XuvTools is developed in a cooperative effort from:
  • Chair of Pattern Recognition and Image Processing [www]
  • Friedrich Miescher Institute for Biomedical Research [www]
  • Center for Biological Systems Analysis [www]
 

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devel:project_files [2010/05/12 15:32]
mario added scene_element_size_um to example
devel:project_files [2010/12/22 20:06] (current)
mario updated to 1.8.1 standard
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 ====== XuvTools Project Files ====== ====== XuvTools Project Files ======
 +
 +<note important>​
 +This documentation is valid for project files of **XuvTools 1.8.1**. Previous versions can differ significantly. While Xuvtools can read previous project files, they are deprecated and should not be used anymore.
 +</​note>​
  
 ==== Plain Text Format ==== ==== Plain Text Format ====
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 | stackXXXX | string | channel | Key: This id is the prefix for all other information about the stack.\\ Value: an arbitrary string (or number). Must be identical for the same channels | | stackXXXX | string | channel | Key: This id is the prefix for all other information about the stack.\\ Value: an arbitrary string (or number). Must be identical for the same channels |
 | stackXXXX_tile | tileXXXX | tile identifier | Value: Which Tile does the stack belong to? Unique id | | stackXXXX_tile | tileXXXX | tile identifier | Value: Which Tile does the stack belong to? Unique id |
-| stackXXXX_stack_file_id | string | identifier in file | Value: This is the identifier for loading and storing the tile\\ in the file (path, or number of planes, or similar).\\ For tiff-based images, use <start-plane>-<end-plane>,<​channel>,​\\ i.e. "0-7,2" for channel ​2 of an 8 plane tiff. |+| stackXXXX_stack_file_id | string | identifier in file | Value: This is the identifier for loading and storing the stack\\ in the file. For most XuvTools file readers (all except HDF5 based), use <series>,<timepoint>,<​channel>,​\\ i.e. "0,7,0" for series 0, timepoint 7, channel ​0.\\ See extra paragraph below for more details. |
 | stackXXXX_size_pix | vector of integers | Z,Y,X size | Extent of stack, as in the file (not the (scaled) stack extent in memory) | | stackXXXX_size_pix | vector of integers | Z,Y,X size | Extent of stack, as in the file (not the (scaled) stack extent in memory) |
 | stackXXXX_element_size_um | vector of floats | Z,Y,X elm. size | Extent of a single voxel of the dataset, in um | | stackXXXX_element_size_um | vector of floats | Z,Y,X elm. size | Extent of a single voxel of the dataset, in um |
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 ==== Minimal Project File Example ==== ==== Minimal Project File Example ====
- 
-<note tip> 
-**Verified on 2009.12.28** by Mario that the following project file is indeed valid, and can be loaded by XuvTools (revision 3228). 
-To test, change the file path and stack dimensions for your application. 
-</​note>​ 
  
 <​code>​ <​code>​
-xuvstitch_project_version=1,​8,​0+xuvstitch_project_version=1,​8,​1
 scene_element_size_um=1,​1,​1 scene_element_size_um=1,​1,​1
 stack0001=0 stack0001=0
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 stack0001_filename=/​data/​xuvtools_img/​2dstitch/​img01.tif stack0001_filename=/​data/​xuvtools_img/​2dstitch/​img01.tif
 stack0001_size_pix=7,​512,​512 stack0001_size_pix=7,​512,​512
-stack0001_stack_file_id=0-7,0+stack0001_stack_file_id=0,3,0
 stack0001_tile=tile0001 stack0001_tile=tile0001
 stack0002=0 stack0002=0
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 stack0002_filename=/​data/​xuvtools_img/​2dstitch/​img02.tif stack0002_filename=/​data/​xuvtools_img/​2dstitch/​img02.tif
 stack0002_size_pix=7,​512,​512 stack0002_size_pix=7,​512,​512
-stack0002_stack_file_id=0-7,0+stack0002_stack_file_id=0,​3,1
 stack0002_tile=tile0002 stack0002_tile=tile0002
 stackcounter=2 stackcounter=2
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 tile0001_channels=stack0001 tile0001_channels=stack0001
 tile0001_enabled=1 tile0001_enabled=1
-tile0002_abs_pos_um=1,​1,​513+tile0002_abs_pos_um=1,​1,​493
 tile0002_channels=stack0002 tile0002_channels=stack0002
 tile0002_enabled=1 tile0002_enabled=1
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 tiles=tile0001,​tile0002 tiles=tile0001,​tile0002
 </​code>​ </​code>​
 +
 +==== Referencing Image Stacks in Project Files ====
 +
 +XuvTools can make use of a diverse set of image readers/​writers. To provide an abstract interface for referencing image stacks in files, the following attributes are used:
 +| stackXXXX_filename | Type: string | image file name\\ example: /​data/​xuvtools_img/​2dstitch/​img01.tif |
 +| stackXXXX_stack_file_id | Type: string | unique identifier for the series,​timepoint,​channel of the image stack\\ A comma-separated unpadded list of integer values, corresponding to series, timepoint, and channel.\\ example: 0,2,0 |
 +
  
devel/project_files.txt ยท Last modified: 2010/12/22 20:06 by mario
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