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-rw-r--r--.gitignore1
-rw-r--r--Makefile.am19
-rw-r--r--Makefile.in131
-rw-r--r--data/geomatic.ui28
-rw-r--r--data/hdfsee.ui (renamed from data/displaywindow.ui)0
-rw-r--r--src/cell.c60
-rw-r--r--src/cell.h2
-rw-r--r--src/detector.c20
-rw-r--r--src/detector.h1
-rw-r--r--src/displaywindow.c2
-rw-r--r--src/dw-geomatic.c801
-rw-r--r--src/dw-geomatic.h68
-rw-r--r--src/geomatic.c81
-rw-r--r--src/indexamajig.c10
-rw-r--r--src/templates.c60
15 files changed, 1139 insertions, 145 deletions
diff --git a/.gitignore b/.gitignore
index 6e1ca3f1..7957270c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,5 +21,6 @@ src/reintegrate
src/estimate_background
src/check_hkl
src/sum_stack
+src/geomatic
src/.dirstamp
*~
diff --git a/Makefile.am b/Makefile.am
index 8ecce78b..52b842b1 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -12,7 +12,7 @@ noinst_PROGRAMS = tests/list_check
TESTS = tests/list_check
if HAVE_GTK
-bin_PROGRAMS += src/hdfsee
+bin_PROGRAMS += src/hdfsee src/geomatic
endif
if HAVE_CAIRO
@@ -53,6 +53,11 @@ if HAVE_GTK
src_hdfsee_SOURCES = src/hdfsee.c src/displaywindow.c src/render.c \
src/hdf5-file.c src/utils.c src/image.c src/filters.c \
src/thread-pool.c
+
+src_geomatic_SOURCES = src/geomatic.c src/dw-geomatic.c src/render.c \
+ src/hdf5-file.c src/utils.c src/image.c src/filters.c \
+ src/thread-pool.c src/cell.c src/reflist.c src/geometry.c \
+ src/peaks.c src/detector.c
endif
src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
@@ -117,21 +122,21 @@ EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
src/index.h src/filters.h src/diffraction-gpu.h src/cl-utils.h \
src/symmetry.h src/povray.h src/index-priv.h src/geometry.h \
src/templates.h src/render_hkl.h src/stream.h src/thread-pool.h \
- src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h
-
-hdfseedir = $(datadir)/hdfsee
-hdfsee_DATA = data/displaywindow.ui
+ src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h \
+ src/dw-geomatic.h
crystfeldir = $(datadir)/crystfel
crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
- data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat
+ data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
+ data/hdfsee.ui data/geomatic.ui
EXTRA_DIST += data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
- data/defs.h data/diffraction.cl data/displaywindow.ui
+ data/defs.h data/diffraction.cl data/hdfsee.ui \
+ data/geomatic.ui
crystfeldocdir = $(docdir)
crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
diff --git a/Makefile.in b/Makefile.in
index e1f68a5c..588c3418 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -44,7 +44,7 @@ bin_PROGRAMS = src/pattern_sim$(EXEEXT) src/process_hkl$(EXEEXT) \
src/sum_stack$(EXEEXT) $(am__EXEEXT_1) $(am__EXEEXT_2)
noinst_PROGRAMS = tests/list_check$(EXEEXT)
TESTS = tests/list_check$(EXEEXT)
-@HAVE_GTK_TRUE@am__append_1 = src/hdfsee
+@HAVE_GTK_TRUE@am__append_1 = src/hdfsee src/geomatic
@HAVE_CAIRO_TRUE@am__append_2 = src/cubeit
@HAVE_OPENCL_TRUE@am__append_3 = src/diffraction-gpu.c src/cl-utils.c
@HAVE_OPENCL_TRUE@am__append_4 = src/diffraction-gpu.c src/cl-utils.c
@@ -74,11 +74,11 @@ mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
-@HAVE_GTK_TRUE@am__EXEEXT_1 = src/hdfsee$(EXEEXT)
+@HAVE_GTK_TRUE@am__EXEEXT_1 = src/hdfsee$(EXEEXT) \
+@HAVE_GTK_TRUE@ src/geomatic$(EXEEXT)
@HAVE_CAIRO_TRUE@am__EXEEXT_2 = src/cubeit$(EXEEXT)
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(crystfeldir)" \
- "$(DESTDIR)$(crystfeldocdir)" "$(DESTDIR)$(hdfseedir)" \
- "$(DESTDIR)$(scriptdir)"
+ "$(DESTDIR)$(crystfeldocdir)" "$(DESTDIR)$(scriptdir)"
PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
am__dirstamp = $(am__leading_dot)dirstamp
am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT) \
@@ -123,6 +123,20 @@ src_estimate_background_OBJECTS = \
$(am_src_estimate_background_OBJECTS)
src_estimate_background_LDADD = $(LDADD)
src_estimate_background_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
+am__src_geomatic_SOURCES_DIST = src/geomatic.c src/dw-geomatic.c \
+ src/render.c src/hdf5-file.c src/utils.c src/image.c \
+ src/filters.c src/thread-pool.c src/cell.c src/reflist.c \
+ src/geometry.c src/peaks.c src/detector.c
+@HAVE_GTK_TRUE@am_src_geomatic_OBJECTS = src/geomatic.$(OBJEXT) \
+@HAVE_GTK_TRUE@ src/dw-geomatic.$(OBJEXT) src/render.$(OBJEXT) \
+@HAVE_GTK_TRUE@ src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) \
+@HAVE_GTK_TRUE@ src/image.$(OBJEXT) src/filters.$(OBJEXT) \
+@HAVE_GTK_TRUE@ src/thread-pool.$(OBJEXT) src/cell.$(OBJEXT) \
+@HAVE_GTK_TRUE@ src/reflist.$(OBJEXT) src/geometry.$(OBJEXT) \
+@HAVE_GTK_TRUE@ src/peaks.$(OBJEXT) src/detector.$(OBJEXT)
+src_geomatic_OBJECTS = $(am_src_geomatic_OBJECTS)
+src_geomatic_LDADD = $(LDADD)
+src_geomatic_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am_src_get_hkl_OBJECTS = src/get_hkl.$(OBJEXT) src/sfac.$(OBJEXT) \
src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
src/reflections.$(OBJEXT) src/symmetry.$(OBJEXT) \
@@ -259,16 +273,18 @@ am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
am__v_GEN_0 = @echo " GEN " $@;
SOURCES = $(src_calibrate_detector_SOURCES) $(src_check_hkl_SOURCES) \
$(src_compare_hkl_SOURCES) $(src_cubeit_SOURCES) \
- $(src_estimate_background_SOURCES) $(src_get_hkl_SOURCES) \
- $(src_hdfsee_SOURCES) $(src_indexamajig_SOURCES) \
- $(src_partialator_SOURCES) $(src_pattern_sim_SOURCES) \
- $(src_powder_plot_SOURCES) $(src_process_hkl_SOURCES) \
- $(src_reintegrate_SOURCES) $(src_render_hkl_SOURCES) \
- $(src_sum_stack_SOURCES) $(tests_list_check_SOURCES)
+ $(src_estimate_background_SOURCES) $(src_geomatic_SOURCES) \
+ $(src_get_hkl_SOURCES) $(src_hdfsee_SOURCES) \
+ $(src_indexamajig_SOURCES) $(src_partialator_SOURCES) \
+ $(src_pattern_sim_SOURCES) $(src_powder_plot_SOURCES) \
+ $(src_process_hkl_SOURCES) $(src_reintegrate_SOURCES) \
