Up: Component summary
Up: Component summary
Component
BFConvertWrapper for the Bioformats command line tool for converting exotic image formats.
Note, that bfconvert has issues with extracting separate channels. It may be a better approach to extract everything and filter later:
val extr=BFConvert(dir=images, name="%o_C%c_")
val extr1=Array2Folder(Folder2Array(extr, filePattern=".*_C0_.*"), fileMode="@file@")
val extr2=Array2Folder(Folder2Array(extr, filePattern=".*_C1_.*"), fileMode="@file@")
See command line options, http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/conversion.html, of type "bfconvert" in the command line.
| Version | 1.0 |
|---|---|
| Bundle | anima |
| Categories | Image Processing |
| Authors | Ville Rantanen (ville.rantanen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | bash ; Bioformats bftools ; bc (DEB) ; installer (bash) |
| Source files | component.xml bfconv.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | BinaryFolder | Mandatory | Input folder of images, any format recognized by Bioformats library. |
Outputs| Name | Type | Description |
|---|---|---|
| out | ImageList | Output folder of converted TIF images. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| filter | string | ".*" | Case insensitive filtering of input files with GNU grep (ex. "tif") |
| gray | boolean | false | Force output images gray scale - sums RGB channels. |
| multiplier | float | 1 | Multiply output signal. e.g. 12bit camera images need to be multiplied with 4 to use the 16bit image intensity range. |
| name | string | "%o_S%s_Z%z_T%t_C%c" | Output file name, %o: original input file name, %s: series index, %z: Z section index, %c: channel index, %t: timepoint index, %n series name, %w channel name |
| png | boolean | false | Convert output to PNG with imagemagick |
| switches | string | "" | Command line switches to bfconvert. |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
|||
|---|---|---|---|---|---|---|
| case1 | properties | in | out | |||
|
switches=-separate -compression LZW, |
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| case2_png | properties | in | out | |||
|
switches=-separate, |
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