Difference between revisions of "Understanding Image Basics"
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+ | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 6pt; margin-right: 6pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#0023a9"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#0023a9">In this </font>'''</span>chapter<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#0023a9"> . . .</font>'''</span><br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 1pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#0023a9"> [MIPAV_ImageBasics.html#1220264 "Supported graphic formats overview" on page 151]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 1pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#0023a9"> [MIPAV_ImageBasics.html#1220316 "Understanding the MIPAV dimensionality and coordinate system" on page 151]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 1pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#0023a9"> [MIPAV_ImageBasics.html#1220350 "Data types" on page 153]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 1pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#0023a9"> [MIPAV_ImageBasics.html#1220413 "Headers" on page 153]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 1pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#0023a9"> [MIPAV_ImageBasics.html#1220437 "Endianness" on page 154]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 1pt; margin-left: 6pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#0023a9"> [MIPAV_ImageBasics.html#1220445 "Viewing and editing image attributes" on page 154]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div> | ||
This chapter also explains the dimensionality and coordinate system used by MIPAV, the data types MIPAV supports, the header offset information, endianness, and how to view and edit image attributes.It also provides a basic information about image file formats supported by MIPAV. More information about graphic file formats and the formats that MIPAV supports can be found in Appendix C: [MIPAV_AppCSupportedFormats.html#1256636 "Supported formats" ]. | This chapter also explains the dimensionality and coordinate system used by MIPAV, the data types MIPAV supports, the header offset information, endianness, and how to view and edit image attributes.It also provides a basic information about image file formats supported by MIPAV. More information about graphic file formats and the formats that MIPAV supports can be found in Appendix C: [MIPAV_AppCSupportedFormats.html#1256636 "Supported formats" ]. |
Revision as of 16:29, 7 February 2012
1Understanding Image BasicsIn this chapter . . .[MIPAV_ImageBasics.html#1220264 "Supported graphic formats overview" on page 151][MIPAV_ImageBasics.html#1220316 "Understanding the MIPAV dimensionality and coordinate system" on page 151][MIPAV_ImageBasics.html#1220350 "Data types" on page 153][MIPAV_ImageBasics.html#1220413 "Headers" on page 153][MIPAV_ImageBasics.html#1220437 "Endianness" on page 154][MIPAV_ImageBasics.html#1220445 "Viewing and editing image attributes" on page 154]This chapter also explains the dimensionality and coordinate system used by MIPAV, the data types MIPAV supports, the header offset information, endianness, and how to view and edit image attributes.It also provides a basic information about image file formats supported by MIPAV. More information about graphic file formats and the formats that MIPAV supports can be found in Appendix C: [MIPAV_AppCSupportedFormats.html#1256636 "Supported formats" ].
Contents
Supported graphic formats overview
MIPAV supports three categories of graphic file formats: vector (i.e., volume of interest, or VOI), bitmap (i.e., 2D to 5D grayscale or RGB images), and 3D images.Vector file formats are usually used to store line-based elements. These elements can be geometric shapes, such as polygons, curves, or splines. MIPAV can read and generate several vector-formatted file types including the MIPAV lookup table (LUT), MIPAV MTX, MIPAV Graphics Plot (PLT), and MIPAV VOI. See also Appendix C: [MIPAV_AppCSupportedFormats.html#1256636 "Supported formats" on page 562].Bitmap file formats are usually used to store real-world graphics data e.g., photographs or medical images such as CT scans. The data portion of bitmap files contains numerical data that indicates the color of each pixel or voxel in the image. MIPAV can read and generate a number of bitmap formatted file types, such as Adobe Photoshop (PSD), Graphics Interchange File (GIF), Sun Raster (RS), Tagged Image File Format (TIFF), and Truevision Graphics Adapter (TGA).MIPAV uses 3D graphic formatted files to store descriptions of the color and shape of 3D models of real-world and imaginary objects.To support the wide range of image-processing needs of the NIH intramural research community, MIPAV reads and writes the image file types indicated in [MIPAV_AppCSupportedFormats.html#1330116 Table 1], refer to Appendix C: [MIPAV_AppCSupportedFormats.html#1256636 "Supported formats" on page 562].Understanding the MIPAV dimensionality and coordinate system
Internally, MIPAV is designed to store images of any dimensionality and thus is n dimensional. [MIPAV_ImageBasics.html#1220345 Figure 102] is a model of an example 3D-image where each position within the grid represents a voxel.voxel-The smallest distinguishable cube-shaped part of a 3D-image.The voxel in the upper left-most position is considered the origin of the dataset. (A volumetric dataset is a set of cross-sectional images). Ideally, each voxel would be isotropic (i.e., cubic), but clinical datasets are often acquired in such a manner that the resolution in the x and y dimensions is greater than the resolution in the z dimension, thus producing rectangular voxels (elongated in the z direction). This voxel anisotropy is taken into account in the execution of the algorithms found in MIPAV.
