New upstream version 2.52

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.

# $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 \

	libgwydgets \

	libgwymodule \

	app \

	gwyddion \

	modules \

	plugins \

	po \

@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 $

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	libgwydgets \

	libgwymodule \

	app \

	gwyddion \

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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.

  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

- 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.

- 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.

- 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

- 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.

  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.

  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:

- 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.

- 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

  (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.

- 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)

  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.

- 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

    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

    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