Re: [OpenDX2-users] first try - opendx and plotting angular dependent data
Hi Lars, First, welcome to OpenDX! Sounds like you've gotten quite a long way already. You may be interested in the OpenDX forum at http://www.opendx.org/cgi-bin/forum/YaBB.pl It gets more readers than the mailing list, I think. I found that there is the Post module which is supposed to do some interpolation. I just do not know how to use it - where in my net should it appear, just after the Connect module? I think you want Refine, not Post. And yes, after Connect should do it. This is where I am completely lost now. I tried to use the positions (a.x, a.y) and the data value (b) with a compute module, to get (x,y,z). However, as a is a field with two scalars, while b contains only one data value, I get an error (Bad paramater: Inputs must be of same length / Input 1 not matching the master (input 0).). So I tried to change my input b by passing it through a second compute module, which was simply to add the second scalar: [(a),(0)] - but this did not work, same error message. So how do I match the two inputs, to be able to modify the position by the data value? The error message refers to the number of positions/data values, not to their dimensionality. Your original compute expression is probably correct (at least, it would not be the cause of that error message). The problem is upstream of Compute. Somehow, the number of positions received by Compute's a input is different from the number of data values received by the b input. (You didn't insert a Post, did you?) --Joel -- === Joel Richardson, Ph.D. Sr. Research Scientist Mouse Genome Informatics The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax: (207) 288-6132 Bar Harbor, Maine 04609 URL: www.informatics.jax.org === ___ OpenDX2-users mailing list OpenDX2-users@lists.berlios.de https://lists.berlios.de/mailman/listinfo/opendx2-users
Re: [OpenDX2-users] Can DX count from 1 instead of 0?
Mark, OpenDX array indexing always starts at 0. You can easily subtract 1 from all the index numbers in the connections component. To do that, you'll have to import that array as something other than the connections component (maybe as a separate object - put the field and the array in a group and import that). Then inside of dx, run the array through Compute(a-1) and then use Replace to put it back into the field as the connections component. You'll probably also have to set the ref and element type attributes after the Compute, using the Options module. Hope that helps. Cheers, Joel Mark Gesing wrote: Hi, I have some data which is on a grid of cube shaped volume elements. The grid is an 8x8 grid (64 elements), made-up of two layers of nodes (9x9x2=162). My problem is that DX by default numbers the nodes starting at 0-161, whereas the application generating the data (LS-Dyna) numbers the nodes 1-162. Therefore when I try to import the data (following the example on page 254 of the user's guide) I get the error: Begin Execution ERROR: Import: Invalid data: 573rd item in `connections' component (162) is not between 0 and 161 / file 'd3plot.dx' line 14 My .dx file d3plot.dx is as follows: object 1 class array type float rank 1 shape 3 items 162 lsb binary data file d3plot, 260 attribute dep string positions object 2 class array type int rank 1 shape 9 items 64 lsb binary data file d3plot,2204 attribute element type string cubes attribute ref string positions object 3 class array type float rank 0 items 162 lsb binary data file d3plot,4560 attribute dep string positions object irreg positions irreg connections binary file class field component positions value 1 component connections value 2 component data value 3 end (forgive the wierd spacing, I have written a code to auto-generate the .dx file for d3plots with different sized meshes, and I haven't bothered to tweak the format statements yet) Can I get DX to number it's nodes from 1-162 instead of 0-161? If not, is there a way to get DX to subtract 1 from each of the numbers in the connectivity list? I am also open to other solutions. If anyone would like to try things out on my binary file (d3plot) ask me and I'll e-mail it to you, I would attach it to this e-mail, however, it is 3.6 megabytes and I decided it would be poor form to send a large attachment to a list. Thank you very much -- Mark Gesing, MASc. Candidate, Mechanical and Mechatronics Engineering, University of Waterloo [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] (519) 888-4567 x32309 ___ OpenDX2-users mailing list OpenDX2-users@lists.berlios.de https://lists.berlios.de/mailman/listinfo/opendx2-users -- === Joel Richardson, Ph.D. Sr. Research Scientist Mouse Genome Informatics The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax: (207) 288-6132 Bar Harbor, Maine 04609 URL: www.informatics.jax.org === ___ OpenDX2-users mailing list OpenDX2-users@lists.berlios.de https://lists.berlios.de/mailman/listinfo/opendx2-users
Re: [opendx-users] Command execution order
AB, The only way to guarantee that B executes after A is to have B's input depend on A's output. Since WriteImage has no outputs, it gets a little complicated - you have to put WriteImage inside a macro, and have the macro produce an output (e.g., the image file name) that can flow to the System module. Cheers, Joel Anonymous Bosch wrote: I am fairly new to openDX, but using the visual program editor I've managed to do some fairly neat stuff. However, I have a problem with the order in which the commands are carried out on a given page. In my particular example I'm using writeImage to write an image file to disk and then modifying it using the System command. The problem is, the System command executes before writeImage and so there's no file to operate on. I'm sure this is an extremely simple problem, but I haven't yet figured it out. Any help appreciated. AB _ The new MSN Search Toolbar now includes Desktop search! http://toolbar.msn.co.uk/ -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
