Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/AUTHORS
+++ b/AUTHORS
@@ -68,7 +68,7 @@ Niv Levy <nivl2000@gmail.com>
 Vinicius Barboza <vinicius.barboza@lnnano.cnpem.br>
    Otsu thresholding.
 Jeffrey J. Schwartz <schwartz@physics.ucla.edu>
-    WinSTM file import.
+    WinSTM and Anasys XML file import.
 Christian Bühler <christian.buehler@uni-ulm.de>
    Pygwy volume data processing module type and other volume data processing
    improvements.

--- a/Makefile.am
+++ b/Makefile.am
-# $Id: Makefile.am 20680 2017-12-18 18:29:14Z yeti-dn $
+# $Id: Makefile.am 21345 2018-08-27 18:48:04Z yeti-dn $

 SUBDIRS = \
 	m4 \
@@ -8,6 +8,7 @@ SUBDIRS = \
 	libgwydgets \
 	libgwymodule \
 	app \
+	gwyddion \
 	modules \
 	plugins \
 	po \

--- a/Makefile.in
+++ b/Makefile.in
@@ -14,7 +14,7 @@

 @SET_MAKE@

-# $Id: Makefile.am 20680 2017-12-18 18:29:14Z yeti-dn $
+# $Id: Makefile.am 21345 2018-08-27 18:48:04Z yeti-dn $

 VPATH = @srcdir@
 am__is_gnu_make = { \
@@ -92,9 +92,9 @@ build_triplet = @build@
 host_triplet = @host@
 subdir = .
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/m4/gconf-2.m4 \
-	$(top_srcdir)/m4/gettext.m4 $(top_srcdir)/m4/glibc21.m4 \
-	$(top_srcdir)/m4/gtk-doc.m4 $(top_srcdir)/m4/gwy-cc-options.m4 \
+am__aclocal_m4_deps = $(top_srcdir)/m4/gettext.m4 \
+	$(top_srcdir)/m4/glibc21.m4 $(top_srcdir)/m4/gtk-doc.m4 \
+	$(top_srcdir)/m4/gwy-cc-options.m4 \
 	$(top_srcdir)/m4/gwy-enable.m4 $(top_srcdir)/m4/gwy-math.m4 \
 	$(top_srcdir)/m4/gwy-python.m4 $(top_srcdir)/m4/gwy-version.m4 \
 	$(top_srcdir)/m4/iconv.m4 $(top_srcdir)/m4/libtool.m4 \
@@ -288,9 +288,6 @@ EXR_LIBS = @EXR_LIBS@
 FFTW3_CFLAGS = @FFTW3_CFLAGS@
 FFTW3_LIBS = @FFTW3_LIBS@
 FGREP = @FGREP@
-GCONFTOOL = @GCONFTOOL@
-GCONF_SCHEMA_CONFIG_SOURCE = @GCONF_SCHEMA_CONFIG_SOURCE@
-GCONF_SCHEMA_FILE_DIR = @GCONF_SCHEMA_FILE_DIR@
 GETTEXT_PACKAGE = @GETTEXT_PACKAGE@
 GIO_CFLAGS = @GIO_CFLAGS@
 GIO_LIBS = @GIO_LIBS@
@@ -490,6 +487,7 @@ SUBDIRS = \
 	libgwydgets \
 	libgwymodule \
 	app \
+	gwyddion \
 	modules \
 	plugins \
 	po \

