def test_guess_binning(self):
#Mar 345 2300 pixels with 150 micron size
mar = detector_factory("mar345")
shape = 2300, 2300
mar.guess_binning(shape)
self.assertEqual(shape, mar.mask.shape,
"Mar345 detector has right mask shape")
self.assertEqual(mar.pixel1, 150e-6,
"Mar345 detector has pixel size 150µ")
mar = detector_factory("mar345")
shape = 3450, 3450
mar.guess_binning(shape)
self.assertEqual(shape, mar.mask.shape,
"Mar345 detector has right mask shape")
self.assertEqual(mar.pixel1, 100e-6,
"Mar345 detector has pixel size 100µ")
mar = detector_factory("mar165")
shape = 1364, 1364
mar.guess_binning(shape)
self.assertEqual(shape, mar.mask.shape,
"Mar165 detector has right mask shape")
self.assertEqual(mar.pixel1, 118.616e-6,
"Mar166 detector has pixel size 118.616µ")
self.assertEqual(mar.binning, (3, 3), "Mar165 has 3x3 binning")
mar = detector_factory("RayonixLx170")
shape = 192, 384
mar.guess_binning(shape)
self.assertEqual(mar.binning, (10, 10),
"RayonixLx170 has 10x10 binning")
def test_guess_binning(self):
# Mar 345 2300 pixels with 150 micron size
mar = detector_factory("mar345")
shape = 2300, 2300
mar.guess_binning(shape)
self.assertEqual(shape, mar.mask.shape, "Mar345 detector has right mask shape")
self.assertEqual(mar.pixel1, 150e-6, "Mar345 detector has pixel size 150µ")
mar = detector_factory("mar345")
shape = 3450, 3450
mar.guess_binning(shape)
self.assertEqual(shape, mar.mask.shape, "Mar345 detector has right mask shape")
self.assertEqual(mar.pixel1, 100e-6, "Mar345 detector has pixel size 100µ")
mar = detector_factory("mar165")
shape = 1364, 1364
mar.guess_binning(shape)
self.assertEqual(shape, mar.mask.shape, "Mar165 detector has right mask shape")
self.assertEqual(mar.pixel1, 118.616e-6, "Mar166 detector has pixel size 118.616µ")
self.assertEqual(mar.binning, (3, 3), "Mar165 has 3x3 binning")
mar = detector_factory("RayonixLx170")
shape = 192, 384
mar.guess_binning(shape)
self.assertEqual(mar.binning, (10, 10), "RayonixLx170 has 10x10 binning")
p = detector_factory("Perkin")
self.assertEqual(p.pixel1, 200e-6, "raw detector has good pixel size")
self.assertEqual(p.binning, (2, 2), "raw detector has good pixel binning")
p.guess_binning((4096, 4096))
self.assertEqual(p.pixel1, 100e-6, "unbinned detector has good pixel size")
self.assertEqual(p.binning, (1, 1), "unbinned detector has good pixel binning")
def test_nexus_detector(self):
tmpdir = tempfile.mkdtemp()
known_fail = []
if io.h5py is None:
logger.warning("H5py not present, skipping test_detector.TestDetector.test_nexus_detector")
return
for det_name in ALL_DETECTORS:
fname = os.path.join(tmpdir, det_name + ".h5")
if os.path.exists(fname): # already tested with another alias
continue
det = detector_factory(det_name)
logger.info("%s --> nxs" % det_name)
if (det.pixel1 is None) or (det.shape is None):
continue
if (det.shape[0] > 1900) or (det.shape[1] > 1900):
continue
det.save(fname)
new_det = detector_factory(fname)
for what in ("pixel1", "pixel2", "name", "max_shape", "shape", "binning"):
if "__len__" in dir(det.__getattribute__(what)):
self.assertEqual(det.__getattribute__(what), new_det.__getattribute__(what), "%s is the same for %s" % (what, fname))
else:
self.assertAlmostEqual(det.__getattribute__(what), new_det.__getattribute__(what), 4, "%s is the same for %s" % (what, fname))