+ $(src_render_hkl_SOURCES) $(src_sum_stack_SOURCES) \
+ $(tests_list_check_SOURCES)
DIST_SOURCES = $(src_calibrate_detector_SOURCES) \
$(src_check_hkl_SOURCES) $(src_compare_hkl_SOURCES) \
$(am__src_cubeit_SOURCES_DIST) \
- $(src_estimate_background_SOURCES) $(src_get_hkl_SOURCES) \
+ $(src_estimate_background_SOURCES) \
+ $(am__src_geomatic_SOURCES_DIST) $(src_get_hkl_SOURCES) \
$(am__src_hdfsee_SOURCES_DIST) \
$(am__src_indexamajig_SOURCES_DIST) $(src_partialator_SOURCES) \
$(am__src_pattern_sim_SOURCES_DIST) $(src_powder_plot_SOURCES) \
@@ -303,8 +319,7 @@ am__nobase_list = $(am__nobase_strip_setup); \
am__base_list = \
sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
-DATA = $(crystfel_DATA) $(crystfeldoc_DATA) $(hdfsee_DATA) \
- $(script_DATA)
+DATA = $(crystfel_DATA) $(crystfeldoc_DATA) $(script_DATA)
RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
distclean-recursive maintainer-clean-recursive
AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
@@ -559,13 +574,14 @@ EXTRA_DIST = configure m4/gnulib-cache.m4 src/cell.h src/hdf5-file.h \
src/povray.h src/index-priv.h src/geometry.h src/templates.h \
src/render_hkl.h src/stream.h src/thread-pool.h \
src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h \
- data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
- data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff \
- data/sfac/O.nff data/sfac/P.nff data/sfac/S.nff \
- data/sfac/f0_WaasKirf.dat data/defs.h data/diffraction.cl \
- data/displaywindow.ui doc/geometry.txt doc/indexamajig.txt \
- doc/pattern_sim.txt doc/process_hkl.txt doc/symmetry.txt \
- doc/twin-calculator.pdf doc/0-INDEX doc/examples/lcls-dec.geom \
+ src/dw-geomatic.h data/sfac/Ca.nff data/sfac/C.nff \
+ data/sfac/Fe.nff data/sfac/H.nff data/sfac/Mg.nff \
+ data/sfac/N.nff data/sfac/O.nff data/sfac/P.nff \
+ data/sfac/S.nff data/sfac/f0_WaasKirf.dat data/defs.h \
+ data/diffraction.cl data/hdfsee.ui data/geomatic.ui \
+ doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
+ doc/process_hkl.txt doc/symmetry.txt doc/twin-calculator.pdf \
+ doc/0-INDEX doc/examples/lcls-dec.geom \
doc/examples/lcls-june-r0013-r0128.geom \
doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom \
scripts/check-near-bragg scripts/double-hit \
@@ -602,6 +618,11 @@ src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c \
@HAVE_GTK_TRUE@ src/hdf5-file.c src/utils.c src/image.c src/filters.c \
@HAVE_GTK_TRUE@ src/thread-pool.c
+@HAVE_GTK_TRUE@src_geomatic_SOURCES = src/geomatic.c src/dw-geomatic.c src/render.c \
+@HAVE_GTK_TRUE@ src/hdf5-file.c src/utils.c src/image.c src/filters.c \
+@HAVE_GTK_TRUE@ src/thread-pool.c src/cell.c src/reflist.c src/geometry.c \
+@HAVE_GTK_TRUE@ src/peaks.c src/detector.c
+
src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
src/reflections.c src/symmetry.c src/beam-parameters.c \
src/thread-pool.c
@@ -654,13 +675,12 @@ tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
src/utils.c
INCLUDES = "-I$(top_srcdir)/data"
-hdfseedir = $(datadir)/hdfsee
-hdfsee_DATA = data/displaywindow.ui
crystfeldir = $(datadir)/crystfel
crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
- data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat
+ data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
+ data/hdfsee.ui data/geomatic.ui
crystfeldocdir = $(docdir)
crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
@@ -834,6 +854,18 @@ src/estimate_background.$(OBJEXT): src/$(am__dirstamp) \
src/estimate_background$(EXEEXT): $(src_estimate_background_OBJECTS) $(src_estimate_background_DEPENDENCIES) src/$(am__dirstamp)
@rm -f src/estimate_background$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(src_estimate_background_OBJECTS) $(src_estimate_background_LDADD) $(LIBS)
+src/geomatic.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+src/dw-geomatic.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+src/reflist.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+src/geometry.$(OBJEXT): src/$(am__dirstamp) \
+ src/$(DEPDIR)/$(am__dirstamp)
+src/peaks.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
+src/geomatic$(EXEEXT): $(src_geomatic_OBJECTS) $(src_geomatic_DEPENDENCIES) src/$(am__dirstamp)
+ @rm -f src/geomatic$(EXEEXT)
+ $(AM_V_CCLD)$(LINK) $(src_geomatic_OBJECTS) $(src_geomatic_LDADD) $(LIBS)
src/get_hkl.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/beam-parameters.$(OBJEXT): src/$(am__dirstamp) \
@@ -850,7 +882,6 @@ src/hdfsee$(EXEEXT): $(src_hdfsee_OBJECTS) $(src_hdfsee_DEPENDENCIES) src/$(am__
$(AM_V_CCLD)$(LINK) $(src_hdfsee_OBJECTS) $(src_hdfsee_LDADD) $(LIBS)
src/indexamajig.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-src/peaks.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/index.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/diffraction.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
@@ -859,10 +890,6 @@ src/mosflm.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/templates.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-src/geometry.$(OBJEXT): src/$(am__dirstamp) \
- src/$(DEPDIR)/$(am__dirstamp)
-src/reflist.$(OBJEXT): src/$(am__dirstamp) \
- src/$(DEPDIR)/$(am__dirstamp)
src/diffraction-gpu.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/cl-utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -937,8 +964,10 @@ mostlyclean-compile:
-rm -f src/diffraction.$(OBJEXT)
-rm -f src/dirax.$(OBJEXT)
-rm -f src/displaywindow.$(OBJEXT)
+ -rm -f src/dw-geomatic.$(OBJEXT)
-rm -f src/estimate_background.$(OBJEXT)
-rm -f src/filters.$(OBJEXT)
+ -rm -f src/geomatic.$(OBJEXT)
-rm -f src/geometry.$(OBJEXT)
-rm -f src/get_hkl.$(OBJEXT)
-rm -f src/hdf5-file.$(OBJEXT)
