[base] how can i interact with the spot creator plugin from outside the system
Greetings!
I'm trying to understand the genepix tiff spotfinding problem I described
earlier.
I want to interact with the spotfinder plugin with my own program but I
can't create files.
I have this:
images/
|-- 13298608_532-uncompressed.tif
`-- 13298608_635-uncompressed.tif
I want to do something like this:
public class TestImageProblem {
SpotImagesData data;
FileData red;
FileData green;
TestImageProblem() {
data = new SpotImagesData();
data.setGamma(new Float(1.8));
data.setXOffset(2000);
data.setYOffset(2400);
data.setXScale(10);
data.setYScale(10);
data.setSpotsize(24);
java.io.File redfile = new
java.io.File(images/13298608_635-uncompressed.tif);
java.io.File greenfile = new
java.io.File(images/13298608_532-uncompressed.tif);
Pass the data to the spot image creator ( SpotImages.createSpotImages )
}
Can you tell me how to create the appropriate file objects when the files
are here and not connected to the base datbaase?
Thanks!
Chad
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[base] genepix 6.0/6.1, multi-image tif-s, spot finding,
Greetings! I've been troubleshooting a problem that exists when trying to use images generated by Genepix 6.0/6.1 as images for spots. Genepix generates a single, multi-image, 16 bit greyscale TIFF. It's composition is as follows: Index Description 1 635 preview (495x1396 pixels) 2 532 preview (495x1396 pixels) 3 635 image (1884x5472 pixels) 4 523 image (1884x5472) The image offsets and scales are found in the .gpr file that Genepix creates. I used those numbers to try to use the single-image tiff for spots but most of the time it failed with an exception that I described in previous posts: java.lang.ClassCastException: [[B at com.sun.media.jai.opimage.BandMergeOpImage.shortLoop(BandMergeOpImage.java:3 41) Once in a while, though, it would succeed but the spots would be tiny in the images. This is because BASE2 is using indices 1 and 2 for the images in a multi-image tiff. In the case of GenePix 6.0/6.1 these are preview images. If you select 'Export Images' in Genepix 6.0/6.1 it does not do what you expect. I would expect that it would run it's own version of tiffsplit and generate two 16-bit greyscale tiffs. It actually creates two RGB images with 8 bits in the appropriate colour channel - red or green. These images cannot be imported into BASE (they provide the same exception as above). The reason why this exception is so mysterious can be balmed on JAI. IN core/net/sf/basedb/core/SpotImages.java the method In private RenderedOp loadTiffImage(File file, int band) executes this: RenderedOp image = JAI.create(tiff, params); For the single-image tiffs described above, this call returns the equivalent of an empty image: (PlanarImage[minX=0 minY=0 width=0 height=0 tileGridXOffset=0 tileGridYOffset=0 tileWidth=0 tileHeight=0 sampleModel=null colorModel=null]) It's my opinion that this should somehow throw an exception either through JAI or have this condition be trapped by BASE because, well, the call CLEARLY failed. Can a developer have this throw an exception? It would make image parsing problems MUCH easier to find. RIGHT! Let's return to the problem of the images. As a user of Genepix, I cannot change it's exporting behavior. However, when I use 'tiffsplit' on the commandline to split the GenePix multi-image tiff and import each image (full-size, not preview) into BASE2 separately everything works. This implies that there is not a fundamental problem with the individual GenePix images (as found in the multi-image tiff). BASE1 had a feature in 'Create Spot Images' that allowed you to specify: 'Index of ch1 TIFF' 'Index of ch2 TIFF' Can you please bring back this feature in BASE2? In the meantime I will modify our local copy to do this without prompting. Thanks for your efforts! Chad Matsalla Plant Biotechnology Institute, National Research Council of Canada Saskatoon, Saskatchewan, Canada - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] genepix 6.0/6.1, multi-image tif-s, spot finding,
Nicklas wrote: Nice work! It seems like you have spent some time on this. I certainly have. JAI isn't exactly intuitive. Do you have some code and/or images that can be useful for us? I certainly do. I basically check to see if the user provided one and only one image and if so call 'loadMultiImageTiff' with the indices of the desired images: (in SpotImages.mergeColorImages()) : HashMapString,RenderedOp images = loadMultiTiff(red,index_635,index_532); sourceImages[0] = images.get(635); sourceImages[1] = images.get(532); I'll clean up my code this weekend. Would you like me to send you a diff of some sort? I wrote a Test class based on yours and heavily altered (in parts) SpotImages.java. I certainly have data I can 'lend' you for testing (please email for a url). I'll also ask the Molecular Devices people for a dataset that we can put into the svn for testing.