Changes for page Access data with ImageJ

Last modified by fwilde on 2018/12/18 12:01
From version 14.1
edited by fwilde
on 2016/09/15 16:34
Change comment: There is no comment for this version
To version 15.1
edited by fwilde
on 2018/12/18 12:01
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
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1 1  {{layout}}
2 2  {{layout-section ac:type="two_right_sidebar"}}
3 3  {{layout-cell}}
4 -Currently, at P05 a generic data format is used to store raw and reconstructed data. Generally, this is a binary format in little endian byte order with different data types (uint16, real32, ...) and a header which describes the dataset (rows and columns, data format). This data can either be imported directly in ImageJ or loaded with our plugins.
4 +{{info}}
5 +As of 2017, all images are stored in TIFF format. These can be easily viewed with many image viewers including ImageJ.
6 +{{/info}}
5 5  
8 +\\
9 +
10 +Until 2017 at P05 a generic data format was used to store raw and reconstructed data. This is a binary format in little endian byte order with different data types (uint16, real32, ...) and a header which describes the dataset (rows and columns, data format). This data can either be imported directly in ImageJ or loaded with our plugins.
11 +
6 6  = {{id name="AccessdatawithImageJ-Readthefileheader"/}}Read the file header =
7 7  
8 8  Each image contains a header consisting of the information needed to open the binary raw file. To read the header open the first line of the dataset (e.g. with the {{code language="none"}}head{{/code}} command in Linux or in an editor). The header information is subdivided with underscore symbols, like e.g. {{code language="none"}}PC_2_U_2000_2000_{{/code}}. The first item describes on what kind of computer the data was generated. The second item shows the dimensionailty of the data (2 for an image). The next item is a letter (either B U I L or F ) and describes the data type. A list of te data types can be found in the table below. The last items give the length of the dataset in each dimension. The total header length is not fixed and generally depends on the image dimensions.and count all letters until the carriage return. Add 2 to this number (carriage return has two letters) and this is the header length - e.g. {{code language="none"}}PC_2_U_2000_2000_{{/code}} has 17 letters ansd thus results in a header length of 19.
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16 16  header tag
17 17  )))
18 18  |(((
19 -
25 +\\
20 20  )))|(((
21 21  8 bit
22 22  )))|(((
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30 30  U
31 31  )))
32 32  |(((
33 -
39 +\\
34 34  )))|(((
35 35  16 bit Signed
36 36  )))|(((
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37 37  I
38 38  )))
39 39  |(((
40 -
46 +\\
41 41  )))|(((
42 42  32 bit Signed
43 43  )))|(((
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90 90  [[attach:read_dat.java]]
91 91  {{/panel}}
92 92  
93 -
99 +\\
94 94  
95 -
101 +\\
96 96  {{/layout-cell}}
97 97  
98 98  {{layout-cell}}
Confluence.Code.ConfluencePageClass[0]
Id
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1 -116602068
1 +116602069
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/116602068/Access data with ImageJ
1 +https://confluence.desy.de/spaces/P5I/pages/116602069/Access data with ImageJ