--- a/NEWS
+++ b/NEWS
+2.52 (2018-11-14)
+Application:
+- Translations updated: Czech, French, Russian.
+
+Libraries:
+- libgwyddion: System exp10() is used as backend for our pow10() function when
+  the latter (obsolete one) is not provided by the system.
+- libgwyddion: gwy_math_find_minimum_1d() termination condition was improved.
+- libgwyddion: Function for measuring string width in a fixed font was added.
+- libgwyprocess: GwyDataField function for mean square value was added.
+- libgwyprocess: Broken Laplace exterior in gwy_data_field_ext_convolve()
+  was fixed.  Laplace interpolation producing constant values for data of
+  very small absolute magnitude was corrected.
+- libgwyprocess: gwy_data_field_find_regularization_sigma_for_psf() was
+  improved.
+- libgwyprocess: gwy_data_field_deconvolve_regularized() is a bit faster now.
+- libgwyprocess: PSF reconstruction using least squares problem solution was
+  added, with the corresponding sigma optimisation function.
+- libgwyprocess: Rare crash inside gwy_data_field_fill_grain() was fixed.
+- libgwyprocess: Row corrections (most of Align Rows) are available as library
+  functions.
+- libgwyprocess: Functions for measuring dispersion when data field is taken
+  as a distribution.
+- libgwyprocess: Pixel/voxel size functions for all regular data objects were
+  added.
+- libgwyprocess: Brick z-axis calibration copying function was added.
+- libgwyprocess: gwy_someting_assign() convenience macros were added for all
+  basic data objects.
+- libgwyprocess: Simpler brick functions working with entire XY planes and
+  Z profiles.  Arguments keep_offsets are actually implemented now.  Summary
+  functions working in the XZ plane were fixed.
+- libgwyprocess: Function for taking data field absolute value was added.
+- libgwyprocess: Histogram-like functions possibly trying to create DataLines
+  with negative real size in edge cases were fixed.
+- libgwydgets: GwyDataWindow shows value under mouse pointer also in base
+  (unprefixed) units.
+- libgwydgets, libgwyapp: Off-screen graph rendering uses screen's default
+  visual instead of best which might not work.
+- libgwyapp: Items in data browser can be renamed by plain double-click.
+- libgwyapp: gwy_rect_selection_labels_fill() shows consistent real dimensions
+  and gives consistently the same isel for entire field and no selection
+  present.
+- libgwyapp: Inverted assertion in gwy_app_wait_set_enabled() causing a
+  Critical warning was corrected.
+
+Modules:
+- Anasys XML (new): Imports Analysis studio XML (.axd) files.
+- AFM Workshop spectra (new): Imports AFM workshop single point spectra.
+- Nanosystemz (new): Imports Nanosystemz profilometry data files.
+- Volume plane level (new): Simple levelling of volume data planes.
+- Volume outliers (new): Removal of outliers in volume data planes.
+- Deconvolve (new): Simple regularised deconvolution.
+- Transfer function guess: Windowing option was added.  Zoomed central part of
+  TF can be displayed and extracted.  A second guess method was added, least
+  squares problem solution.  Sigma fitting was improved.  Various GUI
+  improvements.
+- Volume transfer function: Improvements from the image module were integrated.
+  Regularisation parameter can be estimated per plane.
+- Extend: New extended image dimensions are displayed.   Masks and
+  presentations are extended correctly.
+- Dimensions and Units (image and volume): New units are remembered and unit
+  change is applied when function is re-run non-interactively.
+- VTK export: Z-scaling can be specified manually.
+- Crop: Selection dimensions are always ediable when a data window is active.
+- Grain statistics: The grain statistics table can be exported.
+- Pygwy: Missing reference in gwy_app_file_load() was corrected.
+- Line correct: Marking of rows with inverted sign (Mark Inverted Rows) added.
+- Volume and image MFM recalculation: Warnings upon pressing Reset were fixed.
+  They can modify an existing image/volume data.
+- Surffile: Micron symbols written using old MS DOS code pages are recognised.
+- Volume Cut'n'Slice: Multiple-plane selection actually extracts several
+  different planes now.
+- ACF 2D, PSDF 2D: Lines selected in the dialogue for profiles are also
+  selected in the output image.
+- Nanoscope: Reading of text files, broken in 2.51, was fixed.
+- Volumize layers: Preview image has actually the same dimensions as brick
+  XY plane now.
+- Statistical quantities: Entropy was removed as too slow (use the separate
+  Entropy function), scan line discrepancy was added.
+- Nanonis: Vertical flipping can be controlled via a settings value.
+- Cross-correlation: The OK button is insensitive when no image to correlate
+  with is selected, fixing a crash when it was run with no second image.
+- Measure lattice: Vector a₁ being printed second time as a₂ in exported
+  reports was corrected.
+
+Other:
+- Compilation: False positives in tests for supported gcc warning options were
+  hopefully fixed.
+- Python: Python scripts were changed to explicitly say python2 in the shbang
+  lines instead of python.  Standalone gwy module disables progress bars by
+  default.
+- GConf: The obsolete GConf-based thumbnailer support was removed and its
+  schemas are no longer installed.
+- Source code: Source files for gwyddion, the program, were moved from app to
+  separate directory gwyddion.
+
+
 2.51 (2018-06-26)
 Application:
 - Translations updated: Brazilian Portugese, Czech, French, Russian.
@@ -82,7 +179,7 @@ Modules:
  images also changed and match previous versions only statistically.
 - Graph logscale: Logarithm base mishandling was fixed.  Base-2 logarithm and
  negative abscissa handling options were added.
- Statistics Quantities: Volume was added as a new quantity.
+- Statistical quantities: Volume was added as a new quantity.
 - FFT profile: Renamed to 2D PSDF.  It can now both extract profiles and create
  the entire 2D PSDF image.
 - Image export: Font selection having sometimes no effect on the exported
@@ -169,10 +266,10 @@ Modules:
 - ACF 2D: Has a GUI now, supports masking, can pre-level the data, extract
  radial ACF profiles and calculate some statistical parameters.
 - Filters tool: Mean value filter uses circular kernel instead of square.
- Statistical Quantities, Statistical Functions and Row/Column Statistics
+- Statistical quantities, Statistical functions and Row/Column statistics
  tools: Apply button is insensitive when ther is no curve, some repeated
  recalculations were fixed.
- Statistics Quantities: Quantities Sp, Sv and Sz were added.
+- Statistical quantities: Quantities Sp, Sv and Sz were added.
 - Object synthesis: Hexagonal pyramid, full sphere and nuggets shapes were
  added.  Feature up/down direction is now an arbitrary fraction.  There are
  new is now options to avoid stacking and for vertical placement character.
@@ -262,8 +359,8 @@ Modules:
 - Volume swap axes (new): Reorganises data to change X, Y, Z axis roles.
 - Fibre synthesis (new): Generates images from randomly placed fibres.
 - Mask noisify (new): Adds salt and/or pepper noise to the mask.
- Statistical functions tool: Masked one-dimensional ACF, HHCF, PSDF, DA and
-  CDA are available now.  Area scale graph was added.
+- Statistical functions: Masked one-dimensional ACF, HHCF, PSDF, DA and CDA are
+  available now.  Area scale graph was added.
 - JPK: Crash when QI/force map loading was cancelled during ‘Scanning files’
  was fixed.
 - Dimensions and Units: A rarely occurring freeze was fixed.
@@ -509,8 +606,8 @@ Modules:
 - Fit sphere: Was removed, use new Fit shape module instead.
 - Row/column statistics tool: Masking support was added.  The misguided fixed
  resolution option was removed.
- Statistical quantities tool: Automatic selection of units and precision for
-  the displayed quantities was improved.
+- Statistical quantities: Automatic selection of units and precision for the
+  displayed quantities was improved.
 - XYZize: XYZ log is created for the new XYZ data, not volume data log.
 - Pygwy: Containers can be directly indexed both by strings and integers
  (quarks).  Overrides for Container methods get_value() and set_value() were
@@ -533,7 +630,7 @@ Modules:
 - Grain statistics: The values are displayed with more significant digits.
 - Raw XYZ import: No longer loses the first data point in the file.
 - Graph cut: The ‘cut all’ setting is remembered, some GUI improvements.
- Cross correlate: Introduced weighting function, result smoothing and
+- Cross-correlation: Introduced weighting function, result smoothing and
  extension and back-correction according to the results.
 - Nanonis: Mask of invalid values is correctly flipped with the data now.
 - JPK: Support for single point spectroscopy was added.
@@ -1005,7 +1102,7 @@ Modules:
  profile, Drift correction: It is possible to select a target graph for the
  curves.
 - Arithmetic: Data fields 2 to 8 are remembered between invocations.
- Calibrate, Merge, Immerse, Attach Presentation, Cross-correlate, FFT, Mark
+- Calibrate, Merge, Immerse, Attach Presentation, Cross-correlation, FFT, Mark
  With, Mask by Correlation, Neural network training: Second image is
  remembered between invocations.
 - Immerse: Detail positions are remembered.
@@ -1261,7 +1358,7 @@ Modules:
  images was corrected.
 - Spectral synthesis: Critical message/crash, occurring when some files were
  loaded but no channel was active while invoking the function, was fixed.
- Cross-correlation: now allowing use of multiple channels and output of
+- Cross-correlation: Now allowing use of multiple channels and output of
  all the results together.

