TOMOGRAPHIC RECONSTRUCTION DATABASE

• Archiving using the database at Albany.

  • The web-based tomography database is designed to make it easy to keep track of the reconstructions. It also serves as a means for archiving all the necessary data from each reconstruction. It was written, and is maintained by Yu Chen.
  • Database location: From SGI workstations, use http://newton15-250/archivedb/search_t.asp.
    From PC's use http://luzon/archivedb/search_T.asp.

• Use of the database to find information on reconstructions.

  • Viewing a database page: You can select the page (i.e. project or reconstruction) you want to see from the default list, or you can generate a new list of pages based on a search. Any word(s) in the database text can be entered, and the search can be refined by any of the categories in the pull-down lists. You can also sort the listed pages according to any of the column headings of the list table, just by clicking on the heading.
  • Security: You can look at all the information on any page, and you can download any of the data which was archived, but editing the information or uploading more data requires a password.
  • Downloads: Click on the category of data you want to download. You will be prompted for where you want to put the downloaded file. Each category has only one associated file. In the case of the "raw data files", "marker files", and "procedure and other doc files", the original individual files will have been saved as a single zipped, compressed file. Accordingly, they will end in Z. After you download the zipped files, you will have to extract the original files.
  • Extracting zipped files:On the PC, you can use WINzip to extract any or all of the files desired. On the SGI, you will have to uncompress, then tar the file, which will restore all the original files. For "raw data files" type uncompress raw.tar.Z, then tar xvf raw.tar. For "marker files" type uncompress mrk.tar.Z, then tar xvf mrk.tar. For "procedure and other doc files" type uncompress misc.tar.Z, then tar xvf misc.tar.

• Entering information in the database

  • Entering a new reconstruction: Chose any existing database page, then click on the "Add" button. A blank database page will appear, ready to edit. When you choose the author from the list, you will have to use the password for that author for any future editing. If you know the password, you can change it any time. If you chose "other" as an author, the data will not be password protected.
  • Pasting text: You can paste large text blocks into the database windows. For example, you can paste in your whole "info.dat" text, if you are still making one in addition to the information you put in the database. You should paste in all the marker alignment results, from the data saved in the errors files. Although the windows are small in the edit mode, when the data is displayed your text will look as it did in your original window.
  • Saving text: Just click on the "Save" button. Important: You must first save the text before uploading any data files. If you put in all the text, then click on "Upload Image and Other Files" without having saved the text, the text will be blank.
  • To upload data files:Type the complete location path of the file you want to upload in the appropriate box. This information is just a record of where the files were originally. When you click on "Upload Image and Other Files", you can either again type (or paste) the complete location path of the files in the boxes provided, or you can use the browse utility provided. You don't have to fill in all the boxes at each upload.
  • Sample image:You should prepare a JPG image of a sample z-slice from the volume. It will be used on the database page as an aid in identifying the reconstruction. You will be asked for this file when you do an upload. A small version of the image will be shown when the database page is displayed. If you click on the small image, you will get the full-size image. So you could alternatively put a montage of several slices, or some slices and a model here.
  • Compressing/zipping files:The "raw data files", "marker files", and "procedure and other doc files" have to be zipped and compressed to only one file per category. On the PC, use WINzip. On the SGI, this can be done on a single command line. For example, to make a compressed file of all the raw images, use tar cvf - raw* | gzip > raw.tar.Z. For the marker document files, use tar cvf - d_* | gzip > mrk.tar.Z. For all the other document files (assuming you use the naming conventions suggested in this webpage), use tar cvf - A* S* b* c* i* | gzip > misc.tar.Z This will make the three files: raw.tar.Z, mrk.tar.Z, and misc.tar.Z which you can put into the database. If you wish to save more than one reconstructed volume, you can zip them together using tar cvf - vol* | gzip > vol.tar.Z
  • Archiving:Storing data in the database is an alternative to archiving it on a CDROM. The database is maintained and backed up with the intention of being a "safe" place for long-term archiving.