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== XDS crashes ==
== XDS crashes ==


XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer.  
XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer, or (rarely) it is due to improper inputs ([[Problems#INTEGRATE_cell_and.2For_distance_run_away.3B_xds_crashes_or_has_to_be_killed|this]] is the only example I know of).  


If it crashes for the second reason, these are the things to try/consider:
If it crashes for the second reason, these are the things to try/consider:
=== read error ===
... may result in e.g.
forrtl: severe (24): end-of-file during read, unit 2, file bin1_01.tmp
Any error message that XDS prints out afterwards is just a follow-up error. The most likely cause of the problem is that your disk is full, or your quota exceeded. You must fix the root problem before you can continue.


=== huge frames leading to overflow of the shell's stack limit ===
=== huge frames leading to overflow of the shell's stack limit ===
Line 14: Line 22:
  ulimit -s 102400  
  ulimit -s 102400  
The numbers above mean a 10-fold increase over the default, and should be enough. I've found this to be necessary for unusually large frames (32 MB).
The numbers above mean a 10-fold increase over the default, and should be enough. I've found this to be necessary for unusually large frames (32 MB).
xds_par in this case also might need an increase of the environment variable OMP_STACKSIZE (e.g. "setenv OMP_STACKSIZE 128M").


=== memory consumption exceeding the 4GB barrier when using the 32bit binary ===
xds_par in this case also might need an increase of the environment variable OMP_STACKSIZE (e.g. "setenv OMP_STACKSIZE 128M").


As pointed out by James Holton, the memory consumed by huge frames in combination with many threads may be larger than 32 bits allow. Execution then stops with
According to http://stackoverflow.com/questions/13264274/why-segmentation-fault-is-happening-in-this-openmp-code one should also check the "virtual address space limit" with ulimit (increase with ulimit -v) .
forrtl: severe (41): insufficient virtual memory
The workaround is to limit the [http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html MAXIMUM_NUMBER_OF_PROCESSORS], or to use XDS instead of XDS_PAR. An even better solution is to switch to the 64bit binary, but that of course requires a 64bit operating system.


=== Problems with OpenMP ===
=== Problems with OpenMP ===
Line 26: Line 31:
If the "xds_par" binary crashed, try "xds". xds_par uses OpenMP for parallelization, which adds complexity. If it works with xds, but not with xds_par, then there is a chance that some environment variable needs to be set/changed. In any case the XDS developers would like to learn about this.
If the "xds_par" binary crashed, try "xds". xds_par uses OpenMP for parallelization, which adds complexity. If it works with xds, but not with xds_par, then there is a chance that some environment variable needs to be set/changed. In any case the XDS developers would like to learn about this.


=== limitation of the parallel 32bit binary  ===
As of March 2021, Thomas Hauß (HZB) reported an OpenMP-related problem that is due to a bug in a library that the ifort compiler links into xds_par. It is unknown to us which version of the compiler has or does not have this bug. The bug has been seen with xds_par (VERSION Jan 31, 2020  BUILT=20200417) and is a crash with error message containing:
 
<pre>
The 32bit OpenMP binary may not be able to allocate enough storage when using many threads (e.g. >10). The error message might be something like:
OMP: Error #13: Assertion failure at z_Linux_util.cpp(2361).
 
OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
OMP: Error #34: System unable to allocate necessary resources for OMP thread:
forrtl: error (76): Abort trap signal
  OMP: System error #11: Resource temporarily unavailable
Image              PC                Routine            Line        Source           
xds_par            00000000005620C4  Unknown              Unknown  Unknown
libpthread-2.17.s  00002ADC08AAA630  Unknown              Unknown  Unknown
libc-2.17.so      00002ADC08EF1387  gsignal              Unknown  Unknown
libc-2.17.so      00002ADC08EF2A78  abort                Unknown  Unknown
xds_par            000000000063FB83  Unknown              Unknown  Unknown
xds_par            000000000062BDFF  Unknown              Unknown  Unknown
xds_par            000000000060748C  Unknown              Unknown  Unknown
xds_par            000000000067980E  Unknown              Unknown  Unknown
xds_par            000000000063D737  Unknown              Unknown  Unknown
xds_par            000000000063EC58  Unknown              Unknown  Unknown
xds_par            0000000000629A0E  Unknown              Unknown  Unknown
xds_par            0000000000419056  xds_                    21586 MAIN_XDS.f90
xds_par            0000000000418951  MAIN__                      1  MAIN_XDS.f90
xds_par            0000000000415862  Unknown              Unknown  Unknown
libc-2.17.so      00002ADC08EDD555  __libc_start_main    Unknown  Unknown
xds_par            0000000000415769  Unknown              Unknown  Unknown
</pre>
The bug is not related to the xds_par source code, but also happens with other software. The workaround is to set the environment variable
    bash: export KMP_INIT_AT_FORK=FALSE
    tcsh: setenv KMP_INIT_AT_FORK FALSE


=== 64bit binary on a 32 bit operating system ===
=== 64bit binary on a 32bit operating system ===


If the error message is e.g.
If the error message is e.g.
Line 39: Line 64:
or
or
  -bash: /usr/local/bin/xds: cannot execute binary file
  -bash: /usr/local/bin/xds: cannot execute binary file
make sure to use the 32bit version of XDS instead - you try to run the 64bit version on a 32bit operating system; this won't work.
you try to run the 64bit version on a 32bit operating system; this won't work. Since October 2015, you need a 64bit Linux operating system to run XDS because the 32bit version is no longer provided.
 
=== CPU without SSE2 support ===
 
If the error message is
 
forrtl: severe (168): Program Exception - illegal instruction
Image              PC        Routine            Line        Source
xds                08055250  Unknown              Unknown  Unknown
xds                0804B3F6  Unknown              Unknown  Unknown
 
this means that unfortunately the CPU of your machine is too old to be supported by XDS (which in this respect is compiled with the default options of the ifort compiler). This may happen e.g. with old AMD CPUs that don't support SSE2 (on Linux check the ''flags'' field of /proc/cpuinfo for the presence of the sse2 flag).


According to [http://en.wikipedia.org/wiki/SSE2#Notable_IA-32_CPUs_not_supporting_SSE2] the following Intel-compatible CPUs did not implement SSE2 after SSE2 was introduced (2001):
* AMD CPUs prior to Athlon 64, including all Socket A-based CPUs
* Intel CPUs prior to Pentium 4
* VIA C3
* Transmeta Crusoe


=== ASSERT VIOLATION ===
=== ASSERT VIOLATION ===
Line 76: Line 85:
since otherwise, FRAME.cbf is overwritten by INTEGRATE.  
since otherwise, FRAME.cbf is overwritten by INTEGRATE.  


To look at '''all''' spot positions found by COLSPOT, you could try
To look at '''all''' spot positions found by COLSPOT, you can use the COLSPOT tab of [[XDSGUI]]. This nicely shows ice rings, and may also help to find shaded regions on the detector.
echo "set yrange [] reverse ; plot 'SPOT.XDS' us 1:2 w dots" | gnuplot -persist
 
This may also help to find shaded regions on the detector.
=== ugly diffraction pattern ===
 
