Raw Header - TomoVision
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1. Axial Sagittal Coronal and Oblique From the Patient Info page study_num serie_num image_num patient_name patient_id patient_age XV The Raw_Header Program xvi patient_sex patient_weight hospital physician radiologist2. Raw Header User s Manual Rev 8 April 2007 WD omsYision division of VIRTUAL MAGIC INC MONTREAL CANADA Raw_Header USER S MANUAL Raw_Header Copyright 1997 2005 by Yves Martel Distribution rights by TomoVision ALL RIGHTS RESERVED TomoVision 4559 Pontiac Montreal Qc Canada H2J 2T2 For questions regarding Raw_Header call 514 522 3559 or FAX 514 522 3559 during Eastern standard time business hours or e mail supportOtomovision com Information in this document is subject to change without notice and does not represent a commitment on the part of TomoVision Virtual Magic Inc It is against the law to copy this software in any fashion or any medium TomoVision is a division of Virtual Magic Inc 1 The Raw Header Program The TomoVision s libraries can recognize a large number of medical image format Unfortunately it can not recognize all of them Raw_Header provide a mechanism to help read some of the image format that the libraries would otherwise be unable to read As long as the image data is uncompressed Raw_Header should help you to make some sense out of it In order to read the image we need to generate a new header that will enable the libraries to understand the image data Raw_Header creates this header The image file is not modified a second file with the extension hdr is created instead containing the new header information Raw_Header can also be used to modify the infor
3. X floats If pixel plane is 3 or 4 then O means that each pixel is created from 3 or 4 for RGBA consecutive pixel_ swap pixel_pading file_offset image_ offset file_name The Raw Header Program values and 1 means that the pixels are represented by color planes For 16 and 32 bit integer pixels 0 means a LITTLE ENDIAN pixel value and 1 is BIG ENDIAN For float values the 4 configurations of the 4 bytes used to create the float value are possible O ABCD 1 DCBA 2 CDAB and 3 BADC This is the value used to fill out any portion of the image outside the field of view Number of bytes to skip at the beginning of the image file Number of bytes to skip at the begnning of each image in the image file Name of the file containing the pixel data This file must be in the same directory as the header file From the Image Geometry page inc_x inc_y inc_z thickness org_x y and z dir_h_x y and z dir_v_x y and Z axis_syst axis_trust Horizontal distance between each pixels Vertical distance between each pixels Distance between each slice Thickness of each slice Position in coordinate system of the center of the upper left pixel Components of the horizontal direction vector from left to right Components of the vertical direction vector from top to bottom 0 DICOM system 1 GE system 2 Siemens system 1 if the left and top label have been defined slice_orientation The accepted values are
4. e Their values can be one of Unknown Anterior Posterior Head Feet Left Right You also have to select the axis system that you want to use for this image You have a choice among the 3 most popular axis systems for medical scanners xi The Raw_Header Program Image Ordering The image ordering in conjunction with the slice spacing will be used to compute the image origin of the other opened images if you click on the Apply to All Files button xii The Raw_Header Program 1 4 The Patient Info This section will enable you to add or edit the patient information to the image It has 2 regions one to enter the study series and image numbers of this image the other to enter the textual information associated with the image z Raw Image Header C TomoVision Images Problemes KodakPACS unknown data C Pixel Format2 Y Image Geometry i Patient Info Study Num Serie Num nage Nun Patient Name junknown data O Patient ID SaaS Patient Age ASA es Patient Sex A eee Patient Weight Se eee Hospital Name EPA REIS Physician Name Radiologist Name AAA IS eee Comment 1 EA Comment 2 pen File d unknown data gt oi a xiii The Raw_Header Program 2 The Header File Format XIV The Header file format is loosely based on the university of Waterloo IM format The header is entirely composed of lines of ASCII text Each line is terminated by th
5. e Raw_Header Program taken that the images are opened in the same order as the order specified with the Image Ordering buttons of the Image Geometry section Write Headers The program will create 1 new header for each opened image The header will have the same name as the opened image but with the hdr extension Exit Exit the program At typical raw file look like this magic RAW_DATA 291 was zel pixel_size 16 pixel_plane l pixel_sign 0 pixel_swap 0 pixel ding 321169 file _offset 3072 image_offset 0 file_name ctl Ines 0 UES 7 3 Icy ARAS Tio ae 2839 0 00010 thickness 2 5000 DIAS gt 28 2 2000 orgy 5 1254 ome 2339 27S Che m s0 O00 Glz In ys L 0000 Cll m 480 006 0 As 0000 e ay 00000 Cui wy 4280 0000 axis_syst 0 axis aus 8 Al slice_orientation Axial serie_num 289 image_num 12804 patient_name Anonymous paren stele WALZ Savoie hospitali Sie Elias lain Glosjoskieedl physician Anonymous Sample raw header file vi The Raw_Header Program 1 1 The File Format tab This section is split in 4 regions Image Format Pixel Format Image Format Suggestions and an Image preview nage Header E lmages Raw C THEAD File Format File Header Hea a Height Computed Size ma Real File Size m a m aa Image Format In this region you can change the image file structure information The image file is composed
