cpp_decomp

Operates decompression of compressed image stored in TIFF file.

internal

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

Yohann Demont

Tools for Imaging Flow Cytometry

Gautier Stoll

Guido Kroemer

Jean-Pierre Marolleau

Loïc Garçon

cpp_decomp function

<dl><dt>fname</dt>
<dd>string, path to file.</dd>
<dt>offset</dt>
<dd>std::size_t, position of the beginning of compressed image.</dd>
<dt>nbytes</dt>
<dd>uint32_t, number of bytes of compressed image.</dd>
<dt>imgWidth</dt>
<dd>R_len_t, Width of the decompressed image. Default is 1.</dd>
<dt>imgHeight</dt>
<dd>R_len_t, Height of the decompressed image. Default is 1.</dd>
<dt>nb_channels</dt>
<dd>R_len_t, number of channels of the decompressed image. Default is 1.</dd>
<dt>removal</dt>
<dd>uint8_t, object removal method. Only apply for 30818 compression. Default is 0. 
-1, for clipped removal: height OR width clipped pixels will be set to -1. 
-2, height clipped removal: height clipped pixels will be set to -1. 
-3, width clipped removal: width clipped pixels will be set to -1. 
-4, only keep background: background pixels will be set to 1 and all others to 0. 
-5, only keep foreground: foreground pixels will be set to 1 and all others to 0.</dd>
<dt>compression</dt>
<dd>uint32_t, compression algorithm used. Default is 30818.</dd>
<dt>verbose</dt>
<dd>bool, whether to display information (use for debugging purpose). Default is false.</dd></dl>

Arguments

IFC_object Decompression — cpp_decomp

<dl>

<dt>fname</dt>
<dd>string, path to file.</dd>


<dt>offset</dt>
<dd>std::size_t, position of the beginning of compressed image.</dd>


<dt>nbytes</dt>
<dd>uint32_t, number of bytes of compressed image.</dd>


<dt>imgWidth</dt>
<dd>R_len_t, Width of the decompressed image. Default is 1.</dd>


<dt>imgHeight</dt>
<dd>R_len_t, Height of the decompressed image. Default is 1.</dd>


<dt>nb_channels</dt>
<dd>R_len_t, number of channels of the decompressed image. Default is 1.</dd>


<dt>removal</dt>
<dd>uint8_t, object removal method. Only apply for 30818 compression. Default is 0. 
-1, for clipped removal: height OR width clipped pixels will be set to -1. 
-2, height clipped removal: height clipped pixels will be set to -1. 
-3, width clipped removal: width clipped pixels will be set to -1. 
-4, only keep background: background pixels will be set to 1 and all others to 0. 
-5, only keep foreground: foreground pixels will be set to 1 and all others to 0.</dd>


<dt>compression</dt>
<dd>uint32_t, compression algorithm used. Default is 30818.</dd>


<dt>verbose</dt>
<dd>bool, whether to display information (use for debugging purpose). Default is false.</dd>

</dl>

cpp_decomp: IFC_object Decompression

Description

Arguments