[opendx-users] [Fwd: string processing modules available]
Hey DX'ers, I am pleased to announce the availability of a set of free, open-source modules for OpenDX that provide significantly enhanced string processing capabilities. These modules define a new category, bdxStrings, and include functions such as regular expression matching, substring extraction, and enhanced formatting and parsing. I wrote them some time ago and have been using them regularly. I decided it was about time to release them in case others might also find them useful. For details and downloads, go here: http://www.informatics.jax.org/~jer/biodx This is a beta release. Please suggest changes and improvements, and report any bugs to me. Thanks! Cheers, Joel -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] 3-D problem
Samuel, How are you importing your data, and what happens downstream of the import? There must be some step where you are coverting 12.5-17.5 to 0-60... Joel samuel verstraete wrote: Hi, This only solves my problem in a way... Indeed it's not a sheet of paper anymore but now the axes are still going from 0 to 60... Is there any where that i can adjust the labels of the axes? gr, Samuel Verstraete On Tue, 27 Sep 2005 09:12:59 -0400 Joel Richardson [EMAIL PROTECTED] wrote: Samuel, Use Scale to adjust the aspect, e.g., give it a scaling vector of [1, 1, 100]. AutoAxes will show the unscaled coordinates. Joel samuel verstraete wrote: Hi, I'm using opendx for 3-d visualisation of a 3-D grid. So basically the VolumeRendering.net program. Now i have a small problem. The data i work with are only 5 deep (Z) and 500 in X and Y. So what you basically see is a sheet of paper that has some depth but is hardly worth looking at. The simplest sollution to this is of course to change the unit of the Z-delta in the Data Prompter (importer). this gives satisfying results but then the axes are not right anymore. (instead of going from 12.5 to 17.5 they go from 0 to 60.) I don't want that. Do you guys know of any better sollution? Prolly this is quite a simple question but i just started trying this program and i must say that it's not so easy ;) gr, Samuel Verstraete -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 === -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] 3-D problem
Samuel, Use Scale to adjust the aspect, e.g., give it a scaling vector of [1, 1, 100]. AutoAxes will show the unscaled coordinates. Joel samuel verstraete wrote: Hi, I'm using opendx for 3-d visualisation of a 3-D grid. So basically the VolumeRendering.net program. Now i have a small problem. The data i work with are only 5 deep (Z) and 500 in X and Y. So what you basically see is a sheet of paper that has some depth but is hardly worth looking at. The simplest sollution to this is of course to change the unit of the Z-delta in the Data Prompter (importer). this gives satisfying results but then the axes are not right anymore. (instead of going from 12.5 to 17.5 they go from 0 to 60.) I don't want that. Do you guys know of any better sollution? Prolly this is quite a simple question but i just started trying this program and i must say that it's not so easy ;) gr, Samuel Verstraete -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
[opendx-users] Java Explorer question
I've been experimenting with Java Explorer (with a fair amount of success) and I'm wondering if there is any way - by hook or by crook - to make objects in a scene hypertext links - when the user clicks on one while in Pick mode, the end result is the object's URL target is opened in a new browser window. My gut tells me this is not supported, nor will it be easy to implement. Obviously, my net has to somehow communicate the URL to the applet, which must open the new browser window. Assuming this is not currently possible, I'm willing to dig in and try to implement it, if that seems like a good idea. It would sure be useful for the things I'm trying to do. Any advice from the experts? Thanks in advance, Joel -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] FEA Grid Visulization
If by number the positions, you mean you want the number 1 to appear in the scene at the first position, 2 at the second, and so on, here's one way... To get n, Extract(positions) and feed to Inquire(items). Feed this to Enumerate to generate the integer list 1 .. n. Replace the data in the original field with this list. Send this to AutoGlyph; set the glyph type to text, and the ratio to 1.0. Color to taste. Cheers, Joel Jon Pitt wrote: Hi, I'm trying to visualize a grid generated by an FEA package. I can get the connections drawn and change their color, but I would like to number the positions. Does anyone know how to do this? I would also like to further extend this to the faces and cells themselves, but starting with the positions would be great! Thank you, Jon Pitt University Park, PA 16802 [EMAIL PROTECTED] -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] How to exclude part of data