if (det.mask is not None) or (new_det.mask is not None):
self.assert_(numpy.allclose(det.mask, new_det.mask), "%s mask is not the same" % det_name)
if det.shape[0] > 2000:
continue
try:
r = det.calc_cartesian_positions()
o = new_det.calc_cartesian_positions()
except MemoryError:
logger.warning("Test nexus_detector failed due to short memory on detector %s" % det_name)
continue
self.assertEqual(len(o), len(r), "data have same dimension")
err1 = abs(r[0] - o[0]).max()
err2 = abs(r[1] - o[1]).max()
if det.name in known_fail:
continue
if err1 > 1e-6:
logger.error("%s precision on pixel position 1 is better than 1µm, got %e" % (det_name, err1))
if err2 > 1e-6:
logger.error("%s precision on pixel position 1 is better than 1µm, got %e" % (det_name, err2))
# self.assert_(err1 < 1e-6, "%s precision on pixel position 1 is better than 1µm, got %e" % (det_name, err1))
# self.assert_(err2 < 1e-6, "%s precision on pixel position 2 is better than 1µm, got %e" % (det_name, err2))
if not det.IS_FLAT:
err = abs(r[2] - o[2]).max()
self.assert_(err < 1e-6, "%s precision on pixel position 3 is better than 1µm, got %e" % (det_name, err))
# check Pilatus with displacement maps
# check spline
# check SPD sisplacement
shutil.rmtree(tmpdir)
def test_nexus_detector(self):
tmpdir = tempfile.mkdtemp()
known_fail = [] #TODO: fix broken detectors
# print(tmpdir)
for det_name in ALL_DETECTORS:
fname = os.path.join(tmpdir, det_name + ".h5")
if os.path.exists(fname): #already tested with another alias
continue
# print fname
det = detector_factory(det_name)
if (det.pixel1 is None) or (det.shape is None):
continue
# print(det)
det.save(fname)
new_det = detector_factory(fname)
# print new_det
for what in ("pixel1", "pixel2", "name", "max_shape", "shape",
"binning"):
if "__len__" in dir(det.__getattribute__(what)):
self.assertEqual(det.__getattribute__(what),
new_det.__getattribute__(what),
"%s is the same for %s" % (what, fname))
else:
self.assertAlmostEqual(
det.__getattribute__(what),
new_det.__getattribute__(what), 4,
"%s is the same for %s" % (what, fname))
if det.shape[0] > 2000:
continue
r1, r2 = det.calc_cartesian_positions()
o1, o2 = new_det.calc_cartesian_positions()
err1 = abs(r1 - o1).max()
err2 = abs(r2 - o2).max()
if det.name not in known_fail:
self.assert_(
err1 < 1e-6,
"%s precision on pixel position 1 is better than 1µm, got %e"
% (det_name, err2))
self.assert_(
err2 < 1e-6,
"%s precision on pixel position 2 is better than 1µm, got %e"
% (det_name, err2))
if (det.mask is not None) or (new_det.mask is not None):
self.assert_(numpy.allclose(det.mask, new_det.mask),
"%s mask is not the same" % det_name)
#check Pilatus with displacement maps
#check spline
#check SPD sisplacement
shutil.rmtree(tmpdir)
def test_non_flat(self):
"""
tests specific to non flat detectors to ensure consistency
"""
a = detector_factory("Aarhus")
# to limit the memory footprint, devide size by 100
a.binning = (10, 10)
t0 = time.time()
n = a.get_pixel_corners(use_cython=False)
t1 = time.time()
a._pixel_corners = None
c = a.get_pixel_corners(use_cython=True)
t2 = time.time()
logger.info("Aarhus.get_pixel_corners timing Numpy: %.3fs Cython: %.3fs" % (t1 - t0, t2 - t1))
self.assert_(abs(n - c).max() < 1e-6, "get_pixel_corners cython == numpy")
# test pixel center coordinates
t0 = time.time()
n1, n2, n3 = a.calc_cartesian_positions(use_cython=False)
