Tomo Reconstruction Tips & Tricks (AM-TOMO)

Questions:

Answers:

The width, length and bit depth of TIFF images can be determined in many different ways. For example, the Linux command tiffinfo can be used to print information about the input TIFF file(s) in the following way: tiffinfo [options] input1.tif input2.tif...

For example,

Linux command

tiffinfo 06029.tif

displays the following summary information:

Linux output from tiffinfo

TIFFReadDirectory: Warning, 06029.tif: unknown field with tag 65000 (0xfde8) encountered.
TIFF Directory at offset 0x146d308 (21418760)
  Image Width: 4008 Image Length: 2672
  Bits/Sample: 16
  Sample Format: unsigned integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 2672
  Planar Configuration: single image plane
  Make: Unknown
  Model: Unknown
  Tag 65000: 727733745.824557

It is sometimes desirable to reconstruct a sub-set, or a slab, of slices rather than the complete set. The recon_arrayxml.py script is capable of accomplishing this task with the help of the F- and L-options.
For example,
Linux command
```
python2.6 /dls_sw/i13/software/gda/config/tomography_scripts/recon_arrayxml.py -I settings.xml -o ../../reconstruction/564/ -C 2000.5 -F 1299 -L 1300
```
will reconstruct a slab consisting of exactly 1 slice (=1300-1299), namely that indexed 1299.
The contents of your settings.xml file under the ROI tag need to be modified in the following way:

<ROI>
        <Type info="Standard, Rectangle">Rectangle</Type>
        <Xmin>580</Xmin>
        <Xmax>3000</Xmax>
        <Ymin>1225</Ymin>
        <Ymax>1725</Ymax>
        <OutputWidthType info="Standard, Given">Standard</OutputWidthType>
        <OutputWidth>500</OutputWidth>
        <Angle>0.0</Angle>
</ROI>

where the above values of Xmin, Xmax, Ymin, and Ymax need to be changed to whatever values you would like to use in your reconstruction. Incidentally, these coordinates can be determined, for example, by looking at the original projection images in ImageJ.

The information about all current SGE jobs can be found with the help of the qstat command. The state of a successfully submitted job is indicated by the status code qw or r. If a job encountered a problem, then its status code is Eqw or Rr. The possible status codes are:

d(eletion)

E(rror)

h(old)

r(unning)

R(estarted)

s(uspended)

S(uspended)

t(ransferring)

T(hreshold)

w(aiting)

For a more detailed explanation of all possible job states, see the table displayed below:

Category	SGE Letter Code	Description
Pending
	qw	Job is in the queue and waiting to be executed.
	hqw	Job is in the queue and waiting to be executed but it is not elligible for execution due to a hold request or because it is waiting for completion of all the jobs in its job dependecies.
	hRqw	Job is in the queue and waiting to be executed after being Restarted but it is not elligible for execution due to a hold request or because it is waiting for completion of all the jobs in its job dependecies.
Running
	r	Job is running.
	t	Job is transferring and about to be executed.
	Rr	Job is running after being Restarted.
	Rt	Job is transferring after being Restarted.
Suspended
	s ts	Job is suspended.
	S tS	The queue containing the job is Suspended and therefore the job is also suspended.
	T tT	At least one suspend Threshold of the queue containing the job has been exceeded and therefore the job has been suspended as a consequence.
	Rs Rts RS RtS RT RtT	Job is in the Suspended category after being Restarted.
Error
	Eqw Ehqw ERqw	Job in the Pending category is in the Error state due to its job properties and therefore could not be executed.
Deletion
	dr dt dRr dRt ds dts dS dtS dT dtT dRs dRts dRS dRtS dRT dRtT	Job in the Running or Suspended category which has been marked for deletion via the qdel command.

If a SGE job is in the Eqw state, then the following command:

Linux command

qstat -j job_id | grep "error reason"

can be used to diagnose the errors (please replace the job_id argument with your particular job's identifier).

An SGE job can be deleted with the help of the qdel command:
Linux command
```
qdel job_id 
```
The nxs2tiff command can be used to extract TIFF images from a GDA scan NeXus file:
Linux commands
```
module load tomography; nxs2tiff -h
```
outputs a brief description of its arguments. To use it, please follow the following 3-argument pattern:
Linux command
```
nxs2tiff -d /nexus/internal/path/to/data /path/to/nexus/file /path/to/output/directory
```
For example,
Linux command
```
nxs2tiff -d /entry1/instrument/pco1_hw_hdf/data /dls/i13/data/2013/cm5937-1/7724.nxs /dls/i13/data/2013/cm5937-1/processing/raw/7724/projections 
```
Please note that nxs2tiff does not create output directory, so the latter needs to be created manually prior to executing nxs2tiff. Please also note that the first input path, corresponding to the d (for data) option, is not a path to a HDF5 file but an internal path to data inside your GDA scan NeXus file (incidentally, the name of that NeXus file needs to be specified in the second input path).
If there are any issues, your qsub log files can be found in /dls/tmp/tomopy; please examine your latest run_nxs2tiff.sh.e* style file stored in that directory to diagnose any problems.