You can run the data through Histogram, then run the histo through Include to keep only the bins that have at least N occurrences, then Statistics to get the min/max pressures. Then feed your original data through Include, using this min/max. Joel Jonathan Matheson wrote: I can get a good image that way but I am looking for a way to do this automatically. I am using it for a computational fluid dynamics simulation so the pressure range is always different depending on the shape and other parameters. Also, my cfd program calls dx once it writes the dx files so the user can immediately see the image. Because the pressure range depends on the individual problem you'd have to specify the range each time which is not very practical. My range is so big now that the good data (data outside the shape surface) appears all one colour because it occupies a very small range of the colourmap. If I use 'statistics' to find the max and min it gives me the garbage values from within the shape. I need to somehow use the boundary of the shape dx file to exclude the data inside of it and then search for the max and min outside. I can't find a way to split up the 'data' or get rid of part of it. I can exclude all of it easily enough but that's certainly no help. Thanks, Jon Chris Pelkie wrote: Using only the Colormap Editor (once you install Colormap and a Color, double-click the Colormap module), you can modify the normally linear colormap to any shape you want. You can also type in min and max values right there to constrain what gets colored (it invalidates the data outside your range, just like Include). So you can pretty quickly trim outliers, or leave them in, but by adding new control points, make a colormap that pushes all the colors down and up to wrap around the 'good' data. Note the 'histogram' function of Colormap Editor can help identify where the 'good' data is. To see all the above, you have to run the data flow from your imported field into the 1st input of Colormap. Also run this same output to the 1st input of Color. Then run the 1st output of Colormap to 2nd input of Color. Samples show this clearly. On Aug 9, 2005, at 9:47 PM, Jonathan Matheson wrote: I am importing 2 3D dx files into my .net program. One of them contains pressure values in the ‘data’ field. The other shape file has only ‘positions’ and triangular ‘connections’ fields with no data. The pressure values within the shape are garbage and I need to make my program ignore them. The problem is that outside of the shape the pressures are all pretty close but inside they are really high and really low. As a result of this my colour map does not show the pressure differences outside the shape. I can manually set the max and min values through the ‘include’ function but dx is automatically called from another program and that is not an option. I am looking for a way to search for the max and min pressure values while ignoring those that are inside the shape. If I could do that I can set those values in the ‘include’ function and everything will display properly. Thanks, Jon ___ Chris Pelkie Scientific Visualization Producer 622 Rhodes Hall, Cornell Theory Center Ithaca, NY 14853 (607) 254-8794 -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] Configuring OpenDX on a Mac
I should have checked more thoroughly. It's only the DX main menu that fails to recognize the directory setting. Run visual program and Edit visual program both go to the root (curiously, with a double slash at the start. I.e., I end up at // not /). However, the VPE dialogs (open, load macros, file interactors, etc.) all start at the desired directory. I tried setting DXHOST to unix and tried adding -host unix to DXARGS (and I am logging out/in each time), but with the same behavior - the launcher window goes away, but no dx. Just curious - what is the ~/.dx-ad config file? Is it safe/recommended to add parameter settings there? As I said, setting DX*host there does work. Thanks again for the help. Joel David Thompson wrote: I tested the DXARGS specifically because this was the most interesting and it worked with no problems (changed my directory to my Desktop). Can you check it again? Can you check it on the command line and see if it works? I guess, I should also know what you mean by it doesn't work (mine made all FileSelectors and Open/Save dialogs default to the Desktop folder I set it to.) Remember you have to log out and log in each time you make a change to the environment.plist file (its only read once at log in time.) Can you set the -host localhost okay via the command line? You could also try to set DXHOST=unix which will just assume a localhost but not even try to look up the machine name. David === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] Configuring OpenDX on a Mac
Problem solved...mostly. I stumbled across a config file in my home
directory. The file is named .dx-ad, and is not documented anywhere
that I've been able to find. The VPE uses it to save things like
which module categories are expanded. The settings in this file
take effect whether DX is started from the command line or from the
launcher. By looking at dx source code,
and playing around a bit, I was able to come up with the following.
(This may not be the most robust way to go about this, but it
got me over the hurdle.)
1. To achieve the same effect as setting DXMACROS, you can define the
variable DX*macros.
2. To achieve the same effect as setting DXMDF, you can define the
variable DX*userModuleDescriptionFile.
3. I did not see any way to achieve the same effect as setting
DXMODULES. (DX*modules doesn't do anything.)
As a workaround, the MDF file can give the complete
path to the loadable file.
4. Looking at the dx source code, it seems that setting the variable
DX*directory should set the working directory, but it doesn't. Whenever
I launch dx from the icon, the working directory is always root.
Cheers,
Joel
Joel Richardson wrote:
Hey DXers,
I am running the Vis Inc. distribution of OpenDX 4.3.2 on a Powerbook
G4 running OSX 10.3.9.
I've got a bunch of macros and runtime loadable modules that I'd
like to have available every time I start dx. Similarly, I'd like
the working directory to be set to a particular location.
The standard mechanism (setting env variables) works fine if I
invoke dx from the command line. But if I launch it via the application
icon or open a .net file, my settings have no effect. The variables
are set in my .bashrc file.
