Difference between revisions of "Allocating Memory in MIPAV"
(→Opening image files) |
(→MIPAV window) |
||
Line 467: | Line 467: | ||
|+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 10. Expanded MIPAV window showing toolbars, image slider, and more menus after the first image is opened. See also "MIPAV toolbars". | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 10. Expanded MIPAV window showing toolbars, image slider, and more menus after the first image is opened. See also "MIPAV toolbars". | ||
|- | |- | ||
− | |||
− | |||
| | | | ||
[[Image:ExpandedMIPAVWindow.jpg|center]] | [[Image:ExpandedMIPAVWindow.jpg|center]] | ||
− | |}<br clear="all" /><br / | + | |}<br clear="all" /><br /> |
Revision as of 18:34, 16 February 2012
When you run MIPAV for the first time you must specify the amount of memory that you would like to allocate, so that MIPAV can take the full advantage of the memory resources available in your machine.
Figure 3. Change Java-Runtime Memory Allocation dialog box
You must restart of MIPAV for the changes to take effect. To exit MIPAV, select File > Exit. Then, restart the software.
Contents
To allocate additional memory
The first step is to view how much memory is currently being used and to free needlessly reserved memory. Then, if necessary, you may need to allocate additional memory.
Figure 4. Memory Monitor dialog box
If you need more memory, you can allocate virtual memory or disk swap space if there is free space on your hard drive. For instructions on how to do this, refer to the documentation for your system. If you cannot assign more virtual memory or disk swap space, you may need to install additional memory.
As Java-based programs run, they often leave old variables, objects, or constructors in memory. For instance, if you delineate a VOI, the coordinates of the contours may remain in memory even after you close the image. Java provides a method called the garbage collector (or memory recycling) that automatically freeing objects that are no longer referenced by the program and clears all unnecessarily reserved memory. Generally, the software does this automatically when free memory becomes very limited. However, you can run the garbage collector at any time to free memory by clicking the Memory Usage button. Refer to Figure 5.
Repeat the steps described in "Allocating memory in MIPAV".
Figure 5. Running the garbage collector to free the memory in MIPAV
Opening and loading image files
MIPAV displays images in windows, or frames, that you can move or arrange around the desktop (Figure 6). You can display as many image datasets as needed as long as your computer has enough allocated memory.
Note: The amount of memory required depends on the number of image datasets that are open and the size of each image file. For more information, refer to "Managing memory resources".
You can either open or load an image file. When you open an image file, MIPAV displays the image in a new image window. Loading an image file imports the file into an image window in which another image file is open. In other words, two image files share a common image window.
Understanding image windows
An image window Figure 6 consists of a title bar and an image itself.
Figure 6. An image window
The title bar displays:
- the image file name, e.g. "3DHead";
- the number of the current slice and the total number of slices in the dataset, e.g. 62/124;
- the magnification level, e.g. M:1.0.
- The number of the current slice is also shown in the lower left corner of the image.
You can move an image window around your desktop by clicking the title bar and dragging the window to a new location.
Sometimes, depending on the view, a toolbar or menu bar also appears in the image window. For example, the image window using the light box view contains a toolbar and menu bar. See also Displaying images using the lightbox view.
Image A and Image B
In MIPAV, the first image opened in an image window (see "Understanding image windows")") is referred to as Image A. When you load, or import, a second image in the same window, MIPAV refers to the second image as Image B.
Supported formats
You can use MIPAV to open or load files of a variety of medical and generic graphics and multimedia file formats. Table 1 lists the format, extension, and whether MIPAV can read or write files of a particular format. The extension, which is the last few characters of a file name including the period, indicates the file format. For example, in the file name DOE255.ima, the extension .ima indicates that the file is stored in DICOM format. In the table, the Read column indicates that MIPAV can display image files of a particular format. When a file is read, it is stored in main memory so that MIPAV can access it. The Write column means that MIPAV can copy the data from the memory to a storage destination, such as your hard disk. In this context, writeis synonymous with save.
For more information on file formats, the list of supported formats and other information, refer to Chapter 4 in the MIPAV User's Guide.
