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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revisione514081ac649120c9c6550382920625266f22571 (tree)
Time2014-10-20 16:55:49
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Add: ASCII -> 2D/3D-Graph by GNUPLOT (But, required to specify gnuplot path ...)

new file: TIPS/Gnuplot/Makefile/Makefile
new file: TIPS/Gnuplot/Makefile/Makefile-lib

Modify: help message by "make" or "make help".
modified: 2DClustering/2DClustering1/Makefile
modified: CTFCorrection/CTFCorrection1/Makefile
modified: CTFCorrection/CTFCorrection2/Makefile
modified: CTFCorrection/CTFCorrection3/Makefile
modified: CTFCorrection/CTFCorrection4/Makefile
modified: CTFCorrection/CTFCorrection5/Makefile
modified: CTFCorrection/CTFCorrection6/Makefile
modified: SingleParticle/3DReconstruction/Makefile
modified: SingleParticle/3DReconstruction0/Makefile
modified: SingleParticle/3DReconstruction1/Makefile
modified: SingleParticle/3DReconstruction4/Makefile
modified: SingleParticle/3DReconstructionRadon/Makefile
modified: SingleParticle/Reference0/Makefile
modified: SingleParticle/Reference1/Makefile
modified: Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
modified: Tomography/Tomography0/Makefile
modified: Tomography/Tomography1/Makefile
modified: Tomography/Tomography2/Makefile
modified: Tomography/Tomography4/Makefile
modified: Tomography/Tomography5/Makefile
modified: Tomography/Tomography6/Makefile
modified: Tomography/Tomography7/Makefile

Change Summary

Incremental Difference

--- a/2DClustering/2DClustering1/Makefile
+++ b/2DClustering/2DClustering1/Makefile
@@ -2,18 +2,24 @@
22 # Makefile for 2D Clustering
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=2DClustering
57
68 #
79 # Preparetion
810 # xxxx.roi
911 # Makefile.config
1012 #
13+#### INCLUDE ####
14+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
1115 include Makefile.config
1216
1317 .SUFFIXES: .roi .preshrink .pad .padlst .log .logIn
1418 .SUFFIXES: .logps
1519 .SUFFIXES: .padsortlst .clstlst .clstref .fitlst .clstavg .normfitlst .normclstavg .norm .prop .subprop .subproplst .subpropmon .fit .fitCent .clstavgCent .normclstavgpad
1620
21+help_2DClustering::
22+ make Menu;
1723 #
1824 Menu::
1925 @echo "------------ How to use this Makefile-------------------"
--- a/CTFCorrection/CTFCorrection1/Makefile
+++ b/CTFCorrection/CTFCorrection1/Makefile
@@ -1,6 +1,11 @@
1+#### Root Makefile ####
2+MAKE_ROOT=CTFCorrection1
3+
14 .SUFFIXES: .tif .mrc .cen .nor .fft .ctfinfoauto \
25 .ctfinfo .ctf .ctfps
36
7+#### INCLUDE ####
8+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
49 -include TIFS
510 -include MRCS
611 -include CENS
@@ -19,7 +24,7 @@ RESOLUTION=3.80
1924 JN=-j 4
2025
2126 #####################
22-Help::
27+help_CTFCorrection1::
2328 @echo "----- How To Use -----"
2429 @echo "1. Prepare files(xxxx.tif) to be analyzed."
2530 @echo "2. make TIF2CTF"
--- a/CTFCorrection/CTFCorrection2/Makefile
+++ b/CTFCorrection/CTFCorrection2/Makefile
@@ -2,6 +2,9 @@
22 # This is Makefile for CTF Correction Demo.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=CTFCorrection2
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 INI_MRC_EXT=inimrc
@@ -17,6 +20,7 @@ GRID=grid
1720 #### Suffixes rule ####
1821
1922 #### INCLUDE ####
23+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
2024 -include Makefile.config
2125
2226 #### Definition ####
@@ -62,6 +66,9 @@ JOP_NUM=-j 3
6266
6367
6468 ##### Commands #####
69+help_CTFCorrection2::
70+ @echo "This is Makefile for CTF Correction Demo."
