def get_h5(self,dfile,time) :
"""Retrives 2D image from event.
@run run number
@time time-stamp
"""
if dfile == 0 :
filename = self.dataset_name + '.h5'
else :
filename = self.dataset_name + '__' + str(dfile).zfill(4) + '.h5'
f = h5py.File(filename,'r')
# Ascert that time-stamp exist in file
if time in f.keys():
self.image = f[time][self.detector_address]['HistData'].value
else:
self.image = None
self.img = None
return
# Apply common mode correction
if self.comm == 1:
self.image = pnccd_tbx.common_mode(img = self.image,
edge = self.param1,
side = self.param2,
plot = self.param4)
elif self.comm == 2:
self.image = pnccd_tbx.common_mode_hart(img = self.image,
msk = self.mask,
max_int = self.param1,
max_com = self.param2,
length = self.param3,
orient = self.orient,
plot = self.param4)
# Apply geometry
self.img = pnccd_tbx.get_geometry(img = self.image,
gap = self.gap,
shift = self.shift,
orient = self.orient)
# Check if nQ > smallest dimension/2 then we extend the image with zero values
if self.nQ > min(self.img.shape[0]/2,self.img.shape[1]/2) :
self.img = pnccd_tbx.extend_image(img = self.img)
# Check if carttesian coord background image exists
if self.cart :
self.img = self.img - self.backimg
def get_h5(self,dfile,time) :
"""Retrives 2D image from event.
@run run number
@time time-stamp
"""
if dfile == 0 :
filename = self.dataset_name + '.h5'
else :
filename = self.dataset_name + '__' + str(dfile).zfill(4) + '.h5'
f = h5py.File(filename,'r')
# Ascert that time-stamp exist in file
if time in f.keys():
self.image = f[time][self.detector_address]['HistData'].value
else:
self.image = None
self.img = None
return
# Apply common mode correction
if self.comm == 1:
self.image = pnccd_tbx.common_mode(img = self.image,
edge = self.param1,
side = self.param2,
plot = self.param4)
elif self.comm == 2:
self.image = pnccd_tbx.common_mode_hart(img = self.image,
msk = self.mask,
max_int = self.param1,
max_com = self.param2,
length = self.param3,
orient = self.orient,
plot = self.param4)
# Apply geometry
self.img = pnccd_tbx.get_geometry(img = self.image,
gap = self.gap,
shift = self.shift,
orient = self.orient)
# Check if nQ > smallest dimension/2 then we extend the image with zero values
if self.nQ > min(self.img.shape[0]/2,self.img.shape[1]/2) :
self.img = pnccd_tbx.extend_image(img = self.img)
# Check if carttesian coord background image exists
if self.cart :
self.img = self.img - self.backimg
def get_image(self,evt) :
"""Retrives 2D image from event.
@run run number from Psana
@time time-stamp from Psana
"""
self.run_nr = int(evt.run())
self.evt = evt
self.img = self.src.image(self.evt)
# Check if nQ > smallest dimension/2 then we extend the image with zero values
if self.nQ > min(self.img.shape[0]/2,self.img.shape[1]/2) :
self.img = pnccd_tbx.extend_image(img = self.img)
# Check if carttesian coord background image exists
if self.cart :
self.img = self.img - self.backimg
# CM correction, Make sure that no other CM is already implemented
self.img = pnccd_tbx.common_mode(self.img, 150 , 100 , plot = 0)
self.img = self.img*self.msk
def get_image(self, evt):
"""Retrives 2D image from event.