t1 = time.time()
c1, c2, c3 = a.calc_cartesian_positions(use_cython=True)
t2 = time.time()
logger.info("Aarhus.calc_cartesian_positions timing Numpy: %.3fs Cython: %.3fs" % (t1 - t0, t2 - t1))
self.assert_(abs(n1 - c1).max() < 1e-6, "cartesian coord1 cython == numpy")
self.assert_(abs(n2 - c2).max() < 1e-6, "cartesian coord2 cython == numpy")
self.assert_(abs(n3 - c3).max() < 1e-6, "cartesian coord3 cython == numpy")
def test_detector_imxpad_s140(self):
"""
The masked image has a masked ring around 1.5deg with value
-10 without mask the pixels should be at -10 ; with mask they
are at 0
"""
imxpad = detector_factory("imxpad_s140")
# check that the cartesian coordinates is cached
self.assertEqual(hasattr(imxpad, '_pixel_edges'), True)
self.assertEqual(imxpad._pixel_edges, None)
y, x = imxpad.calc_cartesian_positions()
self.assertEqual(imxpad._pixel_edges is None, False)
# now check that the cached values are identical for each
# method call
y1, x1 = imxpad.calc_cartesian_positions()
self.assertEqual(numpy.all(numpy.equal(y1, y)), True)
self.assertEqual(numpy.all(numpy.equal(x1, x)), True)
# check that a few pixel positions are ok.
self.assertAlmostEqual(y[0, 0], 2.5 * 130e-6 / 2.)
self.assertAlmostEqual(y[3, 0], y[2, 0] + 130e-6)
self.assertAlmostEqual(y[119, 0], y[118, 0] + 130e-6 * 3.5 / 2.)
self.assertAlmostEqual(x[0, 0], 2.5 * 130e-6 / 2.)
self.assertAlmostEqual(x[0, 3], x[0, 2] + 130e-6)
self.assertAlmostEqual(x[0, 79], x[0, 78] + 130e-6 * 3.5 / 2.)
def test_non_flat(self):
"""
tests specific to non flat detectors to ensure consistency
"""
a = detector_factory("Aarhus")
t0 = time.time()
n = a.get_pixel_corners(use_cython=False)
t1 = time.time()
a._pixel_corners = None
c = a.get_pixel_corners(use_cython=True)
t2 = time.time()
logger.info(
"Aarhus.get_pixel_corners timing Numpy: %.3fs Cython: %.3fs" %
(t1 - t0, t2 - t1))
self.assert_(
abs(n - c).max() < 1e-6, "get_pixel_corners cython == numpy")
# test pixel center coordinates
t0 = time.time()
n1, n2, n3 = a.calc_cartesian_positions(use_cython=False)
t1 = time.time()
c1, c2, c3 = a.calc_cartesian_positions(use_cython=True)
t2 = time.time()
logger.info(
"Aarhus.calc_cartesian_positions timing Numpy: %.3fs Cython: %.3fs"
% (t1 - t0, t2 - t1))
self.assert_(
abs(n1 - c1).max() < 1e-6, "cartesian coord1 cython == numpy")
self.assert_(
abs(n2 - c2).max() < 1e-6, "cartesian coord2 cython == numpy")
self.assert_(
abs(n3 - c3).max() < 1e-6, "cartesian coord3 cython == numpy")
def test_detector_imxpad_s140(self):
"""
The masked image has a masked ring around 1.5deg with value
-10 without mask the pixels should be at -10 ; with mask they
are at 0
"""
imxpad = detector_factory("imxpad_s140")
# check that the cartesian coordinates is cached
self.assertEqual(hasattr(imxpad, '_pixel_edges'), True)
self.assertEqual(imxpad._pixel_edges, None)
y, x, z = imxpad.calc_cartesian_positions()
self.assertEqual(imxpad._pixel_edges is None, False)
# now check that the cached values are identical for each
# method call
y1, x1, z1 = imxpad.calc_cartesian_positions()
self.assertEqual(numpy.all(numpy.equal(y1, y)), True)
self.assertEqual(numpy.all(numpy.equal(x1, x)), True)
self.assertEqual(z, None)
self.assertEqual(z1, None)
# check that a few pixel positions are ok.
self.assertAlmostEqual(y[0, 0], 2.5 * 130e-6 / 2.)