If the spots are split or unclean, you may get a seemingly terrible match between observed and calculated spot positions:
***** REFINED SOLUTION BASED ON INDEXED REFLECTIONS IN SUBTREE # 1 *****
REFINED VALUES OF DIFFRACTION PARAMETERS DERIVED FROM      2916 INDEXED SPOTS
REFINED PARAMETERS:  AXIS BEAM ORIENTATION CELL
STANDARD DEVIATION OF SPOT    POSITION (PIXELS)    11.74
STANDARD DEVIATION OF SPINDLE POSITION (DEGREES)    5.94
which leads to very many reflections being rejected from refinement:
  ***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP #  1 *****
      1594 OUT OF    27897 SPOTS INDEXED.
        0 REJECTED REFLECTIONS (REASON: OVERLAP)
    26303 REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION)
The fix is to e.g. double the parameters
MAXIMUM_ERROR_OF_SPOT_POSITION=  6.0
MAXIMUM_ERROR_OF_SPINDLE_POSITION=  4.0
which then leads to less rejections:
***** INDEXING OF OBSERVED SPOTS IN SPACE GROUP #  1 *****
    11669 OUT OF    27897 SPOTS INDEXED.
        2 REJECTED REFLECTIONS (REASON: OVERLAP)
    16226 REJECTED REFLECTIONS (REASON: TOO FAR FROM IDEAL POSITION)
and surprisingly good integration.


=== IDXREF ends with !!! ERROR !!! message ===
=== IDXREF ends with !!! ERROR !!! message ===
Line 107: Line 138:
  THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.
  THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.