71+
6572 all2::
6673 make InitialCTFDataFromMRC;
6774 make ProcessForInput;
--- a/CTFCorrection/CTFCorrection3/Makefile
+++ b/CTFCorrection/CTFCorrection3/Makefile
@@ -2,6 +2,9 @@
22 # This is Makefile for CTF Correction Demo.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=CTFCorrection3
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 INI_MRC_EXT=inimrc
@@ -14,6 +17,7 @@ OUT_CTF_EXT=ctf
1417 #### Suffixes rule ####
1518
1619 #### INCLUDE ####
20+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
1721 -include Makefile.config
1822
1923 #### Definition ####
@@ -49,6 +53,9 @@ JOP_NUM=-j 3
4953 #### Rules of the list created ####
5054
5155 ##### Commands #####
56+help_CTFCorrection3::
57+ @echo "This is Makefile for CTF Correction Demo."
58+
5259 all3::
5360 make InitialCTFDataFromMRC;
5461 make ProcessForInput;
--- a/CTFCorrection/CTFCorrection4/Makefile
+++ b/CTFCorrection/CTFCorrection4/Makefile
@@ -2,6 +2,8 @@
22 # This is Main Makefile for CTF Correction Demo.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=CTFCorrection4
57
68 #### Input extention ####
79 # These extensions must all be different.
@@ -15,6 +17,7 @@ OUT_CTF_EXT=ctf
1517 #### Suffixes rule ####
1618
1719 #### INCLUDE ####
20+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
1821 -include Makefile.config
1922
2023 #### Definition ####
@@ -42,6 +45,9 @@ JOP_NUM=-j 3
4245 #### Rules of the list created ####
4346
4447 ##### Commands #####
48+help_CTFCorrection4::
49+ @echo "This is Makefile for CTF Correction Demo."
50+
4551 all4::
4652 make InitialCTFDataFromMRC;
4753 make ProcessForInputLoop;
--- a/CTFCorrection/CTFCorrection5/Makefile
+++ b/CTFCorrection/CTFCorrection5/Makefile
@@ -2,6 +2,9 @@
22 # This is Makefile for CTF Correction Demo(MultiCompensation).
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=CTFCorrection5
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 INI_MRC_EXT=inimrc
@@ -15,6 +18,7 @@ OUT_TIFF_EXT=tiff
1518 #### Suffixes rule ####
1619
1720 #### INCLUDE ####
21+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
1822 -include Makefile.config
1923
2024 #### Definition ####
@@ -51,6 +55,9 @@ JOP_NUM=-j 3
5155
5256
5357 ##### Commands #####
58+help_CTFCorrection5::
59+ @echo "This is Makefile for CTF Correction Demo(MultiCompensation)."
60+
5461 all3::
5562 make InitialCTFDataFromMRC;
5663 make ProcessForInput;
--- a/CTFCorrection/CTFCorrection6/Makefile
+++ b/CTFCorrection/CTFCorrection6/Makefile
@@ -2,6 +2,8 @@
22 # This is Main Makefile for CTF Correction Demo.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=CTFCorrection6
57
68 #### Input extention ####
79 # These extensions must all be different.
@@ -15,6 +17,7 @@ OUT_CTF_EXT=ctf
1517 #### Suffixes rule ####
1618
1719 #### INCLUDE ####
20+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
1821 -include Makefile.config
1922
2023 #### Definition ####
@@ -43,6 +46,9 @@ JOP_NUM=-j 3
4346 #### Rules of the list created ####
4447
4548 ##### Commands #####
49+help_CTFCorrection6::
50+ @echo "This is Main Makefile for CTF Correction Demo."
51+
4652 all6::
4753 make InitialCTFDataFromMRC;
4854 make ProcessForInput;
--- a/SingleParticle/3DReconstruction/Makefile
+++ b/SingleParticle/3DReconstruction/Makefile
@@ -2,10 +2,14 @@
22 # Eos for 3D reconstrucion from 2D rois using 3D initail reference
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=3DReconstruction
7+
58 .SUFFIXES: .3d .ref3d .ref2d .pad .padtmp .mask .maskfit .fit .fitmask .roi .corinfo .3dinfo .3dlst .3d .3dsm .3dsmCenter .ds6 .3dsmds6 .corinfo2 .corinfolst .cormap .parcorinfolst .parcorinfolstsort .gnuplotcorinfolst .3dlstselect .monlst .mon .ref2dtmp
69
710 SHELL=/bin/bash
811
12+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
913 -include ROIs
1014 -include CORINFOs
1115 -include PADs
@@ -187,6 +191,9 @@ CORINFO2s::
187191 echo "" >> CORINFO2s
188192
189193 ##############
194+help_3DReconstruction:
195+ @echo "Eos for 3D reconstrucion from 2D rois using 3D initail reference."