self.assertAlmostEqual(y[3, 0], y[2, 0] + 130e-6)
self.assertAlmostEqual(y[119, 0], y[118, 0] + 130e-6 * 3.5 / 2.)
self.assertAlmostEqual(x[0, 0], 2.5 * 130e-6 / 2.)
self.assertAlmostEqual(x[0, 3], x[0, 2] + 130e-6)
self.assertAlmostEqual(x[0, 79], x[0, 78] + 130e-6 * 3.5 / 2.)
def test_detector_imxpad_s140(self):
"""
The masked image has a masked ring around 1.5deg with value
-10 without mask the pixels should be at -10 ; with mask they
are at 0
"""
imxpad = detector_factory("imxpad_s140")
# check that the cartesian coordinates is cached
self.assertEqual(hasattr(imxpad, 'COORDINATES'), False)
y, x = imxpad.calc_cartesian_positions()
self.assertEqual(hasattr(imxpad, 'COORDINATES'), True)
# now check that the cached values are identical for each
# method call
y1, x1 = imxpad.calc_cartesian_positions()
self.assertEqual(numpy.all(numpy.equal(y1, y)), True)
self.assertEqual(numpy.all(numpy.equal(x1, x)), True)
# check that a few pixel positiopns are ok.
self.assertAlmostEqual(y[0], 130e-6 / 2.)
self.assertAlmostEqual(y[1], y[0] + 130e-6)
self.assertAlmostEqual(y[119], y[118] + 130e-6 * 3.5 / 2.)
self.assertAlmostEqual(x[0], 130e-6 / 2.)
self.assertAlmostEqual(x[1], x[0] + 130e-6)
self.assertAlmostEqual(x[79], x[78] + 130e-6 * 3.5 / 2.)
def test_nexus_detector(self):
tmpdir = tempfile.mkdtemp()
known_fail = []
if io.h5py is None:
logger.warning("H5py not present, skipping test_detector.TestDetector.test_nexus_detector")
return
for det_name in ALL_DETECTORS:
fname = os.path.join(tmpdir, det_name + ".h5")
if os.path.exists(fname): # already tested with another alias
continue
det = detector_factory(det_name)
if (det.pixel1 is None) or (det.shape is None):
continue
det.save(fname)
new_det = detector_factory(fname)
for what in ("pixel1", "pixel2", "name", "max_shape", "shape", "binning"):
if "__len__" in dir(det.__getattribute__(what)):
self.assertEqual(det.__getattribute__(what), new_det.__getattribute__(what), "%s is the same for %s" % (what, fname))
else:
self.assertAlmostEqual(det.__getattribute__(what), new_det.__getattribute__(what), 4, "%s is the same for %s" % (what, fname))
if (det.mask is not None) or (new_det.mask is not None):
self.assert_(numpy.allclose(det.mask, new_det.mask), "%s mask is not the same" % det_name)
if det.shape[0] > 2000:
continue
try:
r = det.calc_cartesian_positions()
o = new_det.calc_cartesian_positions()
except MemoryError:
logger.warning("Test nexus_detector failed due to short memory on detector %s" % det_name)
continue
self.assertEqual(len(o), len(r), "data have same dimension")
err1 = abs(r[0] - o[0]).max()
err2 = abs(r[1] - o[1]).max()
if det.name in known_fail:
continue
self.assert_(err1 < 1e-6, "%s precision on pixel position 1 is better than 1µm, got %e" % (det_name, err2))
