TestingApp

The FABLE applications are now at stage where is time do some serious testing and evalution of the documentation for the applications.

Test teams

Some test teams have been formed.

• Simulators (both near and farfield) and Fabian
  • Jon
  • Carsten
  • Larry
  • Allan
• Preprocessing
  • Erik ML
  • Henning O
  • Larry
• ImageD11
  • Erik ML
  • Henning FP
  • Larry
  • Christian
• Grainspotter
  • Larry
  • Carsten
  • Christian

Furthermore Ulrich Lienert from APS will do some test have give us some feed back.

What to do

• Is it possible based on the documentation to download and install the programs
• Is it clear from the documentation what the program does, what its limits are and how it interfaces to the other programs.
• Technical performanece - bugs, inconsistencies etc.
• General user friendliness

Programs to test

Here is the list of program releases to test.

• fable.preprocessing release 1.2
• fabian release 0.5.0
• ImageD11 release 1.0.1
• fabio release fabio-numpy 0.0.1
• quesi-nearfield_simulator release 0.6
• simul_farfield release 1.4.6
• GrainSpotter release 0.3

They are available from on the sourceforge download page

Test cases

To get a spread in complexity three different structures have been selected for testing the farfield simulator.
For the ones testing ImageD11 and/or Grainspotter a file called Orientations.txt for each simulation can be used to compare if the grains have been determined correctly. Furthermore compare the global parameters fitted with ImageD11 with the values used for the simulations.

Test 1

One of the most frequent space groups for optically active small molecule compounds is P21 therefore the first test is of the optically active compoundR-(+)-2-phenoxypropionic acid, so it a farely small compound with low symmetry.
The structure of the compound can be found in a cif format here
Input files for simul_farfield as well as output, including the diffraction images can be downloaded here
The diffraction data has been collected in five zip files (notice these on the old teamsites.risoe.dk/synch not the new synch as the remaining files):
FableTest1_data_p1s.zip
FableTest1_data_p2s.zip
FableTest1_data_p3s.zip
FableTest1_data_p4s.zip
FableTest1_data_p5s.zip

Parameters used for the simulation

Beam energy
Beam energy: 24.344 keV

Detector specs
The Frelon2k 2x2 binned was emulated 1024x1024 pixels.
beam center y: 511.5 pixels
beam center z: 511.5 pixels
pixelsize y: 93.6 microns
pixelsize z: 96.2 microns
detector tilt y: 0.0 radians
detector tilt z: 0.0 radians
detector to sample: 95.0 mm

Grain orientations
The grain orientations can be seen here for comparison with Grainspotter results.

Images
Filetype: tif.gz (NB! Detector parameters for .tif files in ImageD11 are: o11=o22=-1 and o12=o21=0)
name stem (prefix): FableTest?1_25gr
Omega range: -90 to 90 degrees
Omega step size: 0.5 degrees

Structure
Unit cell: a = 8.5312 Å, b = 4.8321 Å, c = 10.125 Å, β = 92.031 deg
Lattice centering: P

Test 2

Another frequent space group is the orthorhombic Pnma, hence the second compound, (Mn(cyclam)(HCOO))(CF3SO3)(ClO4) , chosen is one that crystallize is this one.
For testing simul_farfield a cif file (structure information) can be found here
For testing ImageD11 - and maybe Grainspotter a data set has been simulated.
Input files for simul_farfield as well as output, including the diffraction images can be downloaded here
The diffraction data has been collected in three zip files:
FableTest2_data_p1.zip
FableTest2_data_p2.zip
FableTest2_data_p3.zip

Parameters used for the simulation

Beam energy
Beam energy: 24.344 keV

Detector specs
The Frelon2k was emulated 2048x2028 pixels.
beam center y: 1025.7 pixels
beam center z: 1022.1 pixels
pixelsize y: 0.04677648 microns
pixelsize z: 0.04808150 microns
detector tilt y: -0.03 radians
detector tilt z: -0.06 radians
detector to sample: 145.0 mm

Grain orientations
The grain orientations can be seen here for comparison with Grainspotter results.

Images
Filetype: tif.gz (NB! Detector parameters for .tif files in ImageD11 are: o11=o22=-1 and o12=o21=0)
name stem (prefix): FableTest?2_50gr_
Omega range: -90 to 90 degrees
Omega step size: 1.0 degrees

Structure
Unit cell: a = 10.169 Å, b = 12.744, c = 16.181 Å
Lattice centering: P

Test 3

For this test is the structure of tin(IV)porphyrin nitrophenolate chosen for primarily two reasons. Firstly because it crystallizes in the space group R3bar, secondly because it has a reasonably large unit cell ~12000 Å3.
For testing simul_farfield a cif file (structure information) can be found here
For testing ImageD11 - and maybe Grainspotter a data set has been simulated. Input files for simul_farfield as well as output, including the diffraction images can be downloaded here
The diffraction data has been divided into four zip files:
FableTest3_data_p1.zip
FableTest3_data_p2.zip
FableTest3_data_p3.zip
FableTest3_data_p4.zip

Parameters used in the simulation

Beam energy
Beam energy: 24.344 keV

Detector specs
The Frelon2k was emulated 2048x2028 pixels.
beam center y: 1012.4 pixels
beam center z: 1026.2 pixels
pixelsize y: 0.04677648 microns
pixelsize z: 0.04808150 microns
detector tilt y: 0.05 radians
detector tilt z: -0.10 radians
detector to sample: 215.0 mm

Grain orientations
The grain orientations can be seen here for comparison with Grainspotter results.

Images Filetype: tif.gz (NB! Detector parameters for .tif files in ImageD11 are: o11=o22=-1 and o12=o21=0)
name stem (prefix): FableTest?3_40gr_
Omega range: -180 to 0 degrees
Omega step size: 0.5 degrees

Structure
Unit cell: a = b = 36.6819 Å, c = 10.4431 Å, γ = 120 deg
Lattice centering: R