Difference between revisions of "Allocating Memory in MIPAV"
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Revision as of 17:10, 8 February 2012
Contents
Allocating memory in MIPAV
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.
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
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
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, write is synonymous with save.
testing
File format |
Extencion |
Supports |
Open |
Save |
Does not support |
---|---|---|---|---|---|
AFNI |
header HEAD, data BRIK |
See [MIPAV_AppCSupportedFormats.html#1330966 "AFNI" ] |
Y |
Y[#1330166 1] |
|
header HDR, data IMG |
See [MIPAV_AppCSupportedFormats.html#1259280 "Analyze files" ] |
Y |
Y |
TBD | |
Apple Macintosh |
PICT |
TBD. |
Y |
Y |
|
ASCII text |
TXT |
MIPAV defined ascii text surface format. The text surface file records the triangle mesh vertices, normal and connectivity. |
Y |
Y |
|
Audio Video Interleave |
AVI |
Uncompressed RLE8 See [MIPAV_AppCSupportedFormats.html#1331497 "Audio Video Interleave (AVI) files" ] |
Y |
Y[#1330210 2] |
TBD |
BFLOAT |
BFLOAT |
TBD. |
Y |
Y |
|
d3pro, reco, acqp, 2dseq |
See [MIPAV_AppCSupportedFormats.html#1259300 "Bruker data format" ] |
Y |
Y |
TBD | |
Cheschire |
IMC, IMG |
TBD |
Y |
Y |
TBD |
Cheschire Overlay |
OLY |
TBD |
Y |
N |
|
DCM, IMA |
See [MIPAV_AppCSupportedFormats.html#1259305 "Digital Imaging and Communications in Medicine (DICOM) files" ] |
Y |
Y |
TBD | |
DM3 |
DM3 |
TBD |
|||
FTS |
See [MIPAV_AppCSupportedFormats.html#1259307 "FITS" ] |
Y |
Y |
TBD | |
FreeSurfer surface |
See [MIPAV_AppCSupportedFormats.html#1259310 "FreeSurfer image and surface files" ] |
Y |
Y |
TBD | |
FreeSurfer image |
COR |
INFO for the header file and NNN for each slice where NN is the number of the slice |
Y |
Y |
TBD |
SIG |
See [MIPAV_AppCSupportedFormats.html#1259314 "GE - Genesis 5X and LX" ] |
Y |
Y |
TBD | |
GE Signa 4.x |
GEDNO |
TBD |
Y |
N |
TBD |
ICS, IDS |
See [MIPAV_AppCSupportedFormats.html#1259321 "ICS (Image Cytometry Standard)" ] |
Y |
Y |
TBD | |
HDR |
TBD |
Y |
Y |
TBD | |
Laser Scanning Microscope (Zeiss) |
LSM |
See [MIPAV_AppCSupportedFormats.html#1259334 "Laser Scanning Microscope (Zeiss)" ] |
Y |
N |
TBD |
LIFF |
LIFF |
See [MIPAV_AppCSupportedFormats.html#1259338 "LIFF" ] |
TBD | ||
Magnetron Vision |
IMA |
TBD |
Y |
Y |
|
MAP |
MAP |
TBD |
Y |
N |
|
Medical Image Network Common Data Form (including ROIs) |
MNC |
See [MIPAV_AppCSupportedFormats.html#1259341 "Medical Image NetCDF (MINC) files" ] |
Y |
Y |
TBD |
MEDIVISION |
BIN |
TBD |
Y |
Y |
TBD |
MetaMorph Stack |
STK |
TBD |
Y |
Y |
TBD |
Medical Research Council |
MRC |
See [MIPAV_AppCSupportedFormats.html#1259345 "Medical Research Council (MRC)" ] |
Y |
Y |
TBD |
MGH/MGZ volume format |
MGH, MGZ |
MGH for uncompressed storage; MGZ or.MGH.GZ for compressed storage |
Y |
Y |
TBD |
MICRO-CAT (LOG) |
LOG, CT |
See [MIPAV_AppCSupportedFormats.html#1259347 "MICRO-CAT" ] |
TBD | ||
MINC 1.0, 2.0 |
MNC |
See [MIPAV_AppCSupportedFormats.html#1259341 "Medical Image NetCDF (MINC) files" ] |
Y |
Y |
|
MIPAV-specific file formats | |||||
MIPAV LUT |
LUT |
See [MIPAV_AppCSupportedFormats.html#1259356 "MIPAV (LUT) files" ] |
|||
MIPAV MTX |
MTX |
See [MIPAV_AppCSupportedFormats.html#1259359 "MIPAV (MTX) files" ] |
|||
MIPAV PLT |
PLT |
See [MIPAV_AppCSupportedFormats.html#1259365 "MIPAV (PLT) files" ] |
|||
MIPAV SUR |
SUR |
See [MIPAV_AppCSupportedFormats.html#1342166 "MIPAV (SUR) files" ] |
|||
MIPAV TXT |
TXT |
See also [MIPAV_AppCSupportedFormats.html#1343221 "MIPAV text file format" on page 583] |
|||
MIPAV VOI |
VOI, XML |
See [MIPAV_AppCSupportedFormats.html#1259371 "MIPAV (VOI) files" ] |
|||
MIPAV XML |
XML |
Full support, see [MIPAV_AppCSupportedFormats.html#1259376 "MIPAV XML" ] |
N/A | ||
End of MIPAV-specific file formats | |||||
MRC |
MRC |
TBD |
Y |
Y |
|
Nearly Raw Raster Data (NRRD) |
