MeV UED MicroED

to_cbf.py

import os
import numpy as np
import sys
import fabio
from glob import glob
from scipy.signal import medfilt2d

header = {
    'beam_center_x': 512,
    'beam_center_y': 512,
    'bit_depth_readout': 32,
    'count_time': 0.099996,
    'countrate_correction_applied': 1,
    'description': 'UED',
    'detector_distance': 0.150,
    'detector_number': 'E-08-0102',
    'detector_readout_time': 3.78e-06,
    'efficiency_correction_applied': 1,
    'flatfield_correction_applied': 1,
    'frame_time': 0.1,
    'pixel_mask_applied': 0,
    'sensor_material': 'Si',
    'sensor_thickness': 0.00032,
    'threshold_energy': 4680000,
    'virtual_pixel_correction_applied': 1,
    'x_pixel_size': 9.5e-06,
    'y_pixel_size': 9.5e-06,
}


files = sorted(glob(sys.argv[-1]))
print(sys.argv[-1])
print("found %d files" % len(files))

for idx, fn in enumerate(files):

    out_fn = "img_%04i.cbf" % (idx+1,)
    print(idx, fn, '-->', out_fn)

    frame_data = np.genfromtxt(fn)

    frame_data[frame_data < 0.0]  = 0.0

    frame_data = medfilt2d(frame_data, 9)

    cbf = fabio.cbfimage.cbfimage(header=header, data=frame_data.astype(np.int32))
    cbf.write(out_fn)

    os.system('adxv -sa img_%04i.cbf img_%04i.img' % (idx+1,idx+1))

ued.ins

TITL ued1 in P 1 2(1) 1
CELL 0.002650  5.441     7.208    33.988  90.000  86.400  90.000
ZERR 2.00 0.25 0.25 0.25 0.0 3.0 0.0
LATT -1
SYMM -X,Y+1/2,-Z
SFAC C  0.208  0.922  0.702  5.018  1.144 16.523  0.425 47.300  0.030 =
  0.0 0.0 0.000 0.770 12.011
SFAC H  0.042  0.991  0.103  3.924  0.205 11.597  0.170 31.984  0.006 =
  0.0 0.0 0.000 0.310 1.008
SFAC O  0.308  1.088  0.733  4.593  0.710 13.052  0.185 33.768  0.048 =
  0.0 0.0 0.000 0.660 15.999
SFAC N  0.216  0.843  0.649  4.055  0.968 12.693  0.345 36.058  0.032 =
  0.0 0.0 0.000 0.700 14.007
SFAC S  0.610  1.173  1.367  6.371  2.268 18.858  0.808 49.703  0.108 =
  0.0 0.0 0.000 1.030 32.060
UNIT 38 42 0 0 0
HKLF 4
END

XDS.INP

!*****************************************************************************
!
! XDS input file created by TJL Feb 2020 for solving MeV UED structure
! - 4.2 MeV e-
! - yaw geometry
! - median filter spots
!
!*****************************************************************************

!====================== DETECTOR PARAMETERS ==================================
! DETECTOR=UED
 MINIMUM_VALID_PIXEL_VALUE=0
 OVERLOAD= 32768  
 GAIN=1.0  ! pixel contents is interpreted as X-ray counts
 QX=0.0095  QY=0.0095  ! [mm]
 NX= 1024  NY= 1024    !  1M 

 UNTRUSTED_ELLIPSE=     445 545    465  565
 TRUSTED_REGION=0.02 1.41 !Relative radii limiting trusted detector region

 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0


!====================== JOB CONTROL PARAMETERS ===============================
 JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 !JOB= CORRECT


!====================== GEOMETRICAL PARAMETERS ===============================
 ORGX= 488  ORGY= 510      !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2
 DETECTOR_DISTANCE= 1500   !(mm)

 ROTATION_AXIS= 0.0 1.0 0.0

 OSCILLATION_RANGE=0.2

 X-RAY_WAVELENGTH=0.00265           !Angstroem
 INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
 FRACTION_OF_POLARIZATION=0.5 !default=0.5 for unpolarized beam
 POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0


!======================= CRYSTAL PARAMETERS =================================
! TJL : only use if known a priori
! SPACE_GROUP_NUMBER=1
! UNIT_CELL_CONSTANTS= 77.4   77.4   77.4  90.0  90.0  90.0


