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

--
Hwansoo Suh, Ph.D.
Visiting Scholar at Stanford University and 
R&D Staff Member
Device Lab.
Samsung Advanced Institute of Technology
Suwon, Korea
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Haeberle, Tobias | 17 Dec 10:32 2015
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Processing Phase Data

Hello,

I want to process some phase data from an AFM scan and correlate it with the topography data. Unfortunately,
gwyddion can’t open the phase image (.tif format). I get the error: 

`````
The type of data is unknown.  Please report it to the developers.

Full file path: .../Img2015_1217_08404721_2INPUT_B.tif.

Loaded using: joel.
`````

The AFM is a JOEL system. I have no problem reading the topography data images. Or is there a
misunderstanding on my part and gwyddion is not designed to look at phase data? 

Thank you!

Best regards
Tobias
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David Nečas (Yeti | 14 Dec 17:14 2015
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User influence survey


Hello all,

we are currently trying to investigate the influence of humans on
quantitative AFM results, in particular on the data processing part.

We would be therefore grateful if you helped us by spending several
minutes of your time by participating in a short survey at

    http://gwyddion.net/survey2/

The survey consists of processing of a couple images (well, three in
fact) and reporting one parameter for each.  No forms with hundreds of
odd questions are involved.  So it should be fun – and if we get enough
responses for statistics it will be also useful as the statistical
results will be used in a paper focusing on the user influence in SPM
data processing.

Please distribute this request to your colleagues who use AFM.

Thank you in advance.

Best regards,

Yeti & Petr

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Andrés Muñiz Piniella | 1 Dec 12:53 2015
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Faq028

http://gwyddion.net/faq.php#faq028

If I run on windows7 it crashes.

If I only run the Datafield method it works.

So something in the process module function is not working for me.

I'll use the former so no problem for me.


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Nicolas.Vanderesse | 1 Dec 00:15 2015
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Pygwy with Windows 7

Hello all,

I am trying to write scripts for processing multiple LEXT files. I'm running Gwyddion 2.43 Win32 on Windows 7 Enterprise 64bit with Python 2.7.10.

I have read http://gwyddion.net/documentation/pygwy.php and copied-pasted the "Data processing module example" script into a .py file.

The fact is that I cannot even have the script running.
I even don't know if I'm saving the file in the right place, nor where it should appear when Gwyddion is restarted. In Data process/Correct Data, I guess.

I have no $HOME/.gwyddion/  directory. Rather, I have a $HOME/gwyddion/ directory, without point (actually C:\Users\[myname]\gwyddion).

It contains the following subfolders:
[.]             [..]            gwyddion.log    [modules]       [neuralnetwork]
[plugins]       recent-files    settings        [ui]

No "pygwy" subfolder.

So I tried several things:
- creating the folder \gwyddion\pygwy and copying my script into it.
- Replicating \gwyddion into \.gwyddion with the pygwy subfolder.
- Copying my script into \modules\process

That's pretty much about it.

Besides, I can't find the Pygwy console, but as far as I understand, this is a common issue when using Gwyddion in Windows. As a matter of fact, it seems to me that using Gwiddion in Windows is not the best practice...

Thanks in advance if anyone has time to help me.
And many thanks for the program anyway, I find it very useful for my work.
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Peter Eaton | 30 Nov 19:36 2015
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Windows version 3D view bug

Hi, strange that it cannot reproduced.
I can reproduce it on at least 3 computers. These are running windows 7 and 10. It *only* happens when 3D window is maximised.

Last month I ran a class on data processing, and about 20% of the student's reports had this effect in their images.
Yes, perhaps removing the "preview mode" completely will fix this and not impact performance too much.
Pete.
____________________________________________________________________________
Atomic Force Microscopy
Dr Peter Eaton and Dr Paul West
Available through all good bookshops, or direct from Oxford University Press at:
http://ukcatalogue.oup.com/product/9780199570454.do http://afmhelp.com


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Andrés Muñiz Piniella | 30 Nov 13:05 2015
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How to Open Topography first

Hi,
How would I get my SM4 files to open 'Topography' container first?

Is it something i can costumize using pygwy module plugin FILE?




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David Nečas (Yeti | 25 Nov 18:00 2015
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Gwyddion 2.43 was released


Gwyddion 2.43 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.43/
  (all released files)

  http://gwyddion.net/download/2.43/
  (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, Italian, Russian.

