luis vazquez | 17 May 10:37 2016
Picon

"calculate 1D statistical functions" on masked regions?

Hi,

I am interested in performing on a masked image some analysis by using 
the "calculate 1D statistical functions" tool (for instance ACF). I want 
to do it only on the masked regions. In principle, it seems that the 
tool allows it as at the left bottom of the window appears the "Masking 
Mode" section in which one can choose to exclude/include the masked 
regions or use the entire image. However, this option appears always as 
inactive and it is not possible to do these choices. In contrast, this 
is not the case for the "Statistical quantities" tool where it works 
without problems. So,  does this option really work (and how) in the 
"calculate 1D statistical functions" tool?

Thanks in advance,

regards,

Luis

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Anjan Gupta | 11 May 06:04 2016
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Conventional Cross-correlation

Hello,
        I want to calculate the conventional cross-correlation image between the normalized topography and conductance images taken simultaneously. I have not been able to do using Gwyddion so far and I am wondering if it is possible to do it using Pygwy. If I understand the cross-correlation is evaluated in some of the modules like mutual crop.
      Another thing I was wondering about if the arithmatic module can allow use of quantities like Average(d1), StdDev(d1), etc. This way one can at least get zero shift cross-correlation between two images easily. It is possible still by noting these values from image statistics but it is cumbersome and prone to error when one does it for large data.

Thanks in appreciation.
      -Anjan.
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David Nečas (Yeti | 26 Apr 19:08 2016
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Gwyddion 2.45 was released


Gwyddion 2.45 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.45/
  (all released files)

  http://gwyddion.net/download/2.45/
  (source code)

Released files are signed with PGP/GnuPG key

  "David Nečas (Yeti) <yeti <at> gwyddion.net>", id 62A07732
  fingerprint = 263F 9B1E C1E0 5261 C689  D83B 00FD D1D0 62A0 7732

-----------------------------------------------------------------------------

This is a stable version continuing the 2.x series, backward compatible with
previous 2.x versions.

More information about Gwyddion is available at

  http://gwyddion.net/

Bugs should be reported to

  klapetek <at> gwyddion.net

the mailing list, or the project's web forum at SourceForge.

-----------------------------------------------------------------------------

Summary of changes:
Application:
- New translation: British English (accompanied with unification of the default
  language to US English).
- Translations updated: Czech, French, Russian.
- Program messages: Are written to the log file by default on all platforms,
  on Unix in addition to the console.
- Command line: New options --log-to-console and --no-log-to-console permit
  controlling independently where the messages go (and where they do not).
- Program messages: Can be displayed in the GUI using Info → Program Messages.
- Files: The current file can be closed using Ctrl-W (or File → Close in the
  menu).
- Tips of the day: Were updated and can be displayed on startup if enabled.