 Other:
@@ -1896,7 +1993,7 @@ Modules:
 - MapVue: Support for old OptiCode files was added.
 - Profile: Modified to display calibration data if present.
 - Read value: Modified to display calibration data if present.
- Statistics: Modified to display calibration data if present.
+- Statistical quantities: Modified to display calibration data if present.
 - Statistical functions: Modified to display calibration data if present.
 - DOS spectrum: Calculates absolute value of (dI/dU)/(I/U) and does not
  removing the contact potential.
@@ -1958,7 +2055,7 @@ Modules:
 - Spectral synthesis: Generated data can be added to an existing surface.
 - Mask Editor tool: New editing tools were added: paintbrush, eraser,
  and bucket filling and unfilling.
- Statistical functions tool: Radially averaged ACF was added.
+- Statistical functions: Radially averaged ACF was added.
 - Arithmetic: Has a preview, expressions can work with mask values, units of
  the result can be specified, the number of fields was increased to 8.
 - Threshold: Renamed to Limit Range in the menus; can cut off outliers given
@@ -2294,7 +2391,8 @@ Modules:
  (in 2.12 Save button did both actions and Copy did not do anything).
 - Nanoscope: Physical y-size is recalculated to conserve the pixel
  y-size/x-size ratio in all files now.  This affects non-square images.
- Stats tool: Angles are exported in degrees as stated, instead of radians.
+- Statistical quantities: Angles are exported in degrees as stated, instead of
+  radians.
 - HDF4 file: PSI files are flipped vertically to follow the convention.
 - All tools: Somewhat inconsistent conversion between pixel and real
  coordinates were unified.
@@ -2430,8 +2528,8 @@ Modules:
 - RHK SPM32 (SM2): Support for spectra was added.
 - MI file: Reading of ASCII image files was actually implemented.
 - Plugin-proxy: Memory overflow in dump file reading was fixed.
- Surf: Added export to Surf files
- stpfile: Improved support for extended source modes.
+- Surffile: Surf files can be exported.
+- STP file: Improved support for extended source modes.


 2.9 (2007-10-19)
@@ -2656,7 +2754,7 @@ Modules:
  properly.
 - Color Range tool: It is possible to set default color mapping type applied
  when none is specifically set. Manual range setting was enabled.
- Statistical functions tool: Radial PSDF was added.
+- Statistical functions: Radial PSDF was added.
 - Mask editor tool: New option to prevent merging of grains by growing mask.
 - Read Value: Can shift data values to make the currently selected point lie
  on the zero plane.
@@ -2792,8 +2890,8 @@ Modules:
 - Nanonis: Import of non-square images was hopefully fixed.
 - Convolution filter: Minor user interface fixes.
 - Edge: Laplacian no longer clears border lines of pixels of output.
- Statistical functions tool: The labels on x and y axes match how the
-  quantities are denoted in the user guide.
+- Statistical functions: The labels on x and y axes match how the quantities
+  are denoted in the user guide.