@@ -985,8 +1014,10 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/diffraction.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dirax.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/displaywindow.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/dw-geomatic.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/estimate_background.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/filters.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geomatic.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/geometry.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/get_hkl.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/hdf5-file.Po@am__quote@
@@ -1075,26 +1106,6 @@ uninstall-crystfeldocDATA:
test -n "$$files" || exit 0; \
echo " ( cd '$(DESTDIR)$(crystfeldocdir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(crystfeldocdir)" && rm -f $$files
-install-hdfseeDATA: $(hdfsee_DATA)
- @$(NORMAL_INSTALL)
- test -z "$(hdfseedir)" || $(MKDIR_P) "$(DESTDIR)$(hdfseedir)"
- @list='$(hdfsee_DATA)'; test -n "$(hdfseedir)" || list=; \
- for p in $$list; do \
- if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
- echo "$$d$$p"; \
- done | $(am__base_list) | \
- while read files; do \
- echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(hdfseedir)'"; \
- $(INSTALL_DATA) $$files "$(DESTDIR)$(hdfseedir)" || exit $$?; \
- done
-
-uninstall-hdfseeDATA:
- @$(NORMAL_UNINSTALL)
- @list='$(hdfsee_DATA)'; test -n "$(hdfseedir)" || list=; \
- files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
- test -n "$$files" || exit 0; \
- echo " ( cd '$(DESTDIR)$(hdfseedir)' && rm -f" $$files ")"; \
- cd "$(DESTDIR)$(hdfseedir)" && rm -f $$files
install-scriptDATA: $(script_DATA)
@$(NORMAL_INSTALL)
test -z "$(scriptdir)" || $(MKDIR_P) "$(DESTDIR)$(scriptdir)"
@@ -1524,7 +1535,7 @@ check: check-recursive
all-am: Makefile $(PROGRAMS) $(DATA) config.h
installdirs: installdirs-recursive
installdirs-am:
- for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(crystfeldir)" "$(DESTDIR)$(crystfeldocdir)" "$(DESTDIR)$(hdfseedir)" "$(DESTDIR)$(scriptdir)"; do \
+ for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(crystfeldir)" "$(DESTDIR)$(crystfeldocdir)" "$(DESTDIR)$(scriptdir)"; do \
test -z "$$dir" || $(MKDIR_P) "$$dir"; \
done
install: install-recursive
@@ -1581,7 +1592,7 @@ info: info-recursive
info-am:
install-data-am: install-crystfelDATA install-crystfeldocDATA \
- install-hdfseeDATA install-scriptDATA
+ install-scriptDATA
install-dvi: install-dvi-recursive
@@ -1629,8 +1640,7 @@ ps: ps-recursive
ps-am:
uninstall-am: uninstall-binPROGRAMS uninstall-crystfelDATA \
- uninstall-crystfeldocDATA uninstall-hdfseeDATA \
- uninstall-scriptDATA
+ uninstall-crystfeldocDATA uninstall-scriptDATA
.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all check-am \
ctags-recursive install-am install-strip tags-recursive
@@ -1646,15 +1656,14 @@ uninstall-am: uninstall-binPROGRAMS uninstall-crystfelDATA \
install-binPROGRAMS install-crystfelDATA \
install-crystfeldocDATA install-data install-data-am \
install-dvi install-dvi-am install-exec install-exec-am \
- install-hdfseeDATA install-html install-html-am install-info \
- install-info-am install-man install-pdf install-pdf-am \
- install-ps install-ps-am install-scriptDATA install-strip \
- installcheck installcheck-am installdirs installdirs-am \
- maintainer-clean maintainer-clean-generic mostlyclean \
- mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
- tags tags-recursive uninstall uninstall-am \
- uninstall-binPROGRAMS uninstall-crystfelDATA \
- uninstall-crystfeldocDATA uninstall-hdfseeDATA \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-scriptDATA install-strip installcheck \
+ installcheck-am installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-compile \
+ mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am uninstall-binPROGRAMS \
+ uninstall-crystfelDATA uninstall-crystfeldocDATA \
uninstall-scriptDATA
diff --git a/data/geomatic.ui b/data/geomatic.ui
new file mode 100644
index 00000000..e35b0973
--- /dev/null
+++ b/data/geomatic.ui
@@ -0,0 +1,28 @@
+<ui>
+ <menubar name="displaywindow">
+
+ <menu name="file" action="FileAction">
+ <menuitem name="loadgeom" action="LoadGeomAction" />
+ <separator />
+ <menuitem name="close" action="CloseAction" />
+ </menu>
+
+ <menu name="view" action="ViewAction">
+ <menuitem name="images" action="ImagesAction" />
+ <separator />
+ <menuitem name="boostint" action="BoostIntAction" />
+ <separator />
+ <menuitem name="col" action="ColAction" />
+ <menuitem name="monoscale" action="MonoAction" />
+ <menuitem name="invmonoscale" action="InvMonoAction" />
+ <separator />
+ <menuitem name="colscale" action="ColScaleAction" />
+ </menu>
+
+ <menu name="help" action="HelpAction">
+ <menuitem name="about" action="AboutAction" />
+ </menu>
+
+ </menubar>
+
+</ui>
diff --git a/data/displaywindow.ui b/data/hdfsee.ui
index 7975ad4f..7975ad4f 100644
--- a/data/displaywindow.ui
+++ b/data/hdfsee.ui
diff --git a/src/cell.c b/src/cell.c
index 0be76ff3..c53f63b4 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -938,3 +938,63 @@ void cell_fudge_gslcblas()
STATUS("%p\n", cblas_sgemm);
}
#endif
+
+
+UnitCell *rotate_cell(UnitCell *in, double omega, double phi, double rot)
+{
+ UnitCell *out;
+ double asx, asy, asz;
+ double bsx, bsy, bsz;
+ double csx, csy, csz;
+ double xnew, ynew, znew;
+
+ cell_get_reciprocal(in, &asx, &asy, &asz, &bsx, &bsy,
+ &bsz, &csx, &csy, &csz);
+
+ /* Rotate by "omega" about +z (parallel to c* and c unless triclinic) */
+ xnew = asx*cos(omega) + asy*sin(omega);
+ ynew = -asx*sin(omega) + asy*cos(omega);
+ znew = asz;
+ asx = xnew; asy = ynew; asz = znew;
+ xnew = bsx*cos(omega) + bsy*sin(omega);
+ ynew = -bsx*sin(omega) + bsy*cos(omega);
+ znew = bsz;
+ bsx = xnew; bsy = ynew; bsz = znew;
+ xnew = csx*cos(omega) + csy*sin(omega);
+ ynew = -csx*sin(omega) + csy*cos(omega);
+ znew = csz;
+ csx = xnew; csy = ynew; csz = znew;
+
+ /* Rotate by "phi" about +x (not parallel to anything specific) */
