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General:
Why Gwyddion?
I found a bug, what should I do?
How to cite/refer to Gwyddion?
What systems and architectures Gwyddion runs on?
Can we use proprietary plug-ins?
Why I cannot make data view selections or rotate 3D view in KDE?
I am trying to run Gwyddion remotely on Unix and it takes forever to start
I closed a data window, the file was completely closed and I lost valuable changes. How do I prevent that?
Versions and releases:
When it will be finished?
When a new version will be released?
How can I get notified of new releases?
What new features will be in the next version?
My distro/port collection only offers ancient Gwyddion. Can you update it?
What are the quirky names attached to each version number?
What is version 2.xx.20yyyyyy and where can I get it?
What is a development snapshot/nightly build?
How do I apply a patch?
Files and file formats:
I am suddenly unable to open/save files. It worked mere moments ago!
My microscope files load wrong or I get an error message
while opening them, what should I do?
Why I cannot load my microscope files?
How to associate SPM files with Gwyddion in MS Windows?
How do I send large data files to you, do you have an FTP upload area?
What is the best method to automatically load my raw data?
My program will write data that should be consumed by Gwyddion. What format should I use?
How do I write a GSF file in Python?
Data processing:
What the strange PSDF values mean?
How can I export an image of the data?
I opened an XYZ data file and can't do anything with it
How can I process all images in a file using pygwy?
Where is the list of functions usable with gwy_process_func_run()?
How do I use pygwy with Python 3?
Extending and developing:
Why C programming language?
Why to use Gtk+ library?
Can I use my own routines with this software?
Can I use other graphical library (Qt, MFC) with the program
Will my plug-ins work with future versions of Gwyddion?
Will my modules work with future versions of Gwyddion?
I linked Gwyddion with --as-needed and it broke. How to fix it?
How do I write a module in C++?
Can I speed up make install when working on a single module?
How can I expedite integration of my module/patch?
See the explanation.
Please report it to Petr, the mailing list or the web forum at SourceForge.
Be as specific as possible. This means listing the operating system and environment, what exactly you were doing, and the exact error message (if any) or how the program crashed (if it crashed).
Also please try to if check the problem is still present in the latest stable version. If a bug only occurs in old versions and has already been fixed, you can expect a suggestion to upgrade.
For file loading-related bugs please provide the file that causes problems to make reproducing the bug possible. If you experience crashes on a Unix-based system a gdb trace or valgrind output will also be helpful for locating the bug.
A paper about Gwyddion has been published in Central European Journal of Physics (which was later renamed to Open Physics). It can be cited as follows:
David Nečas, Petr Klapetek, Gwyddion: an open-source software for SPM data analysis, Cent. Eur. J. Phys. 10(1) (2012) 181-188
BibTeX record:
@Article{Necas2012,
author = {Nečas, David and Klapetek, Petr},
affiliation = {CEITEC — Central European Institute of Technology, Masaryk University Kamenice 753/5, 625 00 Brno, Czech Republic},
title = {Gwyddion: an open-source software for {SPM} data analysis},
journal = {Central European Journal of Physics},
publisher = {Versita, co-published with Springer-Verlag GmbH},
issn = {1895-1082},
keyword = {Physics and Astronomy},
pages = {181-188},
volume = {10},
issue = {1},
year = {2012},
doi = {10.2478/s11534-011-0096-2},
}
If you refer to Gwyddion in a software context it is also useful to give the
URL http://gwyddion.net/.
Many Gwyddion related algorithms are also described in book on Quantitative Data Processing in Scanning Probe Microscopy published by Elsevier (ISBN: 9780128133477). It includes description of many ideas in (and behind) Gwyddion, as well as basics of different physical quantities measurements and interpretation using Scanning Probe Microscopy techniques, like AFM, FFM, STM, EFM, MFM, SThM, SNOM, etc.
A list of Gwyddion-related publications is provided on a separate page.
