Re: [opendx-dev] OpenDX data model confusion
Hi Matt, Sounds like you are on the right track. The simplest way to get your data into DX is probably just to create a delimited text file and use ImportSpreadsheet (be sure to set the delimiter input to whatever you use in the file (comma, tab, space, ...) timesource1 source2 source3 0.1 53.2101.9 82.9 0.2557.0100.2 82.9 0.4 68.697.382.5 ... ... ... ... The Plot module (under Annotation) will draw the lines for you. It wants a field with a 'positions' component containing the X values, and a 'data' component containing the Y. So, to draw the line for one of your sources, you could rename the time component as 'positions', then mark the data source component you want to plot, then pass it to Plot: ImportSpreadsheet | | "time" | | "positions" | | | Rename | | "source1" | | Mark | | Plot | Image To plot all three source lines at once, Mark each one separately, collect the results into a group, and pass that to Plot: yourfield | | "time" | | "positions" | | | Rename | |-+---+ | | | | "source1" | "Source2" | "Source3" | | | | | | Mark MarkMark | | | +-+ | ++ | | | Collect | Plot | Image To create a scatter plot, say source1 vs. source2, rename source1 to positions, mark source2, and add a "scatter" attribute with a value of 1, just before Plot: yourfield | | "source1" | | "positions" | | | Rename | | "source2" | | Mark | | "scatter" | | | | 1 Options | Plot | Image For more information, check out the documentation for Plot. Hope this helps. Cheers, Joel Matt Genovese wrote: Hello, I am a little confused regarding the OpenDX data model, and would like to solicit input from those who understand it better than I. My project is fairly simple: I am writing a C program to capture data as time progresses, and plot it in DX. There are one or more axes (sources of data values), and obviously the time-axis is another source of data (there can actually be multiple discrete time axes, but I'll keep it simple for now). Note that time does not progress at a constant rate. The goal is to be able to plot any axis vs. a time axis. However, more generally, I'd like to be able to plot any axis vs. any other axiswhich is really a scatter plot. The points on the scatter plot are correlated (linked) by the discrete time which they were captured in the simulation. I'd like to understand how to best assemble this into the DX data model. My attempt is to group all the axes under a DX Field. Each axis is essentially a DX Array of data, which is a component of the Field. However, does this allow me to formulate the time-based plots or scatter plots I am looking for? The Arrays I was building are scalar (rank 0) - just raw values (doubles) obtained over time...one for each axis. I am also confused as to the "rank" and "shape" parameters, and how they affect organization of the data in the Arrayso perhaps this is part of my problem. So for example, my thinking is that if I had 3 data sources, and they're sampled over time, I have: 4 "axes" - 4 DX Arrays as components under 1 DX Field object. Three of the arrays are one-dimensional and contain the data values, and the fouth array is one-dimensional and contains the capture times for all points. Then the three data arrays are somehow linked to the fourth array to correlate the data value with time-of-capture. Again, I'm worried I am going about this all-wrong. I hope this is not too vague. Thanks in advance for any guidance you can provide. Best Regards, Matt
Re: [opendx-dev] Compiling outboard module on MacOSX 10.4 Tiger
Here's what someone sent me a while back. Hope this helps. Cheers, Joel Tan Meng YUE wrote: Hi, I am porting a RenderMan outboard module from Linux to OSX. I have got OpenDX 4.3.2 running on OSX Tiger with no problem but the module compilation on OSX Tiger seems quite different from that in Linux. Does anyone have a sample Makefile which show one how to link the various libraries and build dynamical libraries on OSX Tiger. I have also encountered a DXAddModule() function not found error during the linkage. Cheers -- === 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 === dxRunTimeMacOS.rtf Description: RTF file
[opendx-dev] OK, my face IS red (ImportSpreadsheet)
Ok, just ignore those last two postings. I discovered another bug. I will go away now and stop bothering you... Joel - Begin Forwarded Message - Date: Fri, 16 Jul 2004 14:23:13 -0400 (EDT) From: Joel Richardson <[EMAIL PROTECTED]> Subject: Re: ImportSpreadsheet bugfixes To: opendx2-dev@lists.berlios.de Mime-Version: 1.0 The file I posted yesteday introduced a bug that is fixed in the attached file. (I wasn't handling "!filter" filenames properly.) Sorry about that. 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 === - End Forwarded Message - ======= 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-dev] new modules, seeking feedback
Hello developers, As part of a bioinformatics project, I have developed several runtime-loadable modules that may be of general interest. Before contributing them to the public (or inflicting them upon the innocent, depending on your point of view) I was wondering if someone(s) on this list might be willing to give them a once-over. I'm especially interested in advice on their interface, comments on usability, etc. These modules augment DX's string handling capabilities. (Some of this might be better done as enhancements to Compute, but I didn't want to go there...) Anyway, here's a brief rundown: strFormat - 'souped up' Format, e.g., can format a table into a string list strParse - 'souped up' Parse. e.g., can parse a string list into a table strSplice - substring manipulation: extraction, insertion, deletion strJoin - 'vertical' string concatenation, with separators strRegex - finds regular expression matches strRegsub - makes substitutions at regex matches strRegsplit - splits strings at regex matches. (The regex modules use GNU regex.c) I have compiled them only under solaris, so I have no idea what kind of portability problems may lurk. They just use standard C string functions, so it shouldn't be too bad. If you are interested/willing to test them out or at least look over the man pages, please let me know. 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 ===
[opendx-dev] Bugfix for ImportSpreadsheet
Hello, In a previous email, I asked about ImportSpreadsheet's tendency to munge large integers. E.g., 96933478 becomes 96933480. (http://opendx.npaci.edu/mail/opendx-users/2003.06/msg00046.html) I have traced this to line 1337 of import_ss.c, in the function _dxf_isnumber(). The data value has just been parsed as a float. Then, if no decimal point is found, the float is converted to an int: *d = (int)f; But it's too late because there's not enough precision in the float to represent large ints. Re-parsing the input as an integer fixes it: sscanf(p+(*p=='$'), "%d", d); I have verified this on my local installation. 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 ===
