added a figure to show another sequence type (globules without trap)
This sequence `soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0` needs to be processed for the article so I wanted to describe why the preprocessing doesn't give ideal results on it and how to improve it.
This commit is contained in:
parent
af6fdffdd3
commit
fcd9dde587
55
doc/Makefile
55
doc/Makefile
|
|
@ -9,6 +9,15 @@ lipase.pdf: lipase.tex graphics
|
||||||
TRAPS_VISIBLE_CONVERTER=convert -contrast-stretch 2%x1% -resize 25%
|
TRAPS_VISIBLE_CONVERTER=convert -contrast-stretch 2%x1% -resize 25%
|
||||||
|
|
||||||
GENERATED_GRAPHICS=\
|
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_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_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
|
graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000039_DM300_nofilter_vis_000.png
|
||||||
|
|
@ -16,17 +25,49 @@ GENERATED_GRAPHICS=\
|
||||||
.PHONY: graphics
|
.PHONY: graphics
|
||||||
graphics: $(GENERATED_GRAPHICS)
|
graphics: $(GENERATED_GRAPHICS)
|
||||||
|
|
||||||
graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000000_DM300_nofilter_vis_000.png : $(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_nofilter_vis_000.tif
|
# creates a rule to list min and max of imanges in an info file for the given sequence
|
||||||
$(TRAPS_VISIBLE_CONVERTER) "$<" "$@"
|
# 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 > "$$@"
|
||||||
|
|
||||||
graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000019_DM300_nofilter_vis_000.png : $(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000019_DM300_nofilter_vis_000.tif
|
graphics/$(subst /,_,$(1))_$(2)_%$(3).png : $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/%$(3).tif graphics/$(subst /,_,$(1))_$(2)_$(3).info
|
||||||
$(TRAPS_VISIBLE_CONVERTER) "$<" "$@"
|
convert -level $(4)x$(5) -resize 25% "$$<" "$$@"
|
||||||
|
endef
|
||||||
|
|
||||||
|
# creates a rule to convert tif images into png for the given sequence
|
||||||
|
# $1 : dir_path : eg soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1
|
||||||
|
# $2 : pos_dir : eg Pos0
|
||||||
|
# eg it will create graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_%.png from $(RAW_IMAGES_ROOT_PATH)/soleil2016/GGHL_rDGL_SGF55_lambda_Em_cinsuite_1/Pos0/%.tif
|
||||||
|
define GENERATE_TRAP_SEQUENCE_IMAGES_CONVERSION_RULE
|
||||||
|
graphics/$(subst /,_,$(1))_$(2)_%.png : $(RAW_IMAGES_ROOT_PATH)/$(1)/$(2)/%.tif
|
||||||
|
$(TRAPS_VISIBLE_CONVERTER) "$$<" "$$@"
|
||||||
|
endef
|
||||||
|
|
||||||
graphics/res_soleil2018_GGH_GGH_2018_cin2_phiG_I_327_vis_-40_1_Pos0_img_000000039_DM300_nofilter_vis_000.png : $(RAW_IMAGES_ROOT_PATH)/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000039_DM300_nofilter_vis_000.tif
|
# manually worked out sensible min and max values from graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_nofilter_vis_000.info
|
||||||
$(TRAPS_VISIBLE_CONVERTER) "$<" "$@"
|
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
|
.PHONY: clean
|
||||||
clean:
|
clean:
|
||||||
rm -f $(GENERATED_GRAPHICS)
|
rm -f $(GENERATED_GRAPHICS) graphics/*.info
|
||||||
rm -f lipase.pdf lipase.aux lipase.fls lipase.log lipase.fdb_latexmk lipase.dvi;
|
rm -f lipase.pdf lipase.aux lipase.fls lipase.log lipase.fdb_latexmk lipase.dvi;
|
||||||
|
|
|
||||||
|
|
@ -258,6 +258,77 @@
|
||||||
\label{fig:trap_sequence1}
|
\label{fig:trap_sequence1}
|
||||||
\end{figure}
|
\end{figure}
|
||||||
|
|
||||||
|
\begin{figure}
|
||||||
|
\centering
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_nofilter_vis_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 0}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
~
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_nofilter_vis_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 19}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
~
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_nofilter_vis_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 39}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
\\
|
||||||
|
\centering
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_327-353_fluo_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 0, 327nm - 353nm}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
~
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_327-353_fluo_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 19, 327nm - 353nm}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
~
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_327-353_fluo_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 39, 327nm - 353nm}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
\\
|
||||||
|
\centering
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000000_DM300_420-480_fluo_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 0, 420nm - 480nm}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
~
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000019_DM300_420-480_fluo_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 19, 420nm - 480nm}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
~
|
||||||
|
\begin{subfigure}[b]{0.3\textwidth}
|
||||||
|
\includegraphics[width=1.0\textwidth]{graphics/soleil2016_GGHL_rDGL_SGF55_lambda_Em_cinsuite_1_Pos0_img_000000039_DM300_420-480_fluo_000.png}
|
||||||
|
%\includegraphics[width=\textwidth]{1.png}
|
||||||
|
\caption{Frame 39, 420nm - 480nm}
|
||||||
|
%\label{fig:1}
|
||||||
|
\end{subfigure}
|
||||||
|
|
||||||
|
\caption{Example of trap sequence (\texttt{soleil2016/GGHL\_rDGL\_SGF55\_lambda\_Em\_cinsuite\_1/Pos0})}
|
||||||
|
\label{fig:sequence_gghl1}
|
||||||
|
\end{figure}
|
||||||
|
|
||||||
\subsection{computing the circularness image}
|
\subsection{computing the circularness image}
|
||||||
|
|
||||||
\label{sec:circularness}
|
\label{sec:circularness}
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue