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User Story #4317 (closed)

Opened 13 years ago

Closed 12 years ago

ROI model-database alignment

Reported by: wmoore Owned by:
Priority: major Milestone: OMERO-4.4
Component: Specification Keywords: n.a.
Cc: jburel, ajpatterson, jamoore Story Points: n.a.
Sprint: n.a. Importance: n.a.
Total Remaining Time: 0.0d Estimated Remaining Time: n.a.

Description (last modified by wmoore)

Some differences between what the model supports and what the database contains or clients write to DB.

ROI model: http://www.ome-xml.org/browser/Documentation/Graphics/ROI/2010-04/Ome-ROI-overview-standard.png

Looking at the Shape table:

  • Does not have 'marker' column ('arrow' etc in the model)
  • 'path' is not supported
  • Line is not supported by measurement tool. Uses polyline.
  • 'transform' model says this should be a String with 6 numbers. Database contains strings such as "rotate(0, 100,50)"
  • font weight (not used?)
  • 'Verdana' in DB, not in model.

Measurement tool behavior

 Attribute   Write        Read                Model
-----------------------------------------------------
FontStyle     'italic'      no          'Bold', 'Italic', BoldItalic, Regular
FontSize      no           yes                 int
FontFamily   'VERDANA'    only 'Courier' ignores 'Helvetica', 'Arial', TimesNewRoman
LineI       polyline     line or polyline
  • FontFamily is not editable - 'VERDANA' by default, FontStyle is ALWAYS saved as 'italic' regardless of existing value.

Database shape table:

          Column          |          Type          | Modifiers 
--------------------------+------------------------+-----------
 discriminator            | character varying(31)  | not null
 id                       | bigint                 | not null
 permissions              | bigint                 | not null
 fillcolor                | integer                | - no e.g.
 fillrule                 | character varying(255) | - no e.g.
 fontfamily               | character varying(255) | 
 fontsize                 | integer                | 
 fontstretch              | character varying(255) | 
 fontstyle                | character varying(255) | 
 fontvariant              | character varying(255) | 
 fontweight               | character varying(255) | 
 g                        | character varying(255) | 
 locked                   | boolean                | 
 strokecolor              | integer                | 
 strokedasharray          | character varying(255) | 
 strokedashoffset         | integer                | 
 strokelinecap            | character varying(255) | 
 strokelinejoin           | character varying(255) | 
 strokemiterlimit         | integer                | 
 strokewidth              | integer                | 
 thec                     | integer                | 
 thet                     | integer                | 
 thez                     | integer                | 
 transform                | character varying(255) | 
 vectoreffect             | character varying(255) | 
 version                  | integer                | 
 visibility               | boolean                | 
 points                   | text                   | 
 textvalue                | text                   | 
 cx                       | double precision       | 
 cy                       | double precision       | 
 anchor                   | character varying(255) | 
 baselineshift            | character varying(255) | 
 decoration               | character varying(255) | 
 direction                | character varying(255) | 
 glyphorientationvertical | integer                | 
 writingmode              | character varying(255) | 
 x                        | double precision       | 
 y                        | double precision       | 
 d                        | text                   | 
 height                   | double precision       | 
 rx                       | double precision       | 
 width                    | double precision       | 
 bytes                    | bytea                  | 
 ry                       | double precision       | 
 x1                       | double precision       | 
 x2                       | double precision       | 
 y1                       | double precision       | 
 y2                       | double precision       | 
 creation_id              | bigint                 | not null
 external_id              | bigint                 | 
 group_id                 | bigint                 | not null
 owner_id                 | bigint                 | not null
 update_id                | bigint                 | not null
 roi                      | bigint                 | not null
 pixels                   | bigint                 | 
 roi_index                | integer                | not null
 pg_geom                  | polygon                | 
  • Why is textValue not an attribute of the omero.model.Shape superclass - it is implemented in every subclass. FontFamily?, fontSize etc are attributes of Shape superclass.

Change History (21)

comment:1 Changed 13 years ago by wmoore

omero=# select textvalue, fillcolor, fillrule, fontfamily, fontsize, fontstretch, fontstyle, fontvariant, fontweight from shape order by id desc;
     textvalue     | fillcolor  | fillrule | fontfamily | fontsize | fontstretch | fontstyle | fontvariant | fontweight 
-------------------+------------+----------+------------+----------+-------------+-----------+-------------+------------
                   | 1073741824 |          | VERDANA    |       12 |             | italic    |             | bold
 Text-not-showing! | 1090453504 |          | VERDANA    |       12 |             | italic    |             | bold
 Cool rectangle    | 1073741824 |          | VERDANA    |       12 |             | italic    |             | bold