Libraries:
- libgwyprocess: Functions for erosion, dilation, opening and closing
  morphological operations with arbitrarily shaped flat structuring elements
  were added.
- libgwyprocess: A function for alternating sequential filters with flat
  discs was added.
- libgwyprocess: gwy_data_field_grain_simple_dist_trans() can perform all
  types of distance transforms now, including true Euclidean.
- libgwyprocess: Functions for mask growing and shrinking using any available
  distance measure were added.
- libgwyprocess: A function for mask inversion was added.
- libdraw: GwySelection has a method for moving it in the plane (may not be
  meaningful or supported for all subclasses).
- libgwydgets: GwySelectionGraphArea and GwySelectionGraphPoint support crop
  and move methods now.
- libgwyapp: Drag'n'drop of selections from Selection Manager tool to
  channels works for images with offset top-left corner.
- libprocess: A function for trimming empty border rows and columns from
  a mask data field was added.
- libgwyapp: Functions for obtaining quark keys of various common items
  (range, palette, title, meta, ...) in the file were added.
- libgwyddion: New functions gwy_fopen() and gwy_fprintf() were added,
  wrapping the C library functions.  As they reside within Gwyddion they are
  always compiled with the same C library on MS Windows (unlike g_fopen()),
  making FILE pointer passing possible.
- libgwydgets: Graph selections that are either along x or y have now an
  "orientation" property, similar to GwySelectionAxis.
- libgwyddion: GwyContainer items are serialised in lexical order (this is
  not a functional change; the order is still not guaranteed by the format).
- libgwydgets: GwyColorAxis updates properly after exact range inversion.

Modules:
- Sensofarx (new): Imports Sensofar PLUx data files.
- Princeton SPE (new): Imports Princeton Instruments camera SPE files.
- Mask morph (new): Elementary mophological operations with masks, possibly
  using another mask as the structuring elements.
- Mask of Disconnected (new): Mark local outliers that have values
  disconnected to the distribution of other values.
- Rawfile: NaN in floating point data are handled by masking and replacement.
  It is possible to specify a raw value representing missing data.  Support
  for two-byte half and six-byte Pascal floating point formats was added.
  Reading of 64bit integer formats was fixed.
- Filters tool: Minimum and maximum filters now use circular neighbourhoods.
  Opening and closing filters and alternating sequential filters with flat
  discs were added.  The filters can be applied only to masked/unmasked parts
  of the image.
- Rank: Local normalisation and value range filter options were added.
- Nanoscantech: Unit and scale reading was updated.
- Mask editor tool: The distance type used for Grow and Shrink is
  controllable now, with true Euclidean distance being the default.  Using
  bucket fill on an image with no mask creates a mask and fills it entirely.
- Profile tool: Possible crash when starting to take a profile with masking
  was fixed.
- Axis, Ellipse, Line, Point and Rectangle layers: Support for the move
  peration was added.
- Selection manager tool: Selections are distributed correctly from and to
  images with offset top-left corner.
- Pygwy: Python 2.4 is now required.  New wrappers for grain numbering and
  grain quantity calculation were added.
- Slice volume, Align rows: It is possible to select a target graph for
  extracted curves.
- Align rows: All the methods consistently keep the mean correction to zero,
  preserving absolute data values.  A Critical warning message in column
  aligment of non-square images when mask was present but ignored was fixed.
- Mark by threshold, Mark by edge detection, Facet analysis: The mask can be
  combined with mask already present on the image using union or intersection.
- Mark by threshold: Reset button now really resets all the settings.
- Color range tool: Can reverse the mapping for fixed ranges.  Mapping range
  is no longer reset to full upon data change.
- Object synthesis: Features created on the surface can be positive, negative
  or randomly ehtier now.
- NT-MDT: Hybrid mode data are split to upward and downward movement.
- CSM: Image dimensions from Benyuan header are ignored now and BMP
  dimensions are always used.
- Nanoscope: Calculation of dimensions of non-square images was improved
  (hopefully).
- Image export: Smaller pixel-per-inch values are possible for vector formats
  and the values are also no longer rounded to integers.
- WSxM: Horizontally flipped exported channels were fixed.
- Omicron flat: Files with non-standard names are loaded now, with no related
  data loaded alongside.  The original result filename is displayed as the
  filename when possible.
- Critical dimensions: No longer crashes or produces NaNs when the profile
  does not conform to Step profile according to the norm.
- GWYXYZF: Incorrect memory freeing, possibly causing leaks or crashes, was
  fixed.

Other:
- Gwyddion can use either minizip or libzip for opening of ZIP-compressed
  file formats.  The former is used if both are found.
- Configure checks for gtk-doc at least 1.10, required to build the
  documentation (older versions were actually insufficient even before).
- RPM requires rubypick only on RedHat-based distros.

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

Thanks all who contributed,

Yeti

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Peter Eaton | 11 Nov 16:52 2015
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Windows version 3D view bug

Hi, There is a bug present in the 3D view export that has been present for some time. I have just checked and it is still present in v 2.42.

Here's what happens:
Take a height image, use the "Display a 3D view of data" tool. Maximise the 3D window. Arrange image as desired, use the "save 3D view to an image" button. Save the file.
Now, opening the file, it seems the data is displayed at low resolution, compared to what you see on the screen. Similar to the "preview" that appears when rotating the image on the screen.
If I reduced the size of the window (i.e. "de-maximise" it), so it's floating, and then "save 3D view to an image", I get a normal, good output. Only when maximised does this happen.
But this affects our work a lot, because the normal thing to do is to maximise the window before out put to increase the resolution, and also because this way, we can control easily that all images are output at exactly the same size.

Thanks for all your hard work on Gwyddion!
regards,
Pete.

____________________________________________________________________________
Atomic Force Microscopy
Dr Peter Eaton and Dr Paul West
Available through all good bookshops, or direct from Oxford University Press at:
http://ukcatalogue.oup.com/product/9780199570454.do http://afmhelp.com

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