plischer / ccd-analyze

Scripts to analyze CCDs

ccd-analyze

Scripts to analyze CCDs

Usage:

cd src
groovy <SCRIPT> <DATADIR>

For example look at the runall.sh. It downloads data from CHB's Sample CCDAs repo and runs over them.

Contributing

This is what your script should look like

/**
 * This script prints the frequency of each section in the CCD
 */
import groovy.transform.BaseScript

@BaseScript CcdAnalysis script

def <K, V> Map<K, V> combineMaps(Map<K, List<V>> accum, Map<K, V> b) {
    accum + b.collectEntries { k, v -> [k, (accum[k] ?: []) + v] }
}

def result = files.parallelStream().map { File file ->
    def xml = new XmlSlurper().parse(file.newInputStream())
    def sections = xml.component.structuredBody.component.section

    sections.collectEntries { section ->
        [[e-mail](), section.title.text()]
    }
}.reduce([:]) {accum, newMap -> combineMaps(accum, newMap) }.collect {k, v ->
    [k, [count: v.size(), title: v.head()] ]
}

result.each {k, v -> println "$k - ${v.count} - ${v.title}" }

1. Give a clear groovydoc on top that explains what the script does.
2. Declare the @BaseScript to be CcdAnalysis. That lets users run all scripts in an identical way.
3. Use the property files to access all CCDs available to you.
4. Name your script in a meaningful way, e.g. SectionFrequency.groovy
5. Optionally if you need static typing, use @Grab('com.github.rahulsom:ihe-iti:0.8') .

For every other aspect, this is just another groovy script.

Recommended:

• Try to parallelize script execution. Everyone has a multi core processor these days, and many people crunch 1000s of CCDs with this.

Creating a pull request

1. Fork the repo
2. Clone it
3. Write your script, tweak an existing script
4. Send a pull request
5. Wait for Travis to run some tests
6. Wait for me to merge it