196+
190197 First::
191198 cp $(INITIAL).3d $(TARGET).ref3d
192199 touch *.roi
--- a/SingleParticle/3DReconstruction0/Makefile
+++ b/SingleParticle/3DReconstruction0/Makefile
@@ -2,6 +2,9 @@
22 # This is makefile of Sample for 3D-Reconstrucion.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=3DReconstruction0
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 IN_PDB_EXT=pdb
@@ -30,6 +33,7 @@ IN_TIFF_EXT=mrc
3033 #### INCLUDE ####
3134 SHELL=/bin/bash
3235
36+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3337 -include IN_ROI_LIST
3438 -include IN_PAD_LIST
3539 -include IN_CORR_LIST
@@ -220,7 +224,7 @@ IN_TIFF_LIST2::
220224 echo "" >> 3D_LIST_LIST
221225
222226 #### Commands ####
223-Help::
227+help_3DReconstruction0::
224228 @echo "This is makefile of Sample."
225229
226230 Initial::
--- a/SingleParticle/3DReconstruction1/Makefile
+++ b/SingleParticle/3DReconstruction1/Makefile
@@ -2,6 +2,9 @@
22 # This is makefile of Sample for 3D-Reconstrucion.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=3DReconstruction1
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 IN_PDB_EXT=pdb
@@ -30,6 +33,7 @@ IN_TIFF_EXT=mrc
3033 #### INCLUDE ####
3134 SHELL=/bin/bash
3235
36+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3337 -include IN_ROI_LIST
3438 -include IN_PAD_LIST
3539 -include IN_CORR_LIST
@@ -220,7 +224,7 @@ IN_TIFF_LIST2::
220224 echo "" >> 3D_LIST_LIST
221225
222226 #### Commands ####
223-Help::
227+help_3DReconstruction1::
224228 @echo "This is makefile of Sample."
225229
226230 Initial::
--- a/SingleParticle/3DReconstruction4/Makefile
+++ b/SingleParticle/3DReconstruction4/Makefile
@@ -2,6 +2,9 @@
22 # This is makefile of Sample for 3D-Reconstrucion.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=3DReconstruction4
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 IN_PDB_EXT=pdb
@@ -30,6 +33,7 @@ IN_TIFF_EXT=mrc
3033 #### INCLUDE ####
3134 SHELL=/bin/bash
3235
36+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3337 -include IN_ROI_LIST
3438 -include IN_PAD_LIST
3539 -include IN_CORR_LIST
@@ -220,7 +224,7 @@ IN_TIFF_LIST2::
220224 echo "" >> 3D_LIST_LIST
221225
222226 #### Commands ####
223-Help::
227+help_3DReconstruction4::
224228 @echo "This is makefile of Sample."
225229
226230 Initial::
--- a/SingleParticle/3DReconstructionRadon/Makefile
+++ b/SingleParticle/3DReconstructionRadon/Makefile
@@ -2,6 +2,9 @@
22 # This is a Makefile to make 3D-Data using the RadonTransform from 2D-Datas and 3DList.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=3DReconstructionRadon
7+
58 #### Input extention and listname ####
69 IN_3D_EXT=fit
710 IN_3DLIST_EXT=3dlst
@@ -12,6 +15,7 @@ IN_3DLIST_EXT=3dlst
1215 SHELL=/bin/bash
1316
1417 #### INCLUDE ####
18+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
1519 -include IN_3D_LIST
1620
1721 #### Definition ####
@@ -40,7 +44,7 @@ IN_3D_LIST::
4044
4145
4246 #### Commands ####
43-Help::
47+help_3DReconstructionRadon::
4448 @echo "This is a Makefile to make 3D-Data using the RadonTransform from 2D-Datas and 3DList."