 Other:
 - Unix compilation: Confusion between AM_FOO and FOO variables in makefiles was

--- a/README
+++ b/README
@@ -34,6 +34,7 @@ Subdir dependencies (fully resolved):
    libgwydgets:  libgwyddion libprocess libdraw
    libgwymodule: libgwyddion libprocess libdraw libgwydgets
    app:          libgwyddion libprocess libdraw libgwydgets libgwymodule
+    gwyddion:     libgwyddion libprocess libdraw libgwydgets libgwymodule app
    modules:      libgwyddion libprocess libdraw libgwydgets libgwymodule app
    devel-docs:   libgwyddion libprocess libdraw libgwydgets libgwymodule app
    po:           libdraw libgwydgets libgwymodule app modules
@@ -46,7 +47,8 @@ Subdir contents:
    libdraw:      Gwyddion drawing library
    libgwydgets:  Gwyddion widget library
    libgwymodule: Gwyddion module library
-    app:          Gwyddion application library (libgwyapp), main application
+    app:          Gwyddion application library
+    gwyddion:     Main program (gwyddion)
    modules:      Standard modules (file, graph, layer, process, tool, ...)
    plugins:      Standard and sample plug-ins (file, process)
    thumbnailer:  Tool for creating thumbnails of SPM data

--- a/aclocal.m4
+++ b/aclocal.m4
@@ -2545,7 +2545,6 @@ AC_SUBST([am__tar])
 AC_SUBST([am__untar])
 ]) # _AM_PROG_TAR

-m4_include([m4/gconf-2.m4])
 m4_include([m4/gettext.m4])
 m4_include([m4/glibc21.m4])
 m4_include([m4/gtk-doc.m4])

--- a/app/Makefile.am
+++ b/app/Makefile.am
-# $Id: Makefile.am 21207 2018-06-25 09:29:12Z yeti-dn $
+# $Id: Makefile.am 21624 2018-11-13 13:48:03Z yeti-dn $

 libgwyddion = $(top_builddir)/libgwyddion/libgwyddion2.la
 libgwymodule = $(top_builddir)/libgwymodule/libgwymodule2.la
@@ -7,8 +7,6 @@ libgwydraw = $(top_builddir)/libdraw/libgwydraw2.la
 libgwydgets = $(top_builddir)/libgwydgets/libgwydgets2.la

 libgwyapp2includedir = $(pkgincludedir)/app
-uidatadir = $(pkgdatadir)/ui
-

 if MODULE_DEPENDENCIES
 libgwyapp_libadd = \
@@ -47,23 +45,11 @@ libgwyapp2include_HEADERS = \
 	wait.h

 noinst_HEADERS = \
-	mac_integration.h\
-	authors.h \
 	gwyappfilechooser.h \
-	gwyappinternal.h \
-	gwyddion.h \
-	release.h \
-	toolbox.h
-
-uidata_DATA = toolbox.xml
+	gwyappinternal.h

-bin_PROGRAMS = gwyddion
 lib_LTLIBRARIES = libgwyapp2.la

-BUILT_SOURCES = \
-	authors.h \
-	release.h
-
 if OS_MSWIN
 no_undefined = -no-undefined
 export_symbols = -export-symbols libgwyapp2.def
@@ -72,11 +58,10 @@ libgwyapp2_la_DEPENDENCIES = libgwyapp2.def
 endif

 # Must init
-EXTRA_DIST = \
-	README.objdata \
-	toolbox.xml
+EXTRA_DIST =
 CLEANFILES = libgwyapp2.def
 MAINTAINERCLEANFILES =
+BUILT_SOURCES =

 MKENUM_NAME = gwyapptypes
 MKENUM_ID = GWY_APP_TYPES
@@ -107,20 +92,16 @@ libgwyapp2.def: $(libgwyapp2_la_OBJECTS)
 		| awk -F' ' '($$2=="T" && $$3 ~ /^gwy_/){print "     ",$$3}'; \
 	done | sort >>libgwyapp2.def

-AM_CFLAGS = $(darwin_cflags) @GTK_MAC_CFLAGS@ @FFTW3_CFLAGS@ @UNIQUE_CFLAGS@ @COMMON_CFLAGS@ @GIO_CFLAGS@
-AM_CPPFLAGS = -I$(top_srcdir)
-AM_LDFLAGS = $(darwin_ldflags)
-
 # In following order do:
 # Any code change     C:   R++: A
 # Any iface change    C++: 0:   A
 # Adding ifaces       C:   R:   A++
 # Changing ifaces     C:   R:   0
-libversion = -version-info 21:0:21
+libversion = -version-info 21:1:21
 #libversion = -release @LIBRARY_RELEASE@
-libgwyapp2_la_LDFLAGS = @GTKGLEXT_LIBS@ @GIO_LIBS@ @BASIC_LIBS@ $(win32_libs) -export-dynamic $(no_undefined) $(export_symbols) $(libversion)
-libgwyapp2_la_CPPFLAGS = -DG_LOG_DOMAIN=\"GwyApp\" $(AM_CPPFLAGS)
-libgwyapp2_la_LIBADD = $(libgwyapp_libadd)
+AM_CFLAGS = @COMMON_CFLAGS@ @GIO_CFLAGS@
+AM_LDFLAGS = @GTKGLEXT_LIBS@ @GIO_LIBS@ @BASIC_LIBS@ $(win32_libs) -export-dynamic $(no_undefined) $(export_symbols) $(libversion) $(libgwyapp_libadd)
+AM_CPPFLAGS = -DG_LOG_DOMAIN=\"GwyApp\" -I$(top_srcdir)

 libgwyapp2_la_SOURCES = \
 	app.c \
@@ -150,37 +131,5 @@ libgwyapp2_la_SOURCES = \
 	validate.c \
 	wait.c