This is printed out for you to actually read, and take action accordingly. In most cases you just change the JOBS - line in XDS.INP to read
This is printed out for you to actually read, and take action accordingly. In most cases you just change the JOB= line in XDS.INP to read
  JOB= DEFPIX INTEGRATE CORRECT
  JOB= DEFPIX INTEGRATE CORRECT
and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES).
and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES).
=== IDXREF produces too short cell parameter(s) ===
The first table "CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS" should show close-to-integer difference vectors. The following is an example how it should ''not'' look like:
  #  COORDINATES OF REC. BASIS VECTOR    LENGTH  1/LENGTH
    1  -0.0000476-0.0014008-0.0044654  0.0046802    213.67
    2  -0.0101960-0.0056194 0.0019466  0.0118037      84.72
    3  -0.0145331 0.0238225-0.0071754  0.0288134      34.71
CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS
  #  COORDINATES OF VECTOR CLUSTER  FREQUENCY      CLUSTER INDICES 
    1  0.0004199-0.0012633-0.0043826    2442.      0.97    -0.04    -0.00
    2  0.0101757 0.0060701-0.0019630    2175.    -0.03    -1.02      0.01
    3 -0.0076118 0.0114167-0.0040603    1965.      0.13      0.04      0.50    <---- half-integer indices!?
    4  0.0100552 0.0071646 0.0025337    1944.    -1.01    -0.99      0.01
    5  0.0072840-0.0101455 0.0084405    1841.    -1.10    -0.01    -0.49    <---- half-integer indices!?
    6  0.0000976 0.0027828 0.0089584    1792.    -2.00      0.00    -0.00
    7  0.0103103 0.0043851-0.0063902    1790.      0.98    -1.02      0.00
    8  0.0025742 0.0163995-0.0098507    1760.      0.95    -0.99      0.51    <---- half-integer indices!?
    9  0.0068686-0.0089437 0.0128884    1724.    -2.08      0.03    -0.49    <---- half-integer indices!?
  10 -0.0174443 0.0123504 0.0161324    1694.    -4.01      0.99      0.52    <---- half-integer indices!?
  11  0.0272195-0.0050005-0.0136142    1678.      2.99    -1.97    -0.50    <---- half-integer indices!?
  ...
PARAMETERS OF THE REDUCED CELL (ANGSTROEM & DEGREES)
    34.71    84.72    213.67    90.35    90.27    90.06
Do you see the half-integer difference vectors in the last column? This clearly indicates that the third axis above the table (with 1/length=34.71) actually should be twice that size. If this happens, the histogram of indexed spots often has two equally-large subtrees:
SUBTREE    POPULATION
    1          976
    2          972
    3          10
    4            7
    5            6
Remedy: take the reduced cell (as found below the table), but double the 34.71, and stick it into the line
UNIT_CELL_CONSTANTS=69.42    84.72    213.67    90.35    90.27    90.06
in XDS.INP. To make XDS actually ''use'' that line, specify
SPACE_GROUP_NUMBER=1
and leave the space group determination for later.
Alternatively, try several well-separated SPOT_RANGEs instead of 1. For example, instead of
SPOT_RANGE=1 900
try e.g.
SPOT_RANGE=1 100
SPOT_RANGE=801 900
In the cases where I've tried this, this splitting of SPOT_RANGE into several wedges always resulted in IDXREF picking up the correct cell.
The reason for the indexing failure in these cases seems to be the fact that the crystal changed its orientation within the SPOT_RANGE by more than ~ 0.1°.
'''The other reason for this failure mode''' - but in this case there is only one SUBTREE with high POPULATION - is when the default <code>SEPMIN= 6.00 CLUSTER_RADIUS= 3</code> are used, but the spots are closer than 6 pixels. This often happens with Pilatus data; the recommendation for this detector is to use <code>SEPMIN= 4.00 CLUSTER_RADIUS= 2</code> in XDS.INP, or even <code>SEPMIN= 2.00 CLUSTER_RADIUS= 1</code>.
=== Difference vectors are neither integers nor halfs ===
This can happen if SPACE_GROUP_NUMBER is wrong, i.e. the user "forces" a lattice (e.g. body-centered) that does not match the true one (which may be primitive). So the first thing to try is SPACE_GROUP_NUMBER=0.
Sometimes, IDXREF nevertheless finds no good lattice:
  #  COORDINATES OF VECTOR CLUSTER  FREQUENCY      CLUSTER INDICES
    1  0.0090336-0.0044767 0.0137041    1636.      0.99      0.99    -0.00
    2 -0.0239422 0.0085088 0.0078304    1556.    -2.00      1.00      0.00
    3  0.0088799 0.0092726 0.0077661    1555.      0.50      0.50    -0.56
    4 -0.0000164 0.0138382-0.0058215    1486.    -0.49    -0.49    -0.56    <---- 0.56 is neither close to 0.5 nor to 0 or 1
    5 -0.0148222 0.0040131 0.0216634    1468.    -1.00      2.00    -0.00
    6  0.0098829 0.0070246-0.0042191    1430.      0.50    -0.50    -0.44    <---- same here
    7 -0.0030325 0.0110238 0.0056577    1422.    -0.50      0.50    -0.44    <----  and here
...
If it is not a case of SEPMIN and CLUSTER_RADIUS being too large (see above), try to increase INDEX_ERROR - in this case, it indexes beautifully with INDEX_ERROR=0.14 .
=== IDXREF produces too long axes ===
This may (rarely) happen when MAXIMUM_NUMBER_OF_JOBS is > 1. In this case, different JOBS' COLSPOT runs may report some reflections twice in SPOT.XDS. Since their phi values are close, they correspond to long unit cell parameters. This happens more easily if the mosaicity is high and therefore reflections extend over the borders between JOBs.
This effect may be mitigated by having as many SPOT_RANGEs as JOBs, and leaving gaps between the SPOT_RANGEs.
=== IDXREF prints !!! WARNING !!! message ===
If you see
!!! WARNING !!! REFINEMENT DID NOT CONVERGE
                LAST CORRECTION SHIFT WAS  6.1E-02 (should be <  1.0E-03)
then try the following: find the line
REFINE(IDXREF)= ...
in XDS.INP. If it is commented out with a !, remove the !. Then, change it to have
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! POSITION
i.e. remove POSITION from the list of refinable parameters. Once that is done, save XDS.INP and re-run the IDXREF step.
This problem occurs if the POSITION value (called DISTANCE in former XDS versions) is large, and XDS cannot refine it meaningfully.
If this does not help, try to refine even less items, e.g. leave out AXIS.
=== IDXREF prints ERROR IN REFINE !!! RETURN CODE IS IER= 0 ===
This is due to either wrong inputs in XDS.INP, or due to bad data, e.g. spots from many crystals whose diffraction patterns overlap. The first possibility applies if the diffraction pattern is clean. The second applies if the diffraction pattern is ugly, and unsuitable for indexing. In that case, maybe try a different SPOT_RANGE.