4549
4650 All::
--- a/SingleParticle/Reference0/Makefile
+++ b/SingleParticle/Reference0/Makefile
@@ -2,6 +2,9 @@
22 # This is makefile of Sample for 3D-Reconstrucion.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=Refernce0
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 INI_PDB_EXT=pdb
@@ -38,6 +41,7 @@ DST_1D_EXT=1ddst
3841 #### INCLUDE ####
3942 SHELL=/bin/bash
4043
44+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
4145 -include BASE_ROI_LIST
4246 -include IN_ROI_LIST
4347 -include ROI_SINO_LIST
@@ -267,7 +271,7 @@ IN_1D_LIST::
267271 echo "" >> IN_1D_LIST
268272
269273 #### Commands ####
270-Help::
274+help_Refernce0::
271275 @echo "This is makefile of Sample."
272276
273277 Initial::
--- a/SingleParticle/Reference1/Makefile
+++ b/SingleParticle/Reference1/Makefile
@@ -2,6 +2,9 @@
22 # This is makefile of Sample for 3D-Reconstrucion.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=Refernce1
7+
58 #### Input extention ####
69 # These extensions must all be different.
710 INI_PDB_EXT=pdb
@@ -38,6 +41,7 @@ DST_1D_EXT=1ddst
3841 #### INCLUDE ####
3942 SHELL=/bin/bash
4043
44+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
4145 -include BASE_ROI_LIST
4246 -include IN_ROI_LIST
4347 -include ROI_SINO_LIST
@@ -267,7 +271,7 @@ IN_1D_LIST::
267271 echo "" >> IN_1D_LIST
268272
269273 #### Commands ####
270-Help::
274+help_Refernce1::
271275 @echo "This is makefile of Sample."
272276
273277 Initial::
--- a/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
+++ b/Small Tools/mrcImage/mrcImageFourierNeighborCorrelation/Makefile/Makefile
@@ -46,9 +46,16 @@ Initial::
4646 make InputBackImage;
4747 make InputMaskImage;
4848
49+Exe::
50+ make FSC;
51+
4952 all::
5053 make Initial;
51- make FSC;
54+ make Exe;
55+ make Final;
56+
57+Final::
58+
5259
5360 help_mrcImageFourierNeighborCorrelation::
5461 @echo
--- /dev/null
+++ b/TIPS/Gnuplot/Makefile/Makefile
@@ -0,0 +1,65 @@
1+#
2+# This is Main Makefile for Gnuplot.
3+#
4+
5+#### Root Makefile ####
6+MAKE_ROOT=Gnuplot
7+
8+#### Input extention ####
9+INI=mrc
10+IN_GNU=txt
11+GNU_X_SIZE=480
12+GNU_Y_SIZE=480
13+GNU_Z_SIZE=480
14+
15+#### Suffixes rule ####
16+# Defined at Sub
17+
18+#### INCLUDE ####
19+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
20+-include Makefile-lib
21+
22+#### Definition ####
23+# Path of Input File
24+# Basically, use a linked data from /SampleData.
25+INPUT_PATH=${EOS_HOME}/tutorial/SampleData/XXXX.mrc
26+
27+### FileData
28+FILE_NAME=Input
29+
30+#### Rules of the list created ####
31+# Defined at Sub
32+
33+##### Commands #####
34+# Defined at Sub basically
35+Initial::
36+# $(RM) $(FILE_NAME).$(INI);
37+# ln -s $(INPUT_PATH) $(FILE_NAME).$(INI);
38+ mrcImageGaussDisc -o "$(FILE_NAME).$(INI)"
39+ mrcImageInfo -i "$(FILE_NAME).$(INI)" -x -o "$(FILE_NAME)-2d.$(IN_GNU)";
40+ mrcImageMakeDump -i "$(FILE_NAME).$(INI)" -o "$(FILE_NAME)-3d.$(IN_GNU)";
41+
42+Exe::
43+ make Exe2D;
44+ make Exe3D;
45+
46+Exe2D::
47+ @export IN_GNU_FILE_NAME=$(FILE_NAME)-2d; \
48+ export OUT_GNU_FILE_NAME=$(FILE_NAME)-2d; \
49+ export OUT_GNU=png; \
50+ export VIEW_GNU_FILE_NAME=2D; \
51+ make gnuplot2D;
52+
53+Exe3D::
54+ @export IN_GNU_FILE_NAME=$(FILE_NAME)-3d; \
55+ export OUT_GNU_FILE_NAME=$(FILE_NAME)-3d; \
56+ export OUT_GNU=png; \
57+ export VIEW_GNU_FILE_NAME=3D; \
58+ make gnuplot3D;
59+
60+all::
61+ make Initial;
62+ make Exe;
63+
64+##### Commands(Input to Output) #####
65+# Defined at Sub
--- /dev/null
+++ b/TIPS/Gnuplot/Makefile/Makefile-lib
@@ -0,0 +1,99 @@
1+#
2+# This is Sub Makefile for Gnuplot.