I'm able to make the macros visible by placing them under
${HOME}/Library/Application Support/OpenDX/macros
as described in the distribution notes. But I cannot make
my loadables visible, and the working directory is always /.
Thanks in advance,
Joel
--
===
Joel Richardson, Ph.D. Phone: (207) 288-6435
The Jackson Laboratory Fax: (207) 288-6132
600 Main Street URL: www.informatics.jax.org
Bar Harbor, Maine 04609
===
Re: [opendx-users] Configuring OpenDX on a Mac
David,
Thanks - this works as advertised ... mostly!
1. Setting DXMDF, DXMODULES, and DXMACROS in ~/.MacOSX/environment.plist
works just fine.
2. Setting DXARGS to change the working directory does not work - I
still end up at the root dir.
3. Also, I'd like to set host to localhost. (Otherwise ssh complains,
and I have to open a connection manually from VPE.)
If I set DXHOST (or add -host localhost to DXARGS) in
environment.plist, dx fails to launch. I see the launcher
progress bar, but it just goes away, and there's no dx main menu.
I *can* set DX*host in ~/.dx-ad, however.
Thanks,
Joel
David Thompson wrote:
Joel,
You can set the following environment variables to override things:
DXMDF=path2mdf/file.mdf
DXMACROS=path2macrosdirectory
DXARGS=-directory /workingpath
.bashrc is not consulted from an app that is not started from a
terminal. You can follow the thread on Apple's X11 mailing list for more
information on environment variables and apps, see
http://lists.apple.com/archives/x11-users/2004/Dec/msg00085.html
Your best bet would be to place these variables in the
~/.MacOSX/environment.plist as mentioned here
http://developer.apple.com/documentation/MacOSX/Conceptual/BPRuntimeConfig/Concepts/EnvironmentVars.html
By the way, you will need to logoff and login for environment.plist to
take effect.
A technote from Apple talks about creating this file
http://developer.apple.com/qa/qa2001/qa1067.html.
I just tried it out to make sure it works and it does as I state. I will
make sure to add this to the documentation for the next release. It
really is a nice feature. If you have the Property List Editor from the
developer tools, it can help to make sure the syntax is correct.
David
Hey DXers,
I am running the Vis Inc. distribution of OpenDX 4.3.2 on a Powerbook
G4 running OSX 10.3.9.
I've got a bunch of macros and runtime loadable modules that I'd
like to have available every time I start dx. Similarly, I'd like
the working directory to be set to a particular location.
The standard mechanism (setting env variables) works fine if I
invoke dx from the command line. But if I launch it via the
application icon or open a .net file, my settings have no effect. The
variables
are set in my .bashrc file.
I'm able to make the macros visible by placing them under
${HOME}/Library/Application Support/OpenDX/macros
as described in the distribution notes. But I cannot make
my loadables visible, and the working directory is always /.
Thanks in advance,
Joel
--
===
Joel Richardson, Ph.D. Phone: (207) 288-6435
The Jackson Laboratory Fax: (207) 288-6132
600 Main Street URL: www.informatics.jax.org
Bar Harbor, Maine 04609
===
--
===
Joel Richardson, Ph.D. Phone: (207) 288-6435
The Jackson Laboratory Fax: (207) 288-6132
600 Main Street URL: www.informatics.jax.org
Bar Harbor, Maine 04609
===
[opendx-users] Configuring OpenDX on a Mac
Hey DXers,
I am running the Vis Inc. distribution of OpenDX 4.3.2 on a Powerbook
G4 running OSX 10.3.9.
I've got a bunch of macros and runtime loadable modules that I'd
like to have available every time I start dx. Similarly, I'd like
the working directory to be set to a particular location.
The standard mechanism (setting env variables) works fine if I
invoke dx from the command line. But if I launch it via the application
icon or open a .net file, my settings have no effect. The variables
are set in my .bashrc file.
I'm able to make the macros visible by placing them under
${HOME}/Library/Application Support/OpenDX/macros
as described in the distribution notes. But I cannot make
my loadables visible, and the working directory is always /.