self.assert_(err2 < 1e-6, "%s precision on pixel position 2 is better than 1µm, got %e" % (det_name, err2))
if not det.IS_FLAT:
err = abs(r[2] - o[2]).max()
self.assert_(err < 1e-6, "%s precision on pixel position 3 is better than 1µm, got %e" % (det_name, err))
# check Pilatus with displacement maps
# check spline
# check SPD sisplacement
shutil.rmtree(tmpdir)
def test_Xpad_flat(self):
d = detector_factory("Xpad S540 flat")
cy = d.calc_cartesian_positions(use_cython=True)
np = d.calc_cartesian_positions(use_cython=False)
self.assert_(numpy.allclose(cy[0], np[0]),
"max_delta1=" % abs(cy[0] - np[0]).max())
self.assert_(numpy.allclose(cy[1], np[1]),
"max_delta2=" % abs(cy[1] - np[1]).max())
def test_nexus_detector(self):
tmpdir = tempfile.mkdtemp()
known_fail = [] #TODO: fix broken detectors
# print(tmpdir)
for det_name in ALL_DETECTORS:
fname = os.path.join(tmpdir, det_name + ".h5")
if os.path.exists(fname): #already tested with another alias
continue
# print fname
det = detector_factory(det_name)
if (det.pixel1 is None) or (det.shape is None):
continue
# print(det)
det.save(fname)
new_det = detector_factory(fname)
# print new_det
for what in ("pixel1", "pixel2", "name", "max_shape", "shape", "binning"):
if "__len__" in dir(det.__getattribute__(what)):
self.assertEqual(det.__getattribute__(what), new_det.__getattribute__(what), "%s is the same for %s" % (what, fname))
else:
self.assertAlmostEqual(det.__getattribute__(what), new_det.__getattribute__(what), 4, "%s is the same for %s" % (what, fname))
if det.shape[0] > 2000:
continue
r1, r2 = det.calc_cartesian_positions()
o1, o2 = new_det.calc_cartesian_positions()
err1 = abs(r1 - o1).max()
err2 = abs(r2 - o2).max()
if det.name not in known_fail:
self.assert_(err1 < 1e-6, "%s precision on pixel position 1 is better than 1µm, got %e" % (det_name,err2))
self.assert_(err2 < 1e-6, "%s precision on pixel position 2 is better than 1µm, got %e" % (det_name, err2))
if (det.mask is not None) or (new_det.mask is not None):
self.assert_(numpy.allclose(det.mask, new_det.mask), "%s mask is not the same" % det_name)
#check Pilatus with displacement maps
#check spline
#check SPD sisplacement
shutil.rmtree(tmpdir)
def test_Detector_pickle(self):
det = self.ai.detector
dets = dumps(det)
self.assertTrue(dets, "pickle works")
rest = loads(dets)
self.assertTrue(rest, "unpickle works")
self.assertEqual(rest.shape, self.ai.detector.MAX_SHAPE)
# test the binning
mar = detector_factory("RayonixMx225")
mar.guess_binning((2048, 2048))
self.assertEqual(mar.binning, (3, 3), "binning OK")
mars = dumps(mar)
marr = loads(mars)
self.assertEqual(mar.binning, marr.binning, "restored binning OK")
def test_detector_rayonix_sx165(self):
"""
rayonix detectors have different pixel size depending on the binning.