-gwyddion_SOURCES = \
-	about.c \
-	gwyddion.c \
-	mac_integration.c \
-	remote.c \
-	remote-unique.c \
-	remote-win32.c \
-	remote-x11.c \
-	splash.c \
-	tips.c \
-	toolbox.c \
-	toolbox-editor.c \
-	toolbox-spec.c
-
-gwyddion_LDADD = @COMMON_LDFLAGS@ @GTK_MAC_LIBS@ @GTKGLEXT_LIBS@ @FFTW3_LIBS@ @UNIQUE_LIBS@ @GIO_LIBS@ @BASIC_LIBS@ $(LIBXMU) \
-	libgwyapp2.la \
-	$(libgwymodule) \
-	$(libgwydgets) \
-	$(libgwydraw) \
-	$(libgwyprocess) \
-	$(libgwyddion)
-
-if MAINTAINER_MODE
-authors.h: ${top_srcdir}/AUTHORS $(top_srcdir)/utils/gen-authors.py
-	$(AM_V_GEN)$(PYTHON) $(top_srcdir)/utils/gen-authors.py $(top_srcdir)/AUTHORS header >authors.h
-
-release.h: ${top_srcdir}/NEWS Makefile $(top_builddir)/config.h
-	$(AM_V_GEN)echo '/* This is a 'GENERATED' file. */' >release.h
-	$(AM_V_at)echo '/*< private_header >*/' >>release.h
-	$(AM_V_at)sed -n 1p ${top_srcdir}/NEWS | sed -e 's/^.*(/#define RELEASEDATE 0x/' -e 's/)/u/' -e 's/-//g' >>release.h
-endif
-
 clean-local:
 	rm -f core.* *~
--- a/app/Makefile.in
+++ b/app/Makefile.in
--- a/app/README.objdata
+++ b/app/README.objdata
-
-Data set on various gwyddion objects by main app (g_object_set_data()).
-May change, namely many may get some "gwy-app-" prefix.
-
-Toolbox (gwy_app_main_window_get()):
-    "accel_group":       The toolbox's main accelerator group
-
-Process menu:
-    "gwy-app-menu-repeat-last":    Menu item representing repeat-last
-    "gwy-app-menu-reshow-last":    Menu item representing reshow-last
-
-`Recent Files' menu items:
-    "filename":          The file name
-
-Toolbar show/hide buttons:
-    "arrow":             The arrow widget
-    "key":               Settings key holding visibility for this toolbox
-                         ("/app/toolbox/visible/SOMETHING")
-
-Data Containers:
-    "metadata-browser"   If set, there is already a metadata browser active for
-                         this data and the pointer is its window widget.
-
-# $Id: README.objdata 20681 2017-12-18 18:37:24Z yeti-dn $
--- a/app/app.c
+++ b/app/app.c
 /*
- *  $Id: app.c 20678 2017-12-18 18:26:55Z yeti-dn $
+ *  $Id: app.c 21435 2018-09-11 12:39:53Z yeti-dn $
 *  Copyright (C) 2003-2006,2013-2017 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
@@ -241,20 +241,23 @@ gwy_app_main_window_get(void)

 /**
 * gwy_app_main_window_set:
- * @window: A window.
+ * @window: A window, presumably the Gwyddion toolbox.
+ *
+ * Sets the main application window.
 *
- * Sets Gwyddion main application window (toolbox) for
- * gwy_app_main_window_get().
+ * This function is probably only useful in Gwyddion itself and should be
+ * ignored.
 *
- * This function can be called only once and should be called at Gwyddion
- * startup so, ignore it.
+ * It needs to be called exactly once at Gwyddion startup.
+ * It restores the toolbox position and makes gwy_app_main_window_get() work.
 **/
 void
 gwy_app_main_window_set(GtkWidget *window)
 {
    g_return_if_fail(GTK_IS_WINDOW(window));
    if (gwy_app_main_window && window != gwy_app_main_window) {
-        g_critical("Trying to change app main window");
+        g_critical("The main window was already set to %p.",
+                   gwy_app_main_window);
        return;
    }

@@ -1684,52 +1687,25 @@ change_brick_preview(GwyDataWindow *data_window)
        return;
    }

