lipase/doc/Makefile

RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images)


# pdflatex is called twice to ensure cross references are found
lipase.pdf: lipase.tex graphics
	pdflatex lipase.tex; pdflatex lipase.tex

# command used to convert traps sequences in the visible into png with maximum contrast
TRAPS_VISIBLE_CONVERTER=convert -contrast-stretch 2%x1% -resize 25%

GENERATED_GRAPHICS=\
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_nofilter_vis_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_nofilter_vis_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_nofilter_vis_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_327-353_fluo_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_327-353_fluo_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_327-353_fluo_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_420-480_fluo_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_420-480_fluo_000.png \
	graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_420-480_fluo_000.png \
	graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000000_DM300_nofilter_vis_000.png \
	graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000019_DM300_nofilter_vis_000.png \
	graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000039_DM300_nofilter_vis_000.png

.PHONY: graphics
graphics: $(GENERATED_GRAPHICS)

# creates a rule to list min and max of imanges in an info file for the given sequence
# creates a rule to convert tif images into png for the given sequence
# $1 : dir_path : eg soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1
# $2 : pos_dir : eg Pos0
# $3 : channel_suffix : eg 420-480_fluo_000
# $4 : min_value : the maximum pixel value for this channel (eg 631)
# $5 : max_value : the maximum pixel value for this channel (eg 1441)
# eg it will create graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_%.png from $(RAW_IMAGES_ROOT_PATH)/soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0/%.tif
define GENERATE_CHANNEL_IMAGES_CONVERSION_RULE
graphics/$(subst /,_,$(1))_$(2)_$(3).info:
	convert $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/*$(3).tif -format "%[filename] %[min] %[max]\n" info: 2>/dev/null > "$$@"

graphics/$(subst /,_,$(1))_$(2)_%$(3).png : $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/%$(3).tif graphics/$(subst /,_,$(1))_$(2)_$(3).info
	convert -level $(4)x$(5) -resize 25% "$$<" "$$@"
endef

# creates a rule to convert tif images into png for the given sequence
# $1 : dir_path : eg soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1
# $2 : pos_dir : eg Pos0
# eg it will create graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_%.png from $(RAW_IMAGES_ROOT_PATH)/soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0/%.tif
define GENERATE_TRAP_SEQUENCE_IMAGES_CONVERSION_RULE
graphics/$(subst /,_,$(1))_$(2)_%.png : $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/%.tif
	$(TRAPS_VISIBLE_CONVERTER) "$$<" "$$@"
endef

# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_nofilter_vis_000.info
SEQ_GGHL_RDGL_SGF55_VIS_MIN_VALUE = 13000
SEQ_GGHL_RDGL_SGF55_VIS_MAX_VALUE = 65535  # yes, the images are saturated!
$(eval $(call GENERATE_CHANNEL_IMAGES_CONVERSION_RULE,soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1,Pos0,nofilter_vis_000,$(SEQ_GGHL_RDGL_SGF55_VIS_MIN_VALUE),$(SEQ_GGHL_RDGL_SGF55_VIS_MAX_VALUE)))

# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_327-353_fluo_000.info
SEQ_GGHL_RDGL_SGF55_F340_MIN_VALUE = 631
SEQ_GGHL_RDGL_SGF55_F340_MAX_VALUE = 1441
$(eval $(call GENERATE_CHANNEL_IMAGES_CONVERSION_RULE,soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1,Pos0,327-353_fluo_000,$(SEQ_GGHL_RDGL_SGF55_F340_MIN_VALUE),$(SEQ_GGHL_RDGL_SGF55_F340_MAX_VALUE)))

# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_420-480_fluo_000.info
SEQ_GGHL_RDGL_SGF55_F450_MIN_VALUE = 700
SEQ_GGHL_RDGL_SGF55_F450_MAX_VALUE = 1800
$(eval $(call GENERATE_CHANNEL_IMAGES_CONVERSION_RULE,soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1,Pos0,420-480_fluo_000,$(SEQ_GGHL_RDGL_SGF55_F450_MIN_VALUE),$(SEQ_GGHL_RDGL_SGF55_F450_MAX_VALUE)))

$(eval $(call GENERATE_TRAP_SEQUENCE_IMAGES_CONVERSION_RULE,res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1,Pos0))

.PHONY: clean
clean:
	rm -f $(GENERATED_GRAPHICS) graphics/*.info
	rm -f lipase.pdf lipase.aux lipase.fls lipase.log lipase.fdb_latexmk lipase.dvi;