Example #1
0
def generate_q_bins(rmax, qmax, pixel_size, distance, wavelength):
    """
    Generate the Q bins at the resolution of the detector
    Parameters
    -----------
    rmax: float
        The maximum radial distance on the detector
    qmax: float
        The maximum Q on the detector
    pixel_size: float
        The size of the pixels, in the same units as rmax
    distance: float
        The sample to detector distance, in the same units as rmax
    wavelength: float
        The wavelength of the x-rays

    Returns
    -------
    ndarray:
        The bin edges, suitable for np.histogram or
        scipy.stats.binned_statistic
    """
    base_pixels = np.arange(0, rmax, pixel_size)
    pixel_bottom = base_pixels
    pixel_top = base_pixels + pixel_size
    tthb = np.arctan(pixel_bottom / distance)
    ttht = np.arctan(pixel_top / distance)
    dq = twotheta_to_q(ttht, wavelength) - twotheta_to_q(tthb, wavelength)
    fq = np.linspace(0, qmax, len(dq))
    b = np.zeros(len(fq) + 1)
    b[1:] = dq + fq
    return b
Example #2
0
def test_q_twotheta_conversion():
    wavelength = 1
    q = np.linspace(0, 4 * np.pi, 100)
    assert_array_almost_equal(q,
                              core.twotheta_to_q(
                                  core.q_to_twotheta(q, wavelength),
                                  wavelength),
                              decimal=12)
    two_theta = np.linspace(0, np.pi, 100)
    assert_array_almost_equal(two_theta,
                              core.q_to_twotheta(
                                  core.twotheta_to_q(two_theta, wavelength),
                                  wavelength),
                              decimal=12)
Example #3
0
def test_q_twotheta_conversion():
    wavelength = 1
    q = np.linspace(0, 4 * np.pi, 100)
    assert_array_almost_equal(q,
                              core.twotheta_to_q(
                                  core.q_to_twotheta(q, wavelength),
                                  wavelength),
                              decimal=12)
    two_theta = np.linspace(0, np.pi, 100)
    assert_array_almost_equal(two_theta,
                              core.q_to_twotheta(
                                  core.twotheta_to_q(two_theta,
                                                     wavelength),
                                  wavelength),
                              decimal=12)
	def angularIntegrationBackDetector(n_bins=100,center=(265,655),min_bin=40,max_bin=800,threshold=(0.001,10000)):
	    ''' 
	    Does the circular integration and q-calibration on the back
	    detector, with an additional threshold masking
	    '''
	
	    # -- parameters
	    Ldet = 5080. # detector to sample distance 
	    dpix = 0.055 # um (pixel size)
	    energy = 8.4 #keV
	
	    # -- constants
	    h = 4.135667516*1e-18 #kev*sec
	    c = 3*1e8 #m/s
	    lambda_ = h*c/energy*1e10 # wavelength of the X-rays
	
	    # -- calulate q-range
	    width,spacing = float(max_bin-min_bin)/float(n_bins),0
	    edges = roi.ring_edges(min_bin, width, spacing, n_bins)
	    two_theta = utils.radius_to_twotheta(Ldet, edges*dpix)
	    q_val = utils.twotheta_to_q(two_theta, lambda_)
	    q = np.mean(q_val, axis=1)
	
	    # -- apply threshold mask data
	    self.data[data<threshold[0]]=0
	    self.data[data>threshold[1]]=0
	
	    # -- angular average 
	    Iq= circularAverage(self.data,calibrated_center=center,nx=n_bins,min_x=min_bin,max_x=max_bin)
	    print q.shape,Iq[1].shape
	    return Iq[0],Iq[1]
Example #5
0
def generate_q_bins(rmax, pixel_size, distance, wavelength, rmin=0):
    """
    Generate the Q bins at the resolution of the detector
    Parameters
    -----------
    rmax: float
        The maximum radial distance on the detector in distance units.
        Note that this should go to the bottom edge of the pixel.
    pixel_size: float
        The size of the pixels, in the same units as rmax
    distance: float
        The sample to detector distance, in the same units as rmax
    wavelength: float
        The wavelength of the x-rays
    rmin: float, optional
        The minimum radial distance on the detector in distance units. Defaults
        to zero. Note that this should be the bottom of the pixel

    Returns
    -------
    ndarray:
        The bin edges, suitable for np.histogram or
        scipy.stats.binned_statistic
    """
    pixel_bottom = np.arange(rmin, rmax, pixel_size)
    pixel_top = pixel_bottom + pixel_size

    bottom_tth = np.arctan(pixel_bottom[0] / distance)
    top_tth = np.arctan(pixel_top / distance)

    top_q = twotheta_to_q(top_tth, wavelength)

    bins = np.zeros(len(top_q) + 1)

    bins[0] = twotheta_to_q(bottom_tth, wavelength)
    bins[1:] = top_q
    return bins
Example #6
0
def calculate_g2(data,mask=None,g2q=180,center = [265,655]):
    '''
    Calculates the intensity-intensity temporal autocorrelation using
    scikit-beam packages on the back detector
    for a q-range (g2q) and width (width, num_rings,spacing) 
    '''

