def calibrated_pixels_to_q(detector_size, pyfai_kwargs):
"""
For a given detector and pyfai calibrated geometry give back the q value
for each pixel in the detector.
Parameters
-----------
detector_size : tuple
2 element tuple defining the number of pixels in the detector. Order is
(num_columns, num_rows)
pyfai_kwargs: dict
The dictionary of pyfai geometry kwargs, given by pyFAI's calibration
Ex: dist, poni1, poni2, rot1, rot2, rot3, splineFile, wavelength,
detector, pixel1, pixel2
Returns
-------
q_val : ndarray
Reciprocal values for each pixel shape is [num_rows * num_columns]
"""
if geo is None:
raise RuntimeError("You must have pyFAI installed to use this "
"function.")
a = geo.Geometry(**pyfai_kwargs)
return a.qArray(detector_size)
def testGeometryFunctions(self):
func, statargs, varargs, kwds, expectedFail = self.param
kwds["pixel1"] = 1
kwds["pixel2"] = 1
g = geometry.Geometry(**kwds)
g.wavelength = 1e-10
t0 = time.time()
oldret = getattr(g, func)(*statargs, path=varargs[0])
t1 = time.time()
newret = getattr(g, func)(*statargs, path=varargs[1])
t2 = time.time()
logger.debug("TIMINGS\t meth: %s t=%.3fs\t meth: %s t=%.3fs" % (varargs[0], t1 - t0, varargs[1], t2 - t1))
maxDelta = abs(oldret - newret).max()
msg = "geo=%s%s max delta=%.3f" % (g, os.linesep, maxDelta)
if expectedFail:
self.assertNotAlmostEquals(maxDelta, 0, 3, msg)
else:
self.assertAlmostEquals(maxDelta, 0, 3, msg)
logger.info(msg)
def __display3dDialog(self):
from ..dialog.Detector3dDialog import Detector3dDialog
dialog = Detector3dDialog(self)
settings = self.model().experimentSettingsModel()
detector = settings.detectorModel().detector()
image = settings.image().value()
mask = settings.mask().value()
colormap = CalibrationContext.instance().getRawColormap()
geometry = None
fittedGeometry = self.model().fittedGeometry()
if fittedGeometry.isValid():
from pyFAI import geometry
geometry = geometry.Geometry()
model_transform.geometryModelToGeometry(fittedGeometry, geometry)
dialog.setData(detector=detector,
image=image, mask=mask, colormap=colormap,
geometry=geometry)
dialog.exec_()
qsize = map_x.size
qshape = map_x.shape
qimg = np.fromiter((image[(i, j)] for i, j in np.nditer([map_y.astype(int),
map_x.astype(int)])), dtype=np.float, count=qsize).reshape(qshape)
qimg[mask] = 0.0
return (
np.rot90(qimg, 3), qpar, qvrt)
return
if __name__ == '__main__':
import fabio, pylab as plt, time
filename = 'Burst/calibration/AGB_5S_USE_2_2m.edf'
image = fabio.open(filename).data
sdd = 0.283351
cen_y = 0.005363
cen_x = 0.040123
pixel = 0.000172
geo = geometry.Geometry(sdd, cen_y, cen_x, 0, 0, 0)
geo.set_wavelength(1.23984e-10)
geo.set_pixel1(0.000172)
geo.set_pixel2(0.000172)
t0 = time.clock()
qimg = remesh(image, filename, geo)
t1 = time.clock() - t0
print 'remesh clock time = %f' % t1
plt.imshow(np.log(qimg + 5))
plt.show()
# okay decompiling remesh.pyc
def test_remesh():
filename = 'GIWAXS_sfloat_2m.gb'
center = [632., 69.5]
pixel = [172E-06, 172E-06]
poni = np.multiply(center, pixel)
dist = 300.
det = detectors.Pilatus2M
g = geometry.Geometry(dist=0.3,
poni1=poni[1],
poni2=poni[0],
pixel1=pixel[0],
pixel2=pixel[1],
wavelength=0.123984E-09)
data = np.fromfile(filename, dtype=np.float32).reshape(1679, 1475)
data = np.flipud(data)
ai = np.deg2rad(0.14)
lims = [[0, 20], [0, 20]]
res = [512, 512]
# default qp-qz, same size as detector
img, x, y = camsaxs.remesh(data, g, ai)
box = [x.min(), x.max(), y.min(), y.max()]
plt.imshow(np.log(img + 4), origin='lower', extent=box)
plt.title('qp_qz_full.png')
plt.show()
plt.figure()
img, x, y = camsaxs.remesh(data,
g,
ai,
res=res,
coord_sys='qp_qz',
out_range=lims)
box = [x.min(), x.max(), y.min(), y.max()]
plt.imshow(np.log(img + 4), origin='lower', extent=box)
plt.title('qp_qz_roi.png')
plt.show()
plt.figure()
img, x, y = camsaxs.remesh(data, g, ai, coord_sys='qy_qz')
box = [x.min(), x.max(), y.min(), y.max()]
plt.imshow(np.log(img + 4), origin='lower', extent=box)
plt.title('qy_qz_full.png')
plt.show()
plt.figure()
img, x, y = camsaxs.remesh(data, g, ai, res=res, coord_sys='qy_qz')
box = [x.min(), x.max(), y.min(), y.max()]
plt.imshow(np.log(img + 4), origin='lower', extent=box)
plt.title('qy_qz_roi.png')
plt.show()
plt.figure()
img, x, y = camsaxs.remesh(data, g, ai, coord_sys='theta_alpha')
box = [x.min(), x.max(), y.min(), y.max()]
plt.imshow(np.log(img + 4), origin='lower', extent=box)
plt.title('th_al_full.png')
plt.show()
plt.figure()
lims = [[-0.1, 0.1], [0, 0.2]]
res = [2000, 2000]
img, x, y = camsaxs.remesh(data,
g,
ai,
res=res,
coord_sys='theta_alpha',
out_range=lims)
box = [x.min(), x.max(), y.min(), y.max()]
plt.imshow(np.log(img + 4), origin='lower', extent=box)
plt.title('th_al_roi.png')
plt.show()