Operating system-wise, Gwyddion is known to work on GNU/Linux, Microsoft Windows, Mac OS X, and FreeBSD. Architecture-wise, it has been tested on i386, AMD64, and PowerPC. It should work on any Unix-like system where Gtk+ and other dependencies work.
The core developers do not prepare executables for all these systems, but a number of people maintain packages for various platforms and systems. The known packages are listed at the download page.
Yes, you can. You can use a plug-in with other than open source license. However, such a plug-in cannot be a part of the program, but can be distributed separately. Also note the difference between plug-ins, i.e. standalone programs reading/writing/processing some data, that can be independent works, and modules that are always derived works of Gwyddion.
Most likely you use the Oxygen theme of KDE. Unfortunately, its creators decided to enable moving windows by clicking in any inactive area by default, despite not being able to detect inactive areas reliably. And they refuse to change this default.
Run oxygen-settings and disable the odd behaviour by selecting
Drag windows from title bar only in Widget Style → General → Windows'
drag mode.
This is often caused by DRI3. Try running Gwyddion as follows:
LIBGL_DRI3_DISABLE=1 gwyddion
If it does not help or you get errors on startup, the last resort is disabling 3D completely, including any attempts to check whether it is even available:
gwyddion --disable-gl
Of course, the 3D view will not be available in such case.
By saving valuable changes after you make them. Files can be saved (to the GWY format) by pressing Ctrl-S.
When all windows (image, graph, volume) of a file are closed the entire file is closed. There is no Do you want to save… prompt.
This has the advantage that if you use the program to view various data and experiment with them you will not be pestered with questions when you want to discard the experiments.
The disadvantage is, of course, that changes can be indeed lost. Save the data explicitly when you make changes you want to preserve.
The developers are not in principle against some Do you want to save… prompt but they are not much interested in such thing and are unlikely to implement it themselves. Patches that add such prompt and also preserve the current operation mode will be considered for inclusion.
Since Gwyddion is intended as a framework the for development and sharing of new analytical methods, everlasting continuous development is expected.
Furthermore, there seems to be no shortage of new or changed SPM data formats. As part of the Gwyddion mission is enabling SPM users to analyse data acquired by all kinds of instruments in the same way, this also requires an ongoing development.
When the amount of changes warrants a new release.
Assuming a reasonable development pace, this policy means new versions are typically released a few times per year (see the version statistics). Sometimes the development is slower so it takes longer.
As many other projects have realized, waiting until features are finished leads to excessive delays. Hence features that are not ready yet are simply omitted from the release. Do not take it personally if you have a personal interest in something left out – since we do not wait, another release, meaning another chance, will occur soon.
If you are subscribed to either gwyddion-users or gwyddion-devel mailing list you will receive notifications by e-mail.
If you are a SourceForge.net user, you can subscribe to project Gwyddion, see the big button Subscribe to Updates. The service sends information about updates to the project and it is configurable to some degree using ‘Subscriptions’ settings in your SourceForge account. However, setting it up to only get notifications of new releases does not seem possible at this moment.
SourceForge also offers a RSS feed for project activity, see the top right corner of the Files tab.
We also send notifications using some software release aggregation services du jour. Currently you can watch new releases at Freshcode.
See the NEWS file in the subversion repository.
This file reflects the state of current development snapshots, more or less. It is often updated with some delay. On the other hand it can also mention features that have been added to the program but are not yet complete. But if something appeared in the NEWS file it is almost certain it will be present in the next stable version.
Then there are things we just plan or would like to have in the software but their implementation has not started yet. They may not actually appear in the upcoming version and are not listed anywhere.
In short, no.
When a new version is released we publish three things:
All other packages, ports, formulas, … are maintained by other people on their own schedule. We try to track known packaging efforts on the download page but we have no control over them. The person who can create an updated version of Gwyddion package is most likely the same one who created the current one.