@run run number from Psana
@time time-stamp from Psana
"""
self.run_nr = int(evt.run())
self.evt = evt
self.img = self.src.image(self.evt)
# Check if nQ > smallest dimension/2 then we extend the image with zero values
if self.nQ > min(self.img.shape[0] / 2, self.img.shape[1] / 2):
self.img = pnccd_tbx.extend_image(img=self.img)
# Check if carttesian coord background image exists
if self.cart:
self.img = self.img - self.backimg
# CM correction, Make sure that no other CM is already implemented
self.img = pnccd_tbx.common_mode(self.img, 150, 100, plot=0)
self.img = self.img * self.msk
def __init__(self,
dataset_name = None,
detector_address = None,
data_type = 'idx',
mask_path = None,
mask_angles = None,
mask_widths = None,
backimg_path = None,
backmsk_path = None,
geom_path = None,
det_dist = None,
det_pix = 0.075,
beam_l = None,
mask_thr = None,
nQ = None,
nPhi = None,
dQ = 1,
dPhi = 1,
cent0 = None,
r_max = None,
dr = None,
dx = None,
dy = None,
r_0 = None,
q_bound = None,
peak = None,
dpeak = None):
"""The fluctuation scattering class stores processing parameters,
initiates mask and background data and retrieves 2D images
from events. Processing options of the 2D images include:
* Transform from cartesian to polar coordinates
* Beam center refinement
* Dynamic masking
* Normalization % SAXS calculation
* Particle sizing
* Computation of in-frame 2-point angular auto-correlations using FFTs
@param dataset_name Experiment name and run number
@param detector_address Adress to back or front detector
@param data_type Type of data file format (h5 or xtc in the formats: idx|idx_ffb|smd|smd_ffb|h5)
@param mask_path Full path to static image mask
@param mask_angles Center of angluar slices (deg) that should be masked out (due to jet streaks etc), [Ang1 Ang2 ...]
@param mask_widths Width of angular slices (deg) that should be masked out (due to jet streaks etc), [delta1 delta2 ...]
@param backimg_path Full path to background image
@param backmsk_path Full path to background mask
@param geom_path Full path to geometry file (for h5 format)
@param det_dist Override of detecor distance (in mm)
@param det_pix Pixel size (in mm)
@param beam_l Override of beam wavelength (in Angstrom)
@param mask_thr Threshold for dynamic masking
@param nQ Number of Q-bins to consider (in pixels)
@param nPhi Number of Phi-bins to consider (in pixels)
@param dQ Stepsize in Q (in pixels)
@param dPhi Stepsize in Phi (in pixels)
@param cent0 Initial beam center coordinates [xc,yc]
@param r_max Maximum radial value to use for beamcenter refinement (in pixels)
@param dr Stepsize in r (in pixels)
@param dx Gridsize for beam center refinement in x, i.e xc+/-dx (in pixels)
@param dy Gridsize for beam center refinement in y, i.e yc+/-dy (in pixles)
@param r_0 Starting value for particle radius refinement [in Ang]
@param q_bound Upper and Lower boundaries of q for Particle radius refinement [in Ang^-1]
@param peak Q-values for peak maxima [q_peak1 q_peak2 ...]
@param dpeak Delta Q used for peak integration of peak maxima [delta_q1 delta_q2 ...]
"""
# Initialize parameters and configuration files once
self.data_type = data_type
self.dataset_name = dataset_name
self.detector_address = detector_address
if (self.data_type == 'idx') or (self.data_type == 'idx_ffb') or (self.data_type == 'smd') or (self.data_type == 'smd_ffb') or (self.data_type == 'xtc') :
self.ds = DataSource(self.dataset_name)
self.src = Detector(self.detector_address, self.ds.env())
if mask_path is None : # Create a binary mask of ones, default mask only works for xtc/ffb
evt = self.ds.events().next()
self.mask_address = self.src.mask(evt,calib=True,status=True)
self.msk = self.src.image(evt,self.mask_address)
self.mask = np.copy(self.msk)
else:
self.msk = np.loadtxt(mask_path)
self.mask = np.copy(self.msk)
if geom_path is not None :
geom = np.genfromtxt(geom_path,skiprows=1)
self.gap = geom[0]
self.shift = geom[1]
self.orient = geom[2
]
self.comm = geom[3]
self.param1 = geom[4]
self.param2 = geom[5]
self.param3 = geom[6]
self.param4 = geom[7]
if (self.data_type == 'h5'):
if mask_path is None : # Create a binary mask of ones
## Add default binary mask here ## Default pnCCD dimensions
dim1 = 1024
dim2 = 1024
self.mask = np.ones((dim1,dim2))
else:
self.mask = np.loadtxt(mask_path)
# Apply geometry
self.msk = pnccd_tbx.get_geometry(img = self.mask,
gap = self.gap,
shift = self.shift,
orient = self.orient)
if self.detector_address == 'pnccdFront' :
evt = self.ds.events().next()
gain = self.src.gain(evt)
self.gain = self.src.image(evt,gain)
self.cart = 0
self.flat = 0
if backimg_path is None :
self.backimg = None
else :
self.backimg = np.loadtxt(backimg_path).astype(np.float64)
# Check if background image in cartesian coordinates exists
if (self.backimg.shape == self.msk.shape):
self.cart = 1 # Remove bg before transform to polar coordinates
if backmsk_path is None :
self.backmsk = None
else :
self.backmsk = np.loadtxt(backmsk_path).astype(np.float64)
# Check if flat-field image exists
if (self.backmsk is None) and (self.backimg is not None) and (self.cart==0):
self.pcflat = pnccd_tbx.dynamic_flatfield(self.backimg)
self.flat = 1
if det_dist is None : # Get detector distance from events
for run in self.ds.runs():
self.det_dist = cspad_tbx.env_distance(self.detector_address, run.env(), 577)
else :
self.det_dist = det_dist
self.det_pix = det_pix
if beam_l is None : # Get wavelength from event, note it can change slightly between events. So in the future use average.