1 file with extension of.NRRD or 2 files with extension of.NHDR for header file and.RAW,.TXT,.HEX,.RAW.GZ, or.RAW.BZ2 for data file |
Y |
Y |
||
NIFTI |
2 files with header HDR and data IMG; or a single file.NII |
See [MIPAV_AppCSupportedFormats.html#1259382 "NIFTI" ] |
Y |
Y |
|
OSM |
WU |
TBD |
|||
Optical Coherence Tomography |
TMG |
TBD |
Y |
Y |
|
Phillips |
PAR and PARV2 for header files and REC and FREC for data files |
PAR and PARV2 for header files and REC and FREC for data files See [MIPAV_AppCSupportedFormats.html#1332108 "Phillips PAR/REC" ] |
Y |
Y |
TBD |
PICT |
PICT |
Encoding of black and white images as bitmap mode PICTs. Encodes grayscale images from 2 to 8-bits as palette mode (PICT format does not have grayscale mode). Encodes palette images as palette mode PICTS, encodes other images as a 24-bit 3 component directed bits PICT. Decoding of black and white and up to (and including) 32-bit color PICT images. Also supports the decoding of compressed PICT images. |
Y |
Y |
N/A |
Polygon File Format or Stanford Triangle Format |
PLY |
See [MIPAV_AppCSupportedFormats.html#1342572 "Polygon File Format" on page 587] |
Y |
Y |
|
QT |
See [MIPAV_AppCSupportedFormats.html#1259408 "QuickTime-Apple" ] |
Y |
Y |
TBD | |
RAW |
See [MIPAV_AppCSupportedFormats.html#1259413 "Raw data files" ] |
Y |
Y |
TBD | |
Siemens CT |
Old Siemens Somatom CT format (DR3) |
Y |
Y |
TBD | |
IMA |
See [MIPAV_AppCSupportedFormats.html#1259422 "Siemens - Magnetom Vision" ] |
Y |
Y |
TBD | |
Siemens MicroCAT |
LOG, CT |
See also [MIPAV_AppCSupportedFormats.html#1259347 "MICRO-CAT" ] |
Y |
Y |
|
SPM |
SPM |
TBD |
Y |
Y |
|
STL |
STLA, STLB |
See also [MIPAV_AppCSupportedFormats.html#1341589 "STL (ASCII and Binary)" on page 590] |
Y |
Y |
|
Truevision Graphics Adapter |
Encodes index color images in an uncompressed TGA palette format; encodes other images in an uncompressed 24-bit TGA format. Decodes black and white, palette, true color uncompressed images. Decodes 16-bit, 24-bit, and 32-bit true color variants (can include loading of alpha channel). |
Y |
Y |
N/A | |
Washington University OSM dataset Structure |
WU |
TBD |
Y |
Y |
TBD |
Common raster file formats | |||||
Adobe Photoshop |
PSD |
Encoding of bitmap, grayscale, RGB, and index mode images. Also supports the encoding of RLE compression for all image variants. Decoding of Adobe Photoshop v 2.5 images (and above) with the following modes: bitmap, grayscale, palette, and RGB. |
Y |
Y |
Alpha saving |
PIC |
See [MIPAV_AppCSupportedFormats.html#1259296 "BIORAD" ] |
Y |
Y |
TBD | |
GIF |
Decoding of interlaced images and images with a transparency information set. See also [MIPAV_AppCSupportedFormats.html#1259318 "Graphics Interchange Format (GIF) files" ] |
Y |
N |
Encoding of a GIF file Decoding of multiframe GIFs using the multiframe load mechanism | |
Joint Photographics Experts Group |
See [MIPAV_AppCSupportedFormats.html#1259331 "Joint Photographic Experts Group (JPEG/JFIF) files" ] |
Y |
Y |
TBD | |
Microsoft Windows Bitmap |
BMP, DIB |
Encoding of Index Color Model images as uncompressed BMP palette formats. Other Color Model images are encoded as uncompressed 24-bit BMP formatted files. Decoding of BMP version 2.x through 4.x files. Also supports the encoding of OS/2 variant files. Supports the encoding of true color and palette images, as well as Run-Length Encoding 8 (RLE8) and RLE4 images. See [MIPAV_AppCSupportedFormats.html#1259350 "Microsoft Windows Bitmap (BMP) files" ] |
Y |
Y |
Decoding of old versions of BMP files (prior to version 2.x) |
Microsoft Windows Cursor |
CUR |
Y |
Y |
||
Microsoft Windows icon |
ICO |
Y |
Y |
||
PC Paintbrush File Format |
Encoding of PCX files including uncompressed and RLE-compressed support. Full support for decoding of PCX files. See [MIPAV_AppCSupportedFormats.html#1259396 "PC Paintbrush (PCX) files" ] |
Y |
Y |
N/A | |
PNG |