Version numbers are nicely structured and algorithmically comparable. But it is difficult to associate anything with a version number, especially for software with so many versions as Gwyddion. Hence Yeti started to nickname the releases. The first release bearing a name was 2.8, called “Freedom for Fourier”. And with a few exceptions, all versions released since then also carry a name.
The names characterise important features or development process of each version for easier recalling what it was about. But they often do so in a peculiar, cryptic, whimsical, tangential or arcane manner. While “The TIFF Toll” only poorly masks the developers' opinion on TIFF libraries, “Too Technical Tears” may be more difficult to decipher. There are no formal naming rules – Yeti evidently likes alliteration though.
Each night (if you live in a time zone around GMT, as most Gwyddion developers do), an automated build and packaging of Gwyddion is performed. This results in so-called nightly snapshot that consists of whatever is in the code repository at that moment. Its version number is constructed by appending the current date to the previous stable version number. Hence it appears between the stable versions by the usual sorting rules:
2.29 < 2.29.20120902 < 2.30 stable snapshot stable
You can download the latest snapshot from the Download page here. Note that the package file is always called Gwyddion-head, i.e. the actual version number can be only seen after unpacking, but you can also see the build date displayed in the download table. Since the automated build can fail and sometimes the source code is not properly updated from SourceForge please always check the date inside the program when testing the development snapshots (and if unsure then ask).
The snapshots contain all the latest features – and bugs. If you are told to try a nightly build (namely because it contains a feature or bugfix you requested) then the developer telling you this thinks it should be usable now. But the scary warnings on the download page still apply.
Also, the snapshot to try is typically the next one which will be available for download the following day.
Development snapshot and nightly build refer to the same thing, automatically created Gwyddion packages capturing the current state of its development. They are described in detail in another entry.
Patches are applied by running the patch program (see patch(1) for details):
patch -p1 <gwyddion-patch-name.patch
in the unpacked source code before executing ./configure.
Occasionally, patches may also need -p0 instead of
-p1. Admittedly, we are not completely consistent in the patch
level.
All patches we publish are source code patches (which is the classical meaning of patch, even though you can find all kinds of updates being called ‘patches’ nowadays). Any binary package updates, which are much rarer than patches, are released as complete packages.
Please check that the file type is set to ‘Automatically detected’ (for file opening) or ‘Automatic by extension’ (for saving/exporting) in the file dialogue. The file type selector is in the lower part of the window, below the file list.
Selecting a specific file type means Gwyddion will not perform any automatic detection and simply assume this file type. When it does not match the actual format you will get an error message (for file opening) or the file is saved in an unexpected format (for saving/exporting).
Report it as a bug – preferably in the mailing list or web forum. Since microscope producers frequently update their file formats, it may happen that Gwyddion loads your data incorrectly even if the file format is supported in general.
In order to improve the import and fix the problem, the developers need:
On the other hand, sending Gwyddion screenshots is usually pointless as the developers can try to open the files in Gwyddion themselves and see what happens. What they cannot do is opening the files in your original microscope software for comparison.
So, do not send Gwyddion screenshots unless it is clear that other people are not able to observe the same Gwyddion behaviour. But do send screenshots of correctly loaded data (in other software).
If you have microscopy data in a format Gwyddion cannot open please contact us and send file format documentation, sample data files, information what kind of data these files contain and what they should look like when loaded correctly, and generally any available information that can be helpful for adding support for the file format to Gwyddion.
We would like to support as many SPM file formats as feasible. Nevertheless, the mere knowledge that someone somewhere in the world has some files that Gwyddion cannot open is, no matter how saddening, not sufficient to actually implement support for the file format. And if we do not even know about it, the import module for your file format is unlikely to miraculously appear.
So do not just wait. If you want to open your files in Gwyddion then do something about it.
Of course, you can also write a file import module yourself (and you are encouraged to do so) and submit it for inclusion to Gwyddion. There is page describing the file format situation in details.
