WARNING: The installation of Motif V1.2 for VMS, or (apparently) an upgrade to VMS V6.1 (VAX) kills older versions MDP. On the VAX, old versions of MDP will have access violations when images are to be displayed. On AXP, image windows are put up, but the images themselves are missing. These problems are due, it would seem, to bugs in the shared libraries for the FORTRAN binding of XLib. The release of MDP V94.100 and later use alternate code which is believed to bypass these problems. DEC has been alerted (don't hold your breath...). UNIX versions of MDP use the C library for XLib calls.
- MAJOR CHANGES
- The versions of the software for the Alpha machines have been re-built using
Integer*8 for the pointers to the array addresses. This is necessary for OSF/1
(64-bit technology strikes!), and is tolerated by OpenVMS/AXP: it does not work
for VMS/VAX or Ultrix. The code in the source areas has been modified to
contain the I*8 variables, which need to be altered to I*4 for re-compilation
on the 32-bit machines. Since this code is fairly static, this does not seem
to be too much of a burden. While this is a major chenge internally for the
MDPP, it should not affect users.
- The VMS version of the program has been recompiled using the V6.2 FORTRAN
compiler (VAX and AXP). As a result image sizes have reduced somewhat, and
some minor probably cosmetic buglets were found and fixed. The reason for
mentioning this is that this has caused the re-compilation of code that has
existed (on the VAX anyway) un-touched for possibly as long as 10 years...
This means that some of these programs may `explode' if run now. I need to
know urgently if there are problems so that these new bugs can be fixed
and the revised code made available via FTP.
-The algoritm for `popping' arrays has been changed. In the past a byte
arrays was just thrown up on the screen, without attempting to fix the display
to correspond to the array. Now, the mapping calculation is done to
(hopefully) get a close match between the display obtained with regular `DV'
and that obtained with `ZI', for example. This involves a lot more
computation, but on an Alpha, its no big deal.
- `MT' has been altered to allow the user to specify an output format.
-`VL' now computes the layer-line powers when it runs. This allows you to
follow individual layerlines in a regression search, for example: the powers
are loaded into output registers
-`XL' now loads layerline altitudes into output registers.
- NEW COMMANDS
None.
- BUG FIXES
-A problem was found in the Motif Menu driver such that sub-menus nested
below two-deep crashed the program.
-A major bug has been found in the UNIX versions of the program
which caused attempts to `malloc' additional memory to lead to a Segmentation
Fault (what else?). This affected several programs, notably `VD' (for byte
arrays) and `DK' (which was completely dead).
-A bug has been found in the management of the display in all versions of the
program. This bug caused the image to jump by a pixel when re-popped over an
existing image.
-A bug that caused points marked on the screen to be placed at the bottom
left-hand corner of larger pixels has been fixed. The marks are now in the middle, as near as possible. Part of the same can-of-worms was the inaccuracy of vector drawing, especially in the FTs, now also fixed.
-`DV' probably failed to put the image title into line printer over-print
image output. This is now fixed.
-`EL' The program was found to generate contaminated layerlines for arrays
wider than 80 pixels if the array was `in core': the disk version was fine.
The `core' version is fixed now. This is quite horrible, but there are two
saving graces: first, if the error hit the array was so screwed up, you could
not help but notice. Secondly, nearly every helix ever processed has been
narrower than 80 pixels. This is how the error survived, unnoticed, for about
15 years. Yuck!
-`FF' The code in the FFT section of the distribution did not support prime
factors up to 53, and I build at least one set of software with this stuff. It
should be OK now.
-`MV' The conversion of an array to `Movie' format will not be done a second
time if the array to be viewed is already converted.
-`XL' just blew up! It shouldn't any more.
-A pre-beta release of the OSF/1 version of the program (left for FTP)
contained many bugs due to the increased (64-bit) size of array pointers (which
the program still considered 32-bit).
- KNOWN BUGS
- There appears to be a problem with the color-table allocations on UNIX in
cases when other programs use up all the colors and then release them. In this
case, MDP (UNIX) does not seem to get the overlay plane graphics working
properly and lines that should erase, don't. I am not able to re-produce the
conditions so that I can figure out the problem, which is a pain since it is
not all that rare an event. The (basically unacceptable) workaround is to
terminate your X-session, and restart it. If/when I figure this out, there
will be a FTPable image for the two UNIX platforms.
-`XL' was written to allow layerlines to be extracted at non-integer sampling
levels. It seems clear now that simple FT is not the way to do this. A
revised method is expected to be developed and distributed in the next release
of the MDPP.
-MAJOR CHANGES
- The Alpha version now uses IEEE internal floating-point format. Therefore
the libraries supplied here are incompatible with those in the V93.100
distribution: do not mix these libraries! There are command files that can be
used to recompile the libraries called `compile-alpha.com'. Use these to
rebuild the libraries by defining the `fr.com' procedure appropriately.