6. e characters lt CR gt and lt LF gt 0x0D and Ox0A Everything on a line following a or a will be considered as comments and can be disregarded by the program The header is composed of a series of keywords value pairs The keyword and values are separated by Each pair of keyword and values are separated by one or more separation characters The recognized separators are space comma t tab or n new line If a value contains a space it should be placed between quotes Example file_name file name with spaces in the name You can use lowercase or uppercase indifferently in the keywords the program converts all the keywords characters to uppercase before parsing the header However the values are case sensitive The first keyword values pair should always be magic RAW_DATA The recognized keywords and their permitted values are From the File Format page x Horizontal resolution in pixels y Vertical resolution in pixels Z Number of images in the file pixel_size Number of bytes per pixels The accepted values are 8 16 and 32 pixel_plane Number of pixel planes The accepted values are 1 for B amp W images 3 for RGB images and 4 for RGBA images pixel_sign O if the pixel values are unsigned 1 if they are signed pixel_config Used only for float and color pixels If pixel plane is 1 then a value of 1 is used for IEEE floats 2 for Data General floats and 3 for VA
7. he actual image is surrounded by a padding to make the image square The pixels from this padding will usually mess up some image computation like histograms and dynamic range The Raw_Header Program 1 3 The Image Geometry tab In this section you will be able to specify the physical dimensions and orientations of the image This section is composed of 4 regions the Pixel Metrics the Image Origin the Image Orientation and the Image Ordering Raw Image Header C TomoVision Images Problemes KodakPACS unknown data olx Pixel Metrics Image Origin Image Orientation This region will specify the physical dimensions of a pixel in the image We need its width and height in mm the slice thickness and if you want to create a 3D data set you need the spacing between each slice This value will be used to fix the other image s origin if you use the Apply to All Files button The sign of the slice spacing is affected by the axis system and the image ordering information This region is used to specify the position of the bottom left corner of the image The values are specified in the patient s 3D coordinates system If the image orientation is oblique we will also use this region to specify the horizontal and vertical orientation of the image The image can be either Axial Sagittal Coronal or Oblique The Label A is the label at the top of the image the Label B is on the left side of the imag
8. he graphic window the vertical and horizontal scroll bars can be used to scroll the image The Raw_Header Program The image will show you a representation of all the pixels in the file Each byte from the file that is not used to create the image is represented by a black amp white pixel The colors range from black for a byte of value 0 and white for a byte of value 255 If there is an uncompressed image in the file it should be easy to discern its pattern You then have to click on the different pixels of the image File Header Image Width Image Height Image Header Padding value You click on the first pixel of the image This will fix the size of the file header Note that the first image actually starts after the file header and the first image header As long as the image header is not known it is assumed to be 0 To help in the image information identification the pixels following the file header will be displayed using the Pixel Format defined in the Pixel Format section You click on the first pixel of the second line of the image This will fix the width of the images You click on the last pixel of the image This will fix the images height You click on the first pixel of the second image If your file has more than 1 image this will fix the size of each image s header You click on a pixel inside the PATA padding region of the image For some image modality like CT t
