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acdc.make
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# MIT License
# Copyright (c) 2023 Hoel Kervadec
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
CC = python3.9
PP = PYTHONPATH="$(PYTHONPATH):."
SHELL = zsh
.PHONY: all geodist train plot view view_labels npy pack report weak
red:=$(shell tput bold ; tput setaf 1)
green:=$(shell tput bold ; tput setaf 2)
yellow:=$(shell tput bold ; tput setaf 3)
blue:=$(shell tput bold ; tput setaf 4)
reset:=$(shell tput sgr0)
# RD stands for Result DIR -- useful way to report from extracted archive
RD = results/acdc
# CFLAGS = -O
# DEBUG = --debug
EPC = 100
BS = 8 # BS stands for Batch Size
K = 4 # K for class
G_RGX = (patient\d+_\d+_\d+)_\d+
B_DATA = [('img', png_transform, False), ('gt', gt_transform, True)]
NET = ENet
# NET = Dummy
TRN = $(RD)/ce \
$(RD)/diceloss \
$(RD)/boundary
GRAPH = $(RD)/val_dice.png $(RD)/tra_dice.png \
$(RD)/tra_loss.png \
$(RD)/val_3d_dsc.png
BOXPLOT = $(RD)/val_3d_dsc_boxplot.png
PLT = $(GRAPH) $(HIST) $(BOXPLOT)
REPO = $(shell basename `git rev-parse --show-toplevel`)
DATE = $(shell date +"%y%m%d")
HASH = $(shell git rev-parse --short HEAD)
HOSTNAME = $(shell hostname)
PBASE = archives
PACK = $(PBASE)/$(REPO)-$(DATE)-$(HASH)-$(HOSTNAME)-acdc.tar.gz
all: pack
train: $(TRN)
plot: $(PLT)
pack: $(PACK) report
$(PACK): $(PLT) $(TRN)
$(info $(red)tar cf $@$(reset))
mkdir -p $(@D)
tar cf - $^ | pigz > $@
chmod -w $@
# tar -zc -f $@ $^ # Use if pigz is not available
# Data generation
data/ACDC-2D: OPT = --seed=0 --retain 25
data/ACDC-2D: data/acdc
$(info $(yellow)$(CC) $(CFLAGS) preprocess/slice_acdc.py$(reset))
rm -rf $@_tmp $@
$(PP) $(CC) $(CFLAGS) preprocess/slice_acdc.py --source_dir="data/acdc/training" --dest_dir=$@_tmp $(OPT)
mv $@_tmp $@
data/acdc: data/acdc.lineage data/acdc.zip
$(info $(yellow)unzip data/acdc.zip$(reset))
md5sum -c $<
rm -rf $@_tmp $@
unzip -q $(word 2, $^) -d $@_tmp
rm $@_tmp/training/*/*_4d.nii.gz # space optimization
mv $@_tmp $@
data/ACDC-2D/train/img data/ACDC-2D/val/img: | data/ACDC-2D
data/ACDC-2D/train/gt data/ACDC-2D/val/gt: | data/ACDC-2D
# Trainings
$(RD)/ce: OPT = --losses="[('CrossEntropy', {'idc': [0, 1, 2, 3]}, 1)]"
$(RD)/ce: data/ACDC-2D/train/gt data/ACDC-2D/val/gt
$(RD)/ce: DATA = --folders="$(B_DATA)+[('gt', gt_transform, True)]"
$(RD)/diceloss: OPT = --losses="[('DiceLoss', {'idc': [0, 1, 2, 3]}, 1)]"
$(RD)/diceloss: data/ACDC-2D/train/gt data/ACDC-2D/val/gt
$(RD)/diceloss: DATA = --folders="$(B_DATA)+[('gt', gt_transform, True)]"
$(RD)/boundary: OPT = --losses="[('BoundaryLoss', {'idc': [0, 1, 2, 3]}, 1)]"
$(RD)/boundary: data/ACDC-2D/train/gt data/ACDC-2D/val/gt
$(RD)/boundary: DATA = --folders="$(B_DATA)+[('gt', dist_map_transform, False)]"
# Template
$(RD)/%:
$(info $(green)$(CC) $(CFLAGS) main.py $@$(reset))
rm -rf $@_tmp
mkdir -p $@_tmp
printenv > $@_tmp/env.txt
git diff > $@_tmp/repo.diff
git rev-parse --short HEAD > $@_tmp/commit_hash
$(CC) $(CFLAGS) main.py --dataset=$(dir $(<D)) --batch_size=$(BS) --group --schedule \
--n_epoch=$(EPC) --workdir=$@_tmp --csv=metrics.csv --n_class=4 --metric_axis 1 2 3 \
--compute_3d_dice \
--grp_regex="$(G_RGX)" --network=$(NET) $(OPT) $(DATA) $(DEBUG)
mv $@_tmp $@
# Plotting
$(RD)/val_3d_dsc.png $(RD)/val_dice.png $(RD)/tra_dice.png: COLS = 1 2 3
$(RD)/tra_loss.png: COLS = 0
$(RD)/tra_loss.png: OPT = --dynamic_third_axis
$(RD)/val_dice.png $(RD)/tra_loss.png $(RD)/val_3d_dsc.png: plot.py $(TRN)
$(RD)/tra_dice.png: plot.py $(TRN)
$(RD)/val_3d_dsc_boxplot.png: COLS = 1 2 3
$(RD)/val_3d_dsc_boxplot.png: moustache.py $(TRN)
$(RD)/%.png:
$(info $(blue)$(CC) $(CFLAGS) $< $@$(reset))
$(eval metric:=$(subst _hist,,$(@F)))
$(eval metric:=$(subst _boxplot,,$(metric)))
$(eval metric:=$(subst .png,.npy,$(metric)))
$(CC) $(CFLAGS) $< --filename $(metric) --folders $(filter-out $<,$^) --columns $(COLS) \
--savefig=$@ --headless $(OPT)
# Viewing
view: $(TRN)
viewer/viewer.py -n 3 --img_source data/ACDC-2D/val/img data/ACDC-2D/val/gt \
$(addsuffix /best_epoch/val, $^) --crop 10 \
--display_names gt $(notdir $^) --no_contour -C $(K)
report: $(TRN)
$(info $(yellow)$(CC) $(CFLAGS) report.py$(reset))
$(CC) $(CFLAGS) report.py --folders $(TRN) --metrics val_3d_dsc val_dice --axises 3 $(DEBUG)