):
self.result[key] = val
def getMask(self):
return self.mask
def removeMask(self):
self.mask = None
def createMask(self, low, high, dataset=None):
if dataset is None:
if self.dataset is None:
print "No reference dataset to mask"
return
else:
dataset = self.dataset
maskMaker = MakeMask(low, high)
# arrayListDataset = ArrayList(dataset.exec(maskMaker));
# self.mask=DataSet(arrayListDataset.get(0));
self.mask = maskMaker.value(dataset).get(0).cast(Dataset.FLOAT64)
return self.mask
def applyMask(self, mask=None, dataset=None):
if dataset is None:
if self.dataset is None:
print "No dataset to mask"
return
else:
dataset = self.dataset
if mask is None:
if self.mask is None:
print "No mask provided, please create new mask"
return dataset
else:
mask = self.mask
maskedDataet = dataset * mask
# if self.alive:
# self.display(maskedDataet);
return maskedDataet
def display(self, dataset=None):
if dataset is None:
if self.dataset is None:
print "No dataset to display"
return
else:
dataset = self.dataset
if self.panel:
RCPPlotter.imagePlot(self.panel, dataset)
else:
print "No panel set to display"
raise Exception(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
def rescan(self, scanNumber):
"""
To re-do the data analysis based on the data set generated in the previous scan
Input: scanNumber: the old scan that created a list of data files
Output: a new SRS data file that re do the data analysis
"""
self.data.loadSRS(scanNumber)
self.data.info()
#find the file name
#load dataset from the file
#do the analysis and get result
#save into a new srs file
def __getitem__(self, key):
if self.result == None:
self.getPosition()
return self.result[key]
### Psduco Device Interface method implementations:
def asynchronousMoveTo(self, exposureTime):
if self.passive:
print "The Detector Analyser " + self.name + " only works with existing detector data, no new data will be collected."
return
self.dataset = None
self.result = None
self.detector.asynchronousMoveTo(exposureTime)
# self.detector.setCollectionTime(t);
# self.detector.collectData();
def isBusy(self):
if self.passive:
return False
else:
return self.detector.getStatus() == Detector.BUSY
def getPosition(self):
self.loadDataset()
result = [self.detector.getCollectionTime(), self.filename]
if self.processors != None:
for processor in self.processors:
result += list(self.getResult(processor, self.dataset))
self.setResult(result)
if self.alive:
self.display()
return result
def __init__(self):
self.data = ScanFileHolder()
class PilatusPseudoDeviceClass(DetectorBase, ShutterDeviceClass):
DETECTOR_STATUS_IDLE, DETECTOR_STATUS_BUSY, DETECTOR_STATUS_PAUSED, DETECTOR_STATUS_STANDBY, DETECTOR_STATUS_FAULT, DETECTOR_STATUS_MONITORING = range(
6)
def __init__(self, name, panelName, detectorName, shutterName=None):
self.setName(name)
self.setInputNames(['exposure'])
self.setExtraNames([])
# self.setOutputFormat(['%.2f']);
self.setLevel(7)
self.panel = panelName
self.detector = vars(gdamain)[detectorName]
self.detectorInfo = None
self.data = ScanFileHolder()
self.exposureTime = 0
self.sum = 0
self.maxpix = 0
# self.filePath = None;
# self.filePrefix = None;
# self.fileFormat = "%s%s%4.4d.tif";
# self.fileNumber = self.detector.getFileNumber();
self.logScale = False
self.alive = True
ShutterDeviceClass.__init__(self, shutterName)
# DetectorBase Implementation
def getPosition(self):
return self.readout()
# def asynchronousMoveTo(self,newExpos):
# self.setCollectionTime(newExpos)
# self.collectData();
def getCollectionTime(self):
self.exposureTime = self.detector.getCollectionTime()
return self.exposureTime
def setCollectionTime(self, newExpos):
self.exposureTime = newExpos
self.detector.setCollectionTime(self.exposureTime)
def collectData(self):
self.openShutter()
self.detector.collectData()
return
def readout(self):
self.closeShutter()
self.fileNumber = self.detector.readout()
fileName = self.getFullFileName()
if not self.fileExists(fileName, 100):
logger.simpleLog("PilatusDetectorPseudoDevice.readout(): File '" +
fileName + "' does not exist!")