Thanks in advance,
Joel
--
===
Joel Richardson, Ph.D. Phone: (207) 288-6435
The Jackson Laboratory Fax: (207) 288-6132
600 Main Street URL: www.informatics.jax.org
Bar Harbor, Maine 04609
===
[opendx-users] JavaDX/MacOSX question
I have just started looking into JavaDX. I've gotten pretty far but have just run into a wall. Everything is works fine if I run the web browser on the same machine as JavaDX. I see the server status on the Status.html page, and the demos all seem to work. But when I try it from a different machine, the applet is not able to connect, and the JavaDX console window shows no traffic (I've got -verbose and -debug both turned on.) Locally, I'm accessing the pages with http://, not file:// A possibly related problem is that stopserver also is not able to connect - it just hangs. I have to kill the server process manually. Anyone know of something obvious that might be going on? Thanks in advance! Joel === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] simple plotting
Hi Dan, I haven't looked at your data, but from your description, you need to do something like the following: tbl = ImportSpreadsheet(...); in1 = Mark(tbl, 'x'); in2 = Mark(tbl, 'y'); in3 = Mark(tbl, 'z'); tbl2 = Compute(float([$0, $1, $2]), in1, in2, in3); tbl3 = Unmark( tbl2, positions); tbl4 = Mark( tbl3, velocity); At this point, you've got a field with the desired positions and the velocity column marked as data. You can do further computations on the data, if needed, and then pass it to Glyph or AutoGlyph. Cheers, Joel Dan Patnaude wrote: Maybe this is a fundamental misunderstanding of how DX treats things on my part. I've updated the data so that I now have four columns: x,y,z,radial velocity The x, y, and z positions describe a position in space, and the data at that position is the radial velocity. If I assume an age and distance to the remnant, I can decompose the radial velocity into components vx, vy, and vz, but I am still at a loss. When I read in the spreadsheet, how do I tell DX to associate v_radial (or vx,vy,vz) with the position (x,y,z)? I don't understand how to tell DX that the 1st three columns denote positions, but the 4th column (or 4th, 5th and 6th columns) are data associated with those positions; i.e. column 4 is the x component of the velocity at the position (x,y,z). Moreover, if I do create a three vector for the velocity components, I can't seem to pass it to the 4th tab in Construct. It returns the following error: ERROR: Construct: Invalid data: origin must be a vector or vector list Here is the layout: ImportSpreadSheet=Mark(x),Mark(y),Mark(z),Mark(vx),Mark(vy),Mark(vz) Mark(x,y,z)-Compute([x,y,z]) Mark(vx,vy,vz)-Compute([vx,vy,vz]) [x,y,z]-Construct.origin [vx,vy,vz]-Construct.data A little more insight would be helpful. I can't imagine that this is as much of a hassle as it seems to be. I've attached the network and data in case anyone would be kind enough to play around with it. On May 20, 2005, at 5:29 PM, Chris Pelkie wrote: I'm not sure if you mean you want all the arrows to originate at 0,0,0, as if you snapshot the 'explosion', or if you want each arrow to originate at its x,y,z position, but be directed radially away from 0,0,0. In either case, the solution is the same, but the 'positions' are different. To draw 3-d arrow glyphs in space, you need to have 3-d positions and 3-d data (dep on those positions). You didn't specify what you Mark'ed (I assume column0, column1, column2), so after creating the 3-vector and (unnecessarily Unmark'ing) you have 3-d data on the 1-d positions (a line) autocreated by ImportSpreadsheet (and usually, but not always, worthless). So to emanate all from the origin, compute the 3-vectors as you have already, then feed this array to the 4th input of a Construct. Set origin to 0,0,0. This creates a field with as many 0,0,0 positions as there are data items in the input array. Autoglyph. Color with Autocolor or Color/Colormap. Image. done. To do the second layout, separately Compute the array of 3-d positions and feed it to Construct(origin) and the data array to the same Construct's 4th input (which I can't think of the formal name of off the top of my head, either data or input). Same net as above. Use Print(rd) to watch how each operation changes the data field at the output of each module. Chris Pelkie Vice President (607) 257-8335 Conceptual Reality Presentations, Inc. 30 West Meadow Drive Ithaca, NY 14850 On May 19, 2005, at 19:41, Daniel Patnaude wrote: Hi- I'm trying to do something which intuitively ought to be quite simple: I have a data file which looks like: x_pos,y_pos,v_radial The data is of ~ 450 ejecta knots in a supernova remnant (3c58 for the curious). I basically want to make a 'kaboom' type 3-d distribution with the coords x,y,v_rad, since v_rad is effectively a measure of the z displacement from the center. The positions should be marked by an arrow which points radially away from (0,0,0), has a length proportional to the data, and optionally a color based on the value (bluer for positive, redder for negative values). Is this an easy thing to do? So far, all I've been able to do is: ImportSpreadSheet-(Mark x 3, for each value)-Compute (to make a vector)-Unmark-Autoglyph-Image but this only makes a distribution of circles, which looks nice, but isn't quite what I have in mind. Any suggestions? Thanks, Dan Daniel Patnaude Smithsonian Astrophysical Observatory 60 Garden St MS-02 Cambridge, MA 02138 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] (617) 496-2087 -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL
[opendx-users] random(a,b) function crashes?