Gwyddion can open over 120 different SPM data formats. Many of them bear
file extensions that are non-unique, such as .dat,
.xml or .tif, or numbered like .001,
.002, etc. This makes SPM files problematic to associate in MS
Windows where the file type is determined from the extension. Hence, by
default only .gwy is associated with Gwyddion.
Other file extensions need to be associated manually. The correct command for the ‘open’ action is
C:\Program Files\Gwyddion\bin\gwyddion.exe --remote-new "%1"
where C:\Program Files\Gwyddion has to be replaced with the
actual installation path if Gwyddion is installed elsewhere. If you simply
select Gwyddion in Default Programs → File Associations for the
file extension, it will work but each file will open in a new Gwyddion
instance.
The easiest way to set it is probably using a utility such as Default
Programs Editor or FileTypesMan and setting/changing the ‘open’ command. You
can also edit the registry using regedit and set
HKCR\FILE-TYPE-NAME\shell\open\command to the command,
where FILE-TYPE-NAME is the name of the file type for
the extension.
Unfortunately, we do not have any public FTP upload space.
The preferred method of sending large files is to upload them to a file hosting service/file deposit of your choice and send the link.
When you post a message to the SourceForge discussion you can attach files to the post using the ‘Add attachments’ button.
Not preferred, but also possible is to send files by e-mail. In such case compress the files with 7zip, xz or zip because:
Please do not send large files directly to the mailing lists; messages exceeding certain size are rejected as most people do not appreciate receiving unsolicited huge files.
Generally, we try to implement automatic loading of all kinds of file formats, however rarely used, using file import modules. Please always contact the developers about the support for your file format directly in Gwyddion if there is at least a slight chance it will help also other people.
Sometimes your raw data may be too raw though.
In this case complement the data file with a standalone
NRRD (Nearly Raw
Raster Data) header referring to the raw file using datafile
and specifying the dimensions and other properties. Loading this header into
Gwyddion will then load the raw data.
The biggest advantage of this method is that no modification of the raw file is necessary. You just accompany it with a small text header file. For instance, for a matrix of text values it can look like:
NRRD0004 type: float encoding: ascii dimension: 2 sizes: 128 64 units: "m" "m" sampleunits: "V" axismins: 0 0 axismaxs: 5e-6 2.5e-6 datafile: data.txt
The header for binary data would specify encoding as
raw and possibly give a few other parameters like the byte
position where the data start (using byteskip). But otherwise
it works exactly the same.
NRRD is supported since Gwyddion version 2.25. The nrrdfile
module can read 1D, 2D and 3D data in all reasonable representations, including
compressed formats and hexadecimal encoding.
For single-channel data, there are several good choices:
The last option also applies to complex data as the effort required to save complex data files depends on many factors and no single format fits all uses. Of course, the ultimate Gwyddion format is GWY but it is among the most complex. A small standalone library for reading and writing of Gwyddion files, libgwyfile, is now available under a very permissive license, i.e. you can generally use it also in closed-source software.