raise Exception("No File Found Error")
if self.alive:
self.display()
return fileName
def getStatus(self):
return self.detector.getStatus()
def createsOwnFiles(self):
return True
def toString(self):
self.getPosition()
return "Latest image file: " + self.getFullFileName()
def stop(self):
self.closeShutter()
## Extra Implementation
def setAlive(self, newAlive=True):
self.alive = newAlive
def setLogScale(self, newLogScale=True):
self.logScale = newLogScale
def setPanel(self, newPanelName):
self.panel = newPanelName
def getDetectorInfo(self):
return self.detectorInfo
def singleShot(self, newExpos):
"""Shot single image with given exposure time"""
if self.getStatus() != Detector.IDLE:
print 'Pilatus not available, please try later'
return
self.openShutter()
self.setCollectionTime(newExpos)
self.setNumOfImages(1)
self.collectData()
while self.getStatus() != Detector.IDLE:
sleep(self.exposureTime / 2.0)
return self.readout()
def multiShot(self, newExposureTime, newExposurePeirod, newNumberOfImages):
"""Shot single image with given exposure time"""
if self.getStatus() != Detector.IDLE:
print 'Pilatus not available, please try later'
return
self.openShutter()
self.setCollectionTime(newExposureTime)
self.setExposurePeriod(newExposurePeirod)
self.setNumOfImages(newNumberOfImages)
self.collectData()
while self.getStatus() != Detector.IDLE:
sleep(self.exposureTime * newNumberOfImages / 5.0)
self.closeShutter()
print 'Done, file number is: ' + str(self.getFileNumber())
return self.detector.getMultipleFullFileNames()
def display(self, file=None):
if file == None:
file = self.getFullFileName()
# self.data.loadPilatusData(file)
self.data.load(PilatusTiffLoader(file))
dataset = self.data.getAxis(0)
if self.panel:
if self.logScale:
RCPPlotter.imagePlot(self.panel, DatasetMaths.lognorm(dataset))
#For RCP GUI
else:
RCPPlotter.imagePlot(self.panel, dataset)
#For RCP GUI
else:
print "No panel set to display"
raise Exception(
"No panel_name set in %s. Set this or set %s.setAlive(False)" %
(self.name, self.name))
def triggerOn(self, interval):
# self.detector.start();
self.detector.trigger()
self.triggerFlag = True
while self.triggerFlag:
sleep(interval)
self.readout()
def triggerOff(self):
self.triggerFlag = False
self.detector.stop()
## Pilatus Implementation
def setFile(self, subDir, newFilePrefix):
"""Set file path and name"""
pilatusDataDir = InterfaceProvider.getPathConstructor(
).createFromDefaultProperty()
# pilatusDataDir = InterfaceProvider.getPathConstructor().createFromProperty("gda.pilatus.datadir");
fullPath = os.path.join(pilatusDataDir, subDir)
if not os.path.exists(fullPath):
print "Warning: Pilatus image path does not exist. Create new"
print "OS Command: " + "umask 0002; mkdir -p " + fullPath
os.system("umask 0002; mkdir -p " + fullPath)
