Explore: Sampling Over Files

Suggest edits
Documentation > Explore > Direct Sampling

Contents

Data processing often revolves about massive computation using big bunch of files. Model inputs come in many shapes; this is why OpenMOLE features some file exploration functions to manipulate your datasets as easily as possible.

Exploring a set of files 🔗

OpenMOLE introduces the concept of Domains as a variable ranging along a set of files. For instance, to run a program over a set of files in a subdirectory you may use:
val f = Val[File]

DirectSampling(
  evaluation = myModel,
  sampling = f in (workDirectory / "dir"
)

To explore files located in several directories:
val i = Val[Int]
val f = Val[File]

DirectSampling(
  evaluation =  myModel,
  sampling =
    (i in (0 to 10)) x
    (f in (workDirectory / "dir").files("subdir${i}", recursive = true).filter(f => f.isDirectory && f.getName.startsWith("exp")))
)

The filter modifier filters the initial file sampling according to a predicate. You can filter using any function taking a File and producing a Boolean (see the corresponding javadoc or create your own). Some predicate functions available out of the box are startsWith(), contains(), endsWith() .
val f = Val[File]

DirectSampling(
  evaluation = myModel,
  sampling = (f in (workDirectory / "dir") filter(_.getName.endsWith(".nii.gz")) )
)

Searching in deep file trees can be very time consuming and irrelevant in some cases where you know how your data is organised. By default the file selector only explores the direct level under the directory you've passed as a parameter. If you want it to explore the whole file tree, you can set the option recursive to true as in files(recursive = true).


If you wish to select one single file for each value of i you may use the select operation:
val i = Val[Int]
val f = Val[File]

DirectSampling(
  evaluation = myModel,
  sampling =
    (i in (0 to 10)) x
    (f in (workDirectory / "dir").files("subdir${i}", recursive = true).filter(f => f.isDirectory && f.getName.startsWith("exp")))
)

Files vs Paths 🔗

As its name suggests, the files selector manipulates File instances and directly injects them in the dataflow.

If you plan to delegate your workflow to a local cluster environment equipped with a shared file system across all nodes, you don't need data to be automatically copied by OpenMOLE.

In this case, you might prefer the paths selector instead. Paths works exactly like files and accept the very same options. The only difference between the two selectors is that paths will inject Path variables in the dataflow.

Path describes a file's location but not its content. The explored files won't be automatically copied by OpenMOLE when using Path, so this does not fit a grid environment for instance.

import java.nio.file.Path

val dataDir     = "/vol/vipdata/data/HCP100"

val subjectPath = Val[Path]
val subjectID   = Val[String]

DirectSampling(
  evaluation = myModel,
  sampling = subjectPath in File(dataDir).paths(filter=".*\\.nii.gz") withName subjectID
)

More details on the difference between manipulating Files and Paths can be found in the dedicated entry of the FAQ.

More examples 🔗

You can find full examples using OpenMOLE's capabilities to process a dataset in the following entries of the marketplace:

Going further 🔗

Files can also be injected in the dataflow through Sources. They provide more powerful file filtering possibilities using regular expressions and can also target directories only.