-    if (type == BRICK_PREVIEW_MEAN) {
-        gwy_brick_mean_plane(brick, preview,
-                             0, 0, 0,
-                             brick->xres, brick->yres, -1,
-                             TRUE);
-    }
-    else if (type == BRICK_PREVIEW_MINIMUM) {
-        gwy_brick_min_plane(brick, preview,
-                            0, 0, 0,
-                            brick->xres, brick->yres, -1,
-                            TRUE);
-    }
-    else if (type == BRICK_PREVIEW_MAXIMUM) {
-        gwy_brick_max_plane(brick, preview,
-                            0, 0, 0,
-                            brick->xres, brick->yres, -1,
-                            TRUE);
-    }
-    else if (type == BRICK_PREVIEW_MINPOS) {
-        gwy_brick_minpos_plane(brick, preview,
-                               0, 0, 0,
-                               brick->xres, brick->yres, -1,
-                               TRUE);
-    }
-    else if (type == BRICK_PREVIEW_MAXPOS) {
-        gwy_brick_maxpos_plane(brick, preview,
-                               0, 0, 0,
-                               brick->xres, brick->yres, -1,
-                               TRUE);
-    }
-    else if (type == BRICK_PREVIEW_RMS) {
-        gwy_brick_rms_plane(brick, preview,
-                            0, 0, 0,
-                            brick->xres, brick->yres, -1,
-                            TRUE);
-    }
+    if (type == BRICK_PREVIEW_MEAN)
+        gwy_brick_mean_xy_plane(brick, preview);
+    else if (type == BRICK_PREVIEW_MINIMUM)
+        gwy_brick_min_xy_plane(brick, preview);
+    else if (type == BRICK_PREVIEW_MAXIMUM)
+        gwy_brick_max_xy_plane(brick, preview);
+    else if (type == BRICK_PREVIEW_MINPOS)
+        gwy_brick_minpos_xy_plane(brick, preview);
+    else if (type == BRICK_PREVIEW_MAXPOS)
+        gwy_brick_maxpos_xy_plane(brick, preview);
+    else if (type == BRICK_PREVIEW_RMS)
+        gwy_brick_rms_xy_plane(brick, preview);
    else if (type == BRICK_PREVIEW_CHANNEL) {
        GQuark quark = gwy_app_get_data_key_for_id(cid);
        GObject *field = gwy_container_get_object(cdata, quark);
-        gwy_serializable_clone(field, G_OBJECT(preview));
+        gwy_data_field_assign(preview, field);
    }
    else if (type == BRICK_PREVIEW_SECTION)
-        gwy_brick_extract_plane(brick, preview,
-                                0, 0, level,
-                                brick->xres, brick->yres, -1,
-                                TRUE);
+        gwy_brick_extract_xy_plane(brick, preview, level);
    else {
        g_return_if_reached();
    }

--- a/app/app.h
+++ b/app/app.h
 /*
- *  $Id: app.h 20678 2017-12-18 18:26:55Z yeti-dn $
- *  Copyright (C) 2003-2006 David Necas (Yeti), Petr Klapetek.
+ *  $Id: app.h 21392 2018-09-05 07:53:07Z yeti-dn $
+ *  Copyright (C) 2003-2018 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
 *  This program is free software; you can redistribute it and/or modify
@@ -38,6 +38,7 @@ void         gwy_app_restore_window_position    (GtkWindow *window,
                                                 const gchar *prefix,
                                                 gboolean grow_only);
 GtkWidget*   gwy_app_main_window_get            (void);
+void         gwy_app_main_window_set            (GtkWidget *window);
 void         gwy_app_data_view_change_mask_color(GwyDataView *data_view);
 gboolean     gwy_app_quit                       (void);
 void         gwy_app_init_widget_styles         (void);

--- a/app/data-browser-aux.c
+++ b/app/data-browser-aux.c
 /*
- *  $Id: data-browser-aux.c 20848 2018-03-16 09:41:01Z yeti-dn $
+ *  $Id: data-browser-aux.c 21430 2018-09-11 11:46:00Z yeti-dn $
 *  Copyright (C) 2006-2016 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
@@ -2287,7 +2287,7 @@ _gwy_app_create_brick_preview_field(GwyBrick *brick)
    GwyDataField *preview = gwy_data_field_new(xres, yres, xreal, yreal,
                                               FALSE);

-    gwy_brick_mean_plane(brick, preview, 0, 0, 0, xres, yres, -1, FALSE);
+    gwy_brick_mean_xy_plane(brick, preview);
    return preview;
 }

@@ -2626,9 +2626,9 @@ gwy_app_get_graph_thumbnail(GwyContainer *data,
    if (!gtk_main_level())
        return NULL;

-    visual = gdk_visual_get_best();
+    visual = gdk_visual_get_system();
    g_return_val_if_fail(visual, NULL);
-    cmap = gdk_colormap_new(visual, FALSE);
+    cmap = gdk_colormap_get_system();
    g_return_val_if_fail(cmap, NULL);

    width = MAX(width, max_width);

--- a/app/data-browser.c
+++ b/app/data-browser.c
--- a/app/file.c
+++ b/app/file.c
 /*
- *  $Id: file.c 20678 2017-12-18 18:26:55Z yeti-dn $
+ *  $Id: file.c 21363 2018-08-28 14:39:00Z yeti-dn $
 *  Copyright (C) 2003-2006 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
@@ -131,6 +131,8 @@ gwy_app_set_current_directory(const gchar *directory)
 * load fails, an error dialog is presented.
 *
 * Returns: Container of the just loaded file on success, %NULL on failure.
+ *          The caller does not own the reference, the container is only
+ *          owned by the data browser.
 **/
 GwyContainer*
 gwy_app_file_load(const gchar *filename_utf8,

--- a/app/gwyappinternal.h
+++ b/app/gwyappinternal.h
 /*
- *  $Id: gwyappinternal.h 20678 2017-12-18 18:26:55Z yeti-dn $
- *  Copyright (C) 2004-2016 David Necas (Yeti), Petr Klapetek.
+ *  $Id: gwyappinternal.h 21392 2018-09-05 07:53:07Z yeti-dn $
+ *  Copyright (C) 2004-2018 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
 *  This program is free software; you can redistribute it and/or modify
@@ -116,10 +116,6 @@ typedef struct {
    gchar *message;
 } GwyAppLogMessage;

