def write_smv(self, path: str, i: int) -> str:
"""Write the image+header with sequence number `i` to the directory
`path` in SMV format.
Returns the path to the written image.
"""
img = self.data[i]
h = self.headers[i]
img = np.ushort(img)
shape_x, shape_y = img.shape
phi = self.start_angle + self.osc_angle * (i - 1)
# TODO: Dials reads the beam_center from the first image and uses that for the whole range
# For now, use the average beam center and consider it stationary, remove this line later
mean_beam_center = self.mean_beam_center
try:
date = str(datetime.fromtimestamp(h['ImageGetTime']))
except BaseException:
date = '0'
header = collections.OrderedDict()
header['HEADER_BYTES'] = 512
header['DIM'] = 2
header['BYTE_ORDER'] = 'little_endian'
header['TYPE'] = 'unsigned_short'
header['SIZE1'] = shape_x
header['SIZE2'] = shape_y
header['PIXEL_SIZE'] = self.physical_pixelsize
header['BIN'] = '1x1'
header['BIN_TYPE'] = 'HW'
header['ADC'] = 'fast'
header['CREV'] = 1
header['BEAMLINE'] = self.name # special ID for DIALS
header['DETECTOR_SN'] = 901 # special ID for DIALS
header['DATE'] = date
header['TIME'] = str(h['ImageExposureTime'])
header['DISTANCE'] = f'{self.distance:.4f}'
header['TWOTHETA'] = 0.00
header['PHI'] = '{phi:.4f}'
header['OSC_START'] = f'{phi:.4f}'
header['OSC_RANGE'] = f'{self.osc_angle:.4f}'
header['WAVELENGTH'] = f'{self.wavelength:.4f}'
# reverse XY coordinates for XDS
header['BEAM_CENTER_X'] = f'{mean_beam_center[1]:.4f}'
header['BEAM_CENTER_Y'] = f'{mean_beam_center[0]:.4f}'
header[
'DENZO_X_BEAM'] = f'{mean_beam_center[0]*self.physical_pixelsize:.4f}'
header[
'DENZO_Y_BEAM'] = f'{mean_beam_center[1]*self.physical_pixelsize:.4f}'
fn = path / f'{i:05d}.img'
write_adsc(fn, img, header=header)
return fn
def test_smv(data, header):
out = 'out.smv'
formats.write_adsc(out, data, header)
assert os.path.exists(out)
img, h = formats.read_image(out)
assert np.allclose(img, data)
assert 'value' in h # changes type to str
assert h['string'] == header['string']
beam_x, beam_y = find_beam_center_blur(img)
centers.append((beam_x, beam_y))
# get image center
center_x, center_y = (np.array(img.shape) / 2).astype(int)
shift_x = center_x - beam_x
shift_y = center_y - beam_y
# shift the beam to the center of the image
shifted = ndi.shift(img, (shift_x, shift_y))
if binning > 1:
shifted = ndi.zoom(shifted, scale)
pixel_size = float(header["PIXEL_SIZE"])
header["PIXEL_SIZE"] = str(pixel_size / binning)
header["SIZE1"] = str(shifted.shape[0])
header["SIZE2"] = str(shifted.shape[1])
header["BEAM_CENTER_X"] = str(center_x / binning)
header["BEAM_CENTER_Y"] = str(center_y / binning)
out = fn.stem + "-centered.img"
write_adsc(fname=str(out), data=shifted, header=header)
# Plot centers of the direct beam
beam_x, beam_y = np.array(centers).T
plt.plot(beam_x, beam_y)
plt.xlabel("X axis (px)")
plt.ylabel("Y axis (px)")
plt.show()