+ xnew = asx;
+ ynew = asy*cos(phi) + asz*sin(phi);
+ znew = -asy*sin(phi) + asz*cos(phi);
+ asx = xnew; asy = ynew; asz = znew;
+ xnew = bsx;
+ ynew = bsy*cos(phi) + bsz*sin(phi);
+ znew = -bsy*sin(phi) + bsz*cos(phi);
+ bsx = xnew; bsy = ynew; bsz = znew;
+ xnew = csx;
+ ynew = csy*cos(phi) + csz*sin(phi);
+ znew = -csy*sin(phi) + csz*cos(phi);
+ csx = xnew; csy = ynew; csz = znew;
+
+ /* Rotate by "rot" about the new +z (in-plane rotation) */
+ xnew = asx*cos(rot) + asy*sin(rot);
+ ynew = -asx*sin(rot) + asy*cos(rot);
+ znew = asz;
+ asx = xnew; asy = ynew; asz = znew;
+ xnew = bsx*cos(rot) + bsy*sin(rot);
+ ynew = -bsx*sin(rot) + bsy*cos(rot);
+ znew = bsz;
+ bsx = xnew; bsy = ynew; bsz = znew;
+ xnew = csx*cos(rot) + csy*sin(rot);
+ ynew = -csx*sin(rot) + csy*cos(rot);
+ znew = csz;
+ csx = xnew; csy = ynew; csz = znew;
+
+ out = cell_new_from_cell(in);
+ cell_set_reciprocal(out, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
+
+ return out;
+}
diff --git a/src/cell.h b/src/cell.h
index 17990e2c..09d9144d 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -80,6 +80,8 @@ extern double resolution(UnitCell *cell,
signed int h, signed int k, signed int l);
extern UnitCell *cell_rotate(UnitCell *in, struct quaternion quat);
+extern UnitCell *rotate_cell(UnitCell *in, double omega, double phi,
+ double rot);
extern void cell_print(UnitCell *cell);
diff --git a/src/detector.c b/src/detector.c
index af7b0c0d..154fe660 100644
--- a/src/detector.c
+++ b/src/detector.c
@@ -214,6 +214,7 @@ struct detector *get_detector_geometry(const char *filename)
return NULL;
}
det->n_panels = -1;
+ det->panels = NULL;
do {
@@ -339,7 +340,7 @@ struct detector *get_detector_geometry(const char *filename)
if ( det->n_panels == -1 ) {
ERROR("No panel descriptions in geometry file.\n");
fclose(fh);
- free(det->panels);
+ if ( det->panels != NULL ) free(det->panels);
free(det);
return NULL;
}
@@ -349,56 +350,46 @@ struct detector *get_detector_geometry(const char *filename)
max_y = 0;
for ( i=0; i<det->n_panels; i++ ) {
- STATUS("Panel %i, min_x = %i\n", i, det->panels[i].min_x);
if ( det->panels[i].min_x == -1 ) {
ERROR("Please specify the minimum x coordinate for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, max_x = %i\n", i, det->panels[i].max_x);
if ( det->panels[i].max_x == -1 ) {
ERROR("Please specify the maximum x coordinate for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, min_y = %i\n", i, det->panels[i].min_y);
if ( det->panels[i].min_y == -1 ) {
ERROR("Please specify the minimum y coordinate for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, max_y = %i\n", i, det->panels[i].max_y);
if ( det->panels[i].max_y == -1 ) {
ERROR("Please specify the maximum y coordinate for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, cx = %f\n", i, det->panels[i].cx);
if ( det->panels[i].cx == -1 ) {
ERROR("Please specify the centre x coordinate for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, cy = %f\n", i, det->panels[i].cy);
if ( det->panels[i].cy == -1 ) {
ERROR("Please specify the centre y coordinate for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, clen = %f\n", i, det->panels[i].clen);
if ( det->panels[i].clen == -1 ) {
ERROR("Please specify the camera length for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, res = %f\n", i, det->panels[i].res);
if ( det->panels[i].res == -1 ) {
ERROR("Please specify the resolution for"
" panel %i\n", i);
reject = 1;
}
- STATUS("Panel %i, badrow direction = %c\n", i,
- det->panels[i].badrow);
/* It's OK if the badrow direction is '0' */
/* It's not a problem if "no_index" is still zero */
/* The default peak_sep is OK (maybe) */
@@ -431,3 +422,10 @@ out:
return det;
}
+
+
+void free_detector_geometry(struct detector *det)
+{
+ free(det->panels);
+ free(det);
+}
diff --git a/src/detector.h b/src/detector.h
index 63d4d268..8bd537d1 100644
--- a/src/detector.h
+++ b/src/detector.h
@@ -53,5 +53,6 @@ extern void record_image(struct image *image, int do_poisson);
extern struct panel *find_panel(struct detector *det, int x, int y);
extern struct detector *get_detector_geometry(const char *filename);
+extern void free_detector_geometry(struct detector *det);
#endif /* DETECTOR_H */
diff --git a/src/displaywindow.c b/src/displaywindow.c
index fbf49f77..c2e94e71 100644
--- a/src/displaywindow.c
+++ b/src/displaywindow.c
@@ -857,7 +857,7 @@ static void displaywindow_addmenubar(DisplayWindow *dw, GtkWidget *vbox,
g_signal_connect(dw->ui, "add_widget",
G_CALLBACK(displaywindow_addui_callback), vbox);
if ( gtk_ui_manager_add_ui_from_file(dw->ui,
- DATADIR"/hdfsee/displaywindow.ui", &error) == 0 ) {
+ DATADIR"/crystfel/hdfsee.ui", &error) == 0 ) {
fprintf(stderr, "Error loading message window menu bar: %s\n",
error->message);
return;
diff --git a/src/dw-geomatic.c b/src/dw-geomatic.c
new file mode 100644
index 00000000..c5137e43
--- /dev/null
+++ b/src/dw-geomatic.c
@@ -0,0 +1,801 @@
+/*
+ * dw-geomatic.c
+ *
+ * GUI geometry calibration
+ *
+ * (c) 2006-2011 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <gtk/gtk.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <cairo.h>
+#include <gdk-pixbuf/gdk-pixbuf.h>
+
+#include "dw-geomatic.h"
+#include "render.h"
+#include "hdf5-file.h"
+#include "utils.h"
+#include "cell.h"
+#include "geometry.h"
+#include "peaks.h"
+
+
+static void displaywindow_error(DWGeomatic *dw, const char *message)
+{
+ GtkWidget *window;
+
+ window = gtk_message_dialog_new(GTK_WINDOW(dw->window),
+ GTK_DIALOG_DESTROY_WITH_PARENT,
+ GTK_MESSAGE_WARNING,
+ GTK_BUTTONS_CLOSE, message);
+ gtk_window_set_title(GTK_WINDOW(window), "Error");
+
+ g_signal_connect_swapped(window, "response",
+ G_CALLBACK(gtk_widget_destroy), window);
+ gtk_widget_show(window);
+}
+
+
+static void displaywindow_update(DWGeomatic *dw)
+{
+ gint width;
+
+ if ( dw->image != NULL ) {