For instance using this function:
import array, sys, math def write_gsf(filename, imagedata, xres, yres, xreal=None, yreal=None, xyunits=None, zunits=None, title=None): """Write a Gwyddion GSF file. filename -- Name of the output file. imagedata -- Image data. xres -- Horizontal image resolution. yres -- Vertical image resolution. xreal -- Horizontal physical dimension (optional). yreal -- Vertical physical dimension (optional). xyunits -- Unit of physical dimensions (optional). zunits -- Unit of values (optional). title -- Image title (optional). Image data may be passed as any listable object that can be used to form a floating point array.array(). This includes tuples, lists, arrays, numpy arrays and other stuff. """ data = array.array('f', imagedata) if len(data) != xres*yres: raise ValueError("imagedata does not have xres*yres items") isinf = math.isinf isnan = math.isnan for z in data: if isinf(z) or isnan(z): raise ValueError("GSF files may not contain NaNs and infinities") if sys.byteorder == 'big': data.byteswap() header = ['Gwyddion Simple Field 1.0'] header.append('XRes = %u' % xres) header.append('YRes = %u' % yres) if xreal is not None: header.append('XReal = %.12g' % xreal) if yreal is not None: header.append('YReal = %.12g' % yreal) if xyunits is not None: header.append('XYUnits = %s' % xyunits) if zunits is not None: header.append('ZUnits = %s' % zunits) if title is not None: header.append('Title = %s' % title) header = ''.join(x + '\n' for x in header) l = len(header) sentinel = bytearray() for j in range(4 - l % 4): sentinel.append(0) fh = open(filename, 'wb') fh.write(header.encode('utf-8')) fh.write(sentinel) fh.write(data) fh.close()
Most probably you are looking at the PSDF method of fractal dimension estimation. It uses a log-log plot with arbitrary shifts and scale. Use the statistical functions tool to obtain PSDF in absolute units.
The x axis units are then lateral_unit-1 and y axis units lateral_unit × value_unit2. The normalization corresponds to the PSDF expressions for various surfaces that can be used to fit rms and autocorrelation length of rough surfaces in graph fitting.
The spatial frequencies used in Gwyddion are circular, corresponding to exponentials in the Fourier transform of form exp(iKx), not exp(2πiKx).
Many different PSDF normalizations can be found in the literature, together with reasons why they are better than others. PSDF in Gwyddion is based on the concept of an infinite rough surface (two-dimensional random signal if you want to get mathematical). The measured data is a finite-resolution measurement on a finite area which is assumed to have the same statistical properties as the entire surface.
The total energy of an infinite signal is infinite. Hence a meaningful quantity is the energy per unit area. The PSDF displayed in Gwyddion is exactly that. It is sampled in certain points given by the discrete nature of the calculation, nevertheless, the values should be approximations of W₁(k) that results from continuous Fourier transform of the autocorrelation function of the entire infinite surface.
This has the following nice consequences:
Finally, note that the square of a density of some quantity is not the density of the same quantity squared. Normalizations of PSDF and Fourier coefficients need to be considered separately for continuous distributions.
Some of these points are also illustrated in the roughness evaluation talk by David Nečas.
Using File → Save As and choosing an image format such as PNG or TIFF (or just giving the file the corresponding extension). Recent versions can also export PDF, SVG or EPS images. Please see the user guide for a detailed description.
For a plain export without rulers, false colour bars, etc. you can also press Ctrl-C in an image window to copy it to the clipboard and then paste it to another program.
If you want to represent the data in an image format but not to lose too much information then save it as PNG, TIFF or PPM and select 16bit greyscale for a larger bit depth. Gwyddion also can save and load OpenEXR HDR images that offer even higher bit depths and dynamic ranges.
XYZ data are fundamentally different from image data. One is an arbitrary cloud of points; the other is a regular map of some physical quantity.
XYZ data are more general. Even for measurements in a regular grid, they permit representing exactly all x and y coordinates and their deviations from the ideal grid positions. This flexibility has its price: few image processing algorithms have direct equivalents for XYZ data. Different, more complicated methods are necessary.
XYZ data are a separate data type in Gwyddion. It can open such files and show a preview. It also offers a handful of XYZ data functions in the XYZ data menu. Of these you most likely want to use Rasterise with the Average type interpolation – and create an image. Image processing is what Gwyddion does best. If the x and y coordinates are regular (within some small tolerance), Rasterise should recognise it and offer to create an image directly. Gwyddion, however, never attempts to force XYZ data to images automatically. If data are XYZ (instead of a much simpler image) it should be because there is a reason to keep them that way.
Unfortunately, some misguided software occasionally represents images as XYZ data. This happens even when the software cannot actually work with XYZ data and the points must form a regular grid by definition. So at best the XY part of XYZ just sits there to be ignored, but more likely gets in the way. If you have the choice do not store images as XYZ data. If you do not have the choice use Rasterise – or perhaps strip the useless XY and convert the file to an image data format (like GSF) by a script.