3+#
4+
5+#### Input extention ####
6+# Defined at Main
7+
8+#### Suffixes rule ####
9+.SUFFIXES:
10+
11+#### INCLUDE ####
12+# Use TIPS File.
13+# -include ${EOS_HOME}/tutorial/TIPS/XXXX/Makefile/Makefile-lib
14+
15+#### Definition ####
16+# Defined at Main
17+# gnuplot Application directory path
18+G_PLOT_PATH=${GNUPLOT_PATH}
19+G_PLOT_EXE="${GNUPLOT_PATH}gnuplot"
20+
21+#### Rules of the list created ####
22+
23+
24+##### Commands #####
25+gnuplot2D::
26+ @if [ ! -z $(G_PLOT_EXE) -a ! -z "$(IN_GNU_FILE_NAME).$(IN_GNU)" ] ; then \
27+ if [ ! -z "$(GNU_X_SIZE)" -a ! -z "$(GNU_Y_SIZE)" -a ! -z "$(OUT_GNU_FILE_NAME)" -a ! -z "$(OUT_GNU)" ] ; then \
28+ OPTION1="set terminal png size $(GNU_X_SIZE), $(GNU_Y_SIZE); set output '$(OUT_GNU_FILE_NAME).$(OUT_GNU)' ;"; \
29+ else \
30+ OPTION2="pause -1 ;" ; \
31+ fi; \
32+ if [ -z "$(VIEW_GNU_FILE_NAME)" ] ; then \
33+ VIEW_GNU_FILE_NAME="$(IN_GNU_FILE_NAME).$(IN_GNU)"; \
34+ else \
35+ $(RM) $(VIEW_GNU_FILE_NAME); \
36+ ln -s "$(IN_GNU_FILE_NAME).$(IN_GNU)" $(VIEW_GNU_FILE_NAME); \
37+ VIEW_GNU_FILE_NAME=$(VIEW_GNU_FILE_NAME); \
38+ fi; \
39+ $(G_PLOT_EXE) -e " \
40+ $$OPTION1 \
41+ plot '$$VIEW_GNU_FILE_NAME' ; \
42+ $$OPTION2 \
43+ "; \
44+ $(RM) $(VIEW_GNU_FILE_NAME); \
45+ echo "success gnuplot2D"; \
46+ else \
47+ echo "failed gnuplot2D"; \
48+ fi;
49+
50+gnuplot3D::
51+ @if [ ! -z $(G_PLOT_EXE) -a ! -z "$(IN_GNU_FILE_NAME).$(IN_GNU)" ] ; then \
52+ if [ ! -z "$(GNU_X_SIZE)" -a ! -z "$(GNU_Y_SIZE)" -a ! -z "$(GNU_Z_SIZE)" -a ! -z "$(OUT_GNU_FILE_NAME)" -a ! -z "$(OUT_GNU)" ] ; then \
53+ OPTION1="set terminal png size $(GNU_X_SIZE), $(GNU_Y_SIZE); set output '$(OUT_GNU_FILE_NAME).$(OUT_GNU)' ;"; \
54+ else \
55+ OPTION2="pause -1 ;" ; \
56+ fi; \
57+ if [ -z "$(VIEW_GNU_FILE_NAME)" ] ; then \
58+ VIEW_GNU_FILE_NAME="$(IN_GNU_FILE_NAME).$(IN_GNU)"; \
59+ else \
60+ $(RM) $(VIEW_GNU_FILE_NAME); \
61+ ln -s "$(IN_GNU_FILE_NAME).$(IN_GNU)" $(VIEW_GNU_FILE_NAME); \
62+ VIEW_GNU_FILE_NAME=$(VIEW_GNU_FILE_NAME); \
63+ fi; \
64+ $(G_PLOT_EXE) -e " \
65+ $$OPTION1 \
66+ splot '$$VIEW_GNU_FILE_NAME' ; \
67+ $$OPTION2 \
68+ "; \
69+ $(RM) $(VIEW_GNU_FILE_NAME); \
70+ echo "success gnuplot3D"; \
71+ else \
72+ echo "failed gnuplot3D"; \
73+ fi;
74+
75+help_Gnuplot::
76+ @echo
77+ @echo "Gnuplot"
78+ @echo "This is Sub Makefile for Gnuplot."