+ dw->width = dw->image->width;
+ dw->height = dw->image->height;
+ } else {
+ dw->width = 320;
+ dw->height = 320;
+ }
+
+ width = dw->width;
+ if ( dw->show_col_scale ) width += 20;
+
+ if ( dw->pixbuf != NULL ) {
+ gdk_pixbuf_unref(dw->pixbuf);
+ }
+ if ( dw->image != NULL ) {
+ dw->pixbuf = render_get_image(dw->image, 1, dw->scale,
+ dw->boostint);
+ } else {
+ dw->pixbuf = NULL;
+ }
+
+ if ( dw->col_scale != NULL ) {
+ gdk_pixbuf_unref(dw->col_scale);
+ }
+ dw->col_scale = render_get_colour_scale(20, dw->height, dw->scale);
+
+ gdk_window_invalidate_rect(dw->drawingarea->window, NULL, FALSE);
+}
+
+
+/* Window closed - clean up */
+static gint displaywindow_closed(GtkWidget *window, DWGeomatic *dw)
+{
+ if ( dw->hdfile != NULL ) {
+ hdfile_close(dw->hdfile);
+ }
+
+ exit(0); /* This program only handles one image at a time */
+}
+
+
+static gboolean displaywindow_expose(GtkWidget *da, GdkEventExpose *event,
+ DWGeomatic *dw)
+{
+ cairo_t *cr;
+ Reflection *refl;
+ RefListIterator *iter;
+
+ cr = gdk_cairo_create(da->window);
+
+ /* Blank white background */
+ cairo_rectangle(cr, 0.0, 0.0, da->allocation.width,
+ da->allocation.height);
+ cairo_set_source_rgb(cr, 0.0, 0.0, 1.0);
+ cairo_fill(cr);
+
+ if ( dw->pixbuf != NULL ) {
+ gdk_draw_pixbuf(da->window,
+ da->style->bg_gc[GTK_WIDGET_STATE(da)],
+ dw->pixbuf,
+ 0, 0, 0, 0, dw->width, dw->height,
+ GDK_RGB_DITHER_NONE, 0, 0);
+ }
+
+ if ( (dw->show_col_scale) && (dw->col_scale != NULL) ) {
+ gdk_draw_pixbuf(da->window,
+ da->style->bg_gc[GTK_WIDGET_STATE(da)],
+ dw->col_scale,
+ 0, 0, dw->width, 0, 20, dw->height,
+ GDK_RGB_DITHER_NONE, 0, 0);
+ }
+
+ if ( dw->image->det != NULL ) {
+
+ RefList *peaks;
+ UnitCell *rot;
+
+ dw->image->bw = 0.01;
+ dw->image->div = 0.0;
+ dw->image->profile_radius = 0.0;
+
+ rot = rotate_cell(dw->cell, dw->pos_x/100000.0, dw->pos_y/100000.0, 0.0);
+ peaks = find_intersections(dw->image, rot, 0);
+ cell_free(rot);
+
+ for ( refl = first_refl(peaks, &iter);
+ refl != NULL;
+ refl = next_refl(refl, iter) ) {
+
+ double x, y;
+
+ get_detector_pos(refl, &x, &y);
+ cairo_new_path(cr);
+ cairo_arc(cr, x, y, 3.0, 0.0, 2.0*M_PI);
+ cairo_set_source_rgb(cr, 0.0, 0.0, 1.0);
+ cairo_stroke(cr);
+
+ }
+
+ reflist_free(peaks);
+
+ }
+
+ return FALSE;
+}
+
+
+static gint displaywindow_close(GtkWidget *widget, DWGeomatic *dw)
+{
+ gtk_widget_destroy(dw->window);
+ return 0;
+}
+
+
+static gint displaywindow_set_boostint_response(GtkWidget *widget,
+ gint response,
+ DWGeomatic *dw)
+{
+ int done = 1;
+
+ if ( response == GTK_RESPONSE_OK ) {
+
+ const char *sboostint;
+ float boostint;
+ int scanval;
+
+ sboostint = gtk_entry_get_text(
+ GTK_ENTRY(dw->boostint_dialog->entry));
+ scanval = sscanf(sboostint, "%f", &boostint);
+ if ( (scanval != 1) || (boostint <= 0) ) {
+ displaywindow_error(dw, "Please enter a positive "
+ "value for the intensity boost "
+ "factor.");
+ done = 0;
+ } else {
+ dw->boostint = boostint;
+ displaywindow_update(dw);
+ }
+ }
+
+ if ( done ) {
+ gtk_widget_destroy(dw->boostint_dialog->window);
+ }
+
+ return 0;
+}
+
+
+static gint displaywindow_set_boostint_destroy(GtkWidget *widget,
+ DWGeomatic *dw)
+{
+ free(dw->boostint_dialog);
+ dw->boostint_dialog = NULL;
+ return 0;
+}
+
+
+static gint displaywindow_set_boostint_response_ac(GtkWidget *widget,
+ DWGeomatic *dw)
+{
+ return displaywindow_set_boostint_response(widget, GTK_RESPONSE_OK, dw);
+}
+
+
+/* Create a window to ask the user for a new intensity boost factor */
+static gint displaywindow_set_boostint(GtkWidget *widget, DWGeomatic *dw)
+{
+ struct gmdialog *bd;
+ GtkWidget *vbox;
+ GtkWidget *hbox;
+ GtkWidget *table;
+ GtkWidget *label;
+ char tmp[64];
+
+ if ( dw->boostint_dialog != NULL ) {
+ return 0;
+ }
+
+ if ( dw->hdfile == NULL ) {
+ return 0;
+ }
+
+ bd = malloc(sizeof(struct gmdialog));
+ if ( bd == NULL ) return 0;
+ dw->boostint_dialog = bd;
+
+ bd->window = gtk_dialog_new_with_buttons("Intensity Boost",
+ GTK_WINDOW(dw->window),
+ GTK_DIALOG_DESTROY_WITH_PARENT,
+ GTK_STOCK_CANCEL, GTK_RESPONSE_CLOSE,
+ GTK_STOCK_OK, GTK_RESPONSE_OK, NULL);
+
+ vbox = gtk_vbox_new(FALSE, 0);
+ hbox = gtk_hbox_new(TRUE, 0);
+ gtk_box_pack_start(GTK_BOX(GTK_DIALOG(bd->window)->vbox),
+ GTK_WIDGET(hbox), FALSE, FALSE, 7);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(vbox), FALSE, FALSE, 5);
+
+ table = gtk_table_new(3, 2, FALSE);
+ gtk_table_set_row_spacings(GTK_TABLE(table), 5);
+ gtk_table_set_col_spacings(GTK_TABLE(table), 5);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(table), FALSE, FALSE, 0);
+
+ label = gtk_label_new("Boost Factor:");
+ gtk_misc_set_alignment(GTK_MISC(label), 1, 0.5);
+ gtk_table_attach_defaults(GTK_TABLE(table), GTK_WIDGET(label),
+ 1, 2, 3, 4);
+
+ bd->entry = gtk_entry_new();
+ snprintf(tmp, 63, "%.2f", dw->boostint);
+ gtk_entry_set_text(GTK_ENTRY(bd->entry), tmp);
+ gtk_table_attach_defaults(GTK_TABLE(table), GTK_WIDGET(bd->entry),
+ 2, 3, 3, 4);
+
+ g_signal_connect(G_OBJECT(bd->entry), "activate",
+ G_CALLBACK(displaywindow_set_boostint_response_ac),
+ dw);
+ g_signal_connect(G_OBJECT(bd->window), "response",
+ G_CALLBACK(displaywindow_set_boostint_response), dw);
+ g_signal_connect(G_OBJECT(bd->window), "destroy",
+ G_CALLBACK(displaywindow_set_boostint_destroy), dw);
+ gtk_window_set_resizable(GTK_WINDOW(bd->window), FALSE);
+ gtk_widget_show_all(bd->window);
+ gtk_widget_grab_focus(GTK_WIDGET(bd->entry));
+
+ return 0;
+}
+
+
+static gint displaywindow_about(GtkWidget *widget, DWGeomatic *dw)
+{
+ GtkWidget *window;
+
+ const gchar *authors[] = {
+ "Thomas White <taw@physics.org>",
+ NULL
+ };
+
+ window = gtk_about_dialog_new();
+ gtk_window_set_transient_for(GTK_WINDOW(window),
+ GTK_WINDOW(dw->window));
+
+ gtk_about_dialog_set_name(GTK_ABOUT_DIALOG(window), "geomatic");
+ gtk_about_dialog_set_version(GTK_ABOUT_DIALOG(window), PACKAGE_VERSION);