comment:2 Changed 13 years ago by wmoore

omero=# select g, locked, fillcolor, fillrule, strokecolor, strokedasharray, strokedashoffset, strokelinecap, strokelinejoin, strokemiterlimit, strokewidth from shape order by id desc;
 g | locked | fillcolor  | fillrule | strokecolor | strokedasharray | strokedashoffset | strokelinecap | strokelinejoin | strokemiterlimit | strokewidth 
---+--------+------------+----------+-------------+-----------------+------------------+---------------+----------------+------------------+-------------
   | f      | 1073741824 |          |  -993737532 |                 |                  |               |                |                  |           1
   | f      | 1090453504 |          |  -989856000 |                 |                  |               |                |                  |           1
   | f      | 1073741824 |          |  -993737532 |                 |                  |               |                |                  |           1
Last edited 13 years ago by wmoore (previous) (diff)

comment:3 Changed 13 years ago by jburel

  • Cc jmoore added

comment:4 Changed 13 years ago by wmoore

omero=# select discriminator, transform, vectoreffect, version, visibility, anchor, baselineshift, decoration, direction, glyphorientationvertical, writingmode from shape order by id desc;
 discriminator |                    transform                     | vectoreffect | version | visibility | anchor | baselineshift | decoration | direction | glyphorientationvertical | writingmode 
---------------+--------------------------------------------------+--------------+---------+------------+--------+---------------+------------+-----------+--------------------------+-------------
 text          | none                                             |              |         |            |        |               |            |           |                          | 
 text          | none                                             |              |         |            |        |               |            |           |                          | 
 polyline      | none                                             |              |         |            |        |               |            |           |                          | 
 polygon       | none                                             |              |         |            |        |               |            |           |                          | 
 rect          | none                                             |              |         |            |        |               |            |           |                          | 
 rect          | none                                             |              |         |            |        |               |            |           |                          | 
 rect          | none                                             |              |         |            |        |               |            |           |                          | 
 ellipse       | translate(245.74999251304587 209.50000561479504) |              |         |            |        |               |            |           |                          | 

comment:5 Changed 13 years ago by wmoore

'Line' vv 'Polygon'

discriminator |                                                                                points                                                                                 
---------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
 text          | 
 polyline      | points[137,433, 183,260] points1[137,433, 183,260] points2[137,433, 183,260] mask[0,0] 
 polygon       | points[472,112, 473,162, 378,91, 437,51, 509,68] points1[472,112, 473,162, 378,91, 437,51, 509,68] points2[472,112, 473,162, 378,91, 437,51, 509,68] mask[0,0,0,0,0] 
 rect          | 

comment:6 Changed 13 years ago by wmoore

omero=# select discriminator, d, bytes, roi, pixels, roi_index, pg_geom from shape order by id desc;
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied
 discriminator | d | bytes | roi | pixels | roi_index | pg_geom 
---------------+---+-------+-----+--------+-----------+---------
 polyline      |   |       | 905 |        |         2 | 
 polyline      |   |       | 905 |        |         1 | 
 text          |   |       | 907 |        |         0 | 
 text          |   |       | 906 |        |         0 | 
 polyline      |   |       | 905 |        |         0 | 

... older
 ellipse       |   |       | 646 |        |         1 | ((0,0))
 ellipse       |   |       | 646 |        |         0 | ((0,0))
 ellipse       |   |       | 645 |        |         1 | ((0,0))
 ellipse       |   |       | 645 |        |         0 | ((0,0))

comment:7 Changed 13 years ago by wmoore

  • Description modified (diff)

comment:8 Changed 13 years ago by wmoore

  • Description modified (diff)

comment:9 Changed 13 years ago by wmoore

  • Description modified (diff)

comment:10 Changed 13 years ago by wmoore

  • Description modified (diff)

comment:11 Changed 13 years ago by wmoore

  • Description modified (diff)

comment:12 Changed 13 years ago by wmoore

  • Description modified (diff)

comment:13 Changed 13 years ago by wmoore

  • Type changed from Task to User Story

comment:14 Changed 13 years ago by agilo

  • Status changed from new to accepted

Updated status, related task in progress

comment:15 Changed 13 years ago by jburel

  • Cc dzmacdonald added

comment:16 Changed 13 years ago by jburel

Meeting 21/02/11 attendance: J-M, Andrew, Donald, Will
Topic align model and clients

  • Review Font related attributes
  • Transform in Model, Keep it as it is. Client to replace rot, translate. Implication on upgrade script.
  • Polyline, no changes to implementation. Indicates the model and DB diverge.
  • Remove polygon => polyline close = true. Make sure it is in the DB.
  • No support for line for now.

comment:17 Changed 13 years ago by jburel

  • Milestone changed from OMERO-Beta4.3 to Unscheduled

comment:18 Changed 13 years ago by ajpatterson

  • Cc ajpatterson added; jburel removed
  • Owner changed from ajpatterson to jburel

Story passed to JM as remaining tickets are his.

comment:19 Changed 13 years ago by jburel

  • Cc jburel added; dzmacdonald removed
  • Owner jburel deleted

Not exactly true. No owner to the story, transformations will have to be supported by all the clients for example.

comment:20 Changed 13 years ago by ajpatterson

  • Component changed from Model to Specification

comment:21 Changed 12 years ago by jburel

  • Milestone changed from Unscheduled to OMERO-Beta4.4
  • Resolution set to fixed
  • Status changed from accepted to closed

Discussed during February meeting, All tasks completed, closing.

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