    # -- parameters
    inner_radius = g2q#180 # radius of the first ring
    width = 1
    spacing = 0
    num_rings = 10
    #center = (273, 723) # center of the speckle pattern
    dpix = 0.055 # The physical size of the pixels
    energy = 8.4 #keV
    h = 4.135667516*1e-18#kev*sec
    c = 3*1e8 #m/s
    lambda_ = h*c/energy*1e10 # wavelength of the X-rays  
    Ldet = 5080. # # detector to sample distance 

    # -- average and mask data
    avg_data = np.average(data,axis=0)#*mask

    # -- ring array
    edges = roi.ring_edges(inner_radius, width, spacing, num_rings)

    # -- convert ring to q
    two_theta = utils.radius_to_twotheta(Ldet, edges*dpix)
    q_val = utils.twotheta_to_q(two_theta, lambda_)
    q_ring = np.mean(q_val, axis=1)
 
    # -- ring mask
    rings = roi.rings(edges, center, data[0].shape)
    ring_mask = rings*mask

    # -- calulate g2
    num_levels = 1#7
    num_bufs = 100#2
    g2, lag_steps = corr.multi_tau_auto_corr(num_levels,num_bufs,ring_mask,mask*data)
    
    # -- average
    g2_avg = np.average(g2,axis=1)
    qt = np.average(q_ring)

    # -- standard error
    g2_err = np.std(g2,axis=1)/np.sqrt(len(g2[0,:]))

    return qt,lag_steps[1:],g2_avg[1:],g2_err[1:]
def angular_integration_back_detector(data,
                                      n_bins=100,
                                      mask=None,
                                      center=(265, 655),
                                      min_bin=40,
                                      max_bin=800,
                                      threshold=(0.001, 10000)):
    ''' 
    Does the circular integration and q-calibration on the back
    detector, with an additional threshold masking
    '''

    # -- parameters
    Ldet = 5080.  # detector to sample distance
    dpix = 0.055  # um (pixel size)
    energy = 8.4  #keV

    # -- constants
    h = 4.135667516 * 1e-18  #kev*sec
    c = 3 * 1e8  #m/s
    lambda_ = h * c / energy * 1e10  # wavelength of the X-rays

    # -- calulate q-range
    width, spacing = float(max_bin - min_bin) / float(n_bins), 0
    edges = roi.ring_edges(min_bin, width, spacing, n_bins)
    two_theta = utils.radius_to_twotheta(Ldet, edges * dpix)
    q_val = utils.twotheta_to_q(two_theta, lambda_)
    q = np.mean(q_val, axis=1)

    # -- apply threshold mask data
    data[data < threshold[0]] = 0
    data[data > threshold[1]] = 0

    # -- angular average
    Iq = circular_average(data,
                          calibrated_center=center,
                          mask=mask,
                          nx=n_bins,
                          min_x=min_bin,
                          max_x=max_bin)
    print q.shape, Iq[1].shape
    return Iq[0], Iq[1]
	def calculateG2(self, g2q=180, center=[265,655]):
		"""
		--------------------------------------------
        	Method: SpecklePattern.calculateG2
        	--------------------------------------------
		Calculates the intensity-intensity temporal autocorrelation using
		scikit-beam packages on the back detector
		for a q-range (g2q) and width (width, num_rings,spacing)
        	--------------------------------------------
        	Usage: mySpeckles.calculateG2()
        	--------------------------------------------
                Prerequisites:
		data - data stored as numpy 3D array
                --------------------------------------------
		Arguments: (optional)
		g2q - at which q (pixels) you wanna calculate g2
		center - beam position in the data array (y, x)
		--------------------------------------------
		Returns tuple with:
		qt - q (in Ang-1) at which you calculated g2
		lag_steps[1:] - time array
		g2_avg[1:] - g2 average array
		g2_err[1:] - g2 uncertainty array
		--------------------------------------------
		"""
    		# -- parameters
    		inner_radius = g2q#180 # radius of the first ring
    		width = 1
    		spacing = 0
    		num_rings = 10
    		#center = (273, 723) # center of the speckle pattern
    		dpix = 0.055 # The physical size of the pixels
    		energy = 8.4 #keV
    		h = 4.135667516*1e-18#kev*sec
    		c = 3*1e8 #m/s
    		lambda_ = h*c/energy*1e10 # wavelength of the X-rays
    		Ldet = 5080. # # detector to sample distance
    		