self.beam_l = cspad_tbx.evt_wavelength(self.ds.events().next())
else :
self.beam_l = beam_l
if mask_thr is None : # No dynamic masking
self.thr = None
else :
self.thr = mask_thr
if nQ is None : # Use image dimensions as a guide, leave room for offset beamC
if self.msk.shape[0] > self.msk.shape[1] : # nQ determined by smallest dimension
self.nQ = int(self.msk.shape[1]/2)-20
else :
self.nQ = int(self.msk.shape[0]/2)-20
else :
self.nQ = nQ
if (self.nQ % 10): # Ascert even number, speeds things up massively for FFT
self.nQ = np.floor(self.nQ/10)*10
if (self.nQ % dQ): # Ascert clean divisor
self.nQ = np.floor(self.nQ/dQ)*dQ
if nPhi is None : # Estimate based on 2*pi*nQ
self.nPhi = np.ceil(2*np.pi*self.nQ)
else :
self.nPhi = nPhi
if (self.nPhi % 10): # Ascert even number, speeds things up massively for FFT
self.nPhi = np.ceil(self.nPhi/10)*10
if (self.nPhi % dPhi): # Ascert clean divisor
self.nPhi = np.ceil(self.nPhi/dPhi)*dPhi
self.dQ = dQ
self.dPhi = dPhi
self.mask_angles = mask_angles
self.mask_widths = mask_widths
# Compute slices that should be masked in static mask
if (self.mask_angles is not None) and (self.mask_widths is not None) :
self.mask_angles = (self.mask_angles/360) * self.nPhi
self.mask_widths = (self.mask_widths/360) * self.nPhi
# Check if nQ > smallest dimension/2 then we extend the image with zero values
if self.nQ > min(self.msk.shape[0]/2,self.msk.shape[1]/2) :
self.msk = pnccd_tbx.extend_image(img = self.msk)
self.mask = np.copy(self.msk)
if (cent0 is None) or (sum(cent0) == 0): # Use center of gravity to estimate starting beamC
self.cent0 = [int(round(self.msk.shape[1]/2)) , int(round(self.msk.shape[0]/2))]
else :
self.cent0 = cent0
self.cent = self.cent0 # Default center
if r_max is None : # Default, Use half of nQ
self.r_max = int(self.nQ*(3/4))
else :
self.r_max = r_max
if (self.r_max % dr): # Ascert clean divisor
self.r_max = np.floor(self.r_max/dr)*dr
self.dr = dr
self.dx = dx
self.dy = dy
if r_0 is None :
self.radius = 0
self.score = 0
self.r_0 = r_0
if q_bound is None or sum(q_bound)==0 :
self.q_bound = [None,None]
else :
self.q_bound = [None,self.q_bound]
# Compute q-spacing
self.q = np.arange(0, self.nQ, self.dQ)
self.q = self.q*self.det_pix/self.det_dist*4*np.pi/self.beam_l/2
# Compute Phi (Not accounting for curvature)
self.phi = np.linspace(0, 2*np.pi, self.nPhi/self.dPhi,endpoint=False)
# Compute indices for Peak maxima
if (peak is not None) and (dpeak is not None) :
self.peak = peak
self.dpeak = dpeak
self.ind1 = (self.q >= (self.peak[0] - self.dpeak[0])) & (self.q <= (self.peak[0] + self.dpeak[0]) )
self.ind2 = (self.q >= (self.peak[1] - self.dpeak[1])) & (self.q <= (self.peak[1] + self.dpeak[1]) )
else:
self.peak = None
self.dpeak = None
def __init__(self,
dataset_name=None,
detector_address=None,
data_type='idx',
mask_path=None,
mask_angles=None,
mask_widths=None,
backimg_path=None,
backmsk_path=None,
geom_path=None,
det_dist=None,
det_pix=0.075,
beam_l=None,
mask_thr=None,
nQ=None,
nPhi=None,
dQ=1,
dPhi=1,
cent0=None,
r_max=None,
dr=None,
dx=None,
dy=None,
r_0=None,
q_bound=None,
peak=None,
dpeak=None):
"""The fluctuation scattering class stores processing parameters,
initiates mask and background data and retrieves 2D images
from events. Processing options of the 2D images include:
* Transform from cartesian to polar coordinates
* Beam center refinement
* Dynamic masking
* Normalization % SAXS calculation
* Particle sizing
* Computation of in-frame 2-point angular auto-correlations using FFTs
@param dataset_name Experiment name and run number
@param detector_address Adress to back or front detector
@param data_type Type of data file format (h5 or xtc in the formats: idx|idx_ffb|smd|smd_ffb|h5)
@param mask_path Full path to static image mask
@param mask_angles Center of angluar slices (deg) that should be masked out (due to jet streaks etc), [Ang1 Ang2 ...]
