- ...
pages).1
- If the Version of FIT2D being used has been linked
``dynamically'' then it is dependent on
the required system libraries being available. If it has been linked
``statically'' then it should be completely
independent.
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- ... line2
- Command line options may also be useful, see
Section 20, Page .
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- ...
one3
- The version number may well be different, and some of the
messages notifying you of recent changes may be different.
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- ... using4
- This is useful if
you encounter bugs or problems.
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- ... window5
- This is nothing to do
with FIT2D, but is a property of the X-window system. Depending on
how your X-terminal is set-up it may not be necessary to click, simply
placing the graphics cursor inside the terminal window may be
sufficient.
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- ... same6
- This automatic re-sizing does not presently
work on Windows systems.
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- ...fig-image7
- The images displayed in
this manual deliberately have relatively small numbers of pixels. This is
to prevent the PostScript file of the manual getting too big, and to make
printing reasonably quick. Naturally, most analysis will involve images
with many more pixels. FIT2D can handle very large images and display
them efficiently.
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- ...
versions8
- Other file formats are likely to be added as needed,
so this list is likely to grow.
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- ... formats9
- Crystallographic software package from Molecular
Simulations
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- ...
bins10
- Prior to V9.130 the storage was the opposite way around.
It was changed so that output of radial//Q-space scans could
easily be input and fitted in the MFIT interface. If fitting is
required in the azimuthal direction the command TRANSPOSE can be
used.
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- ... cursor11
- More commands
are available, but these are the most important ones. GNU Readline
documentation describes fully the available possibilities.
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- ... command12
- Previously, <CONTROL>D
(Unix) or <CONTROL>Z (VMS) were the normal "User escape" commands, however
FIT2D now uses the GNU Readline library for terminal input which enables
command line history recall and file name completion, but using <CONTROL>D
for its own purposes.
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- ... menu13
- It is possible that there are still some occasions
when this ``user escape'' option does not work as it should. If this happens
please inform me of the command so that it can be rectified for future
versions.
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- ...
sub-menus14
- For keyboard driven programs many users dislike having to
go up and down many menus and sub-menus to find commands. The calibration
and fitting
operations have nevertheless been put in separate sub-menu to reflect
the much greater specialist knowledge required to use these routines.
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- ... document15
- This is a command that I use for making FIT2D posters, and
documentation.
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- ... size16
- The present implementation is much
faster than the previous version (20 times for 1010 top-hat).
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- ... different17
- There is a mis-conception that
reverse polish notation calculators are ``better''. This is completely
un-true; they are neither better nor worse, just much simpler to program,
as no parser is necessary.
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- ...
user18
- This range is likely to be added to in the future.
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- ... point19
- Normally, a ``file extension'' does not
include the decimal point i.e. is the characters after the
decimal point, however, defining the ``extension'' with or
without the decimal point allows more flexibility.
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- ... file20
- For screen output
the screen itself will provide a limit.
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- ... performed21
- Prior
to V9.164 a similar formula was used, with less user control.
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- ...
system22
- Note: For a short time this input option was called
XRII, until it was realised that there were two different file formats
produced by the two different CCD cameras used with the X-ray image
intensifier systems.
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- ...)23
- Previously
<CONTROL>D (Unix) or <CONTROL>Z (VMS) was used for ``user escape'', but this
has had to be changed owing to the usage of GNU Readline which provides
command history recall and file name completion.
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- ...)24
- This value is chosen to stop overflow and underflow
when performing the normalisation. For the error propagation it is necessary
to divide by the square of the maximum value.
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- ... programs25
-
MOSFLM is a program for the initial indexing and integration of
protein crystallography diffraction patterns written by Andrew
Leslie at
Cambridge, England. DENZO is also a protein crystallography indexing
and integration program, written by Zbyszek
Otwinowski, now at the University
of Texas, USA. INTLAUE is written by various people and is available
from John W Campbell, at DRAL, England.
IDL is a commercial package available for those with money.
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- ... byte26
- ``Big endian'' format is
consistent with the convention for the numbering bits with a byte, and with
normal order of digits within a number. Whereas ``Little Endian'' is
consistent with the manner in which we write (in the ``west'') and think of a
bit/byte stream arriving.
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- ... format27
- Fortran ``g'' format would have been
used, but it is not handled correctly on HP-UX.
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- ... font28
- At present the graphics system only
supports one font family so that the font do not change, but the font family
used: ``Times-Roman'' should be suitable for most purposes.
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- ...##BLANK29
- This special variable was
necessary, since just entering a space or returning will select the
default value. Now a quoted blank may be entered as well.
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- ... fonts30
- At present the graphics system only
supports one font family so that the font do not change, but the font family
used: ``Times-Roman'' should be suitable for most purposes.
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- ... data31
- From V6.11
onwards this option takes account of radial and image pixel sizes.
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- ... size32
- Typically
500 variables can be stored.
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- ...
features33
- At the edge of imaging plate images it is possible to
have a false line of peaks owing to light scatter off the edge. Such a
false line of peaks could be mistaken for genuine peaks and lead to false
distortion values which can lead to a false distortion function. Partially
recorded peaks may also lead to false values for the distortion.
