Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  1. Anchor
    A1
    A1
    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,

    Code Block
    titleLinux command
    tiffinfo 06029.tif
    

    displays the following summary information:

    Code Block
    titleLinux 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
  2. Anchor
    A2
    A2
    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,

    Code Block
    titleLinux 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.

  3. Anchor
    A3
    A3
    The ROI element included in your settings.xml file needs 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 reflect your particular reconstruction needs. Incidentally, these ROI coordinates can be determined, for example, by viewing the original projection images in ImageJ.  

  4. Anchor
    A4
    A4
    The information about all current SGE jobs can be obtained 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: 


    CategorySGE Letter CodeDescription
    Pending
      
     



    qwJob is in the queue and waiting to be executed. 
     

    hqwJob 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
       



    rJob is running.
     

    tJob is transferring and about to be executed.
     

    RrJob is running after being Restarted.
     

    RtJob 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:

      

    Code Block
    titleLinux command
    qstat -j job_id | grep "error reason"

      

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

      

  5. Anchor
    A5
    A5
    The owner of a SGE job can delete it with the help of the qdel command:

      

    Code Block
    titleLinux command
    qdel job_id 



  6. Anchor
    A6
    A6
    The nxs2tiff command can be used to extract TIFF images from a given HDF5 dataset accompanied by a NeXus scan file. One can use this command to extract all or any subset of images from this dataset.

    Code Block
    titleLinux commands
    module load tomography; nxs2tiff -h

    outputs a brief description of the command's arguments:

    Code Block
    titleLinux output
    >nxs2tiff -h
        
    
         Welcome to the DLS compute cluster
    
         For MPI jobs, please use 'module load openmpi'.
    
         If using a different OpenMPI installation,
         or manually specifying path to OpenMPI, option
         '-mca orte_forward_job_control 1'
         must be added to mpirun to ensure cluster functionality.
    
         Please report any issues to linux.manager@diamond.ac.uk
    
    Loading 64-bit scipy, version 0.10.0
    /dls_sw/apps/tomopy/tomopy/src/tifffile.py:2170: UserWarning: failed to import _tifffile.decodepackbits
      warnings.warn("failed to import %s" % module_function)
    /dls_sw/apps/tomopy/tomopy/src/tifffile.py:2170: UserWarning: failed to import _tifffile.decodelzw
      warnings.warn("failed to import %s" % module_function)
    /dls_sw/apps/tomopy/tomopy/src/tifffile.py:2170: UserWarning: failed to import _tifffile.unpackints
      warnings.warn("failed to import %s" % module_function)
    
    Usage: nxs2tiff.py [options] file output_folder
    
    Options:
      --version             show program's version number and exit
      -h, --help            show this help message and exit
      -b BEGIN, --begin=BEGIN
                            projection to begin from
      -s SLICES, --slices=SLICES
                            number of projections to process
      -d DATASET, --dataset=DATASET
                            Select the dataset to read from
      -k KEYS, --image_keys=KEYS
                            Select the image_keys dataset
      -i DIM, --slice_dim=DIM
                            Dimension to slice the data in to create the
                            projections
      -f FORMAT, --format=FORMAT
                            format for the output files
      -r, --robert          output for robert
      --scan=SCAN           scan number if needed (for roberts extraction)
    >
    
    


    The simplest way to use nxs2tiff is to follow the following 3-argument pattern:

    Code Block
    titleLinux command
    nxs2tiff -d /nexus/internal/path/to/dataset /path/to/nexus/file /path/to/output/directory

    Please note that the above command requires the use of absolute paths. The default filename format for all extracted files is: p_%05d.tif (c.f. the f-option above).

    Please also note that the default value for the d-option is /entry1/tomo_entry/instrument/detector/data, so there is normally no need to include this option unless the tomo entry is absent from your Nexus scan file, or is malformed, or if you would like to extract images from a dataset stored in a location different from this default path.