79+ @echo
80+ @echo " (Command):"
81+ @echo " gnuplot2D: view 2D data by gnuplot."
82+ @echo " gnuplot3D: view 3D data by gnuplot."
83+ @echo
84+ @echo " (Setting Data):"
85+ @echo " IN_GNU_FILE_NAME: input file name."
86+ @echo " IN_GNU: input file extention."
87+ @echo " (Note) Input file is required to be 2D or 3D that is delimited by space or tab."
88+ @echo " ====== If the following is set, output the image. ======"
89+ @echo " OUT_GNU_FILE_NAME: output file name."
90+ @echo " OUT_GNU: output file extention."
91+ @echo " GNU_X_SIZE: output tiff size x"
92+ @echo " GNU_Y_SIZE: output tiff size y"
93+ @echo " GNU_Z_SIZE: output tiff size z"
94+ @echo " ====== Option ======"
95+ @echo " VIEW_FILE_NAME: displayfile name on gnuplot."
96+ @echo
97+
98+##### Commands(Input to Output) #####
99+
--- a/Tomography/Tomography0/Makefile
+++ b/Tomography/Tomography0/Makefile
@@ -2,6 +2,9 @@
22 # This is a sample Makefile for electron tomography.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=ElectronTomography0
7+
58 #### Input extention and listname ####
69 # For mrcImageCorrelation
710 IN_CORR_EXT=mask
@@ -24,6 +27,7 @@ IN_MASK_LIST=NROIs
2427
2528 SHELL=/bin/bash
2629
30+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
2731 -include $(IN_TIFF_LIST)
2832 -include $(IN_CORR_LIST)_plus
2933 -include $(IN_CORR_LIST)_minus
@@ -118,7 +122,7 @@ $(IN_MASK_LIST)::
118122 echo "" >> $(IN_MASK_LIST)
119123
120124 #### Commands ####
121-Help::
125+help_ElectronTomography0::
122126 @echo "This is a sample Makefile for electron tomography."
123127
124128 All::
--- a/Tomography/Tomography1/Makefile
+++ b/Tomography/Tomography1/Makefile
@@ -2,6 +2,9 @@
22 # This is a sample Makefile for electron tomography.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=ElectronTomography1
7+
58 #### Input extention and listname ####
69 # For mrcImageCorrelation
710 IN_CORR_EXT=mask
@@ -27,6 +30,7 @@ IN_3D_EXT=fit
2730
2831 SHELL=/bin/bash
2932
33+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3034 -include IN_NOISE_LIST
3135 -include IN_MASK_LIST
3236 -include IN_CORR_LIST_plus
@@ -151,7 +155,7 @@ IN_TIFF_LIST::
151155 echo "" >> IN_TIFF_LIST
152156
153157 #### Commands ####
154-Help::
158+help_ElectronTomography1::
155159 @echo "This is a sample Makefile for electron tomography."
156160
157161 TestData::
--- a/Tomography/Tomography2/Makefile
+++ b/Tomography/Tomography2/Makefile
@@ -2,6 +2,10 @@
22 # This is a sample Makefile for electron tomography.
33 #
44
5+
6+#### Root Makefile ####
7+MAKE_ROOT=ElectronTomography2
8+
59 #### Input extention and listname ####
610 # For mrcImageCorrelation
711 IN_CORR_EXT=mask
@@ -26,6 +30,7 @@ IN_3D_EXT=fit
2630
2731 SHELL=/bin/bash
2832
33+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
2934 -include IN_NOISE_LIST
3035 -include IN_MASK_LIST
3136 -include IN_CORR_LIST_plus
@@ -148,7 +153,7 @@ IN_TIFF_LIST::
148153 echo "" >> IN_TIFF_LIST
149154
150155 #### Commands ####
151-Help::
156+help_ElectronTomography2::
152157 @echo "This is a sample Makefile for electron tomography."