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- ... interest34
- Previously it was necessary to limit the ROI
to the valid region of the interpolating function. This is now performed
automatically.
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- ...Flat-Field
35
- The term ``flood-field'' is
used to refer to a smooth, but not completely uniform radiation, whereas
the term ``flat-field'' is used to refer to a completely uniform radiation.
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- ... used36
- At lower temperatures condensation occurs, unless dry
nitrogen is used.
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- ... decay37
- This works to the
extent that the decay is linear.
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- ...Hammersley_2:38
- Originally a different equation was used,
``fitted'' by eye; the values produced by the two equations are very
similar.
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- ... time39
- Phil Evans at the MRC Cambridge has written software to correct for
the decay taking into account the time that particular hkl reflections were
in the diffracting condition.
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- ... peak40
- Almost
any starting peak may now be used, whereas previously it had to be the lower
left-hand peak of the grid.
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- ... peak41
- It is possible to skip peaks and have
the search only find every other peak or every third peak, but under normal
circumstances every peak will be used.
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- ... peaks42
- This constraint is
caused by the software not by any fundamental reason.
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- ... peaks43
- The peak search is now much
more robust than was previously the case.
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- ... peak44
- Again this is not for any fundamental reason.
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- ... positions.)45
-
At Version 5.7 a bug was fixed (I hope) within NAG routines which could cause
FIT2D to crash depending on the value of an non-initialised variable.
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- ... beam-stop46
- Here the true value of the function is unknown,
but since the data images will also miss this data, the precise values
are unimportant. By removing these points the polynomial will simply
interpolate in this region. If the data points are not removed a much
higher order polynomial would be necessary to fit adequately the sharp
feature of the beam-stop shadow. This may introduce unwanted
oscillations elsewhere in the fit.
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- ...
Y-directions47
- This is the sample to mask distance for data which
has already been corrected for spatial distortion.
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- ... data48
- The input data should be divided by the
``flat-field'' image.
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- ...MADNES
49
- MADNES actually needs both distortion mappings.
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- ...Hammersley_2)50
- In future
versions of the manual references will be given to further papers.
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- ...Piltz51
- A powder
diffraction data analysis
program written by R Piltz which inputs 2-D data and allows spatial distortion
and detector tilt to be taken into account when producing a 1-D circularly
averaged powder scan.
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- ...PLATYPUS52
- Although visually the data is only left to right
reversed.
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- ... system53
- At present this is
experimental and experience may show that other parameters need to be
input, or that parameters may be obtained from other sources.
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- ...
``scan''54
- This option is under development.
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- ...
file55
- The PDS format is a simple ASCII format devised by
Andy Fitch and Andrew Murry for the
storage of angular scan data for input
to Rietveld refinement
programs.
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- ...
form56
- It is necessary to output the PDS format data here, as the
number
of pixels averaged to create one angular bin is not available after this
option is finished
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- ...
replaced57
- At present only one font family is used by the
graphics system so the fonts do not change, but the font family used,
``Times-Roman'' should be suitable for most purposes.
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- ...X58
- The
multiplication sign cannot be used as this has a special purpose for the
Unix operating system.
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- ... invalid59
- At present use of some graphics command,
whilst FIT2D is in this mode will result in a core dump. Gradually, these
commands will be protected, and warning messages will be issued instead.
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- ... font60
- In fact X11R6
allows arbitrary sized fonts to be generated, but this is only available
on a smaller percentage of current X-servers, so this possibility has
deliberately not been exploited.
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- ...
window61
- Or in some cases by simply moving the cursor into a
new window, depending on how the ``window manager'' has been defined.
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- ... minimised62
- On HP booted X-servers
xterm uses colour levels within the first 40, so the terminal window remains
readable, but on Sun booted X-servers this is not the case.
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- ... visual''63
- ``Visual'' and
``PseudoColor'', with the American spelling, are X-11
terminology.
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- ... bug64
- The definition of whether or not a bug is
serious or not rests with the author. Clearly, mis-use of the program, and
annoying features do not count, and mistakes in documentation are unlikely
to count. The offer does not cover bugs that occur within source code not
written by the author e.g. ``jpg'' code (but this seems unlikely).
New (experimental) features are similarly not covered.
The beer will be a standard ``demi pression'' and not a Palais de la bière
tourist sized top price beer. Anyone who ``wins'' a free beer is responsible
for paying their own transport to and from the centre of Grenoble.
Users who find features which work unusually well are invited to offer a free
beer in return
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- ... file65
- Great care must be taken when re-defining
PATH as if a mistake is made it is possible to loss all system
commands.
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- ... Unix66
- This may well be a problem limited to Unix
systems.
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- ... Unix67
- Thanks are due to the
``Free Software Foundation'' (FSF/GNU), without whom a
sensible working environment would not have been possible.
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- ... open68
- END GRAPHICS FILE may be used to make sure that the file is closed
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- ... variable69
- The variable must be separated
from other characters by one or more spaces, a comma, or a <TAB>.
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- ... value70
- Before
Version 5.8 variables only work for character input e.g. file names and
commands, at Version 5.8 treatment of variables for all input, including
integer and real constants was added.
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