Internal documentation from DEC suggests that there will be significant
performance gains in the future from improved compiler technology.
Re-compiling the code for the Alpha with each new compiler release is therefore
a reasonable thing to do.
- Files are now saved in the internal format of the machine that is being
used. Foreign formats are converted on input, and on output only if necessary
(see the docs for the `SV' command). This has considerably speeded the I/O for
the Ultrix programs. Files saved in native format can not be read by
MDPP using V93.100 or lower (unless they are created on a VAX): generally files
to be shared with the (slow) VAX should be saved in VAX internal format.
- The documentation has been reworked to a degree. Most of the obvious errors
have been fixed, including the provision of a doc file for each command (about 14 were found to be missing). Additionally, the documentation has been
provided for the VMS systems as in BOOKREADER form. In order to get the docs
available we have just put them in, without a lot of prettying up: this will have to wait until the next release (if then..)
- New users complained that the buttons on the mouse under DECwindows were
reversed relative to the instructional message on the screen.
Accordingly the button order has been changed. This means
that the buttons now correspond to the description provided by the program (no
bad thing in itself). In order that existing users have their
functionality unchanged, a new logical called
`MDP_REVERSE_MOUSE_BUTTONS' has been added. When this is defined as
`TRUE' (the default) the buttons follow the LH scheme that
MDPP/DECwindows has used now for several years. New sites should,
however, comment out the definition in the MDPP.COM file to use the
button order that is consistent with the program instructions. [OK, this is a
mess, but its the best I can do at this point in time. I hope to fix this in
the next release. Sorry.]
-NEW COMMANDS
- The new Menu-driver created by Suzy Gottesman is the `jewel' of this
release. It uses the same menu scripts that are used for the SMG-based
menu-driver available under VMS, but puts the menus up as MOTIF menu windows.
This works on VMS and Ultrix, so is the mechanism of choice on X-workstations.
Functionality is identical on both platforms. Read the documentation about the
menu system to learn more.
- The `RMAP'/'FMAP' function is now available. Get to it as an option of the
`FI 2' command. This allows better compression of real images to byte: note
this is a `lossy' image transformation. Don't expect too much from it,
especially for Fourier transforms.
- The `XX' command has been enhanced by adding code to read Tim Baker's
"Purdue" image format (options 9 & 10). Thanks to Tony Crowther, we now
have the newest MRC code for their file reading and writing. This has been
`fixed' to read files from most sources (SGI, VAX, Ultrix-RISC, Alpha). Thanks
to these changes MRC file format is now available on all platforms.
- `ET' Extract tile. This is a new command to extract tiles from an image.
The main idea is to be able to extract objects, such as single particles, from
a large field. To go with this program a new file data-type has been created
(called IMG_TILE) that will be propagated to other programs as necessary. The
`FI' command converts between TILEs and 3D images.
- `MV' Movie. This command causes a movie loop to be run in a window. It was
inspired by the movie seen at the Gordon Conference as a part of the IMAGIC system.
- `UB' Unbend. This is an implementation of the MRC's CCUNBENDA program,
originally due to Richard Henderson. The code used in MDPP was obtained from
Mike Schmid.
-BUGS FIXED
- `er 2' caused an error if no image was on the screen.
- `bt' would interpolate data with inappropriate weights on the default
option.
- `io 1' creates a correct true-color image flag: this is largely a cosmetic
fix.
- `nr' did not correctly compute max and min if the signs were changed.
- `sd' generated odd streaks on cut faces of models.
- `ts' crashed MDP if too few points were entered. It now generates an error
message.
- `vd 9' has been enhanced to allow data to be generated for the `et' command
and to produce data consistent with other programs that generate lists of
points.
- The compute-server operation of the Alpha version almost certainly did not
work. This has been tested for the basic tools: the DECCHAN option has not
worked yet, however.
- Array value scanning did not work on the Alpha.
- The max-following cursor did not properly follow.
- Some legitimate FFT files were not correctly recognized by the programs.
- POPing windows sometimes crashed the (VMS) program.
- MRC data files can be read on all platforms (previously only the VAX worked).
This now allows file-exchange with UNIX systems such as SGIs and SUNs that
support the MRC format.
- Some displays (e.g. NCD X-terminals) erroneously fail to create popped
windows in the correct place, or fail to warp the cursor to the correct
location. There is now a trap in the program that gives you time to get the
cursor into the window before extinguishing the popped window. For people
using DEC displays, this manifests as a 0.5sec hesitation before a popped
window can be used. Trust me, its an improvement.
- `jpeg' images can now be created using the Alpha version. A file-close
problem was fixed for VMS, generally.
- All versions of MDPP can now generate CGM files. Some problems
with the CGM image layout and scaling have been fixed as well. GPLOT has been
added as a utility program to view these images.