File formats that MIPAV can read and write
Manufacturer or Application |
Extensions |
Read |
Write |
---|---|---|---|
AFNI |
PSD |
Y |
Y |
AFNI |
HEAD, BRIK |
Y |
Y |
Analyze |
IMG |
Y |
Y |
Audio Video Interleave |
AVI |
Y |
Y |
BIORAD |
PIC |
Y |
N |
Bruker |
2dseq |
Y |
N |
Cheshire |
IMG or IMC |
Y |
Y |
DICOM |
DCM, IMA |
Y |
Y |
FITS |
FTS |
Y |
N |
FreeSurfer image |
COR |
Y |
N |
FreeSurfer surface (ASCII file) |
ASC |
Y |
N |
GE - Genesis 5X and LX |
SIG |
Y |
N |
Graphics Interchange File |
GIF |
Y |
N |
ICS (Image Cytometry Standard) |
ICS |
Y |
N |
Interfile |
HDR |
Y |
N |
Joint Photographics Experts Group |
JPEG, JPG |
Y |
Y |
Laser Scanning Microscope |
LSM |
Y |
Y |
Macintosh PICT |
PICT |
Y |
Y |
Medical Image Network |
MNC |
Y |
Y |
MICRO-CAT |
LOG |
Y |
N |
Microsoft Windows Bitmap |
BMP, DIB |
Y |
Y |
Medical Research Council |
MRC |
Y |
Y |
NIFTI |
Dual file (.HDR & .IMG) or single file (.NII) storage |
Y |
Y |
PC Paintbrush |
PCX, DCX, PCC |
Y |
Y |
Portable Network Graphic |
PNG |
Y |
Y |
QuickTime-Apple |
QT, MOV |
Y |
Y |
RAW |
RAW |
Y |
Y |
Siemens - Magnetom Vision |
IMA |
Y |
N |
Sun Raster |
RS, RAS |
Y |
Y |
Tag Image File Format |
TIFF |
Y |
Y |
Truevision Graphics Adapter |
TGA, VST, VDA, ICB, TPIC |
Y |
Y |
X BitMap |
XBM |
Y |
Y |
XML |
XML |
Y |
Y |
X |
PixMap |
Y |
Y |
Image Browser
You can select the image formats to display using the File > Open Image(A) > Image Browser menu. This opens the Choose Image Filter dialog box. In this dialog box, use the check boxes to select the image types which you would like to use in MIPAV. |
||
Select All |
Selects all image types. | |
Clear |
Removes selection. | |
OK |
Applies the image type selection to MIPAV. | |
Cancel |
Disregards any changes you made in this dialog box and closes the dialog box. |
Opening image files
The Open Image A from disk menu allows you to open an image which is stored on your hard drive (or network drive).
Open Image A menu (Figure 8]) provides you with additional options such as to open a single image file, or image sequence, or Leica series images - the images that were taken on a Leica microscope. You can also call Create Blank Image to create a blank image (refer to "Creating new images").
To open an image file or multifiles
An option on the Open Image dialog box (Figure 8), which appears after you select File > Open Image(A), is as multifile. This option lets you open the image as a multifile.
If you can't find the image,check the files types listed in Files of Type (showing in Figure 9) near the bottom of the dialog box. If the file type you are looking for does not appear in Files of Type, select All Files or All.
To form a 4D dataset in Analyze format, use Open as multifile to open a series of individual 3D Analyze, formatted, consecutively ordered images.For example, you can use Open as multifile to open an array of TIFF, JPEG, BMP, etc., files if their file names meet the following format: foo_001.tiff, foo_002.tiff, foo_003, etc. where foo is the name of the file.
MIPAV window
After the first image is opened, the MIPAV window changes. It includes more menus, the title bar displays more information, and tool bars appear. Because the MIPAV window is context sensitive, it displays or hides commands on the menus depending on the characteristics of the image file that is opened. If you opened a dataset file that contains more than one image, an image slice slider also appears. Refer to Figure 10.
If you prefer for MIPAV to use the style of Open and Save dialog boxes that are used by the operating system (e.g., Microsoft Windows, Unix, or Apple) on your computer, read the section on "Using platform-specific Open and Save dialog boxes".
Loading image files