#catmaid-tools

##TileCATMAID

A standalone command line application to export image tiles representing scale level 0 of the tiled scale pyramids for the CATMAID interface from existing CATMAID image stacks. The program enables to crop a box of interest from an existing CATMAID stack and to export only a subset of the tile set. It is thus easily possible (and desired) to parallelize the export on a cluster.

The main utility of the program is to export resliced (xyz, xzy, zyx) representations of existing CATMAID stacks.

Separation of scale level 0 tile generation and scaling is necessary to enable the desired level of parallelization. One would typically generate the scale level 0 tile set parallelized in volumes that cover a moderate number of source tiles. Only after a z-slice is fully exported, it can be used to generate the scale pyramid. I.e., scaling can be parallelized by z-slice but not within a z-slice.

The TileCATMAID main program comes in the fat jar catmaid-tile.jar that can be generated with Eclipse using catmaid-tile.jardesc. It is executed by:

./java -jar ScaleCATMAID.jar -DsourceBaseUrl=http://...

passing parameters as properties to the JVM virtual machine. It accepts the following parameters, type and default in parantheses:

sourceBaseUrl

base path of the source CATMAID stack (string, ""), not required if sourceUrlFormat includes it

sourceUrlFormat

URL format String to address CATMAID tiles(string, sourceBaseUrl + "%5$d/%8$d_%9$d_%1$d.jpg").

Tiles are addressed, in this order, by their

1. scale_level,
2. scale,
3. x,
4. y,
5. z,
6. tile width,
7. tile height,
8. tile row, and
9. tile column.

Examples:

"http://catmaid.org/my-data/xy/%5$d/%8$d_%9$d_%1$d.jpg"

CATMAID DefaultTileSource (type 1)

"http://catmaid.org/my-data/xy/?x=%3$d&y=%4$d&width=%6d&height=%7$d&row=%8$d&col=%9$d&scale=%2$f&z=%4$d"

CATMAID RequestTileSource (type 2)

"http://catmaid.org/my-data/xy/%1$d/%5$d/%8$d/%9$d.jpg"

CATMAID LargeDataTileSource (type 5)

sourceWidth

width of the source in scale level 0 pixels in xyz orientation (long, 0)

sourceHeight

height of the source in scale level 0 pixels in xyz orientation (long, 0)

sourceDepth

depth of the source in scale level 0 pixels in xyz orientation (long, 0)

sourceScaleLevel

source scale level to be used for export scale level 0 (long, 0)

sourceTileWidth

width of source image tiles in pixels (int, 256)

sourceTileHeight

height of source image tiles in pixels (int, 256)

sourceResXY

source stack x,y-resolution (double, 1.0 )

sourceResZ

source stack z-resolution (double, 1.0 )

minX

minimum x-coordinate of the box in the source stack to be exported in scale level 0 pixels in xyz orientation (long, 0)

minY

minimum y-coordinate of the box in the source stack to be exported in scale level 0 pixels in xyz orientation (long, 0)

minZ

minimum z-coordinate of the box in the source stack to be exported in scale level 0 pixels in xyz orientation (long, 0)

width

width of the the box in the source stack to be exported in scale level 0 pixels in xyz orientation (long, 0)

height

height of the the box in the source stack to be exported in scale level 0 pixels in xyz orientation (long, 0)

depth

depth of the the box in the source stack to be exported in scale level 0 pixels in xyz orientation (long, 0)

orientation

orientation of exported stack, possible values "xy", "xz", "zy" (string, "xy")

tileWidth

width of exported image tiles in pixels (int, 256)

tileHeight

height of exported image tiles in pixels (int, 256)

exportMinZ

first z-section index to be exported (long, 0)

exportMaxZ

last z-section index to be exported (long, depth-1)

exportMinR

first row of tiles to be exported (long, 0)

exportMaxR

last row of tiles to be exported (long, depth-1)

exportMinC

first column of tiles to be exported (long, 0)

exportMaxC

last column of tiles to be exported (long, depth-1)

exportBasePath

base path for the stakc to be exported (string, "")

tilePattern

tilePattern the file name convention for export tile coordinates without extension and base path, must contain "<s>","<z>", "<r>", "<c>" (string, "<z>/<r>_<c>_<s>")

format

image tile file format for export, e.g. "jpg" or "png" (string, "jpg")

quality

quality for export jpg-compression if format is "jpg" (float, 0.85)

type

the type of export tiles, either "rgb" or "gray" (string, "rgb")

interpolation

interpolation scheme used, either nearest neighbor "NN" or n-linear "NL" (string, "NN")

Alternatively, it can be executed by the accompanying Bash-script retile that is called with a config file as its single parameter. The config file contains all parameters in key=value rows (escaped according to Bash's needs).

###Examples:

sourceUrlFormat='http://catmaid.org/stack/%5$d/%8$d_%9$d_%1$d.jpg'
sourceWidth=22775
sourceHeight=18326
sourceDepth=462
sourceScaleLevel=2
sourceTileWidth=256
sourceTileHeight=256
sourceResXY=4.0
sourceResZ=45.0
minX=1300
minY=1000
minZ=0
width=2000	
height=2000
depth=100
orientation=xy
exportBasePath=/var/www/catmaid/test/xy/
tilePattern="<z>/<r>_<c>_<s>"
format=jpg
quality=0.85
type=gray
interpolation=NL