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
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.
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.
- image type - To save space in the database, only JPEG or PNG can be saved
to the database.
- tilt series id - You may manually input a "Tilt Series Database ID". If
the 3D image opened by 3dmod is under a standard path in the database (has
a format of <Database path>/< tilt series id>/... ), or it is downloaded
from the database with "Download Files with Database Structure", the
tilt series id will be automatically detected.
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:
where in each case the text should be contained in single quotes as shown.
In addition, it is possible to specify a different Qt database driver by
providing the name in capitals (the default name is QMYSQL for the
libqsqlmysql driver). To use the libqsqlite driver, add the line
Save image with note in 3dmod snapshot directory
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.