!==================== SELECTION OF DATA IMAGES ==============================
!Generic file name and format (optional) of data images
 NAME_TEMPLATE_OF_DATA_FRAMES=../data/corrected_yaw_data/img_????.img

! DATA_RANGE=1 5
 DATA_RANGE=1 225

 BACKGROUND_RANGE=1 225  !Numbers of first and last data image for background

 SPOT_RANGE=1 225       !First and last data image number for finding spots


!================= PARAMETERS CONTROLLING REFINEMENTS =======================
 REFINE(IDXREF)=BEAM AXIS ORIENTATION CELL  ! POSITION
 REFINE(INTEGRATE)= ORIENTATION POSITION BEAM ! CELL AXIS
 REFINE(CORRECT)=POSITION BEAM ORIENTATION CELL AXIS


!================== CRITERIA FOR ACCEPTING REFLECTIONS ======================
 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 10 30000 !Used by DEFPIX

 INCLUDE_RESOLUTION_RANGE=25 1.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT

!MINIMUM_ZETA=0.05 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT)
!WFAC1=1.0  !This controls the number of rejected MISFITS in CORRECT;
        !a larger value leads to fewer rejections.


!============== DECISION CONSTANTS FOR FINDING CRYSTAL SYMMETRY =============
!Decision constants for detection of lattice symmetry (IDXREF, CORRECT)
! MAX_CELL_AXIS_ERROR=0.03 ! Maximum relative error in cell axes tolerated
! MAX_CELL_ANGLE_ERROR=2.0 ! Maximum cell angle error tolerated

!Decision constants for detection of space group symmetry (CORRECT).
!Resolution range for accepting reflections for space group determination in
!the CORRECT step. It should cover a sufficient number of strong reflections.
 TEST_RESOLUTION_RANGE=8.0 4.5
 MIN_RFL_Rmeas= 50 ! Minimum #reflections needed for calculation of Rmeas
 MAX_FAC_Rmeas=2.0 ! Sets an upper limit for acceptable Rmeas


!============== INTEGRATION AND PEAK PROFILE PARAMETERS =====================
!BEAM_DIVERGENCE=   0.80         !arctan(spot diameter/DETECTOR_DISTANCE)
!BEAM_DIVERGENCE_E.S.D.=   0.080 !half-width (Sigma) of BEAM_DIVERGENCE


!======= PARAMETERS CONTROLLING CORRECTION FACTORS (used by: CORRECT) =======
!MINIMUM_I/SIGMA=3.0 ! min(I/sigma) for reflections used in global refinement 
!SNRC=0.1         ! min(I/sigma) for reflections used for finding corrections
!BATCHSIZE=5.0    ! rotation range covered by a batch of consecutive images 
!CORRECTIONS= DECAY MODULATION ABSORPTION


!====================== INDEXING PARAMETERS =================================
!SEPMIN=4.0       ! default is 6 for other detectors
!LUSTER_RADIUS=2 ! default is 3 for other detectors
 MAXIMUM_ERROR_OF_SPOT_POSITION=6.0
 MAXIMUM_ERROR_OF_SPINDLE_POSITION=4.0
 MINIMUM_FRACTION_OF_INDEXED_SPOTS=0.1

!=========== PARAMETERS DEFINING BACKGROUND AND PEAK PIXELS =================
! TJL Note: the following are critical parameters for spotfinding
 STRONG_PIXEL=2.0                              !used by: COLSPOT
 MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=25          !used by: COLSPOT
 NBX=15  NBY=15  !Define a rectangle of size (2*NBX+1)*(2*NBY+1)
 BACKGROUND_PIXEL=5.0                          !used by: COLSPOT,INTEGRATE

!SIGNAL_PIXEL=3.0                              !used by: INTEGRATE
!A pixel above the threshold contributes to the spot centroid
!FIXED_SCALE_FACTOR=TRUE  !Default is FALSE; used by : INIT,INTEGRATE

Software Used (that is generally useful)

Install these!

• adxv : https://www.scripps.edu/tainer/arvai/adxv.html
• XDS : http://xds.mpimf-heidelberg.mpg.de/
• SHELX : http://shelx.uni-ac.gwdg.de/
• and the fabIO python package: https://pythonhosted.org/fabio/