+ gtk_about_dialog_set_copyright(GTK_ABOUT_DIALOG(window),
+ "(c) 2006-2011 Thomas White <taw@physics.org> and others");
+ gtk_about_dialog_set_comments(GTK_ABOUT_DIALOG(window),
+ "Quick viewer for HDF files");
+ gtk_about_dialog_set_license(GTK_ABOUT_DIALOG(window),
+ "(c) 2006-2011 Thomas White <taw@physics.org>\n");
+ gtk_about_dialog_set_website(GTK_ABOUT_DIALOG(window),
+ "http://www.bitwiz.org.uk/");
+ gtk_about_dialog_set_authors(GTK_ABOUT_DIALOG(window), authors);
+
+ g_signal_connect(window, "response", G_CALLBACK(gtk_widget_destroy),
+ NULL);
+
+ gtk_widget_show_all(window);
+
+ return 0;
+}
+
+
+static gint displaywindow_set_colscale(GtkWidget *widget, DWGeomatic *dw)
+{
+ dw->show_col_scale = 1 - dw->show_col_scale;
+ displaywindow_update(dw);
+ return 0;
+}
+
+
+static void displaywindow_addui_callback(GtkUIManager *ui, GtkWidget *widget,
+ GtkContainer *container)
+{
+ gtk_box_pack_start(GTK_BOX(container), widget, FALSE, FALSE, 0);
+
+ /* Enable overflow menu if this is a toolbar */
+ if ( GTK_IS_TOOLBAR(widget) ) {
+ gtk_toolbar_set_show_arrow(GTK_TOOLBAR(widget), TRUE);
+ }
+}
+
+
+static gint displaywindow_setscale(GtkWidget *widget, GtkRadioAction *action,
+ DWGeomatic *dw)
+{
+ switch ( gtk_radio_action_get_current_value(action) )
+ {
+ case 0 : dw->scale = SCALE_COLOUR; break;
+ case 1 : dw->scale = SCALE_MONO; break;
+ case 2 : dw->scale = SCALE_INVMONO; break;
+ }
+ displaywindow_update(dw);
+
+ return 0;
+}
+
+
+static gint displaywindow_loadgeom_response(GtkWidget *d, gint response,
+ DWGeomatic *dw)
+{
+ if ( response == GTK_RESPONSE_ACCEPT ) {
+
+ char *file;
+ struct detector *det;
+
+ file = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER(d));
+
+ det = get_detector_geometry(file);
+ g_free(file);
+
+ if ( det == NULL ) {
+ displaywindow_error(dw, "Invalid geometry file");
+ return 1;
+ }
+
+ /* Validate geometry */
+ if ( (1+det->max_x != dw->image->width)
+ || (1+det->max_y != dw->image->height) ) {
+
+ displaywindow_error(dw,
+ "Geometry does not match image size");
+ return 1;
+
+ } else {
+
+ if ( dw->image->det != NULL ) {
+ free_detector_geometry(dw->image->det);
+ }
+ dw->image->det = det;
+
+ displaywindow_update(dw);
+ }
+
+ }
+
+ gtk_widget_destroy(d);
+
+ return 0;
+}
+
+
+
+static gint displaywindow_loadgeom(GtkWidget *widget, DWGeomatic *dw)
+{
+ GtkWidget *d;
+
+ d = gtk_file_chooser_dialog_new("Load Geometry File",
+ GTK_WINDOW(dw->window),
+ GTK_FILE_CHOOSER_ACTION_SAVE,
+ GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
+ GTK_STOCK_OPEN, GTK_RESPONSE_ACCEPT,
+ NULL);
+
+ g_signal_connect(G_OBJECT(d), "response",
+ G_CALLBACK(displaywindow_loadgeom_response), dw);
+
+ gtk_widget_show_all(d);
+
+ return 0;
+}
+
+
+static void displaywindow_addmenubar(DWGeomatic *dw, GtkWidget *vbox,
+ int colscale)
+{
+ GError *error = NULL;
+ GtkActionEntry entries[] = {
+
+ { "FileAction", NULL, "_File", NULL, NULL, NULL },
+ { "LoadGeomAction", GTK_STOCK_OPEN, "_Load Geometry", NULL,
+ NULL, G_CALLBACK(displaywindow_loadgeom) },
+ { "CloseAction", GTK_STOCK_CLOSE, "_Close", NULL, NULL,
+ G_CALLBACK(displaywindow_close) },
+
+ { "ViewAction", NULL, "_View", NULL, NULL, NULL },
+ { "ImagesAction", NULL, "Images", NULL, NULL, NULL },
+ { "BoostIntAction", NULL, "Boost Intensity...", "F5", NULL,
+ G_CALLBACK(displaywindow_set_boostint) },
+
+ { "HelpAction", NULL, "_Help", NULL, NULL, NULL },
+ { "AboutAction", GTK_STOCK_ABOUT, "_About Geomatic...",
+ NULL, NULL,
+ G_CALLBACK(displaywindow_about) },
+
+ };
+ guint n_entries = G_N_ELEMENTS(entries);
+
+ GtkToggleActionEntry toggles[] = {
+ { "ColScaleAction", NULL, "Show Colour Scale", NULL, NULL,
+ G_CALLBACK(displaywindow_set_colscale), FALSE },
+ };
+ guint n_toggles = G_N_ELEMENTS(toggles);
+ GtkRadioActionEntry radios[] = {
+ { "ColAction", NULL, "Colour", NULL, NULL,
+ SCALE_COLOUR },
+ { "MonoAction", NULL, "Monochrome", NULL, NULL,
+ SCALE_MONO },
+ { "InvMonoAction", NULL, "Inverse Monochrome", NULL, NULL,
+ SCALE_INVMONO },
+ };
+ guint n_radios = G_N_ELEMENTS(radios);
+
+ dw->action_group = gtk_action_group_new("geomatic");
+ gtk_action_group_add_actions(dw->action_group, entries, n_entries, dw);
+ gtk_action_group_add_toggle_actions(dw->action_group, toggles,
+ n_toggles, dw);
+ gtk_action_group_add_radio_actions(dw->action_group, radios, n_radios,
+ colscale,
+ G_CALLBACK(displaywindow_setscale),
+ dw);
+
+ dw->ui = gtk_ui_manager_new();
+ gtk_ui_manager_insert_action_group(dw->ui, dw->action_group, 0);
+ g_signal_connect(dw->ui, "add_widget",
+ G_CALLBACK(displaywindow_addui_callback), vbox);
+ if ( gtk_ui_manager_add_ui_from_file(dw->ui,
+ DATADIR"/crystfel/geomatic.ui", &error) == 0 ) {
+ fprintf(stderr, "Error loading message window menu bar: %s\n",
+ error->message);
+ return;
+ }
+
+ gtk_window_add_accel_group(GTK_WINDOW(dw->window),
+ gtk_ui_manager_get_accel_group(dw->ui));
+ gtk_ui_manager_ensure_update(dw->ui);
+}
+
+
+struct newhdf {
+ DWGeomatic *dw;
+ char name[1024];
+};
+
+static gint displaywindow_newhdf(GtkMenuItem *item, struct newhdf *nh)
+{
+ hdfile_set_image(nh->dw->hdfile, nh->name);
+ hdf5_read(nh->dw->hdfile, nh->dw->image, 0, 0.0);
+ gtk_widget_set_size_request(GTK_WIDGET(nh->dw->drawingarea),
+ nh->dw->image->width,
+ nh->dw->image->height);
+ displaywindow_update(nh->dw);
+ return 0;
+}
+
+
+static GtkWidget *displaywindow_addhdfgroup(struct hdfile *hdfile,
+ const char *group,
+ DWGeomatic *dw, GSList **rgp)
+{
+ char **names;
+ int *is_group;
+ int *is_image;
+ GtkWidget *ms;
+ int n, i;
+
+ if ( hdfile == NULL ) return NULL;
+
+ names = hdfile_read_group(hdfile, &n, group, &is_group, &is_image);
+ if ( n == 0 ) return NULL;
+
+ ms = gtk_menu_new();
+
+ for ( i=0; i<n; i++ ) {
+
+ GtkWidget *item;
+ GtkWidget *sub;
+
+ if ( names[i] == NULL ) return NULL;
+
+ if ( is_group[i] ) {
+
+ item = gtk_menu_item_new_with_label(names[i]);