Libraries:
- libgwyddion: GwyNLFitter fit returns -1 and NULLs the covariance matrix when
  it gets infinities or NaNs anywhere in the matrix or parameters.
- libgwyddion: New macro gwy_info() emits an INFO-level log message.
- libgwyddion, libgwyprocess: New standard boxed structs GwyXY and GwyXYZ were
  added to gwymath.  GwyTriangulationPointXY and GwyTriangulationPointXYZ are
  now their aliases.
- libgwyprocess: New DataField distortion function that takes explicit list of
  coordinates in the original data field.
- libgwyprocess: GwySurface is a new data object representing XYZ data,
  currently providing just a few basic methods.
- libgwyprocess: GwySpline is a new helper data structure for sampling along
  curves.
- libgwyprocess: Wrong estimated sizes for tip models were corrected.
- libgwyprocess: Two new tip models were added: Parabola and Cone.
- libgwyprocess: Function for filling missing valies in GwyDataLine using
  Laplace data correction was added.
- libgwyprocess: GwyDataField line statistics caulcates rms using local line
  means, not the global mean.
- libgwyprocess: Raw 2D FFT transform using the SimpleFFT backend (i.e. with
  FFTW unavailable) overwriting the input data field was fixed.
- libgwyprocess: New function gwy_data_field_area_renormalize() transforms
  values in just a part of data field.
- libgwyprocess: Crash in gwy_data_field_area_get_entropy_at_scales() for data
  fields filled with a constant value was fixed.
- libgwyprocess: gwy_data_field_clear() no longer sets cached area to zero.
- libgwyprocess: Resampling of constant valued data fields always produces
  constant valued data fields.  This fixes odd rounding error patterns in
  thumbnails for constant valued fields.
- libgwyprocess: Tip dilation and erosion functions were optimised.
- libgwydgets: A large number of new stock icons were added.
- libgwydgets: The gradient can be unset using data window colour axis menu.
  The colour gradient and GL material can be unset in the 3D window as well.
- libgwydgets: Positions of graph labels are remembered and restored.
- libgwydgets: GwyGraphCurveModel has a method for ensuring data points are
  ordered by abscissa.
- libgwydgets: Convenience combo box constructor for graph curves was added.
- libgwydgets: Editability of graph area selections can be controlled.
- libgwydgets: Function for setting graph curve data from a single interleaved
  array was added.
- libgwydgets: Graph and 3D windows can be resized using keyboard, similarly
  to other data windows.
- libgwydgets: GwyDataView with physical aspect ratio resizes itself now when
  the physical dimensions change but pixel dimensions do not.
- libgwymodule: XYZ data processing module management functions were added.
- libgwyapp: All program messages are gathered by the default logger and
  displayed in a text view.
- libgwyapp: Data browser can show warnings and other messages ocurring during
  the opening or merging of specific files.
- libgwyapp: Data browser displays thumbnails for graphs.  A new function for
  graph thumbnail creation was added.
- libgwyapp: Thumbnails are generated from any kind of data found in the image,
  preferring volume, XYZ, channels and then graphs.
- libgwyapp: File open dialogue previews almost all visual data types:
  channels, graphs, volume and xyz.
- libgwyapp: XYZ data support was added to validation, logging, metadata
  browsing, data choosers, enumeration and other places.
- libgwyapp: gwy_app_sync_data_items() only replicates non-empty selections
  now.
- libgwyapp: Functions for enumerating ids of data in a container now work
  also for containers not managed by the data browser.
- libgwyapp: GwyAppFileChooser open dialogue can filter files by name.
- libgwyapp: It is possible to query the current data browser page using
  gwy_app_data_browser_get_current().
- libgwyapp: Data can be duplicated with Ctrl-D, deleted with Ctrl-Delete and
  extracted to a new file with Ctrl-Insert.
- libgwyapp: Zooms and sizes of all kinds data windows are saved and restored
  when the data are displayed again (if they seem sane for the current screen).