    		# -- average and mask data
    		avg_data = np.average(self.data,axis=0)#*mask
    		
    		# -- ring array
    		edges = roi.ring_edges(inner_radius, width, spacing, num_rings)
    		
    		# -- convert ring to q
    		two_theta = utils.radius_to_twotheta(Ldet, edges*dpix)
    		q_val = utils.twotheta_to_q(two_theta, lambda_)
    		q_ring = np.mean(q_val, axis=1)
    		
    		# -- ring mask
    		rings = roi.rings(edges, center, self.data[0].shape)
    		ring_mask = rings*mask
    		
    		# -- calulate g2
    		num_levels = 1 #7
    		num_bufs = 100 #2
    		g2, lag_steps = corr.multi_tau_auto_corr(num_levels,num_bufs,ring_mask,self.mask*self.data)
    		
    		# -- average
    		g2_avg = np.average(g2,axis=1)
    		qt = np.average(q_ring)
    		
    		# -- standard error
    		g2_err = np.std(g2,axis=1)/np.sqrt(len(g2[0,:]))
    		
    		return qt, lag_steps[1:], g2_avg[1:], g2_err[1:]
geo = Geometry(
    detector='Perkin', pixel1=.0002, pixel2=.0002,
    dist=.23,
    poni1=.209, poni2=.207,
    # rot1=.0128, rot2=-.015, rot3=-5.2e-8,
    wavelength=1.43e-11
)
r = geo.rArray((2048, 2048))
q = geo.qArray((2048, 2048))
pixels = np.arange(0, np.max(r), geo.pixel1)
pixel_bottom = pixels
pixel_top = pixels + geo.pixel1
tthb = np.arctan(pixel_bottom / geo.dist)
ttht = np.arctan(pixel_top / geo.dist)
dq = twotheta_to_q(ttht, .143) - twotheta_to_q(tthb, .143)
fq = np.linspace(0, np.max(q), len(dq))

b = np.zeros(len(fq)+1)
b[1:] = dq + fq
int_q = np.zeros(q.shape, dtype=np.int)
for i in range(len(b)-1):
    t_array = (b[i] <= q) & (q < b[i+1])
    int_q[t_array] = i - 1

save_stem = '/mnt/bulk-data/Masters_Thesis/dp/figures/'

for j in [100, 300, 500, 1000]:
    #make some sample data
    Z = 100*np.cos(50*r)**2 + 150
Example #10
0
    def calculateG2(self, g2q=180, center=[265, 655]):
        """
		--------------------------------------------
        	Method: SpecklePattern.calculateG2
        	--------------------------------------------
		Calculates the intensity-intensity temporal autocorrelation using
		scikit-beam packages on the back detector
		for a q-range (g2q) and width (width, num_rings,spacing)
        	--------------------------------------------
        	Usage: mySpeckles.calculateG2()
        	--------------------------------------------
                Prerequisites:
		data - data stored as numpy 3D array
                --------------------------------------------
		Arguments: (optional)
		g2q - at which q (pixels) you wanna calculate g2
		center - beam position in the data array (y, x)
		--------------------------------------------
		Returns tuple with:
		qt - q (in Ang-1) at which you calculated g2
		lag_steps[1:] - time array
		g2_avg[1:] - g2 average array
		g2_err[1:] - g2 uncertainty array
		--------------------------------------------
		"""
        # -- parameters
        inner_radius = g2q  #180 # radius of the first ring
        width = 1
        spacing = 0
        num_rings = 10
        #center = (273, 723) # center of the speckle pattern
        dpix = 0.055  # The physical size of the pixels
        energy = 8.4  #keV
        h = 4.135667516 * 1e-18  #kev*sec
        c = 3 * 1e8  #m/s
        lambda_ = h * c / energy * 1e10  # wavelength of the X-rays
        Ldet = 5080.  # # detector to sample distance

        # -- average and mask data
        avg_data = np.average(self.data, axis=0)  #*mask

        # -- ring array
        edges = roi.ring_edges(inner_radius, width, spacing, num_rings)

        # -- convert ring to q
        two_theta = utils.radius_to_twotheta(Ldet, edges * dpix)
        q_val = utils.twotheta_to_q(two_theta, lambda_)
        q_ring = np.mean(q_val, axis=1)

        # -- ring mask
        rings = roi.rings(edges, center, self.data[0].shape)
        ring_mask = rings * mask

        # -- calulate g2
        num_levels = 1  #7
        num_bufs = 100  #2
        g2, lag_steps = corr.multi_tau_auto_corr(num_levels, num_bufs,
                                                 ring_mask,
                                                 self.mask * self.data)

        # -- average
        g2_avg = np.average(g2, axis=1)
        qt = np.average(q_ring)

        # -- standard error
        g2_err = np.std(g2, axis=1) / np.sqrt(len(g2[0, :]))

        return qt, lag_steps[1:], g2_avg[1:], g2_err[1:]