Hey DX listers, I'm running OpenDX 4.3.2 on Solaris 8. The random() function consistently causes dx to dump core. It does not seem to be a problem for the Mac version. I have checked the bug database at opendx.org and there is no mention of this, although the release note for OpenDX 4.3 mentions a fix to random() for Windows. Has anyone else run into this problem? Is there a workaround or a patch? Thanks, Joel -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
[opendx-users] Plot question
I would like to produce a bar chart that includes error ranges extending above and below the top of each bar. I can see how to do the bars using Plot, but not the error ranges. Does anyone know how to do this? Thanks. Joel -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] Coloring Glyphs with a second parameter
Emmanuelle, Color the field according to the second parameter before sending it to AutoGlyph (or Glyph). E.g., f1 = Mark(myField, parameter1); f2 = AutoColor(f1); f3 = Unmark(f2); f4 = Mark(f3, parameter2); f5 = AutopGlyph(f4); ... Cheers, Joel Emmanuelle Lafont wrote: Hi, I've created glyphs with a size depending on a parameter. Now, I'd like to color them according to the value of another parameter. Is there a way to do that? It seems to me that there is a sample about it, but I can't find it anymore. Any help would be welcome. Thanks! Emmanuelle Lafont - Emmanuelle Lafont NUMTECH 6 allée Alan Turing 63175 AUBIERE Cedex -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
Re: [opendx-users] Window focus on Macs
David, That works perfectly. Thank you so much! Joel David Thompson wrote: Joel, This is the function of the quartz-wm Window manager. It is a pain especially for dx. I've changed my focus policy within the window manager so that it focuses on the window that the mouse is over immediately. It solves the problem you talk about with the ImageWindow always gaining focus. To do that, you need to add the key wm_ffm as true to the com.apple.x11.plist file in your ~/Library/Preferences file. I've read that it can be set using: in terminal defaults write com.apple.x11 xm_ffm true then to delete the behavior if you don't like it, defaults write com.apple.x11 delete wm_ffm I didn't have any luck with this, so I editted the file by hand and added it. Of course you will need to restart X11 whenever you change this file. David I've been running OpenDX on my Mac and mostly everything is great. My one problem is having to first click on a window to make it active, before doing whatever in that window. Since working with OpenDX usually requires frequent switching between windows (control panels, dialog boxes, image windows, etc.) all those extra clicks add up to a real pain. Even worse, focus automatically switches to the image window on every execution, so activities like stepping through values in a control panel becomes a truly frustrating experience. On my Sun box, this is not an issue, because I have it configured to give focus to whichever window the mouse is over. I cannot find a way to do this on a Mac. (I'm running OS X 10.3.6, using Apple's X11 v.1.0 - based on XFree86 4.3.) Does anyone else have this problem, and is there a way around it? Thanks! Joel -- === Joel Richardson, Ph.D. Phone: (207) 288-6435 The Jackson Laboratory Fax: (207) 288-6132 600 Main Street URL: www.informatics.jax.org Bar Harbor, Maine 04609 ===
[opendx-users] Window focus on Macs
I've been running OpenDX on my Mac and mostly everything is great. My one problem is having to first click on a window to make it active, before doing whatever in that window. Since working with OpenDX usually requires frequent switching between windows (control panels, dialog boxes, image windows, etc.) all those extra clicks add up to a real pain. Even worse, focus automatically switches to the image window on every execution, so activities like stepping through values in a control panel becomes a truly frustrating experience. On my Sun box, this is not an issue, because I have it configured to give focus to whichever window the mouse is over. I cannot find a way to do this on a Mac. (I'm running OS X 10.3.6, using Apple's X11 v.1.0 - based on XFree86 4.3.) Does anyone else have this problem, and is there a way around it? Thanks! Joel
Re: [opendx-users] Coloring points based on one component of a vector
Assuming the data component holds the 4-vectors and that the 4th vector element holds the internal variable, you could do this: ...-Compute(a.3)-AutoColor()-... Cheers, Joel I have a 4-vector on an irregular set of points. (A collection of particles with 3 velocities and one internal variable that are at irregular positions in space.) I can easily do the various scatter plot projections that I need with all points black. However, I would like to be able to have the point colored depending on the value of the extra internal variable. Can this be done with OpenDX? Any hints on getting started? Thanks.John Cary -- John R. Cary Professor, Dept. of Physics, University of Colorado, Boulder, CO 80309-0390 [EMAIL PROTECTED] ph. (303) 492-1489fax (303) 492-0642cell (720) 839-5997 === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] How to display polydisperse spheres?