# Check the new path created.
if not os.path.exists(fullPath):
print "Error: Pilatus image path does not exist and can not be created"
return
print "Note: Current Pilatus image path: " + fullPath
self.detector.setFilePath(fullPath)
self.detector.setFilePrefix(newFilePrefix)
def getFilePath(self):
return self.detector.getFilePath()
def getFilePrefix(self):
"""Get filename - not the path"""
return self.detector.getFilePrefix()
def getFileNumber(self):
"""Get filenumber"""
self.fileNumber = self.detector.getFileNumber()
return self.fileNumber
def getFullFileName(self):
"""Returns file path of the LAST CREATED image"""
return self.detector.getFullFileName()
def setThreshold(self, newGain, newThresholdEnergy):
self.detector.setThreshold(newGain, newThresholdEnergy)
return
def getThreshold(self):
return self.detector.getThreshold()
def setExposurePeriod(self, newExpp):
self.detector.setExposurePeriod(newExpp)
return
def getExposurePeriod(self):
return self.detector.getExposurePeriod()
def setNumOfImages(self, number):
self.detector.setNumOfImages(number)
def getNumOfImages(self):
return self.detector.getNumOfImages()
#Additional DLS Luster fix to deal with delay
def fileExists(self, fileName, numberOfTry):
result = False
for i in range(numberOfTry):
if (not os.path.exists(fileName)) or (
not os.path.isfile(fileName)):
if i > 1: #To make a note if tried more than twice
print "File does not exist on try " + str(i + 1)
logger.simpleLog(
"DetectorAnalyser: File does not exist on try " +
str(i + 1))
#check again:
sleep(1)
os.system("ls -la " + fileName)
#To try to update the file system
else:
#To touch the file will change the timestamps on the directory, which in turn causes the client to refetch the file's attributes.
os.system("touch -c " + fileName)
#To check the file size non zero
fsize = os.stat(fileName)[stat.ST_SIZE]
if i > 1: #To make a note if tried more than twice
print "File exists on try " + str(
i + 1) + " with size " + str(fsize)
logger.simpleLog("DetectorAnalyser: File '" + fileName +
"' exists on try " + str(i + 1) +
" with size " + str(fsize))
sizeP100K = 383956L
sizeP2M = 9910196L
if fsize != sizeP100K and fsize != sizeP2M:
print "Wrong file size: " + str(fsize)
logger.simpleLog("DetectorAnalyser: File '" + fileName +
"' has wrong file size: " + str(fsize))
sleep(1)
continue
#The file seems exist with some content inside. Double check to make sure it's available
try:
#To touch the file will change the timestamps on the directory, which in turn causes the client to refetch the file's attributes.
os.system("touch -c " + fileName)
tf = open(fileName, "rb")
tf.close()
result = True
break
except:
print "There are something wrong on the file system !!!"
logger.simpleLog(
"DetectorAnalyser: There are something wrong on the file system !!!"
)
return result
class KeyPositionClass(object):
def __init__(self, xAxisName, yAxisName):
self.xAxisName=xAxisName;
self.yAxisName=yAxisName;
self.data=ScanFileHolder();
def update(self):
self.data.loadSRS();
# self.data.loadSRS("/home/xr56/Dev/gdaDev/gda-config/i07/users/data/operation/83.dat");
def getKeyValues(self, axisName):
self.update();
ds=self.data.getAxis(axisName)
mean = ds.mean();
std = ds.std();
sum = ds.sum();
minval = ds.min();
minpos = ds.minPos();
maxval = ds.max()
maxpos = ds.maxPos()
return [minpos, minval, maxpos, maxval, sum, mean, std];
def getPeak(self, xAxisName=None, yAxisName=None):
if xAxisName is None:
xAxisName = self.xAxisName;
if yAxisName is None:
yAxisName = self.yAxisName;
self.update();
yMax=self.data.getMax(yAxisName);
yPos = self.data.getMaxPos(yAxisName)[0];
xVal=self.data.getMaxPos(xAxisName, yAxisName);
return [xVal, yMax];
def getCentreOfMass(self, xAxisName=None, yAxisName=None):
if xAxisName is None:
xAxisName = self.xAxisName;
if yAxisName is None:
yAxisName = self.yAxisName;
self.update()
xDataSet=self.data.getAxis(xAxisName);
yDataSet=self.data.getAxis(yAxisName);
com = self.data.centroid(xDataSet, yDataSet)
xlist = list(xDataSet.getBuffer())
ylist = list(yDataSet.getBuffer())
second_moment = 0
sum = 0
for x, y in zip(xlist,ylist):
sum += y
second_moment += pow(x-com, 2) * y
normalised_second_moment = second_moment/sum
return [com, normalised_second_moment]
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 __init__(self, xAxisName, yAxisName): self.xAxisName=xAxisName; self.yAxisName=yAxisName; self.data=ScanFileHolder();