Check that the set_binning method works for the sx_165
#personal communication of M. Blum:
self.desired_pixelsizes[4096] = 39.500
self.desired_pixelsizes[2048] = 79.000
self.desired_pixelsizes[1364] = 118.616
self.desired_pixelsizes[1024] = 158.000
self.desired_pixelsizes[512] = 316.000
"""
sx165 = detector_factory("rayonixsx165")
# check the default pixels size and the default binning
self.assertAlmostEqual(sx165.pixel1, 395e-7)
self.assertAlmostEqual(sx165.pixel2, 395e-7)
self.assertEqual(sx165.binning, (1, 1))
# check binning 1
sx165.binning = 1
self.assertAlmostEqual(sx165.pixel1, 395e-7)
self.assertAlmostEqual(sx165.pixel2, 395e-7)
self.assertEqual(sx165.binning, (1, 1))
# check binning 2
sx165.binning = 2
self.assertAlmostEqual(sx165.pixel1, 79e-6)
self.assertAlmostEqual(sx165.pixel2, 79e-6)
self.assertEqual(sx165.binning, (2, 2))
# check binning 4
sx165.binning = 4
self.assertAlmostEqual(sx165.pixel1, 158e-6)
self.assertAlmostEqual(sx165.pixel2, 158e-6)
self.assertEqual(sx165.binning, (4, 4))
# check binning 8
sx165.binning = 8
self.assertAlmostEqual(sx165.pixel1, 316e-6)
self.assertAlmostEqual(sx165.pixel2, 316e-6)
self.assertEqual(sx165.binning, (8, 8))
# check a non standard binning
sx165.binning = 10
self.assertAlmostEqual(sx165.pixel1, sx165.pixel2)
def __init__(self,
detector,
image,
pitch,
beamcenter,
detectordistance,
mask=None,
invert=False):
"""
@param detector: instance of Detector or its name
@param image: 2d array representing the image
@param mask:
@param pitch: floating number in millimeter, representing distance between holes
@param beamcenter: 2d array for the position of the beam, (y,x)-coordinate in Px
@param detectordistance: floating number in meter representing distance between detector and scatterin object
@param invert: set to true if the image of the grid has regular dark spots (instead of bright points)
"""
if isinstance(detector, detectors.Detector):
self.detector = detector
else:
self.detector = detectors.detector_factory(detector)
if isinstance(image, numpy.ndarray):
self.image = image
else:
self.image = fabio.open(image).data
if mask is not None:
if isinstance(mask, numpy.ndarray):
self.mask = mask
else:
self.mask = fabio.open(mask).data.astype(bool)
if self.detector.mask is not None:
self.mask = numpy.logical_or(self.detector.mask, self.mask)
else:
self.mask = numpy.zeros_like(self.image, bool)
if invert:
self.image = self.image.max() - self.image
self.pitch = pitch
self.detectordistance = detectordistance
self.beamcenter = beamcenter
self.coordinates = []
self.good_peaks = []
self.mean_vec = []
self.module_translation = []
self.grid_angle = []
self.grid = []
def test_detector_rayonix_sx165(self):
"""
rayonix detectors have different pixel size depending on the binning.
Check that the set_binning method works for the sx_165
#personal communication of M. Blum:
self.desired_pixelsizes[4096] = 39.500
self.desired_pixelsizes[2048] = 79.000
self.desired_pixelsizes[1364] = 118.616
self.desired_pixelsizes[1024] = 158.000
self.desired_pixelsizes[512] = 316.000
"""
sx165 = detector_factory("rayonixsx165")
# check the default pixels size and the default binning
self.assertAlmostEqual(sx165.pixel1, 395e-7)
self.assertAlmostEqual(sx165.pixel2, 395e-7)
self.assertEqual(sx165.binning, (1, 1))
# check binning 1
sx165.binning = 1
self.assertAlmostEqual(sx165.pixel1, 395e-7)
self.assertAlmostEqual(sx165.pixel2, 395e-7)
self.assertEqual(sx165.binning, (1, 1))
# check binning 2
sx165.binning = 2
self.assertAlmostEqual(sx165.pixel1, 79e-6)
self.assertAlmostEqual(sx165.pixel2, 79e-6)
self.assertEqual(sx165.binning, (2, 2))
# check binning 4
sx165.binning = 4
self.assertAlmostEqual(sx165.pixel1, 158e-6)
self.assertAlmostEqual(sx165.pixel2, 158e-6)
self.assertEqual(sx165.binning, (4, 4))