-/* XXX: Bad name.  Cannot fix it because according to the rules it is now
- * public API. */
-void     gwy_app_main_window_set              (GtkWidget *window);
-
 G_GNUC_INTERNAL
 gint     _gwy_app_get_n_recent_files          (void);


--- a/app/gwymoduleutils-file.c
+++ b/app/gwymoduleutils-file.c
 /*
- *  $Id: gwymoduleutils-file.c 21151 2018-06-15 08:18:55Z yeti-dn $
+ *  $Id: gwymoduleutils-file.c 21435 2018-09-11 12:39:53Z yeti-dn $
 *  Copyright (C) 2007-2016 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
@@ -237,7 +237,6 @@ gwy_app_xyz_title_fall_back(GwyContainer *data,
 guint
 gwy_app_channel_remove_bad_data(GwyDataField *dfield, GwyDataField *mfield)
 {
-    GwySIUnit *funit, *munit;
    gdouble *m = gwy_data_field_get_data(mfield);
    guint i, mcount, n;

@@ -257,9 +256,8 @@ gwy_app_channel_remove_bad_data(GwyDataField *dfield, GwyDataField *mfield)

    gwy_data_field_set_xreal(mfield, gwy_data_field_get_xreal(dfield));
    gwy_data_field_set_yreal(mfield, gwy_data_field_get_yreal(dfield));
-    funit = gwy_data_field_get_si_unit_xy(dfield);
-    munit = gwy_data_field_get_si_unit_xy(mfield);
-    gwy_serializable_clone(G_OBJECT(funit), G_OBJECT(munit));
+    gwy_si_unit_assign(gwy_data_field_get_si_unit_xy(mfield),
+                       gwy_data_field_get_si_unit_xy(dfield));

    gwy_debug("mcount = %u", mcount);


--- a/app/gwymoduleutils.c
+++ b/app/gwymoduleutils.c
 /*
- *  $Id: gwymoduleutils.c 20833 2018-03-13 10:52:02Z yeti-dn $
+ *  $Id: gwymoduleutils.c 21435 2018-09-11 12:39:53Z yeti-dn $
 *  Copyright (C) 2007-2018 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
@@ -788,8 +788,8 @@ gwy_preview_surface_to_datafield(GwySurface *surface,

    gwy_data_field_average_xyz(dfield, densitymap,
                               gwy_surface_get_data_const(surface), n);
-    gwy_serializable_clone(G_OBJECT(gwy_surface_get_si_unit_xy(surface)),
-                           G_OBJECT(gwy_data_field_get_si_unit_xy(dfield)));
+    gwy_si_unit_assign(gwy_data_field_get_si_unit_xy(dfield),
+                       gwy_surface_get_si_unit_xy(surface));

    if (want_densitymap) {
        gwy_data_field_copy(densitymap, dfield, FALSE);
@@ -797,8 +797,8 @@ gwy_preview_surface_to_datafield(GwySurface *surface,
        gwy_si_unit_set_from_string(gwy_data_field_get_si_unit_z(dfield), NULL);
    }
    else {
-        gwy_serializable_clone(G_OBJECT(gwy_surface_get_si_unit_z(surface)),
-                               G_OBJECT(gwy_data_field_get_si_unit_z(dfield)));
+        gwy_si_unit_assign(gwy_data_field_get_si_unit_z(dfield),
+                           gwy_surface_get_si_unit_z(surface));
    }
 }


--- a/app/gwyplaintool.c
+++ b/app/gwyplaintool.c
 /*
- *  $Id: gwyplaintool.c 20678 2017-12-18 18:26:55Z yeti-dn $
- *  Copyright (C) 2006,2014 David Necas (Yeti), Petr Klapetek.
+ *  $Id: gwyplaintool.c 21343 2018-08-27 14:28:40Z yeti-dn $
+ *  Copyright (C) 2006-2018 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
 *  This program is free software; you can redistribute it and/or modify
@@ -1223,17 +1223,27 @@ gwy_rect_selection_labels_fill(GwyRectSelectionLabels *rlabels,
        sel[2] = gwy_data_field_get_xreal(dfield);
        sel[3] = gwy_data_field_get_yreal(dfield);
        isel[0] = isel[1] = 0;
-        isel[2] = xres;
-        isel[3] = yres;
+        isel[2] = xres-1;
+        isel[3] = yres-1;
    }

+    sel[0] = gwy_data_field_jtor(dfield, isel[0]);
+    sel[1] = gwy_data_field_jtor(dfield, isel[1]);
+    sel[2] = gwy_data_field_jtor(dfield, isel[2]+1);
+    sel[3] = gwy_data_field_jtor(dfield, isel[3]+1);
+
+    /* Provide sorted real and pixel selection to the caller; but before we
+     * add offsets and convert to position & size.  The documentation has
+     * always said min and max pixel coordinates, so we must have res-1 there
+     * for full-size selections. */
    if (selreal)
        gwy_assign(selreal, sel, 4);
    if (selpix)
        gwy_assign(selpix, isel, 4);

-    sel[2] -= sel[0];
-    sel[3] -= sel[1];
+    isel[2] -= isel[0] - 1;
+    isel[3] -= isel[1] - 1;
+
    sel[0] += xoff;
    sel[1] += yoff;

