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Makefile
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Makefile
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# Run all commands in one shell
.ONESHELL:
# Default target
.DEFAULT_GOAL := help
.PHONY : help
## help: run 'make help" at commandline
help : Makefile
@sed -n 's/^##//p' $<
.PHONY: list
## list: list all targets in the current make file
list:
@LC_ALL=C $(MAKE) -pRrq -f $(lastword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/^# File/,/^# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | egrep -v -e '^[^[:alnum:]]' -e '^$@$$'
## fiducials_calibration: example commandline to run/test fiducials_calibration.py
fiducials_calibration:
fspython scripts/func_fiducials_calibration.py \
--in_img misc/fiducials_calibration/prospective_without_tissue.jpg \
--points 22 17 40 9 478 25 492 9 18 465 30 451 462 472 478 460 \
--width 272 --height 272 \
--out_file /tmp/cal
## fiducials_correction: example commandline to run/test fiducials_correction.py
fiducials_correction:
fspython scripts/func_fiducials_correction.py \
--in_dir misc/fiducials_correction_input/ \
--calibration_file /tmp/cal.npz \
--out_dir /tmp
## 2pt_correction: example commandline to run/test retrospective correction with 2 points
2pt_correction:
fspython scripts/func_retrospective_correction.py \
--in_img /cluster/vive/MGH_photo_recon/2604_whole/photos/2604.01.JPG \
--points 555 619 231 623 \
--width 65 --height 15 \
--out_dir /tmp
## 3pt_correction: example commandline to run/test retrospective correction with 3 points
3pt_correction:
fspython scripts/func_retrospective_correction.py \
--in_img /cluster/vive/UW_photo_recon/Photo_data/17-0333/17-0333_Images/17-0333\ Image.1.jpg \
--points 1320 4839 6036 399 1264 312 \
--width 290 --height 285 \
--out_dir /tmp
## 4pt_correction: example commandline to run/test retrospective correction with 4 points
4pt_correction:
fspython scripts/func_retrospective_correction.py \
--in_img /cluster/vive/UW_photo_recon/Photo_data/17-0333/17-0333_Images/17-0333\ Image.1.jpg \
--points 1320 4839 5959 4790 1264 312 6036 399 \
--width 290 --height 285 \
--out_dir /tmp
## connected_components: example commandline to run/test connected components script
connected_components:
fspython scripts/func_connected_components.py \
--rectangle_coordinates 431 559 477 602 1131 565 1180 628 1788 572 1841 641 \
--in_img /cluster/vive/MGH_photo_recon/2604_whole/deformed/2604.01_deformed.JPG \
--in_mask /cluster/vive/MGH_photo_recon/2604_whole/photos/masked/2604.01_deformed_masked.png \
--out_dir /tmp
## mask_to_cc:: example to convert masks to connected components
mask_to_cc:
fspython func_mask_to_cc.py \
--in_dir /cluster/vive/MGH_photo_recon/2604_whole/photos/masked \
--out_dir /tmp/cc_temp