153158
154159 TestData::
--- a/Tomography/Tomography4/Makefile
+++ b/Tomography/Tomography4/Makefile
@@ -2,6 +2,9 @@
22 # This is a sample Makefile(ver.2) for electron tomography.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=ElectronTomography4
7+
58 # These extensions must all be different.
69 INI_PDB_EXT=pdb
710 INI_3D1_EXT=ini3d1
@@ -27,6 +30,7 @@ AVE_3D_EXT=3dave
2730 #### INCLUDE ####
2831 SHELL=/bin/bash
2932
33+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3034 -include IN_ROI_LIST
3135 -include DIV_3D_LIST
3236
@@ -126,7 +130,7 @@ FIT_3D_LIST::
126130 ls -1 *.$(FIT_3D_EXT) | sort -t - -k1,1 -k2,2 -k3,3 -k4 -n >> FIT_3D_LIST
127131
128132 #### Commands ####
129-Help::
133+help_ElectronTomography4::
130134 @echo "This is a sample Makefile(Ver2) for electron tomography."
131135
132136 #all: data2mrc COARCreate $(ORIBASE).roiinfo BoxCreate PadAndMul roilstCreate ds6Create
--- a/Tomography/Tomography5/Makefile
+++ b/Tomography/Tomography5/Makefile
@@ -2,6 +2,9 @@
22 # This is a sample Makefile(ver.2) for electron tomography.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=ElectronTomography5
7+
58 # These extensions must all be different.
69 INI_PDB_EXT=pdb
710 INI_3D1_EXT=ini3d1
@@ -32,6 +35,7 @@ SHELL=/bin/bash
3235
3336
3437 #### INCLUDE ####
38+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3539 -include IN_ROI_LIST
3640 -include DIV_3D_LIST
3741
@@ -222,7 +226,7 @@ FIT_3D_LIST::
222226
223227 #### Commands ####
224228
225-help::
229+help_ElectronTomography5::
226230 @echo "----- 3D Reconstruction using Eos ------------"
227231 @echo "#Prepare tif-series"
228232 @echo "make Init ; # Prepare directories"
--- a/Tomography/Tomography6/Makefile
+++ b/Tomography/Tomography6/Makefile
@@ -2,6 +2,9 @@
22 # This is a sample Makefile(ver.2) for electron tomography.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=ElectronTomography6
7+
58 # These extensions must all be different.
69 INI_PDB_EXT=pdb
710 INI_3D1_EXT=ini3d1
@@ -32,6 +35,7 @@ SHELL=/bin/bash
3235
3336
3437 #### INCLUDE ####
38+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3539 -include IN_ROI_LIST
3640 -include DIV_3D_LIST
3741
@@ -222,7 +226,7 @@ FIT_3D_LIST::
222226
223227 #### Commands ####
224228
225-help::
229+help_ElectronTomography6::
226230 @echo "----- 3D Reconstruction using Eos ------------"
227231 @echo "#Prepare tif-series"
228232 @echo "make Init ; # Prepare directories"
--- a/Tomography/Tomography7/Makefile
+++ b/Tomography/Tomography7/Makefile
@@ -2,6 +2,9 @@
22 # This is a sample Makefile for electron tomography.
33 #
44
5+#### Root Makefile ####
6+MAKE_ROOT=ElectronTomography7
7+
58 #### Input extention and listname ####
69 # For mrcImageCorrelation
710 IN_CORR_EXT=mask
@@ -28,6 +31,7 @@ IN_LIST_EXT=roilst
2831
2932 SHELL=/bin/bash
3033
34+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
3135 -include IN_NOISE_LIST
3236 -include IN_MASK_LIST
3337 -include IN_CORR_LIST_plus
@@ -153,7 +157,7 @@ IN_TIFF_LIST::
153157 echo "" >> IN_TIFF_LIST
154158
155159 #### Commands ####
156-Help::
160+help_ElectronTomography7::
157161 @echo "This is a sample Makefile for electron tomography."
158162
159163 TestData::
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