Encodes index images as palette PNG images. Also encodes grayscale formatted images (which include grayscale and direct color) with bit masks saved in grayscale file format. Direct color and RGB are encoded as RGB images with an alpha mask (if mask is available from the image). 16-bit depth images are truncated to 8-bit depth when the image is loaded. Decoding of palette, grayscale, and true color images. Also supports the transparency chunk for palette based images. |
Y |
Y |
Some extension chunks (such as ALPHA) | |
Sun Raster |
RS, RAS |
Encodes 8-bit index color images with or without RLE compression or RGB format for other color models. Decoding of 4, 8, 16, 24, and 32-bit images. Supports the decoding of the old, standard, byte encoded, RGB, TIFF, and IFF format type. See [MIPAV_AppCSupportedFormats.html#1259426 "Sun Raster (RS) files" ] |
Decoding of RAW color map or experimental type images | ||
TARGA |
TGA |
See also [MIPAV_AppCSupportedFormats.html#1339888 "TARGA" on page 591] |
Y |
Y |
|
Tag Image File Format |
TIF, TIFF |
See also [MIPAV_AppCSupportedFormats.html#1259429 "Tag Image File Format (TIFF) files" ] |
Y |
Y |
Tiled |
X BitMap |
XBM |
Encoding of 2-color XBM images. Fully supports the decoding of XBM formatted files. |
N/A | ||
X PixMap |
XPM |
Encoding of XPM palette images. Fully supports the decoding of XPM formatted files. |
Y |
Y |
Decoding of image files with 3 or more characters per pixel/voxel |
End of common raster file formats | |||||
Surface description file formats | |||||
ASCII text |
TXT |
Y |
Y |
||
ASCII Poly |
POLY |
See also [MIPAV_AppCSupportedFormats.html#1340689 "POLY" ] |
Y |
Y |
|
ASCII PLY |
PLY |
See also [MIPAV_AppCSupportedFormats.html#1342572 "Polygon File Format" on page 587] |
|||
ASCII STL |
STL |
See also [MIPAV_AppCSupportedFormats.html#1341589 "STL (ASCII and Binary)" ] |
Y |
Y |
|
Binary STL |
STLB |
See also [MIPAV_AppCSupportedFormats.html#1341589 "STL (ASCII and Binary)" ] |
Y |
Y |
|
Legacy VTK |
VTK |
See also [MIPAV_AppCSupportedFormats.html#1341644 "Legacy VTK" ] |
Y |
Y |
|
MIPAV TXT |
TXT |
See also [MIPAV_AppCSupportedFormats.html#1343221 "MIPAV text file format" on page 583] |
Y |
Y |
|
MIPAV surface files |
SUR |
See also [MIPAV_AppCSupportedFormats.html#1342166 "MIPAV (SUR) files" ] |
Y |
Y |
|
VRML |
WRL |
See also [MIPAV_AppCSupportedFormats.html#1341826 "VRML" ] |
Y |
Y |
|
VTK XML |
VTP |
See also [MIPAV_AppCSupportedFormats.html#1341809 "VTK XML surface" ] |
Y |
Y |
|
XML surface |
XML |
See also [MIPAV_AppCSupportedFormats.html#1343346 "XML surface" ] |
Y |
Y |
[#1330167 1]MIPAV does not save extra information with the AFNI file. It only does the "bare minimum." [#1330214 2]AVIs are saved with encoding options: run-length, MPEG, MPEG-4, QuickTime. However, MIPAV requires the Java Media Framework, which is installed with MIPAV.
|
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. |
{| align="center" |
|- | Select All | Selects all image types. |- | Clear | rowspan="1" colspan="2" | Removes selection. |- | OK | rowspan="1" colspan="2" | Applies the image type selection to MIPAV. |- | Cancel | rowspan="1" colspan="2" | Disregards any changes you made in this dialog box and closes the dialog box. |- | rowspan="1" colspan="3" |
|}
Opening image files
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An option on the Open Image dialog box ([MIPAV_QuickStart.html#2389196 Figure 8]), which appears after you select File > Open Image(A), is Open as multifile. This option lets you open the image as a multifile.
|}
check the files types listed in Files of Type (showing in [MIPAV_QuickStart.html#2614455 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.
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 [MIPAV_QuickStart.html#1020845 Figure 10].
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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 [MIPAV_QuickStart.html#1013570 "Using platform-specific Open and Save dialog boxes" on page 74].
Loading image files
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