@@ -1247,9 +1257,6 @@ gwy_rect_selection_labels_fill(GwyRectSelectionLabels *rlabels,
    }
    gwy_si_unit_value_format_free(vf);

-    isel[2] -= isel[0] - 1;
-    isel[3] -= isel[1] - 1;
-
    gtk_spin_button_set_range(rlabels->pix[RLABEL_X], 0.0, xres - 1.0);
    gtk_spin_button_set_range(rlabels->pix[RLABEL_W], 2.0, xres - isel[0]);
    gtk_spin_button_set_range(rlabels->pix[RLABEL_Y], 0.0, yres - 1.0);

--- a/app/wait.c
+++ b/app/wait.c
 /*
- *  $Id: wait.c 20678 2017-12-18 18:26:55Z yeti-dn $
- *  Copyright (C) 2004-2017 David Necas (Yeti), Petr Klapetek.
+ *  $Id: wait.c 21526 2018-10-28 09:01:13Z yeti-dn $
+ *  Copyright (C) 2004-2018 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
 *  This program is free software; you can redistribute it and/or modify
@@ -155,8 +155,12 @@ gwy_app_wait_create_dialog(GtkWindow *window,
 *
 * This function lets the Gtk+ main loop to run.
 *
+ * It must not be called again once the operation is cancelled, i.e. after
+ * any of the progress reporting functions return %FALSE.
+ *
 * Returns: %TRUE if the operation can continue, %FALSE if user cancelled it
- *          meanwhile.
+ *          meanwhile.  You must always check the return value and cancel
+ *          the operation if it is %FALSE.
 **/
 gboolean
 gwy_app_wait_set_message(const gchar *message)
@@ -198,8 +202,12 @@ gwy_app_wait_set_message(const gchar *message)
 *
 * This function lets the Gtk+ main loop to run.
 *
+ * It must not be called again once the operation is cancelled, i.e. after
+ * any of the progress reporting functions return %FALSE.
+ *
 * Returns: %TRUE if the operation can continue, %FALSE if user cancelled it
- *          meanwhile.
+ *          meanwhile.  You must always check the return value and cancel
+ *          the operation if it is %FALSE.
 **/
 gboolean
 gwy_app_wait_set_message_prefix(const gchar *prefix)
@@ -235,8 +243,12 @@ gwy_app_wait_set_message_prefix(const gchar *prefix)
 * fearing that the program will spend all time updating the GUI and no time in
 * the calculation.
 *
+ * It must not be called again once the operation is cancelled, i.e. after
+ * any of the progress reporting functions return %FALSE.
+ *
 * Returns: %TRUE if the operation can continue, %FALSE if user cancelled it
- *          meanwhile.
+ *          meanwhile.  You must always check the return value and cancel
+ *          the operation if it is %FALSE.
 **/
 gboolean
 gwy_app_wait_set_fraction(gdouble fraction)
@@ -402,8 +414,8 @@ gwy_app_wait_set_enabled(gboolean setting)
    if (!wait_enabled == !setting)
        return;

-    g_return_if_fail(dialog);
-    g_return_if_fail(cancelled);
+    g_return_if_fail(!dialog);
+    g_return_if_fail(!cancelled);
    wait_enabled = !!setting;
 }

@@ -412,7 +424,7 @@ gwy_app_wait_set_enabled(gboolean setting)
 *
 * Checks if a progress dialog was cancelled.
 *
- * Calling this function is only meaningful between gwy_app_wait_cursor_start()
+ * Calling this function is only meaningful between gwy_app_wait_start()
 * and gwy_app_wait_finish().  It returns %TRUE if the computation was
 * cancelled by the user.  This may be occasionaly useful in complex
 * multi-level calculations.  Usually, the return values of

--- a/app/wait.h
+++ b/app/wait.h
 /*
- *  $Id: wait.h 20678 2017-12-18 18:26:55Z yeti-dn $
- *  Copyright (C) 2004-2017 David Necas (Yeti), Petr Klapetek.
+ *  $Id: wait.h 21407 2018-09-07 13:07:11Z yeti-dn $
+ *  Copyright (C) 2004-2018 David Necas (Yeti), Petr Klapetek.
 *  E-mail: yeti@gwyddion.net, klapetek@gwyddion.net.
 *
 *  This program is free software; you can redistribute it and/or modify
@@ -29,9 +29,9 @@ G_BEGIN_DECLS
 void     gwy_app_wait_start             (GtkWindow *window,
                                         const gchar *message);
 void     gwy_app_wait_finish            (void);
-gboolean gwy_app_wait_set_fraction      (gdouble fraction);
-gboolean gwy_app_wait_set_message       (const gchar *message);
-gboolean gwy_app_wait_set_message_prefix(const gchar *prefix);
+gboolean gwy_app_wait_set_fraction      (gdouble fraction)      G_GNUC_WARN_UNUSED_RESULT;
+gboolean gwy_app_wait_set_message       (const gchar *message)  G_GNUC_WARN_UNUSED_RESULT;
+gboolean gwy_app_wait_set_message_prefix(const gchar *prefix)   G_GNUC_WARN_UNUSED_RESULT;
 void     gwy_app_wait_cursor_start      (GtkWindow *window);
 void     gwy_app_wait_cursor_finish     (GtkWindow *window);
 gboolean gwy_app_wait_get_enabled       (void);