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def setUp(self):
self.multiFrameFilename = UtilsTest.getimage("MultiFrame.edf.bz2")[:-4]
self.Frame0Filename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2")[:-4]
self.Frame1Filename = UtilsTest.getimage("MultiFrame-Frame1.edf.bz2")[:-4]
self.ref = edfimage()
self.frame0 = edfimage()
self.frame1 = edfimage()
try:
self.ref.read(self.multiFrameFilename)
except:
raise RuntimeError("Cannot read image multiFrameFilename image %s" % self.multiFrameFilename)
try:
self.frame0.read(self.Frame0Filename)
except:
raise RuntimeError("Cannot read image Frame0File image %s" % self.Frame0File)
try:
self.frame1.read(self.Frame1Filename)
except:
raise RuntimeError("Cannot read image Frame1File image %s" % self.Frame1File)
def setUp(self):
self.multiFrameFilename = UtilsTest.getimage("MultiFrame.edf.bz2")[:-4]
self.Frame0Filename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2")[:-4]
self.Frame1Filename = UtilsTest.getimage("MultiFrame-Frame1.edf.bz2")[:-4]
self.ref = edfimage()
self.frame0 = edfimage()
self.frame1 = edfimage()
try:
self.ref.read(self.multiFrameFilename)
except:
raise RuntimeError("Cannot read image multiFrameFilename image %s" % self.multiFrameFilename)
try:
self.frame0.read(self.Frame0Filename)
except:
raise RuntimeError("Cannot read image Frame0File image %s" % self.Frame0File)
try:
self.frame1.read(self.Frame1Filename)
except:
raise RuntimeError("Cannot read image Frame1File image %s" % self.Frame1File)
def setUp(self):
self.multiFrameFilename = UtilsTest.getimage("MultiFrame.edf.bz2")[:-4]
self.Frame0Filename = UtilsTest.getimage("MultiFrame-Frame0.edf.bz2")[:-4]
self.Frame1Filename = UtilsTest.getimage("MultiFrame-Frame1.edf.bz2")[:-4]
self.ref = edfimage()
self.frame0 = edfimage()
self.frame1 = edfimage()
try:
self.ref.read(self.multiFrameFilename)
except:
raise RuntimeError("Cannot read image multiFrameFilename image %s" % self.multiFrameFilename)
try:
self.frame0.read(self.Frame0Filename)
except:
raise RuntimeError("Cannot read image Frame0File image %s" % self.Frame0File)
try:
self.frame1.read(self.Frame1Filename)
except:
raise RuntimeError("Cannot read image Frame1File image %s" % self.Frame1File)
logger.error("Python h5py module is expected to use this script")
sys.exit(1)
infile = os.path.abspath(options.input_file)
if options.output_file is not None:
outfile = options.output_file
else:
outfile = os.path.splitext(infile)[0] + "_mask.edf"
mask = extract_mask(infile)
if outfile.endswith("msk"):
fabio.fit2dmaskimage.fit2dmaskimage(data=mask).write(outfile)
elif outfile.endswith("tif"):
fabio.tifimage.tifimage(data=mask).write(outfile)
else:
fabio.edfimage.edfimage(header={"data_file": infile}, data=mask).write(outfile)
def writeEDF(self, basename):
"""save the distortion matrices into a couple of files called basename-x.edf and basename-y.edf
"""
try:
from fabio.edfimage import edfimage
#from EdfFile import EdfFile as EDF
except ImportError:
print "You will need the Fabio library available from the Fable sourceforge"
return
self.spline2array()
edfDispX = edfimage(data=self.xDispArray.astype("float32"), header={})
edfDispY = edfimage(data=self.yDispArray.astype("float32"), header={})
edfDispX.write(basename + "-x.edf", force_type="float32")
edfDispY.write(basename + "-y.edf", force_type="float32")
def getBluredData(self):
"""
:return: a blurred image
"""
if self._blured_data is None:
with self._sem:
if self._blured_data is None:
logger.debug("Blurring image with kernel size: %s", self.valley_size)
self._blured_data = gaussian_filter(self.getBinnedData(), [self.valley_size / i for i in self.binning], mode="reflect")
if logger.getEffectiveLevel() == logging.DEBUG:
fabio.edfimage.edfimage(data=self._blured_data).write("blured_data.edf")
return self._blured_data
def exportimage(self):
fabimg = edfimage.edfimage(np.rot90(self.getCurrentTab().imageitem.image))
dialog = QtGui.QFileDialog(parent=None, caption=u"Export image as EDF",
directory=unicode(os.path.dirname(self.getCurrentTab().paths[0])),
filter=u"EDF (*.edf)")
dialog.selectFile(unicode(os.path.dirname(self.getCurrentTab().paths[0])))
filename, ok = dialog.getSaveFileName()
if ok and filename:
fabimg.write(filename)
def findgisaxsarcs2(img, experiment):
img = img.T.copy()
cake, _, _ = integration.cake(img, experiment, mask=experiment.mask) # TODO: refactor these parameters and check .T
maskcake, _, _ = integration.cake(experiment.mask.T, experiment)
from fabio import edfimage
fabimg = edfimage.edfimage(cake)
filename = 'cake.edf'
fabimg.write(filename)
fabimg = edfimage.edfimage(maskcake)
filename = 'cake_MASK.edf'
fabimg.write(filename)
img = inpaint(cake, maskcake)
fabimg = edfimage.edfimage(img)
filename = 'cake_LINEAR_INFILL.edf'
fabimg.write(filename)
maxchis, maxqs = findmaxs(img)
out =[]
for chi, q in zip(maxchis, maxqs):
# roi=np.ones_like(img)
#roi[chi - 10:chi + 10, q - 5:q + 5]=10