    For example, the command given below extracts all images (flat fields, dark fields, and sample projections) in the TIFF format, and then saves the entire sequence of these images in a common directory:

    Code Block
    titleLinux command
    nxs2tiff -d /entry1/instrument/pco1_hw_hdf/data /dls/i13/data/2013/cm5937-3/raw/23912.nxs /dls/i13/data/2013/cm5937-3/processing/raw/23912/projections 

    Please note that the first input path, corresponding to the d (standing for data or dataset) option, is not a path to an HDF5 file but an internal path to a desired dataset inside your NeXus scan file (incidentally, the path to the latter file should be used as the second argument). This internal path can be verified in the usual way using hdfview:

    If your Nexus scan file contains the relevant image-key data, then it is possible to extract and save your images in 3 separate directories depending on whether they are flat fields, dark fields, or sample projections. This can be done with the help of the r and scan options. For example, the command given below:

    Code Block
    titleLinux command
    nxs2tiff -r --scan 23912 /dls/i13/data/2013/cm5937-3/raw/23912.nxs /dls/i13/data/2013/cm5937-3/processing/raw

    extracts sample-projections, flat-field (ff), and dark-field (df) images to <output_folder>/<scan>/projections, <output_folder>/ff1<scan>/projections and <output_folder>/df<scan>/projections, respectively.

    Image typeImage path relative to <output_folder>Image absolute path Comment(s)
    sample projection
    /23912/projections
    /dls/i13/data/2013/cm5937-3/processing/raw/23912/projections
    If default format, p_%05d.tif, is used, filenames of extracted projection images are indexed from 0, e.g. p_00000.tif, p_00001.tif, p_00002.tif, etc.
    flat field
    /ff123912/projections
    /dls/i13/data/2013/cm5937-3/processing/raw/ff123912/projections
    dark field
    /
    If default format, p_%05d.tif, is used, filenames of extracted flat-field images are indexed from 0, e.g. p_00000.tif, p_00001.tif, p_00002.tif, etc.
    dark field
    /df23912/projections
    /dls/i13/data
    /2013/cm5937-3/processing/raw/df23912/projections
    /2013/cm5937-3/processing/raw/df23912/projections
    If default format, p_%05d.tif, is used, filenames of extracted dark-field images are indexed from 0, e.g. p_00000.tif, p_00001.tif, p_00002.tif, etc.

    Please also note that the default value for the k-option is /entry1/tomo_entry/instrument/detector/image_key, so there is normally no need to include this option unless the tomo entry is absent from your Nexus scan file, or is malformed, or if you would like to utilise image keys stored in a location different from this default path.

    To extract a subset of images, please use the b and s options.

    When the nxs2tiff command is executed, the terminal output should contain the following message:

    Code Block
    titleLinux output
    Your job job_id ("run_nxs2tiff.sh") has been submitted


    Please note that nxs2tiff runs the above job on the DLS cluster (one can monitor its progress in the usual way using qstat). The nxs2tiff command does not return until this job is completed. When the job is completed with success, one should see the following final message:

    Code Block
    titleLinux output
    Job job_id exited with exit code 0.

     


    If there are any errors, the message reads as follows:

    Code Block
    titleLinux output
    Job job_id exited with exit code 1.

    The errors can be diagnosed with the help of the relevant qsub log files, which can be found in /dls/tmp/tomopy. Please examine your latest run_nxs2tiff.sh.e* style file, found in that directory. 


  7. Anchor
    A7
    A7
    To view the status of all SGE jobs being run by all users, please execute the following qstat command for all users:

    Code Block
    titleLinux commands
    qstat -u "*"

    or, equivalently,

    Code Block
    titleLinux commands
    qstat -u \*
  8. Anchor
    A8
    A8
    To find out which modules have been loaded (added) to the shell environment, please execute:

    Code Block
    titleLinux commands
    module list


    As usual, for more information about the module command and its various useful switches and sub-commands, please execute 


    Code Block
    titleLinux commands
    man module


    to display the on-line manual pages on module.