@param mask_widths Width of angular slices (deg) that should be masked out (due to jet streaks etc), [delta1 delta2 ...]
@param backimg_path Full path to background image
@param backmsk_path Full path to background mask
@param geom_path Full path to geometry file (for h5 format)
@param det_dist Override of detecor distance (in mm)
@param det_pix Pixel size (in mm)
@param beam_l Override of beam wavelength (in Angstrom)
@param mask_thr Threshold for dynamic masking
@param nQ Number of Q-bins to consider (in pixels)
@param nPhi Number of Phi-bins to consider (in pixels)
@param dQ Stepsize in Q (in pixels)
@param dPhi Stepsize in Phi (in pixels)
@param cent0 Initial beam center coordinates [xc,yc]
@param r_max Maximum radial value to use for beamcenter refinement (in pixels)
@param dr Stepsize in r (in pixels)
@param dx Gridsize for beam center refinement in x, i.e xc+/-dx (in pixels)
@param dy Gridsize for beam center refinement in y, i.e yc+/-dy (in pixles)
@param r_0 Starting value for particle radius refinement [in Ang]
@param q_bound Upper and Lower boundaries of q for Particle radius refinement [in Ang^-1]
@param peak Q-values for peak maxima [q_peak1 q_peak2 ...]
@param dpeak Delta Q used for peak integration of peak maxima [delta_q1 delta_q2 ...]
"""
# Initialize parameters and configuration files once
self.data_type = data_type
self.dataset_name = dataset_name
self.detector_address = detector_address
if (self.data_type == 'idx') or (self.data_type == 'idx_ffb') or (
self.data_type == 'smd') or (self.data_type
== 'smd_ffb') or (self.data_type
== 'xtc'):
self.ds = DataSource(self.dataset_name)
self.src = Detector(self.detector_address, self.ds.env())
if mask_path is None: # Create a binary mask of ones, default mask only works for xtc/ffb
evt = next(self.ds.events())
self.mask_address = self.src.mask(evt, calib=True, status=True)
self.msk = self.src.image(evt, self.mask_address)
self.mask = np.copy(self.msk)
else:
self.msk = np.loadtxt(mask_path)
self.mask = np.copy(self.msk)
if geom_path is not None:
geom = np.genfromtxt(geom_path, skiprows=1)
self.gap = geom[0]
self.shift = geom[1]
self.orient = geom[2]
self.comm = geom[3]
self.param1 = geom[4]
self.param2 = geom[5]
self.param3 = geom[6]
self.param4 = geom[7]
if (self.data_type == 'h5'):
if mask_path is None: # Create a binary mask of ones
## Add default binary mask here ## Default pnCCD dimensions
dim1 = 1024
dim2 = 1024
self.mask = np.ones((dim1, dim2))
else:
self.mask = np.loadtxt(mask_path)
# Apply geometry
self.msk = pnccd_tbx.get_geometry(img=self.mask,
gap=self.gap,
shift=self.shift,
orient=self.orient)
if self.detector_address == 'pnccdFront':
evt = next(self.ds.events())
gain = self.src.gain(evt)
self.gain = self.src.image(evt, gain)
self.cart = 0
self.flat = 0
if backimg_path is None:
self.backimg = None
else:
self.backimg = np.loadtxt(backimg_path).astype(np.float64)
# Check if background image in cartesian coordinates exists
if (self.backimg.shape == self.msk.shape):
self.cart = 1 # Remove bg before transform to polar coordinates
if backmsk_path is None:
self.backmsk = None
else:
self.backmsk = np.loadtxt(backmsk_path).astype(np.float64)
# Check if flat-field image exists
if (self.backmsk is None) and (self.backimg is not None) and (self.cart
== 0):
self.pcflat = pnccd_tbx.dynamic_flatfield(self.backimg)
self.flat = 1
if det_dist is None: # Get detector distance from events
for run in self.ds.runs():
self.det_dist = cspad_tbx.env_distance(self.detector_address,
run.env(), 577)
else:
self.det_dist = det_dist
self.det_pix = det_pix
if beam_l is None: # Get wavelength from event, note it can change slightly between events. So in the future use average.