# check binning 8
sx165.binning = 8
self.assertAlmostEqual(sx165.pixel1, 316e-6)
self.assertAlmostEqual(sx165.pixel2, 316e-6)
self.assertEqual(sx165.binning, (8, 8))
# check a non standard binning
sx165.binning = 10
self.assertAlmostEqual(sx165.pixel1, sx165.pixel2)
def image_test_rings():
rings = 10
mod = 50
detector = detector_factory("Titan")
sigma = detector.pixel1 * 4
shape = detector.max_shape
ai = AzimuthalIntegrator(detector=detector)
ai.setFit2D(1000, 1000, 1000)
r = ai.rArray(shape)
r_max = r.max()
chi = ai.chiArray(shape)
img = numpy.zeros(shape)
modulation = (1 + numpy.sin(5 * r + chi * mod))
for radius in numpy.linspace(0, r_max, rings):
img += numpy.exp(-(r - radius)**2 / (2 * (sigma * sigma)))
return img * modulation
def image_test_rings():
rings = 10
mod = 50
detector = detector_factory("Titan")
sigma = detector.pixel1 * 4
shape = detector.max_shape
ai = AzimuthalIntegrator(detector=detector)
ai.setFit2D(1000, 1000, 1000)
r = ai.rArray(shape)
r_max = r.max()
chi = ai.chiArray(shape)
img = numpy.zeros(shape)
modulation = (1 + numpy.sin(5 * r + chi * mod))
for radius in numpy.linspace(0, r_max, rings):
img += numpy.exp(-(r - radius) ** 2 / (2 * (sigma * sigma)))
return img * modulation
def __init__(self, detector, image, pitch, beamcenter, detectordistance, mask=None, invert=False):
"""
@param detector: instance of Detector or its name
@param image: 2d array representing the image
@param mask:
@param pitch: floating number in millimeter, representing distance between holes
@param beamcenter: 2d array for the position of the beam, (y,x)-coordinate in Px
@param detectordistance: floating number in meter representing distance between detector and scatterin object
@param invert: set to true if the image of the grid has regular dark spots (instead of bright points)
"""
if isinstance(detector, detectors.Detector):
self.detector = detector
else:
self.detector = detectors.detector_factory(detector)
if isinstance(image, numpy.ndarray):
self.image = image
else:
self.image = fabio.open(image).data
if mask is not None:
if isinstance(mask, numpy.ndarray):
self.mask = mask
else:
self.mask = fabio.open(mask).data.astype(bool)
if self.detector.mask is not None:
self.mask = numpy.logical_or(self.detector.mask, self.mask)
else:
self.mask = numpy.zeros_like(self.image, bool)
if invert:
self.image = self.image.max() - self.image
self.pitch = pitch
self.detectordistance = detectordistance
self.beamcenter = beamcenter
self.coordinates=[]
self.good_peaks=[]
self.mean_vec = []
self.module_translation = []
self.grid_angle =[]
self.grid =[]
def __init__(self, detector="detector", shape=None):
"""
@param detector: detector instance or detector name
"""
if type(detector) in types.StringTypes:
self.detector = detectors.detector_factory(detector)
else: # we assume it is a Detector instance
self.detector = detector
if "max_shape" in dir(self.detector):
self.shape = self.detector.max_shape
else:
self.shape = shape
self.shape = tuple([int(i) for i in self.shape])
self._sem = threading.Semaphore()
self.lut_size = None
self.pos = None
self.LUT = None
self.delta0 = self.delta1 = None # max size of an pixel on a regular grid ...
self.integrator = None
def __init__(self, detector="detector", shape=None):
"""
@param detector: detector instance or detector name
"""
if type(detector) in types.StringTypes:
self.detector = detectors.detector_factory(detector)
else: # we assume it is a Detector instance
self.detector = detector
if "max_shape" in dir(self.detector):
self.shape = self.detector.max_shape
else:
self.shape = shape
self.shape = tuple([int(i) for i in self.shape])
self._sem = threading.Semaphore()
self.lut_size = None
self.pos = None
self.LUT = None
self.delta0 = self.delta1 = None # max size of an pixel on a regular grid ...