Modules:
- Straighten path (new): Extracts image sampled along a spline curve and the
  direction perpendicular to the curve.
- Path layer (new): A single spline curve with arbitrary number of points.
- Extract path selection (new): Extracts positions and tangents of sampled 
  path selections as graph curves.
- Find graph peaks (new): Simple location of peaks on graph curves.
- Rasterize XYZ (new): Renders XYZ data to an image.
- XYZ Correct Drift (new): Corrects drift in timestamped XYZ data.
- Coerce (new): Transforms surfaces to have prescribed statistical properties.
- XYZize (new): Creates XYZ data (with regular point grid) from an image.
- Data processing modules with preview: Data with non-square aspect ratio
  should look like in 2.43 again.
- IntelliWave (new): Imports IntelliWave ESD data files (experimental).
- Nano Measuring Machine: Parameters from the main DSC file are imported as
  metadata.
- Align rows: Median difference method no longer changes the overall data tilt.
- Spectro tool: Always disabled ‘Apply’ button (broken in 2.44) works again.
- Points, Lines layers: Numbering works with more than 999 objects.
- 1D FFT filter: GUI was reorganised and the previews enlarged.
- Image export: Support for path selection drawing was added.
- Level: Zero mean value supports masking.  Individual module functions have
  separate settings now.
- Columnar synthesis: New option to continuously ‘melt’ the film during the
  growth.
- RHK SPM32 and SM4: Imported graph curves are sorted by abscissa, fixing
  some graph functionality being broken.
- WSxM: Files starting ‘WSxM file copyright WSxM solutions’ are also
  recognised now.  Single-precision files are loaded correctly.
- Nanoscantech: Support for files using UTF-8 encoding was added.
- GWYXYZF: Byte order handling was corrected to follow the specification.
- GWYXYZF, Raw XZY: The data are loaded a native XYZ data instead of being
  regularised to image upon import.
- Statistical functions: Local range was added as a new quantity.
- Object synthesis: Coverage parameter was fixed to actually mean what the
  documentation describes.  Multiply old values by 4 to get the same coverage.
- Mark disconnected: The operation is undoable now.
- XYZ export: Can export both channels and XYZ data.
- APE DAX: Complete metadata are imported, miscellaneous other improvements.
- Seiko: Image resolutions should be correct for all files, with no guessing
  involved.
- OME TIFF: Data split to several files can be loaded at least file by file
  now, instead of getting a cryptic error message.
- Volumize layers: Memory handling error causing a crash after closing the
  volumized data was fixed.  Units are set properly and can be controlled
  in the module dialogue.
- Volumize: The created volume data are now 1 under the surface (inside the
  material) and 0 above the surface (outside the material).

-----------------------------------------------------------------------------

Thanks all who contributed,

Yeti

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Michele Della Ciana | 24 Apr 19:02 2016
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Installing a module on Gwyddion (using Mac)

Hi! 

My name is Michele and I’m an Italian physics student.

I’m trying to install the minimal module in the totorial's section but when I start gwyddion it says:


(gwyddion:6946): GLib-GObject-WARNING **: cannot register existing type 'gchar'

**

GLib-GObject:ERROR:gvaluetypes.c:455:_g_value_types_init: assertion failed: (type == G_TYPE_CHAR)

Abort trap: 6

logout


and it closes.


To copile the module as a shared library I used: 

gcc -fPIC -shared -o module.so main.cpp `pkg-config --cflags --libs gwyddion`

where main.cpp is the source code of the minimal module.


It compiles fine… the problem occurs when I put the “module.so” file in the module’s directory.

By now I’m using gwyddion just as a library, but I hope to solve the problem!

I think is useful to know that I’m using a mac with OS X Yosemite and I have installed  gwyddion using homebrew!


Sorry for my English, I hope the problem is clear!

Thanks in advance

Michele



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Václav Šmilauer | 27 Mar 20:29 2016
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Gravatar

grain photo segmentation

Hi everybody,

I am new to Gwyddion and would like to try using it for grain size 
analysis from industrial camera images. A typical image is like this: 
http://i.imgur.com/lwuOBeh.jpg (the diagonal separates two types of 
material which has different reflectivity), and I would like to run (at 
some point) unattended analysis of grain size distribution under 
constant conditions (same lighting, similar material).

I was able to use some of the tools provided to improve the picture 
(like Polynomial Background to make the lighting artefacts less visible) 
but I am at loss with segmentation. The simple techniques (e.g. 
watershed) are not suitable, since grains have different luminosity 
(especially the glossy ones).

I will be grateful for hints, pointers or solutions. At this moment, the 
analysis does not have to be unattended, setting parameters or light 
hand-tuning is fine.

Cheers, Václav

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vidyasagar | 18 Mar 01:15 2016
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Hi

Dear sir/madam,

I have downloaded Gwyddion software, but it could not working well in my laptop.
When I opening the file, it says, opening of ....mdt failed. file contrains no (importable) data
Could you plase help me?