+
+ sub = displaywindow_addhdfgroup(hdfile, names[i],
+ dw, rgp);
+ gtk_menu_item_set_submenu(GTK_MENU_ITEM(item), sub);
+
+ } else if ( is_image[i] ) {
+
+ struct newhdf *nh;
+
+ item = gtk_radio_menu_item_new_with_label(*rgp,
+ names[i]);
+
+ if ( *rgp == NULL ) {
+ gtk_check_menu_item_set_active(
+ GTK_CHECK_MENU_ITEM(item), TRUE);
+ } else {
+ gtk_check_menu_item_set_active(
+ GTK_CHECK_MENU_ITEM(item), FALSE);
+ }
+
+ *rgp = gtk_radio_menu_item_get_group(
+ GTK_RADIO_MENU_ITEM(item));
+
+ nh = malloc(sizeof(struct newhdf));
+ if ( nh != NULL ) {
+ strncpy(nh->name, names[i], 1023);
+ nh->dw = dw;
+ g_signal_connect(G_OBJECT(item), "activate",
+ G_CALLBACK(displaywindow_newhdf), nh);
+ }
+
+ } else {
+
+ char *tmp;
+
+ item = gtk_menu_item_new_with_label(names[i]);
+
+ tmp = hdfile_get_string_value(hdfile, names[i]);
+ if ( tmp != NULL ) {
+
+ GtkWidget *ss;
+ GtkWidget *mss;
+
+ mss = gtk_menu_new();
+ ss = gtk_menu_item_new_with_label(tmp);
+ gtk_widget_set_sensitive(ss, FALSE);
+ gtk_menu_shell_append(GTK_MENU_SHELL(mss), ss);
+ gtk_menu_item_set_submenu(GTK_MENU_ITEM(item),
+ mss);
+
+ }
+
+
+ }
+
+ gtk_menu_shell_append(GTK_MENU_SHELL(ms), item);
+
+ free(names[i]);
+
+
+ }
+
+ free(is_group);
+ free(is_image);
+
+ return ms;
+}
+
+
+static GtkWidget *displaywindow_createhdfmenus(struct hdfile *hdfile,
+ DWGeomatic *dw)
+{
+ GSList *rg = NULL;
+
+ return displaywindow_addhdfgroup(hdfile, "/", dw, &rg);
+}
+
+
+static void displaywindow_update_menus(DWGeomatic *dw)
+{
+ GtkWidget *ms;
+ GtkWidget *w;
+
+ ms = displaywindow_createhdfmenus(dw->hdfile, dw);
+
+ if ( ms == NULL ) {
+
+ /* Too bad. You'd better hope that /data/data exists... */
+ ERROR("Couldn't get list of images in HDF file\n");
+ w = gtk_ui_manager_get_widget(dw->ui,
+ "/ui/displaywindow/view/images");
+ gtk_widget_set_sensitive(GTK_WIDGET(w), FALSE);
+
+ /* Add a dummy menu so that the user knows what's going on */
+ ms = gtk_menu_new();
+ w = gtk_ui_manager_get_widget(dw->ui,
+ "/ui/displaywindow/view/images");
+ gtk_menu_item_set_submenu(GTK_MENU_ITEM(w), ms);
+
+ return;
+
+ }
+
+ /* Make new menu be the submenu for File->Images */
+ w = gtk_ui_manager_get_widget(dw->ui, "/ui/displaywindow/view/images");
+ gtk_menu_item_set_submenu(GTK_MENU_ITEM(w), ms);
+
+ gtk_widget_show_all(ms);
+}
+
+
+static gint displaywindow_release(GtkWidget *widget, GdkEventButton *event,
+ DWGeomatic *dw)
+{
+ if ( (event->type == GDK_BUTTON_RELEASE) && (event->button == 1) ) {
+
+ g_signal_handler_disconnect(GTK_OBJECT(dw->drawingarea),
+ dw->motion_callback);
+ dw->motion_callback = 0;
+
+ }
+
+ return 0;
+}
+
+
+static gint displaywindow_motion(GtkWidget *widget, GdkEventMotion *event,
+ DWGeomatic *dw)
+{
+ double x, y;
+
+ x = event->x - dw->motion_origx;
+ y = event->y - dw->motion_origy;
+
+ dw->pos_x += x;
+ dw->pos_y += y;
+
+ /* Schedule redraw */
+ gtk_widget_queue_draw_area(dw->drawingarea, 0, 0,
+ dw->width, dw->height);
+
+ return 0;
+}
+
+
+static gint displaywindow_press(GtkWidget *widget, GdkEventButton *event,
+ DWGeomatic *dw)
+{
+ if ( dw->motion_callback != 0 ) {
+ return 0;
+ }
+
+ if ( (event->type == GDK_BUTTON_PRESS) && (event->button == 1) ) {
+
+ dw->motion_origx = event->x;
+ dw->motion_origy = event->y;
+
+ /* Connect motion callback */
+ dw->motion_callback = g_signal_connect(
+ GTK_OBJECT(dw->drawingarea),
+ "motion-notify-event",
+ G_CALLBACK(displaywindow_motion),
+ dw);
+
+ }
+
+ return 0;
+
+}
+
+
+DWGeomatic *geomatic_open(const char *filename)
+{
+ DWGeomatic *dw;
+ char *title;
+ GtkWidget *vbox;
+ GtkWidget *sw;
+ int wr, hr;
+
+ dw = calloc(1, sizeof(DWGeomatic));
+ if ( dw == NULL ) return NULL;
+ dw->pixbuf = NULL;
+ dw->show_col_scale = 0;
+ dw->col_scale = NULL;
+ dw->boostint_dialog = NULL;
+ dw->boostint = 1;
+ dw->motion_callback = 0;
+ dw->image = NULL;
+ dw->scale = SCALE_COLOUR;
+ dw->pos_x = 0.0;
+ dw->pos_y = 0.0;
+ dw->pos_z = 0.0;
+
+ dw->window = gtk_window_new(GTK_WINDOW_TOPLEVEL);
+
+ if ( filename == NULL ) {
+ title = strdup("No file - geomatic");
+ } else {
+ char *bn = safe_basename(filename);
+ title = malloc(strlen(bn)+14);
+ sprintf(title, "%s - geomatic", bn);
+ free(bn);
+ }
+ gtk_window_set_title(GTK_WINDOW(dw->window), title);
+ free(title);
+
+ g_signal_connect(G_OBJECT(dw->window), "destroy",
+ G_CALLBACK(displaywindow_closed), dw);
+
+ vbox = gtk_vbox_new(FALSE, 0);
+ gtk_container_add(GTK_CONTAINER(dw->window), vbox);
+ displaywindow_addmenubar(dw, vbox, dw->scale);
+
+ /* Open the file, if any */
+ if ( filename != NULL ) {
+
+ dw->hdfile = hdfile_open(filename);
+ if ( dw->hdfile == NULL ) {
+ ERROR("Couldn't open file '%s'\n", filename);
+ return NULL;
+ } else if ( hdfile_set_first_image(dw->hdfile, "/") ) {
+ ERROR("Couldn't select path\n");
+ return NULL;
+ } else {
+ dw->image = calloc(1, sizeof(struct image));
+ hdf5_read(dw->hdfile, dw->image, 0, 0.0);
+ }
+
+ } else {
+ return NULL;
+ }
+
+ dw->drawingarea = gtk_drawing_area_new();
+ gtk_widget_set_size_request(GTK_WIDGET(dw->drawingarea),
+ dw->image->width,
+ dw->image->height);
+ sw = gtk_scrolled_window_new(NULL, NULL);
+ gtk_scrolled_window_set_policy(GTK_SCROLLED_WINDOW(sw),
+ GTK_POLICY_AUTOMATIC,
+ GTK_POLICY_AUTOMATIC);
+ gtk_scrolled_window_add_with_viewport(GTK_SCROLLED_WINDOW(sw),
+ dw->drawingarea);
+ gtk_box_pack_start(GTK_BOX(vbox), sw, TRUE, TRUE, 0);
+
+ wr = dw->image->width;
+ hr = dw->image->height;
+ if ( wr > 640 ) wr = 640;
+ if ( hr > 640 ) hr = 640;
+ gtk_widget_set_size_request(GTK_WIDGET(dw->window), wr, hr);
+
+ g_signal_connect(GTK_OBJECT(dw->drawingarea), "expose-event",
+ G_CALLBACK(displaywindow_expose), dw);
+
+ gtk_window_set_resizable(GTK_WINDOW(dw->window), TRUE);
+ gtk_widget_show_all(dw->window);
+
+ dw->cell = load_cell_from_pdb("1JB0.pdb");
+
+ dw->boostint = 1.0;
+ displaywindow_update(dw);
+