=== IDXREF.LP does not show the expected lattice ===
=== IDXREF.LP does not show the expected lattice ===
Line 115: Line 242:
By specifying the spacegroup and unitcell, you tell XDS that it should index based on those reflections that match that spacegroup and unitcell. In a sense, you _force_ that spacegroup and cell. This will discard other (spurious?) reflections, and usually leads to a clean list of Bravais lattice possibilities.
By specifying the spacegroup and unitcell, you tell XDS that it should index based on those reflections that match that spacegroup and unitcell. In a sense, you _force_ that spacegroup and cell. This will discard other (spurious?) reflections, and usually leads to a clean list of Bravais lattice possibilities.


If the data reduction fails nevertheless (in terms of bad R-factors and [[CORRECT#An estimate for the overall quality of an experimental setup|ISa]] in the [[CORRECT]] step), then chances are that you specified some parameter wrongly, or not accurate enough (ORGY and ORGY are the most likely candidates), or that the crystal does not match your idea about its spacegroup and unit cell. Actually the latter happens pretty frequently (which is why it is always the safest way to collect 180° of spindle rotation unless you know your crystals very well; this is also a good strategy in other respects).
If the data reduction fails nevertheless (in terms of bad R-factors and [[CORRECT#An estimate for the overall quality of an experimental setup|ISa]] in the [[CORRECT]] step), then chances are that you specified some parameter wrongly, or not accurate enough (ORGX and ORGY are the most likely candidates), or that the crystal does not match your idea about its spacegroup and unit cell. Actually the latter happens pretty frequently (which is why it is always the safest way to collect 180° of spindle rotation unless you know your crystals very well; this is also a good strategy in other respects).


If you tell XDS that you do not to know the spacegroup (SPACE_GROUP_NUMBER= 0), then [[IDXREF]] takes all observed reflections into account. By design, the spacegroup decision is then postponed until the CORRECT step, or rather to a run of [[pointless]] after CORRECT, and it may be not vital to closely inspect IDXREF.LP, because CORRECT.LP has basically the same information, plus more.
If you tell XDS that you do not know the spacegroup (SPACE_GROUP_NUMBER= 0), then [[IDXREF]] takes all observed reflections into account. By design, the spacegroup decision is then postponed until the CORRECT step, or rather to a run of [[pointless]] after CORRECT, and it may be not vital to closely inspect IDXREF.LP, because CORRECT.LP has basically the same information, plus more.


=== none of the lattices in IDXREF.LP (except aP) has a good QUALITY OF FIT ===
=== none of the lattices in IDXREF.LP (except aP) has a good QUALITY OF FIT ===
Line 137: Line 264:
== Integration failure ==
== Integration failure ==


=== INTEGRATE stops with error message ===
If INTEGRATE stops after e.g.
If INTEGRATE stops after e.g.
  ******************************************************************************
  ******************************************************************************
Line 147: Line 275:
               BEAM_DIVERGENCE=    BEAM_DIVERGENCE_E.S.D.=  
               BEAM_DIVERGENCE=    BEAM_DIVERGENCE_E.S.D.=  


