README.rst

pl-markimg

Table of Contents

• Abstract
• Description
• Usage
  • Arguments
  • Run
• Development
• Examples

Abstract

An app to mark landmark points and lines on an input image

Description

markimg is a ChRIS ds-type application that consumes upstream information about landmarks in an image, and generates measurement lines on the actual image itself. Additionally, it also generates a mini-report, embedded within the image itself as well a text (JSON) file.

Usage

docker run --rm fnndsc/pl-markimg markimg
    [-j|--inputJsonName <jsonFileName>]
    [-i|--inputImageName <pngFileName>]
    [-p|--pointMarker <pointMarker>]
    [-c|--pointColor <pointColor>]
    [-l|--lineColor <lineColor>]
    [-t|--textColor <textColor>]
    [-s|--textSize <textSize>]
    [-w|--lineWidth <lineWidth>]
    [-q|--textPos <textPosition>]
    [-g|--lineGap <lineGap>]
    [-z|--pointSize <sizeInPixels>]
    [--addText <additionalText>]
    [--addTextSize <additionalTextSize>]
    [--addTextPos <additionalTextPosition>]
    [--addTextColor <additionalTextColor>]
    [--addTextOffset <additionalTextOffsetPosition>]
    [-h|--help]
    [--json] [--man] [--meta]
    [--savejson <DIR>]
    [-v|--verbosity <level>]
    [--version]
    <inputDir> <outputDir>

Arguments

[-j|--inputJsonName <jsonFileName>]
The name of the input JSON file.
Default is 'prediction.json'.

[-i|--inputImageName <pngFileName>]
The name of the input image file.
Default is 'leg.png'.

[-p|--pointMarker <pointMarker>]
A character that represents a point on the image.
Default is 'x'.

[-c|--pointColor <pointColor>]
The color of the character representing points on the image.
Default is 'red'.

[-l|--lineColor <lineColor>]
The color of the line drawn on the input image.
Default is 'red'.

[-t|--textColor <textColor>]
The color of the text placed on the input image.
Default is 'white'.

[-s|--textSize <textSize>]
The size of the text on the input image.
Default is '5'.

[-w|--lineWidth <lineWidth>]
The width of line to be drawn on an input image.
Default is '1'.

[-q|--textPos <textPosition>]
The position of text on an image.
Default is 'right'.

[-g|--lineGap <lineGap>]
Space between lines in pixels.
Default is '20'.

[-z|--pointSize <sizeInPixels>]
The size of points to be plotted on the image.
Default is '10'.

[--addText <additionalText>]
If specified, burn this additional text on the final image.

[--addTextSize <additionalTextSize>]
The size of the additional text to be shown on the image.
Default is 5.

[--addTextPos <additionalTextPosition>]
The position of the additional text to be shown on the image.
Default is right.

[--addTextColor <additionalTextColor>]
The color of the additional text to be shown on the image.
Default is white.

[--addTextOffset <additionalTextOffset>]
If specified, move the additional text using the offset
coordinates (x,y). Accepts a tuple in the form of "x,y"

[-h] [--help]
If specified, show help message and exit.

[--json]
If specified, show json representation of app and exit.

[--man]
If specified, print (this) man page and exit.

[--meta]
If specified, print plugin meta data and exit.

[--savejson <DIR>]
If specified, save json representation file to DIR and exit.

[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.

[--version]
If specified, print version number and exit.

Getting inline help is:

docker run --rm fnndsc/pl-markimg markimg --man

Run

You need to specify input and output directories using the -v flag to docker run.

docker run --rm -u $(id -u)                             \
    -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing      \
    fnndsc/pl-markimg markimg                           \
    /incoming /outgoing

Development

Build the Docker container:

docker build -t local/pl-markimg .

Run unit tests:

docker run --rm local/pl-markimg nosetests

Examples

Put some examples here!