self.integrator = None
def image_test_rings():
"Creating a test image containing gaussian spots on several rings"
rings = 10
mod = 50
detector = detector_factory("Titan")
sigma = detector.pixel1 * 4
shape = detector.max_shape
ai = AzimuthalIntegrator(detector=detector)
ai.setFit2D(1000, 1000, 1000)
r = ai.rArray(shape)
r_max = r.max()
chi = ai.chiArray(shape)
img = numpy.zeros(shape)
modulation = (1 + numpy.sin(5 * r + chi * mod))
for radius in numpy.linspace(0, r_max, rings):
img += numpy.exp(-(r - radius) ** 2 / (2 * (sigma * sigma)))
img *= modulation
img = add_noise(img, 0.0)
return img
def image_test_rings():
"Creating a test image containing gaussian spots on several rings"
rings = 10
mod = 50
detector = detector_factory("Titan")
sigma = detector.pixel1 * 4
shape = detector.max_shape
ai = AzimuthalIntegrator(detector=detector)
ai.setFit2D(1000, 1000, 1000)
r = ai.rArray(shape)
r_max = r.max()
chi = ai.chiArray(shape)
img = numpy.zeros(shape)
modulation = (1 + numpy.sin(5 * r + chi * mod))
for radius in numpy.linspace(0, r_max, rings):
img += numpy.exp(-(r - radius)**2 / (2 * (sigma * sigma)))
img *= modulation
img = add_noise(img, 0.0)
return img
def __init__(self, detector, module):
"""
@param detector: instance of Detector or its name
@param module: Intenger number starting with 0 and row by row
"""
if isinstance(detector, detectors.Detector):
self.detector = detector
else:
self.detector = detectors.detector_factory(detector)
self.module = module
self.module_size = self.detector.MODULE_SIZE
self.module_gap = self.detector.MODULE_GAP
self.max_shape = self.detector.MAX_SHAPE
self.amount = []
self.center_of_module = []
self.amount_x = []
self.amount_y = []
self.module_area = []
self.mask = []
self.mask_grid = []
def __init__(self, detector, module):
"""
@param detector: instance of Detector or its name
@param module: Intenger number starting with 0 and row by row
"""
if isinstance(detector, detectors.Detector):
self.detector = detector
else:
self.detector = detectors.detector_factory(detector)
self.module = module
self.module_size = self.detector.MODULE_SIZE
self.module_gap = self.detector.MODULE_GAP
self.max_shape = self.detector.MAX_SHAPE
self.amount = []
self.center_of_module = []
self.amount_x = []
self.amount_y = []
self.module_area = []
self.mask = []
self.mask_grid = []
def __init__(self, detector="detector", shape=None, method="LUT", device=None, workgroup=8):
"""
@param detector: detector instance or detector name
@param shape: shape of the output image
@param method: "lut" or "csr", the former is faster
@param device: Name of the device: None for OpenMP, "cpu" or "gpu" or the id of the OpenCL device a 2-tuple of integer
@param workgroup: workgroup size for CSR on OpenCL
"""
if type(detector) in types.StringTypes:
self.detector = detectors.detector_factory(detector)
else: # we assume it is a Detector instance
self.detector = detector
if "shape" in dir(self.detector):
self.shape = self.detector.shape
if shape is not None and self.shape != shape:
logger.warning("unconsistency in detector geometry, got %s and expected %s" % (shape, self.shape))
self.shape = shape
else:
self.shape = shape
self.shape = tuple([int(i) for i in self.shape])
self._sem = threading.Semaphore()
self.bin_size = None
self.max_size = None
self.pos = None
self.lut = None
self.delta0 = self.delta1 = None # max size of an pixel on a regular grid ...
self.integrator = None
if not method:
self.method = "lut"
else:
self.method = method.lower()
self.device = device
if not workgroup:
self.workgroup = 8
else:
self.workgroup = int(workgroup)
def test_Xpad_flat(self):
d = detector_factory("Xpad S540 flat")
cy = d.calc_cartesian_positions(use_cython=True)
np = d.calc_cartesian_positions(use_cython=False)
self.assert_(numpy.allclose(cy[0], np[0]), "max_delta1=" % abs(cy[0] - np[0]).max())
self.assert_(numpy.allclose(cy[1], np[1]), "max_delta2=" % abs(cy[1] - np[1]).max())