This is, in fact, two questions because there are two different methods how to do something with the data. Either you can obtain the DataField object representing each channel and call its methods directly (or even modify the pixels directly), or you can apply existing data processing modules. The following script demonstrates both:
# This pygwy script shows how an operation can be preformed with # all channels in the current file. c = gwy.gwy_app_data_browser_get_current(gwy.APP_CONTAINER) ######################################### # Directly calling a DataField method for i in gwy.gwy_app_data_browser_get_data_ids(c): # Get the DataField from the container f = c['/%u/data' % i] planecoeffs = f.fit_plane() f.plane_level(*planecoeffs) # Notify Gwyddion we directly modified the data f.data_changed() ######################################### # Using a data processing module function # Remember what was the current channel. current = gwy.gwy_app_data_browser_get_current(gwy.APP_DATA_FIELD_ID) # Set module options in the settings settings = gwy.gwy_app_settings_get() settings['/module/linematch/method'] = 1 settings['/module/linematch/masking'] = int(gwy.MASK_EXCLUDE) # Execute for i in gwy.gwy_app_data_browser_get_data_ids(c): # Make the data field (image) current for data processing functions gwy.gwy_app_data_browser_select_data_field(c, i) # Run the function gwy_process_func_run('align_rows', c, gwy.RUN_IMMEDIATE) # It's best to select again what was selected when we started gwy.gwy_app_data_browser_select_data_field(c, current)
You can, of course, process only some data based on their properties. Running interactive module functions in a loop is not a good idea in general.
The function names are names of high-level (or at least higher-level) functions provided by data processing modules. Each corresponds to some action available in the Data Process menu. If you extend Gwyddion with a module, the functions it defines will be available the same way as functions of built-in modules.
The list of functions can be obtained by several ways:
The short answer is: You can't, sorry. It only works with Python 2.
The slightly longer answer is that Gwyddion is based on GTK+ 2 and consequently pygwy is based on pygobject/pygtk, which only exist for Python 2. Python 3 language bindings are based on gobject-introspection – which is not recommended for GTK+ 2 (although it kind of works). There is no way the current pygwy can work with Python 3. It will have to be recreated for Python 3, it will be incompatible at least to some degree – and it makes little sense to do this all until Gwyddion itself is ported to GTK+ 3. There is some preparation underway but do not hold your breath.
The core and modules is written in the C language.
This language was chosen as it is well known, standardised and widely spread, there are many important libraries that could be used (Gtk+), and it is relatively easy to bind C functions to other languages. At present Python bindings are available.
Modules can be written in C, C++ or Python.
Plugins can be written in C, C++, Perl, Python and maybe more. The simplest ones can be written in almost any language.
The Gtk+ graphical library is used because of its licensing, portability and capabilities. And also because it is a C library.
Yes, certainly, this is one of the main goals.
There are three basic ways you can extend Gwyddion:
A better alternative to plug-ins may be writing a two-part extension. One part would be a wrapper C module that passes data to and from the other part, which can be an arbitrary external tool or service. This essentially means writing a new small and specialised plug-in proxy module. The advantage is that you can use whatever communication means you want, as opposed to reading and writing files in the dump format, and you can design the wrapper specifically for your third-party tool, language or problem domain. You can also extend Gwyddion in ways beyond what is possible using plug-ins.
Yes you can do it in a form of simple plug-ins. But note, that with using some libraries (MFC) you may produce code that is not portable. This is not problem if you use code for you own, but you might be in a problem when you want to share your plug-in with someone.
Yes, virtually forever.
Even if a decision was made the current plug-in system is so bad that a new one must be designed, Gwyddion architecture would allow the old and new plug-in system to coexist, and the current would be kept for compatibility with existing plug-ins.