then you should reduce the upper limit of the DATA_RANGE, to stop before the problematic frames, and re-run INTEGRATE. In this example, you would modify XDS.INP to have
then there are two ways to resolve this:
* you could insert a line DELPHI=10 (or DELPHI=20, for 10 or 20 degrees batches; the default is 5 degree batches) into XDS.INP and re-run INTEGRATE
* as the error message suggests, you should reduce the upper limit of the DATA_RANGE, to stop before the problematic frames, and re-run INTEGRATE. In this example, you would modify XDS.INP to have
  DATA_RANGE=1 135
  DATA_RANGE=1 135
  JOB=INTEGRATE CORRECT
  JOB=INTEGRATE CORRECT  
Save XDS.INP, run XDS and inspect INTEGRATE.LP, to find the lines (e.g.)
Save XDS.INP, run XDS and inspect INTEGRATE.LP, to find the lines (e.g.)
  BEAM_DIVERGENCE=  0.478  BEAM_DIVERGENCE_E.S.D.=  0.048
  BEAM_DIVERGENCE=  0.478  BEAM_DIVERGENCE_E.S.D.=  0.048
  REFLECTING_RANGE=  1.100  REFLECTING_RANGE_E.S.D.=  0.157
  REFLECTING_RANGE=  1.100  REFLECTING_RANGE_E.S.D.=  0.157
Copy them to XDS.INP. Restore the original DATA_RANGE and continue.
Copy them to XDS.INP. Restore the original DATA_RANGE and continue.
If this problem happens with multiple XDS jobs working on the same data set, you might also get a message like
.../bin1_02.tmp
Image              PC                Routine            Line        Source           
xds_par            0000000000592B91  Unknown              Unknown  Unknown
xds_par            00000000004BEF21  joinintegrate_          8995  MAIN_XDS.f90
xds_par            0000000000410A5B  xds_                    21690  MAIN_XDS.f90
xds_par            000000000040B3A4  MAIN__                      1  MAIN_XDS.f90
xds_par            00000000004083F6  Unknown              Unknown  Unknown
libc.so.6          00007FB40222E830  Unknown              Unknown  Unknown
xds_par            00000000004082E9  Unknown              Unknown  Unknown
which looks like a real crash of the program, but in this case with a known reason.
Another error mode of INTEGRATE (in processing of small-molecule data) is ...
IMAGE IER  SCALE    NBKG NOVL NEWALD NSTRONG  NREJ  SIGMAB  SIGMAR
    5  0  0.975  3968463    1      5      1    0  0.1028  1.3486
    6  0  0.967  3969949    2      2      2    0  0.1688  0.0000
    7  0  0.929  3975306    0      3      0    0  0.0000  0.0000
  !!! ERROR !!! CANNOT ALLOCATE MEMORY
              YOU COULD RERUN THIS STEP WITH SMALLER VALUES FOR THE PARAMETERS
              NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=
              NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=
The error message is misleading in this case: there are too few reflections to build the average profile. The fix is: restart INTEGRATE after inserting e.g.
DELPHI=20 ! default is 5, so try with e.g. 10, 20, 45, 90, 180
in XDS.INP and re-run INTEGRATE.
=== INTEGRATE cell and/or distance run away; xds crashes or has to be killed ===
If during INTEGRATE the cell keeps increasing or the distance decreasing or both, then xds starts to consume large amounts of memory and becomes very slow. This may finally exhaust all available memory, and the job either crashes or has to be killed by the user.
The fix here is to use
REFINE(INTEGRATE)= BEAM POSITION ORIENTATION ! CELL
instead of (what used to be the default until June 2017)
REFINE(INTEGRATE)= BEAM POSITION ORIENTATION CELL
Quite generally, the more conservative setting without CELL refinement is adequate unless your crystals diffract to quite high resolution. A sure sign that you should not be refining CELL is that the refined cell and/or distance values in INTEGRATE.LP fluctuate without obvious physical reason. Moreover, distance ("POSITION") refinement nicely soaks up any cell change resulting from radiation damage.
A compromise (if you suspect that the cell parameters actually change ''differently'') would be
REFINE(INTEGRATE)= BEAM ORIENTATION CELL ! POSITION
This should also avoid the run-away but gives more freedom to the refinement. Of course it requires a refined distance (from IDXREF, or rather from GXPARM.XDS->XPARM.XDS renaming).


== See also ==
== See also ==
Line 159: Line 327:


[[Low dose data]]
[[Low dose data]]
[[Indexing]]
[[IDXREF.LP]]
Kay
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