Because MIPAV's image storage buffer is n-dimensional, it can store 2D, 3D, and 4D medical images. CT and MRI are examples of 3D medical images where the three dimensions (x, y, and z) are spatial dimensions. Other 3D datasets include fluoroscopy volumes, where the first two dimensions are spatial and the third dimension is time.
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Data types
A data type is the classification of a particular type of information. For example, a floating point data type indicates a number with a decimal point. Data read from image files are stored in MIPAV's data structures. MIPAV supports all the basic data types shown in [MIPAV_ImageBasics.html#1220361 Table 1] and may in the future support more composite data types including color and complex numbers. The image data read from the file is stored in a data buffer of the same basic data type, preventing the reduction of image information that results from conversion into a fixed data type.
Table 1. Data types supported by MIPAV Data type Description Boolean 1 bit per pixel/voxel (1 on, 0 off) Signed byte 1 byte per pixel/voxel (-128, 127) Unsigned byte 1 byte per pixel/voxel (0, 255) Signed short 2 bytes per pixel/voxel (-32768, 32767) Unsigned short 2 bytes per pixel/voxel (0, 65535) Integer 4 bytes per pixel/voxel (-231, 231-1) Long 8 bytes per pixel/voxel (-9.22E18, 9.22E18) Float 4 bytes per pixel/voxel (-3.4E38, 3.4E38) Double 8 bytes per pixel/voxel (-1.8E308, 1.8E308) Color 32 3 bytes per pixel/voxel, plus 1 byte; 8 bits per color channel (alpha, red, green, and blue)Headers
If you attempt to open a raw image, you may need to supply MIPAV with the header offset. The header offset indicates the size of the space reserved at the beginning of the file where specific types of information is kept. This space, which is called the header, precedes the image data. If you know the length of the header, enter it in the header offset text box. When MIPAV accesses the file, it skips the header offset and begins to read the image data. Note that not all image file formats have a header.Endianness
Endianness refers to the byte ordering of the data. Some computers order the data with the least significant byte (LSB) first followed by the most significant byte (MSB). This byte order is referred as "little endian" or Intel byte ordering. machines that use little-endian byte ordering are VAXes, Intel x86, and Pentium. The reverse is MSB then LSB, which is referred as "big endian" or Motorola byte ordering. Machines that use big-endian byte ordering are IBM System 3D, RISC, and a Motorola 680x0. MIPAV is biendian; that is, it supports both big- and little-endian byte-ordering formats.Viewing and editing image attributes
Information about the image appears in the Image Information dialog box and in the Image Attributes dialog box.The Image Attributes window displays the name of the image file and information about the resolution of the image. The About Image window displays more detailed information about the image, such as the orientation of the image or the number of bits per pixel or voxel.
Viewing image attributes
To view the attributes of an image, select Image > Attributes > View Header in the MIPAV window. For DICOM datasets, the Image Information dialog box similar to the one shown in [MIPAV_ImageBasics.html#1221393 Figure 103]-a appears. For non-DICOM datasets, an Image Information dialog box similar to the one in [MIPAV_ImageBasics.html#1221393 Figure 103]-b appears.|- |
(a) the Info dialog box for DICOM images|- |
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(b) the Info dialog box for non-DICOM images|}
Editing image attributes
By default, the General page always appears first when the Image Attributes dialog box opens.
Image Attributes dialog box
Apply
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applies the changes to the current image, but doesn't close the dialog box.
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OK
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applies the changes to the current image and closes the dialog box.
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Close
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closes the dialog box without applying the changes to the image.
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Help
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opens the on-line help.
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General tab
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What's the Difference Between Clicking Apply or Clicking OK? Click Apply when you want the dialog box or window to remain open after it makes the change so that you can make further modifications. If instead you click OK, the dialog box or window closes immediately after making the current change.
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