Note: The current plug-in system is actually considered ill-designed. While this does not mean the plug-in support will disappear soon (certainly it will not disappear before Gwyddion 4.0), it is not the preferred method to add routines in other programming languages any more and it cannot be expected to be further developed. See the entry about extending Gwyddion for better alternatives.
Yes, under normal circumstances.
Modules are bound to Gwyddion more tightly than plug-ins, so a substantial change in it may break compatibility. Normally, all new versions are both source and binary level compatible with previous ones and modules linked against old versions work even with the newest one.
Gwyddion 2.0 is neither binary compatible (so modules have to be recompiled) not source compatible (so beside recompilation, some changes in module code are necessary) with 1.x versions. But all 2.x version will be backward compatible with other 2.x versions again.
Actually, there already was a one unplanned incompatible change, in version 1.3, where a serious bug present in previous versions could not be fixed while retaining compatibility. This should not happen again.
--as-needed and it broke. How to fix it?Contrary to the popular belief, linking with --as-needed would
make Gwyddion slow and bloated, not more efficient. So the short answer is:
you fix it by not linking with --as-needed.
On platforms that support it, and that means at least all modern Unix
systems, the main application is linked with some “redundant” libraries
and modules are not linked with anything (unless they need a specific extra
library). Symbols in modules are resolved from the libraries the main
application was linked with. Obviously, --as-needed makes this
optimization impossible and every module then has to be linked with all
libraries it requires – this is less than the full set of libraries
but still much more than none. It takes more time to build (even 2×)
and install (almost 10×) and it makes the program start more slowly (module
loading time increases 2×).
But if you insist then pass --enable-library-bloat option
to configure and all the bloat will be linked in.
Easily. You only need to ensure two elementary things:
libstdc++. This should be obvious but since most C modules do not
need to link explicitly with anything it is easy to forget.In fact, Gwyddion contains a C++ module modules/file/hdrimage.cc although it is written in quite C-like C++ because it also interacts with lots of C libraries.
make install when working on a single module?First, run make install from the corresponding subdirectory.
It will install only modules from this directory.
If you configured Gwyddion with --enable-module-bundling this
is all. The following only applies when module bundling is disabled.
Some module subdirectories in Gwyddion source code are large and running
make install in them can still take considerable time. You can
compile and install only a single module by overriding the Makefile variable
specifying the list of modules. Since we use libtool you need to enter the
.la files, for example:
make install file_LTLIBRARIES=gwyfile.la
or
make install process_LTLIBRARIES=level.la
Patches should have a well-defined purpose: take the code from state A to state B. Do not lump unrelated changes together or mix fully working features with experimental stuff.
Ensure the change cannot cause crashes, hangs or memory leaks. Incomplete implementations can be all right sometimes, especially in the case of reverse-engineered weird file formats. But program defensively and do not assume that a file import module will receive only files it can actually load. Always verify that you read meaningful data sizes, file offsets, etc. and give an error if you do not. Similarly for data processing modules. For instance, if they work with multiple data fields do not assume the file contains data with some specific properties. Check the field properties, for instance using gwy_field_check_compatibility().
Try to implement things in the same manner they are done in other modules, i.e. The Gwyddion Way. First, it simplifies review greatly. Second, it is quite likely that you code will be read and modified by people familiar with Gwyddion code in future. If you are not sure about the recommended or common method of handling something then ask.
On the same note, follow the Gwyddion coding style. You can find a description of the style as devel-docs/CODING-STANDARDS in the source code. Furthermore, there is also a Python script utils/check-coding-style.py which checks the most common or obvious style issues. You can run it as
check-coding-style.py sourcefile.c [othersource.c...]
The script is not perfect and does not catch every deviation while it warns about things which may be acceptable in certain circumstances (namely lines longer than 80 characters). However, if your patch makes the warning count go from 2 to 200 for some file something is clearly amiss.