Question on make file about boundary-loss HOT 2 CLOSED

The makefile are made for GNU Make, where I make heavy use of automatic variables. To describe it quickly, it is simply a list of recipes in the form:

recipe_target: recipe_dependencies
    actions to 
    preform to 
    create the recipe

When you tell make to create recipe a that depends on b, it will first run the recipe for b, and then can do the one for a. If another recipe c also depends on b, it will do it directly without rebuilding b since it already exist. So I am building a chain of dependencies: the plots depends on the trained networks (and their metrics), the training depends on the sliced data, the sliced data depends on the extracted data. This is a really good way to automate the dependencies between sub-parts of the experiments. Take the time to decompose it and you should be able to understand how the different parts interact with each other.

I usually do not write them anymore from scratch, but start from an existing one and simply search and replace any reference to the previous dataset, and then modify the training options if needed. To give you an overview of what you need to change (taking wmh.make as an example):

Change the list of targets that interest you, for instance:

TRN = results/colon/gdl results/colon/gdl_surface_steal

GRAPH = results/colon/val_dice.png results/colon/tra_dice.png \
            results/colon/tra_loss.png \
            results/colon/val_haussdorf.png

HIST =  

Change the archive name:

PACK = $(PBASE)/$(REPO)-$(DATE)-$(HASH)-$(HOSTNAME)-colon.tar.gz

Extraction and slicing: write recipes to extract the data from the archive, and create the png files, training and validation set. This what will take you the most time, and is really task specific. I usually create a target data/colon for the extracted data, and data/COLON for the sliced data.

The options for the training come in two parts:

• the individual ones where you define the loss to use and its parameters (+ which training data to use)
• the common ones, which is mostly for the network architecture, number of classes, batch size, ... Note that those options can be overriden by the individual options if you want to

Apart from that, as long as you replace wmh with colon and WMH with COLON, the rest should work pretty well right away. Make has a few very useful options to debug it:

       -d   Print  debugging  information in addition to normal processing.  The debugging information says which files are being considered for remaking, which file-times are being compared and with what results, which files actually need to be remade, which implicit rules are considered and which are
            applied---everything interesting about how make decides what to do.
       -n, --just-print, --dry-run, --recon
            Print the commands that would be executed, but do not execute them (except in certain circumstances).
       --trace
            Information about the disposition of each target is printed (why the target is being rebuilt and what commands are run to rebuild it).

from boundary-loss.

Hi @HKervadec ,

Thanks for your reply very much. I will try to do ti.

from boundary-loss.