[1] I think that adding parameters for which image to use in a multi-image TIFF should be easy to implement. This can be done earliest at the 2.4 release. Great. Another point: The 'zip' that contains spot images isn't a zip. It looks like a zip, but this[2] is what I see when I try to open it in osx. Can you provide a hint as to how to open it? Thanks! Chad Matsalla Plant Biotechnology Institute, National Research Council of Canada Saskatoon, Saskatchewan, Canada [1] I can't do that with these images - their content is proprietary. [2] chad$ file 20th.zip 20th.zip: Zip archive data, at least v2.0 to extract chad$ zip -v ... This is Zip 2.3+CAN-2004-1010 (November 29th 1999), by Info-ZIP. ... chad$ unzip 20th.zip Archive: 20th.zip End-of-central-directory signature not found. Either this file is not a zipfile, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive. unzip: cannot find zipfile directory in one of 20th.zip or 20th.zip.zip, and cannot find 20th.zip.ZIP, period. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] GROUP clause error
Gretings! I see this as well. It's because this query: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY COUNT(*) DESC should say: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY mapCount DESC Hm. For mysql4, anyway. Any ideas on how this can be repaired for people who are bound to mysql4? Chad Matsalla - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] base-2.3.2 and exporting basefiles - the last line of the bioassay set is absent
Greetings! I've discovered a problem with exporting BASEfiles. I discovered this while trying to run the BASE1PluginExecuter and unsurprisingly found the same problem when trying to export data from a BioassaySet. The problem is that the last row of data is absent from the export. Here's what I observered: 1. The Raw Bioassay has 31200 rows. When I go to the 'Raw Bioassay' page, 'Raw Data' page and 'Export' it I get all of the rows as a tab-delimited text file. Yay! 2. I go Experiments-Chad's Experiment-Bioassay Sets and click 'Export Data', select BASEfile and these parameters: Average on reporters: false Export as matrix or serial basefile: Serial Basefile Fields: Int ch1, Int ch2, position Reporter: Reporter ID, Reporter Name The last row I see exported has the position 31199. Row 31200 is absent. A blank line is at the end of this file. 3. Do everything the same as (2) but select 'Normal Basefile'. The last row I see exported has the position 31199. Row 31200 is absent. No blank line is at the end of this file. Thank you for your help, Chad Matsalla Plant Biotechnology Institute Saskatoon, Saskatchewan - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] can't reconfigure a base1 plugin
Hi All!
So I was intrigued by the problem described in a previous post with the
same subject as this one. I went into the source and put a println above
here: (around line 366 of Base1PluginExecutor)
File f = (File) request.getParameterValue(fileParameter.getName());
System.out.println(File requested is (+f+));
if (f != null)
{
if (f.isInDatabase()) f = File.getById(dc, f.getId());
And to my astonishment I saw this in my console:
File requested is (File[id=4509; name=r-debug.txt])
When I looked closer it seems that occasionally a value appeared in the
box by default but was only visible when you clicked the 'File'
parameter on the left.
So it seems there is no problem. Other users might need to watch out for
that phenomenon, though.
Yippee!
Chad Matsalla
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[base] problems with my trashcan
Nicklas wrote: Are you logged in as the user that is the owner of the experiment? I am logged in as root. Shouldn't root be able to delete anything? Chad Matsalla - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Data cube has already been committed
Greetings All! Is there anything that I can so about this error? I'm completely stuck. I don't really know what a data cube is or how it could have already been committed. Do I need to delete the experiment or something? I can't help but wonder if it has something to do with my trashcan problems. Is there some sort of database validator that I can run to test if my databases are consistent? They are large - 10G. Chad Matsalla - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] can you give spot images a css class?
Greetings!
I'm using base-2.9.2 on tomcat 6.0.18 in Geronimo 2.1.3.
We use Combimatrix 90k arrays and the spot images are tiny (12px). I want to
use CSS to make them bigger. Can you give the spot images a class of
something like 'spotimage' so I can do that?
At the moment I'm using
#rawdata td.cell img { width: 30px; }
and it works but it feels ... wrong. I'd prefer
.spotimage { width: 30px; }
Thanks,
Chad Matsalla
Plant Biotechnology Institute
Saskatoon, Saskatchewan, Canada
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