-KNOWN BUGS
The bug in the FORTRAN runtime library that was present in V1.0 of OpenVMS/AXP
is also present in T1.5 FT3: the same fix (replacement of the RTL) is required
to make MDPP work. It is fixed in FT4, and in the V1.5 release.
The font grabbed by default from some X-servers is wrong. This can be fixed in
the VMS version by defining the logical MDP_DECW_FONT to a working
font. There is no similar work-around for Ultrix at this point.
-CHANGES FOR THE NEXT RELEASE
This is expected to be the last release of the MDPP that includes both the VMS
and UNIX versions together. In future, the VMS and UNIX versions (which I
expect will include a new AlphaOSF/1 version) will be submitted separately to
DECUS. The preliminary version number for the next release is V94.100.
- MAJOR CHANGES
- The system has been ported to the Alpha platform under OpenVMS
- The point-editor for screen points has been enhanced ('VD 5') to allow
points to be moved, and new points inserted into a list.
- NEW COMMANDS
- `GH 1' to generate projections of curved solid rods has been cre
ated. It is used in the compass algorithm for helix straightening.
- BUG FIXES
- The output file option did not work under Ultrix. This has been fixed.
- The display of the image header was screwed up if it containied nulls: this is fixed.
- The loop and macro processors did not work under Ultrix, and the
supplementary files options were broken under VMS. These have been fixed.
- Arrow-key cursor control did not work for the DECwindows drivers.
- `FD' was busted under Ultrix (and VMS too, if you thought about it...)
- `NR' would zero some non-real arrays without warning.
- `TP' did not correctly compute total powers of non-real arrays.
- `TS' had several bugs: in particular parametric distances were
mis-calculated in some cases and buffer arrays would go out of bounds.
-KNOWN BUGS
- There is a known bug in the FORTRAN run-time library shipped with
OpenVMS/AXP V1.0 which crashes any program that attempts to open a
direct-access file and specify an associate variable (HOW do they do these
things??). Now that V1.5 is shipping (in March, 1993) it is unlikely that
anyone will have to deal with this bug which makes it impossible to run MDPP.
If you have unpatched V1.0, you will need the new RTL before MDPP will run. As
an additional Gotcha! once you have installed the fixed RTL there will be a
bogus error message every time you exit MDPP coming from the RTL. I am assured
this will disappear in the newer versions of OpenVMS/AXP. Note these are Alpha
problems, only.
- The Alpha version will probably not support synchronous compute-service due
to the fact that the control for network data reading has changed, and we have
not been able to test (and fix) it yet. This `error' is related to the message
about compilation warnings that you will receive on linking the Alpha version
of MDPP: these warnings can be ignored.
- This version of MDPP for the Alpha has been compiled with default DEC
G-floating internal floating point format. There are hints that this will
impose a performance penalty and that using IEEE floating point will improve
execution times. So we will try and see, but not until
the next release which will be in about 3 months.
- For the most part the utilities for the Alpha have been transferred from the
VAX using the VEST utility. Some of them generated errors: these have not been
checked out, so there is a chance they won't work. The solution is to port the
original code, but this will have to wait for a later release since we are not
responsible for these anyway (excuses, excuses..).
- Other than this there are (as usual) no known bugs. So there! V94.100 (Fifth DECUS release)
This is (yet another) maintenance release of the MDPP. The purpose of
this release is to present the OSF/1 port of the system. This port is a little
less complete that the previous Ultrix port, since we have been unable to
finish the transfer of some of the foreign image formats, specifically, the RLE
library. We have been able to get the BOOKREADER documentation working for
Ultrix & OSF/1 and to re-build the FTP area with these new documents
available. Also, the submission to DECUS will now be split into separate VMS
and UNIX packages. You can still build a consolodated area with the full
VMS+UNIX distribution in it, but you do not have to do so. The effect will be
that the UNIX stuff will be a bit ratty for the next few months as I fill out the material. V93.200 (Fourth DECUS release)
This is a maintenance release of MDPP. There have been
many bug fixes, and the Alpha component has been carefully reworked and
completely recompiled under V6.1 of the FORTRAN compiler to use IEEE
floating-point internally. The major new components are the MOTIF-based
menu-driver that has been provided under both VMS and Ultrix, and the
BOOKREADER documentation. The MOTIF menu-driver (created thanks to Suzy
Gottesman's efforts) allows user-written menus to call MDPP procedures.
V93.200 has been tested under VAX/VMS V6.0 (and works).V93.100 (Third DECUS release)
The major change in this release of the MDPP is the port to Open
VMS/AXP. The VMS gersion now checks to see if you are running on an Alpha and
customizes itself to activate the correct images. This has increased the size
of the distribution since both Alpha and VAX binaries are included, along with
their object libraries. Because of the increased volume of the distribution, a
new procedure, called TAILOR.COM has been included. The easiest way to help
reduce the amount of material, however, is not to take it off the tape by
excluding the unwanted files when the files are restored.