25 Aug 2020

Apply a Recipe on a Batch of Files

Apply a recipe to a batch of files and save results in output directory.


This Xtra proposes a module that allows applying a Recipe to a list of files. For each input file, the recipe results are saved in the specific output directory in am format. Result spreadsheets are also exported as .csv files.

Any recipe using a single input can be used. However, the recipe input type must be compatible with the provided inputs, and errors will appear in the console otherwise.

The inputs must be one file per dataset (e.g. no 3D volume represented as a stack of 2D TIFF).

Multichannel datasets can also be processed, but must be available as a single .am file.
Recipes processing multichannel datasets may be generated thanks to the module 'ChannelSelector', also included in the archive.
Recipes processing grayscale images may be applied to a specific channel of a multichannel input using the Process Channel port.

Use the Recipe Player and Export mode with the recipes provided in this archive to see how to build recipes including multichannel data.

Multiple-Dicom files can also be processed. In this case, the input must be a root directory where each subdirectory contains all the Dicom files related to a single dataset.