self.beam_l = cspad_tbx.evt_wavelength(next(self.ds.events()))
else:
self.beam_l = beam_l
if mask_thr is None: # No dynamic masking
self.thr = None
else:
self.thr = mask_thr
if nQ is None: # Use image dimensions as a guide, leave room for offset beamC
if self.msk.shape[0] > self.msk.shape[
1]: # nQ determined by smallest dimension
self.nQ = int(self.msk.shape[1] / 2) - 20
else:
self.nQ = int(self.msk.shape[0] / 2) - 20
else:
self.nQ = nQ
if (self.nQ %
10): # Ascert even number, speeds things up massively for FFT
self.nQ = np.floor(self.nQ / 10) * 10
if (self.nQ % dQ): # Ascert clean divisor
self.nQ = np.floor(self.nQ / dQ) * dQ
if nPhi is None: # Estimate based on 2*pi*nQ
self.nPhi = np.ceil(2 * np.pi * self.nQ)
else:
self.nPhi = nPhi
if (self.nPhi %
10): # Ascert even number, speeds things up massively for FFT
self.nPhi = np.ceil(self.nPhi / 10) * 10
if (self.nPhi % dPhi): # Ascert clean divisor
self.nPhi = np.ceil(self.nPhi / dPhi) * dPhi
self.dQ = dQ
self.dPhi = dPhi
self.mask_angles = mask_angles
self.mask_widths = mask_widths
# Compute slices that should be masked in static mask
if (self.mask_angles is not None) and (self.mask_widths is not None):
self.mask_angles = (self.mask_angles / 360) * self.nPhi
self.mask_widths = (self.mask_widths / 360) * self.nPhi
# Check if nQ > smallest dimension/2 then we extend the image with zero values
if self.nQ > min(self.msk.shape[0] / 2, self.msk.shape[1] / 2):
self.msk = pnccd_tbx.extend_image(img=self.msk)
self.mask = np.copy(self.msk)
if (cent0 is None) or (
sum(cent0)
== 0): # Use center of gravity to estimate starting beamC
self.cent0 = [
int(round(self.msk.shape[1] / 2)),
int(round(self.msk.shape[0] / 2))
]
else:
self.cent0 = cent0
self.cent = self.cent0 # Default center
if r_max is None: # Default, Use half of nQ
self.r_max = int(self.nQ * (3 / 4))
else:
self.r_max = r_max
if (self.r_max % dr): # Ascert clean divisor
self.r_max = np.floor(self.r_max / dr) * dr
self.dr = dr
self.dx = dx
self.dy = dy
if r_0 is None:
self.radius = 0
self.score = 0
self.r_0 = r_0
if q_bound is None or sum(q_bound) == 0:
self.q_bound = [None, None]
else:
self.q_bound = [None, self.q_bound]
# Compute q-spacing
self.q = np.arange(0, self.nQ, self.dQ)
self.q = self.q * self.det_pix / self.det_dist * 4 * np.pi / self.beam_l / 2
# Compute Phi (Not accounting for curvature)
self.phi = np.linspace(0,
2 * np.pi,
self.nPhi / self.dPhi,
endpoint=False)
# Compute indices for Peak maxima
if (peak is not None) and (dpeak is not None):
self.peak = peak
self.dpeak = dpeak
self.ind1 = (self.q >= (self.peak[0] - self.dpeak[0])) & (
self.q <= (self.peak[0] + self.dpeak[0]))
self.ind2 = (self.q >= (self.peak[1] - self.dpeak[1])) & (
self.q <= (self.peak[1] + self.dpeak[1]))
else:
self.peak = None
self.dpeak = None