Sincerely,
Sagar
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John Dodji Amouzou | 2 Mar 16:32 2016
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Scales conversion (from log scale to linear scale)

Hello,
I recorded AFM images in current sensing mode using Resiscope and PicoView and the Z scale of the recorded images is in log scale. I would like to convert Z scales of current and resistance images into linear scale.
How could I do that?
Thanks for your help.
With regards,
Dodji.
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Andrés Muñiz Piniella | 25 Feb 18:22 2016
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3DPrinting your AFM data

I am sorry as I do not recall who was working on this as well, finally got some time to invest time in it.

I have worked on a little script and procedure that should make it possible to take AFM data (or any data represented in a surface) scale it and transform it into an STL that can be 3D printed.


Happy to walk you through to what I have done. Written explanation attached in comments of python code to get you started.

this can be further streamlined and improved. so that it is a saving module in Gwyddion.


--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

Attachment (PrintGWY.py): application/octet-stream, 4568 bytes
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Andrés Muñiz Piniella | 28 Jan 14:52 2016
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windows 32 bit graph and download issues

I am using 2.44 32 bit on windows xp (yes I know it is old).

I noticed that measure distance in graph gives me a value in length but not height.

I was looking to reinstall again but I get sec_error_unknown_issuer
and the address is 139.143.6.160:9091 when following the link from gwiddion.net download page.

--
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David Nečas (Yeti | 11 Jan 15:13 2016
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Gwyddion 2.44 was released


Gwyddion 2.44 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.44/
  (all released files)

  http://gwyddion.net/download/2.44/
  (source code)

Released files are signed with PGP/GnuPG key

  "David Nečas (Yeti) <yeti <at> gwyddion.net>", id 62A07732
  fingerprint = 263F 9B1E C1E0 5261 C689  D83B 00FD D1D0 62A0 7732

-----------------------------------------------------------------------------

This is a stable version continuing the 2.x series, backward compatible with
previous 2.x versions.

More information about Gwyddion is available at

  http://gwyddion.net/

Bugs should be reported to

  klapetek <at> gwyddion.net

or the mailing list.

-----------------------------------------------------------------------------

Summary of changes:
Application:
- Translations updated: Czech, French, Russian.

Libraries:
- libgwyapp: Potential corruption of recent file list by Save As introduced in
  2.43 was fixed.
- libgwydgets: Gwy3DView no longer downsamples data during changes, all
  operations are done with full-resolution surfaces.  Its "reduced-size"
  property was deprecated and it has no effect.
- libgwydgets: Gwy3DView light source distance from the surface no longer
  scales with Value scale, improving views with small Value scale a lot.
- libgwyddion: gwy_debug() adds timestamp to the messages (where available).
- libprocess: Rare incorrect memory reallocation in Delaunay triangulation was
  fixed.
- libgwyapp: gwy_app_channel_remove_bad_data() now ensures the mask field has
  the same lateral dimensions and units as the data field.
- libgwyprocess: Bogus value returned by gwy_data_field_area_get_entropy() with
  mask exclusion mode was fixed.
- libgwyprocess: Functions for estimation of the entropy of two-dimensional
  point cloud, and for entropy-from-histogram-at-scale curves were added.
- libgwydgets: Graph labels respond to "label-property" changes.  The property
  is also meaningfully updated when user moves the label around.
- libgwyprocess: An iterative cancellable version of function
  gwy_triangulation_triangulate() was added.
- libgwyprocess: Functions for filling area under mask with a value and
  simple data-average correction using unmasked data were added.
- libgwydgets: GwyGraphModel and GwyGraphCurveModel clone() methods were
  implemented.
- libgwyprocess: Euclidean distance transform with from_border=FALSE actually
  work for all cases, previously the border-influenced ares had to be limited.
- libgwyprocess: New function for simple regularisation of XYZ data to a data
  field was added.
- libgwyapp: Data windows hidden and re-shown from the data browser no longer
  lose the window icon showing a data thumbnail.