9. mation from images that can be read by TomoVision s libraries If you create a new raw header for these images and access these images through the new header the information from these new headers will be used The Section Tabs E image Geometry Y Patientinfo A _ The raw header is composed of 4 sections The File Format The Image Format the Image Geometry and the Patient Info The Image Format can be defined either numerically or graphically The 4 tabs will control which of these sections you are manipulating The Program controls ae unknownsdata a cc Open File Current File At the bottom of the window are tools present in all sections Call a Window s File Open interface to open one or more new images in the Raw_Header program Alternatively you can drag and drop files in the Raw_Header window to open new images Select the current image from a list of all the opened images The image list cycles through the images that have been opened in the program The File Format Image Format Image Geometry and Patient information sections enable you to change the header of the current image Apply to All Files You can apply the File Format Image Format Image Geometry and Patient Info of the current image to all the other images presently opened in the program The program will assign origins to the images to create a 3D data set according to the information provided in the Image Geometry section Care should be V Th
10. of a file header followed by a series of images Each of these EN images has an image header followed by the image itself The image is Height by Width pixels This region also provides information on the file size computed g AE REE from the information and the actual file size If the E computed size is in red this means that the number of 2 bytes needed to create the image specifies by the structure is larger than the actual number of bytes in the en file Width x Height pixels Pixel Format Inthisregion you can specify how each pixel is stored in the image Each pixel can be stored as an integer value using 8 16 or 32 bits or a float value using 32 bits the program can recognize 3 float formats IEEE Data General or VAX or a color value using 3 or 4 components of 8 or 16 bits each 1 For 8 16 and 32 bit integer values the value can be either signed or unsigned vii The Raw_Header Program Suggestions Image Preview viii 2 If the pixel is 16 or 32 bits integer values the bytes representing the pixel can be LITTLE ENDIAN unswapped or BIG ENDIAN swapped 3 Ifthe pixel is a float value then the byte order of the value can be ABCD DCBA CDAB or BADC 4 If the pixel is created with 3 color components then the image can be represented by Width x Height color pixels of 3 bytes each or by 3 planes of Width x Height pixels each plane constituting a separate color The order of the colors components can be ei
11. of this window will enable you to view all the images The Raw_Header Program 1 2 The Image Format tab It is sometime difficult to find the correct image format using only a numerical interface This section enables you to specify the image format graphically The interface of this section is composed of a list of buttons for the current parameter a text feed back region a numerical image format input region and a graphical input region Raw Image Header C TomoVision lmages Problemes KodakPACS unknown data olx Current Parameters Text Feedback Numerical Input Graphical input Pixel Format2 gt y Image Header Padding Valu File Header 3 Width y Height Image Header y unknown data u y These buttons are used to specify to the program which of the parameters you want to fix The mouse wheel can be used to change the value of the currently selected parameter The text in this region should help you fix the parameters Once you fix a parameter graphically its value will be displayed here inversely you can enter the numerical value of the parameter and see the results in the graphical input region These values are shared with the Pixel Format section This region is composed of a graphic window a vertical and horizontal scroll bar and a scale slider extreme right The scale slider is used to scale up or down the image in the graphic window If the image does not fit entirely in t
12. ther RGB unswapped or BGR swapped 5 If the pixel is created with 3 color components then the image can be represented by Width x Height triplets of colors or by 3 planes of Width x Height values each plane constituting a separate color 6 If the pixel is created with 4 color components then the image can be represented by Width x Height color pixels of 3 bytes each or by 3 planes of Width x Height pixels each plane constituting a separate color The order of the colors components can be either RGBA unswapped or ABGR swapped 7 If the pixel is created with 3 color components then the image can be represented by Width x Height triplets of colors or by 3 planes of Width x Height values each plane constituting a separate color To help finding the correct combination the minimum and maximum values of the pixels is computed The combination that yield the lowest dynamic range is usually the correct one Once the program knows the pixel format it can make a few guesses about the image format The program assumes that the images are square that they have dimensions that are powers of 2 and that the images are at the end of the file From that it creates a list of suggestions Clicking on one of these suggestions will fill out the Image Format region with the corresponding values Using the Image and Pixel Formats the program displays a preview of the image in this region If the file has more than 1 image a slider at the bottom
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