+ gtk_widget_add_events(GTK_WIDGET(dw->drawingarea),
+ GDK_BUTTON_PRESS_MASK
+ | GDK_BUTTON_RELEASE_MASK
+ | GDK_BUTTON1_MOTION_MASK);
+ g_object_set(G_OBJECT(dw->drawingarea), "can-focus", TRUE, NULL);
+
+ g_signal_connect(GTK_OBJECT(dw->drawingarea), "button-press-event",
+ G_CALLBACK(displaywindow_press), dw);
+ g_signal_connect(GTK_OBJECT(dw->drawingarea), "button-release-event",
+ G_CALLBACK(displaywindow_release), dw);
+
+ if ( dw->hdfile != NULL ) displaywindow_update_menus(dw);
+
+ return dw;
+}
diff --git a/src/dw-geomatic.h b/src/dw-geomatic.h
new file mode 100644
index 00000000..0482d26c
--- /dev/null
+++ b/src/dw-geomatic.h
@@ -0,0 +1,68 @@
+/*
+ * dw-geomatic.h
+ *
+ * GUI geometry calibration
+ *
+ * (c) 2006-2011 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef DW_GEOMATIC_H
+#define DW_GEOMATIC_H
+
+#include <gtk/gtk.h>
+
+#include "cell.h"
+#include "reflist.h"
+
+
+struct gmdialog {
+ GtkWidget *window;
+ GtkWidget *entry;
+};
+
+
+typedef struct {
+
+ GtkWidget *window;
+ GtkWidget *drawingarea;
+ GtkUIManager *ui;
+ GtkActionGroup *action_group;
+ GdkPixbuf *pixbuf;
+ gulong motion_callback;
+
+ struct hdfile *hdfile;
+ struct image *image;
+ int width;
+ int height;
+ double boostint;
+
+ /* Dialog boxes */
+ struct gmdialog *boostint_dialog;
+
+ int show_col_scale;
+ int scale;
+ GdkPixbuf *col_scale;
+
+ double motion_origx;
+ double motion_origy;
+
+ UnitCell *cell;
+ double pos_x;
+ double pos_y;
+ double pos_z;
+
+} DWGeomatic;
+
+/* Return an image display window showing the given filename, or NULL */
+extern DWGeomatic *geomatic_open(const char *filename);
+
+
+#endif /* DW_GEOMATICs_H */
diff --git a/src/geomatic.c b/src/geomatic.c
new file mode 100644
index 00000000..94975c25
--- /dev/null
+++ b/src/geomatic.c
@@ -0,0 +1,81 @@
+/*
+ * geomatic.c
+ *
+ * GUI geometry calibration
+ *
+ * (c) 2006-2011 Thomas White <taw@physics.org>
+ *
+ * Part of CrystFEL - crystallography with a FEL
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <gtk/gtk.h>
+#include <getopt.h>
+
+#include "dw-geomatic.h"
+#include "utils.h"
+#include "render.h"
+
+
+static void show_help(const char *s)
+{
+ printf("Syntax: %s [options] image.h5\n\n", s);
+ printf(
+"GUI geometry calibration.\n"
+"\n"
+" -h, --help Display this help message.\n"
+"\n");
+}
+
+
+int main(int argc, char *argv[])
+{
+ int c;
+ int nfiles;
+
+ /* Long options */
+ const struct option longopts[] = {
+ {"help", 0, NULL, 'h'},
+ {0, 0, NULL, 0}
+ };
+
+ gtk_init(&argc, &argv);
+
+ /* Short options */
+ while ((c = getopt_long(argc, argv, "hp:b:i:c:",
+ longopts, NULL)) != -1) {
+
+ switch (c) {
+ case 'h' :
+ show_help(argv[0]);
+ return 0;
+
+ case 0 :
+ break;
+
+ default :
+ return 1;
+ }
+
+ }
+
+ nfiles = argc-optind;
+
+ if ( nfiles < 1 ) {
+ ERROR("You need to give me a file to open!\n");
+ return -1;
+ }
+
+ if ( geomatic_open(argv[optind]) == NULL ) {
+ ERROR("Couldn't open display window\n");
+ return 1;
+ }
+ gtk_main();
+
+ return 0;
+}
diff --git a/src/indexamajig.c b/src/indexamajig.c
index f1684c8c..6112066c 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -400,12 +400,12 @@ static void process_image(void *pp, int cookie)
image.div = beam->divergence;
image.bw = beam->bandwidth;
- image.profile_radius = 0.005e9;
+ image.profile_radius = 0.0001e9;
- reflections = find_intersections(&image, image.indexed_cell,
- 0);
- //reflections = find_projected_peaks(&image, image.indexed_cell,
- // 0, 0.1);
+ //reflections = find_intersections(&image, image.indexed_cell,
+ // 0);
+ reflections = find_projected_peaks(&image, image.indexed_cell,
+ 0, 0.1);
output_intensities(&image, image.indexed_cell, reflections,
pargs->static_args.output_mutex,
diff --git a/src/templates.c b/src/templates.c
index 79e60aec..37188145 100644
--- a/src/templates.c
+++ b/src/templates.c
@@ -47,66 +47,6 @@ struct template {
};
-UnitCell *rotate_cell(UnitCell *in, double omega, double phi, double rot)
-{
- UnitCell *out;
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- double xnew, ynew, znew;
-
- cell_get_reciprocal(in, &asx, &asy, &asz, &bsx, &bsy,
- &bsz, &csx, &csy, &csz);
-
- /* Rotate by "omega" about +z (parallel to c* and c unless triclinic) */
- xnew = asx*cos(omega) + asy*sin(omega);
- ynew = -asx*sin(omega) + asy*cos(omega);
- znew = asz;
- asx = xnew; asy = ynew; asz = znew;
- xnew = bsx*cos(omega) + bsy*sin(omega);
- ynew = -bsx*sin(omega) + bsy*cos(omega);
- znew = bsz;
- bsx = xnew; bsy = ynew; bsz = znew;
- xnew = csx*cos(omega) + csy*sin(omega);
- ynew = -csx*sin(omega) + csy*cos(omega);
- znew = csz;
- csx = xnew; csy = ynew; csz = znew;
-
- /* Rotate by "phi" about +x (not parallel to anything specific) */
- xnew = asx;
- ynew = asy*cos(phi) + asz*sin(phi);
- znew = -asy*sin(phi) + asz*cos(phi);
- asx = xnew; asy = ynew; asz = znew;
- xnew = bsx;
- ynew = bsy*cos(phi) + bsz*sin(phi);
- znew = -bsy*sin(phi) + bsz*cos(phi);
- bsx = xnew; bsy = ynew; bsz = znew;
- xnew = csx;
- ynew = csy*cos(phi) + csz*sin(phi);
- znew = -csy*sin(phi) + csz*cos(phi);
- csx = xnew; csy = ynew; csz = znew;
-
- /* Rotate by "rot" about the new +z (in-plane rotation) */
- xnew = asx*cos(rot) + asy*sin(rot);
- ynew = -asx*sin(rot) + asy*cos(rot);
- znew = asz;
- asx = xnew; asy = ynew; asz = znew;
- xnew = bsx*cos(rot) + bsy*sin(rot);
- ynew = -bsx*sin(rot) + bsy*cos(rot);
- znew = bsz;
- bsx = xnew; bsy = ynew; bsz = znew;
- xnew = csx*cos(rot) + csy*sin(rot);
- ynew = -csx*sin(rot) + csy*cos(rot);
- znew = csz;
- csx = xnew; csy = ynew; csz = znew;
-
- out = cell_new_from_cell(in);
- cell_set_reciprocal(out, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
-
- return out;
-}
-
-
/* Generate templates for the given cell using a representative image */
IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
struct detector *det,
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-20 14:26:22 +0000