Modules:
- Entropy (new): Visualises entropy calculation for distributions of values
  and slopes.
- Leica (new): Imports Leica LIF CLSM images.
- Nano Measuring Machine (new): Imports NMM profile sets and regularises them
  to raster data.
- DM3: Support for Digital Micrograph DM4 files was added.
- Image export: The number of digits in false colour axis ticks can be
  controlled explicitly.  Very small negative values are displayed as ‘0.0’,
  never the odd ‘-0.0’.
- Magellan: RGB images are accepted and the channels are averaged upon import.
- APE file: Crash when loading files with fewer actual data than reported by
  the channels bit mask was fixed.
- Limit Range: Setting range from fixed colour mapping range was fixed.
- NanoScanTech: Loading from raw binary data blocks was implemented.
- Keyence: File loading no longer fails when assembly information seems
  missing or too short as the module does not actually need it.
- All tools: Sensitivity of Apply buttons and auxiliary controls was corrected
  so that can be activated only when there is actually an active image.
- Processing modules with selections in the dialogue: Critical messages when
  the dialogues were displayed were fixed.
- Spectral synthesis: Possible critical message when re-running the function
  after deleting a channel was fixed.
- Rawfile: Replacement value for missing data can be given as text for text
  formats, e.g. ‘BAD’ or ‘NODATA’.
- Raw XYZ: A bug in point merging was fixed that sometimes caused infinities to
  appear in the data.  Triangulation is remembered and not recomputed when
  not necessary.  A progress bar is shown for the trianguation process and it
  is possible to cancel it.  New interpolation type ‘Average’ was added, which
  is always fast and produces a result similar to a bit fuzzier ‘Round’
  interpolation.  Button ‘Reset Ranges’ permits resetting the data ranges to
  the initial values obtained from the file data ranges.  Point density can be
  plotted as another field.
- GWYXYZF: The regularisation method was improved to ‘Average’ from Raw XYZ.
- Nanoscope: Support for 32bit raw data format used since 9.2 was added.
- JEOL: Support for Phase channels was added.
- Statistical quantities: Deficit of entropy to Gaussian distribution with the
  same dispersion was added as a new quantity.  Unavailable quantities are no
  longer printed to reports.
- MI file: Loading of graphs in ASCII format was implemented.
- RHK SM4: Loading of graph data with small Y size works now.
- Raw graph: Curve data are sorted upon import.
- Grain filter: Options for unused quantities (B or C) are now hidden instead
  of insensitivised to reduce visual clutter.
- Graph function fit, FD curve fit, critical dimension: Function names are
  translated also in reports.
- Ballistic deposition synthesis: Progressive preview works now.
- Align graph: Crash with curves not sorted by abscissa was fixed.
- Renishaw: Timestamps in metadata were corrected.

Other:
- MS Windows packages include OpenEXR support now.
- Broken configure detection of libpython on Fedora 23 (and possibly elsewhere)
  was fixed.
- A script generating MS Visual Studio solution files (and other files) was
  added as utils/gen-gwyddion-vs-sln.py.

-----------------------------------------------------------------------------

Thanks all who contributed,

Yeti

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Hwansoo Suh | 17 Dec 19:41 2015

FYI, Installing Gwyddion on Mac with homebew

Hi, all.

In the official download page of Gwyddion, for Mac, only MacPorts and Fink packages are presented.

But if you prefer Homebrew as your main package manager in Mac OS X, there is an alternative installation method. See http://brewformulas.org/Gwyddion for more information.

Hope this helps mac users who use Gwyddion.

Best,
Hwansoo

--
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Visiting Scholar at Stanford University and 
R&D Staff Member
Device Lab.
Samsung Advanced Institute of Technology
Suwon, Korea
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