Insert Mark(size) before Glyph. (Or have your program name the component data instead of size.) Joel Greetings, I'm following this list for quite a while (basically since I started using dx 3 month ago). I really like this program, but now I've got a problem I couldn't solve so far. I'm sure there is a very simple way of doing it, but I can't see it right now. I've created a program that is generating a box filled (not tightly packed) with spheres of randoms sizes. Its output is of the following structure (assuming 100 spheres): object 1 class array type float rank 1 shape 3 items 100 data follows -0.6902 -5.5948 0. [x,y,z coordinate] ... object 2 class array type float rank 0 items 100 data follows 0. [radius] ... attribute dep string positions object data class field component positions value 1 component size value 2 end How can I display these spheres on their correct positions and with the correct radius according to the size component? At the moment, I'm using Import-Glyph-Image which displays the spheres at the correct position but with the same radius (r=1 IIRC). Do I have to choose a diffent output for my program? (Wouldn't be a problem if so.) Thanks for your help, Kai === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] Princeton Ocean Model, calculating depth from Sigma coordinates
Steve, This just scales the depth back. What I really want is to feed Depth into the Compute module as input B and use the Expression: [a.x, a.y, a.z * [b.x, b.y] / 22] When I do this, I get the following in the Message Window: Error: Compute: Bad parameter: Inputs must be of same length / Input 1 not matching the master (input 0). This means that the number of depth values is different from the number of positions. Compute wants its inputs to be arrays of the same length. It then computes the expression for each set of corresponding elements. As a special case, an input can be a single value (array of length 1), in which case the same value is used throughout. Your expression also has an error - which Compute will complain about next, after the inputs are the same length. If what you want is to multiply a.z by the length of vector b, try: [a.x, a.y, a.z * mag(b) / 22 ] Hope this helps. Cheers, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] Errors importing file into Opendx....please tell me what I am doing wrong!!
Arun, Have you checked the opendx-users archives? I seem to remember other discussions of the bufsize mismatch problem. Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] Execution with SIDE_EFFECTs
David, Thanks for looking into this. I did read the documentation, but obviously didn't quite get it. Going back and reading the documentation a bit on this, it appears that your assumption that adding SIDE_EFFECT results in the module always runs is correct. However, the assumption that the downstream modules assume that the output has changed is incorrect. I was assuming that the downstream modules would _detect_ the change, when they tried to lookup the new input in the cache. I think I must not fully understand how the cache is used or maybe how the executive does its dataflow analysis (or both!) I was also assuming a broader definition of side effect, wherein a module's inputs do not fully define its outputs. The first couple of sentences of section 4.1 of the User's Guide gave me this impression. Cheers, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
[opendx-users] Execution with SIDE_EFFECTs
I have written a small inboard module, getTime, that returns the current system clock, using the gettimeofday() call. The module is marked as having side effects, so it is called on every execution, as expected. The problem is the downstream Compute. I want to use the time of day as a random number seed. Even though the time value is changing, the Compute is *not* being reexecuted, so I'm getting the same random numbers every time. The following also shows the problem. In this net, the first value printed by Echo changes each time, but the second remains fixed. [getTime] | +--+-+ || | [Compute(a)] || [Echo] I can force the Compute to execute by setting the output caching to No results, but I thought that wouldn't be necessary here? I have verified this behavior in verions 4.3.2 and 4.2.0, both on Solaris 8. Am I missing something? Thanks, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] Execution with SIDE_EFFECTs
I just tried that and it has no effect... Somehow, the Compute is not being executed, even though its input is clearly changing. If I change Compute's output to no caching, it forces execution, but that shouldn't be necessary, if I'm understanding things correctly. Joel Have you tried setting the output of getTime to cache No results. I'm betting that Compute is seeing getTime as not changing so it cache's the input value. David I have written a small inboard module, getTime, that returns the current system clock, using the gettimeofday() call. The module is marked as having side effects, so it is called on every execution, as expected. The problem is the downstream Compute. I want to use the time of day as a random number seed. Even though the time value is changing, the Compute is *not* being reexecuted, so I'm getting the same random numbers every time. The following also shows the problem. In this net, the first value printed by Echo changes each time, but the second remains fixed. [getTime] | +--+-+ || | [Compute(a)] || [Echo] I can force the Compute to execute by setting the output caching to No results, but I thought that wouldn't be necessary here? I have verified this behavior in verions 4.3.2 and 4.2.0, both on Solaris 8. Am I missing something? Thanks, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org === -- . David L. Thompson Visualization and Imagery Solutions, Inc. mailto:[EMAIL PROTECTED]5515 Skyway Drive, Missoula, MT 59804 Phone : (406)756-7472 === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] Coordinate trasformation
Mark(positions) - Compute(sqrt(a.x^2 + a.y^2 + a.z^2)) - Unmark(r) ...or something like that. Joel Hi, I have a vector field written in cartesian coordinate system. I would like to extract from it the radial component in spherical coordinate, and plotting it with opendx. Is there a simple way to do it using opendx? Thank you in advance, Marzia === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] positions precision
That limitation is pretty integral since many modules touch the positions component. The likely workaround with DX out of the box is to introduce some coordinate system ransformation (i.e., warping the positions via Mark-Compute-Unmark). These could include logarithmic or removing an offset and rescaling. But thay may not work with the distribution of positions. Perhaps another way is to maintain a private positions as doubles, then offset/scale to floats for the portion being rendered and Replace the positions. That last suggestion makes a lot of sense. Thanks. Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
[opendx-users] ImportSpreadsheet rounds integers??
