Grab With Note Plugin Help


This plugin is designed to grab the display in 3dmod top Slicer or Zap window, and save it as an image with text note and Slicer parameters (if it's a Slicer window) or the center position (if it's a Zap window). The top window is the one with the most recent activity. Select which kind of window you want to grab with the Slicer and Zap radio buttons. The snapshot type is controlled by the JPEG, PNG, and TIFF buttons. The notes will include the image filename; if multiple files are loaded, the name of the current file is shown.

Display Features
When this plugin is open, scale bars will be displayed in the image windows even when the Scale Bar dialog is not open, provided that Show and record scale bar is checked. This will be turned on by default if the image or model file appears to have a pixel size defined.

Another special feature when this plugin is open is that snapshots can be of the full window area, even when a rubber band is drawn in the window. This happens whenever Always snapshot whole window is checked. Thus, you can use a rubber band to outline an area of interest in either type of window. The lasso in the Zap toolbar can also be used for outlining a feature.

This plugin lets you draw multiple arrows in either type of window. The first time you press Add Arrow, it acts just the same as using the arrow button in the window's toolbar. However, you can press it again and draw another arrow, without losing the previously drawn arrows. Press Clear Arrows to remove all arrows from the top window of the selected type. The arrows will also go away when this dialog is closed.

Text Box for Notes Text that you type in the box will appear below the filename and other standard information that is added to the snapshot. The text that you enter will be line-wrapped, but you can use "Enter" to break lines. Adding a note is optional.

Save Image
This button saves the grabbed image with note in the standard 3dmod snapshot directory with default snapshot naming.

Save to Database
If you are using Caltech Tomography Database, this button is present and you may use it to add the grabbed image with note to the database and attach it with a given tilt series ID. A database configuration file must be present.

Setup of Database Image Path on Server
The directory <Database path>/Caps/ should be created by the database administrator and it should be writable. All images are saved under <Database path>/Caps/ with file name formats <tilt series id>_<zap or slicer><file id>.jpg

Setup of Configuration File on User Computer
A configuration file should be located at $IMOD_CALIB_DIR/grabDatabase.ini. By default $IMOD_CALIB_DIR is /usr/local/ImodCalib/ . The configuration file should have 5 lines:
      dbpath '/path/to/database/'
      dbhost 'ip_address_of_host'
      dbname 'database_name'
      dbuser 'username'
      dbpass 'password'
where in each case the text should be contained in single quotes as shown.

Hot Keys
[Shift+W]    Save image with note in 3dmod snapshot directory
[W]    Save image with note in the Caltech Tomography Database. The image will be attached to an existing database tilt series ID. See more details above.
[Ctrl+Shift+W]    Save image with note in the Caltech Tomography Database and in 3dmod snapshot directory

This plugin was created by Jane Ding (hding<at>caltech<dot>edu) with refinements by David Mastronarde.