Hi, I am trying to import a small table of genome coordinates and am getting strange results from ImportSpreadsheet. Here's the file (tab-delimited): group species genechromosome start end Spry2 mouse Spry2 14 9692917496933478 Spry2 human SPRY2 13 7490502774910002 Smad7 mouse Smad7 18 7582490875853511 Smad7 human SMAD7 18 4624623446277097 When I import it, the start and end coordinates have changed a little. For example, the coordinates for the first row have become 96929176 and 96933480, respectively. The others have similar differences. Looks like a rounding error of some kind. I get the same results from both 4.2.0 on Solaris 8 and Win2000. Is this a known bug? Is there a workaround? Thanks for any help. Cheers, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
[opendx-users] Hanging on startup
Hello, I'm experiencing a problem that has been discussed before... OpenDX hangs when a large net is executed from the UI. I have tried the suggested solution, increasing DX_SOCKET_BUFSIZE. But even setting it to the maximum allowed (1048576) doesn't help. So, one question I have is how large is large? My .net file is small (80k) although it does use a number of macros. Even so, the total size is well under 1MB. Is there an alternative workaround? Thanks, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
[opendx-users] substring function?
Hi - In dx, how do I compute a substring, given a string, a starting position, and a length? Thanks, Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
[opendx-users] General DX Robustness Question
First, I want to say what a fantastic tool I think DX is. The breadth and depth of its features have been pretty much boggling my mind since I started using it. It may really BE the best thing since sliced bread. That said, the version I'm using crashes a lot, and in a number of different ways. I'm just wondering if this is normal, specific to my platform, something I'm doing wrong (the most like explanation), or what. If anyone can help me, I'd sure appreciate it. The particulars: I downloaded the binary labelled Solaris Sparc v2.8 based on OpenDX 4.1.3 from the OpenDX web site and installed it in the usual place (/usr/local/dx). My workstation is a SunBlade 1000, running Solaris 8 and CDE. The kinds of problems I'm experiencing include: - VPE crashes a lot. I'm doing a lot of macro development right now. Quite frequently, operations like opening/closing a macro window or reloading macro definitions will cause VPE to die. As a defensive measure, I've been saving every couple of opertaions, and quitting/restarting VPE every couple of saves. - Mangling a macro's .net file. This only happened once, but to a large, complicated macro. It suddenly started producing 100s of syntax errors when trying to load it. I looked at the file and it seemed ok to me (not being a script expert, however). VPE would show the modules, but none of the connections. I ended up rewiring the network. - ImportSpreadsheet causes Signal 11 in the executive. This seems to be connected with categorization, because if I don't categorize any columns, it works fine. - Sometimes zooming in the Image window causes DX to crash and kills my window manager along with my login shell!! - Occasional complaints about bad reference counts. Thanks in advance! Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] General DX Robustness Question
Greg, OK, thanks. That's comforting to know. I will try compiling the source as you suggested and get back to you. Joel No, thats not commonly the case at all. Actually, I can't recall the last time the VPE crashed on me. Needless to say, I don't use Suns, and I do remember that, way back when, we did have problems on Solaris - but back in product days, we tracked everything we encountered down and fixed it. Of course, both Solaris and OpenDX have drifted since then, so new problems can easily arise. I would encourage you to lend us a hand here. Download the source (from www.research.ibm.com/dx) and build it with debugging options set. If you can give us info like the stack trace from core dumps we can get a clue as to whats going wrong. The ImportSpreadSheet problem ought to be easy to track down. UI/VPE problems can be tougher, since there's X below our code. Greg === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
Re: [opendx-users] Newbie computation question
Thanks for the reply. I should have stated my question more clearly, though. I can see how to compute the density in a window around a single position, but I need to compute the density at each of a set of regular positions. I'm using Grid to obtain the regular positions. Do I have to loop through the positions explicitly? Is there a way to do this _without_ loops? I've looked at modules like Sample, Regrid, Map, etc., but to no avail. Thanks again! Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
[opendx-users] Newbie computation question
Hello all, I have a field consisting of integer counts at irregular 1-D positions, e.g.: positiondata = 0.0 12 1.0 5 1.357 2.1 10 ... ... I'd like to compute a density function over x, for a given sliding-window size. Seems trivial, but I can't figure out how to do it. Thanks in advance for any advice! Joel === Joel Richardson, Ph.D. [EMAIL PROTECTED] The Jackson Laboratory Phone: (207) 288-6435 600 Main Street Fax:(207) 288-6132 Bar Harbor, Maine 04609 URL:www.informatics.jax.org ===
