Does there exist a (free) solution for extracting 2D slices from a 4D dataset? I'm thinking of something like the EELS SI Picker tool, or the DM-script one in Dave Mitchell's SITools package. I can currently change the slice being viewed on my 4D data in GMS 3 using the Gatan-provided SI Viewer, but I'm unable to manipulate it in a meaningful way.
To answer the scripting question:
It could be done by scripting and listener scripts, yes.
But there is no need to..
The 4D picker tool in GMS 3 is already free, but you need to use the appropriate free license.
When you go to Gatan's webpage for the free offline GMS you get various choices.
You need the STEMx lincense for the 4D picker tool. See below.
Note that you can use multiple licenses side-by-side, so I would recommend to get the last two or three.
Related
Inevitably (hasn't been updated since 2018) though sadly, Google Poly is closing down. :-(
Is there another 3D mesh API available? Ideally one that also works "out of the box" with Unity? Ideally with the option to filter by low-poly models and such...
If you want free or non free 3d models for unity I want to suggest these websites:
1. Cults 3D
Cults offers its users the perfect range of 3D models – from maker-inspired 3D files all the way to professional high-quality designs. Cults checks each 3D design for printability and organizes them into different groups such as fashion, art, jewelry, home, architecture, or gadgets. The mix of a modern visual interface, a well-arranged database, and a focus on smart, useful & beautiful designs makes browsing through their website a lot of fun. While many models come for free, others come at very affordable prices.
2. Pinshape
Pinshape offers its visitors the opportunity to browse through a great selection of more than 13,000 (free and payable) STL files. Finding great 3D printable models on the website is child’s play: both the visual representation and logical organization of the website are top-notch.
3. 3DShook
The 3DShook website is somewhat similar to Pinshape and Cults but the designs tend to be more focused on ‘fun’ 3D prints for hobbyists. Some models are free but most require a fee. However, 3DShook does offer designs at a very competitive price.
4. Thingiverse
Thingiverse is probably one of the biggest and most popular databases. It has a very active maker community behind it and offers free-to-use STL files only. You don’t even need to open an account in order to download a 3D model from their site. Sometimes the database can seem slightly less organized than the cleaner and simpler design of sites like Pinshape and Cults.
5. GrabCAD
GrabCAD is different than the databases we have looked at so far. Firstly, GrabCad provides you with technical, engineering, and scale models only. Secondly, it lets you filter its database based on the 3D modeling software that the designs were created in. It’s the place to be for anyone looking for more than 27,000 technical 3D files. However, take into account that this website is not intended for 3D printing.
6. 3D Warehouse
The 3D Warehouse simply screams ‘geometrical’. Whether you are looking for architecture, product design or scale models, 3D Warehouse offers anything that was created with the popular 3D modeling software SketchUp. Luckily they also let you filter their database for 3D printable models by selecting ‘Only Show Printable Models’ in their advanced search function. All other models can be made printable thanks to a connection with the 3DPrintCloud.
7. CGTrader
CGTrader offers a dedicated database for 3D printable objects. So far there are more than 13,000 models to choose from. We noticed that there are many printable jewelry designs in particular on this website. While many models are downloadable for free, others come at affordable prices.
8. TurboSquid
TurboSquid is the place to be for downloading the most stunning 3D designs. It doesn’t get any more high-end and professional than this. The problems: the designs are great visually but are not optimized for 3D printing. There is also no filtering option for finding 3D printable models. Furthermore, all models on TurboSquid are premium (payable) files. Quality comes at a price.
9. 3DExport
3DExport is somewhat similar to TurboSquid: This is also a database that focuses on the visual aspects and offers amazing premium 3D models. In addition to this, 3DExport offers its users a filter for finding 3D printable models only.
10. Yeggi
Last but not least we want to mention Yeggi, a search engine for 3D printable models. Yeggi scans all the databases mentioned above, and many more, for 3D printable files. So if you want to search the ‘Google’ of 3D models, this might be the right website for you.
11. Remix 3D
Remix 3D is more than a 3D model database, is the Microsoft community of modelers who want to share their creations. The models on the libraries are organized by categories and they can be used and of course “remixed” on Microsoft Paint 3D and their VR/AR app, Mixed Reality.
source
I need to generate surface generation from a segmented NIFTI file. I can do that easily in 3D slicer but I want to do that in Python. Is it possible to do that in Python?
I tried using VTK model but it is not showing the Surface rendered output.
check out simpleITK. It has tools that can read in series with full 3d awareness, and also generate various surfaces for you.
It isn't an app that will display things for you however, but there are various examples you can find for how to take the output of simpleITK and use with various visualisation options.
You can do that easily by scripting in 3D Slicer. You don't need to use the graphical user interface, just launch a Python script from the command-line. You can put together the script you need from examples in the script repository (for example https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Export_model_nodes_from_segmentation_node).
I am interested in visualizing meteorological and climatological data.
Here we are talking about 2D/3D visualization for weather and climate elements:
Temperature
Pressure
Wind
Example
We have used some tools previously, such as:
GrADS
Surfer (commercial software)
GIS Meteo (commercial software)
What another tools (preferably open source) would you suggest for that purpose nowadays?
I know you mentioned GrADS, but it was the tool I used mostly for development of weather products, a little more intuitive and resource friendly than IDV when I coded, and generally pretty good rate of development. You mentioned Open Source... did you know there is an OpenGrADS (http://opengrads.org/)? Most friends involved in weather product development use a combination of GrADS\OpenGrADS for much of their work. But I agree it doesn't produce knock-your-socks-off graphics.
Another commonly used free program is Gempak, another Unidata product, which really seems to be becoming outdated in my personal opinion).
And then you can talk high end graphics, you're going to pay more. http://moe.met.fsu.edu/~hrw22/movies/WIND_Katrina_2005-08-28_00Z.gif is a great video of Katrina that was produced by someone I knew using Amira. According to Wikipedia, you're looking at
"Cost: $4,000 USD + $800/year support (2009)... although now has much more ugly/complex pricing structure where each feature is priced separately (eg: Amira Mesh Option $360). I believe at NCMIR we pay ~$9000/year for five user-license." Ouch!
I don't have an open source tool, but if you can get access to a Level-II data feed (Level-II is minimally post processed radar data), I and a meteorologist friend use GR2Analyst. I would assume you know enough about weather sources to be able to figure out how to set this up.
If you're looking for an open source (and free) tool that can do 2D and 3D, which also includes access to a wide variety of datasets (obs, model output, remote sensing - radar level 2 and 3, satellite, and more!), then you might want to check out the Unidata Integrated Data Viewer (IDV):
http://www.unidata.ucar.edu/software/idv/
Source code available here:
https://github.com/Unidata/IDV
The interface is a bit complex, but we have some youtube screencasts to help people get up and going:
http://www.youtube.com/user/unidatanews/videos
If you'd like to see a video for a specific thing, we are taking requests :-) (email support-idv#unidata.ucar.edu). We do yearly training workshops as well, and those materials are available online here:
http://www.unidata.ucar.edu/software/idv/docs/workshop/
Cheers!
Sean
Panoply is a multiplataform desktop option if data is available in formats such NetCDF, HDF or GRIB.
I extracted the following text from his site that describes some of the characteristics:
Slice and plot geo-gridded latitude-longitude, latitude-vertical, longitude-vertical, or time-latitude arrays from larger multidimensional variables.
Slice and plot "generic" 2D arrays from larger multidimensional variables.
Slice 1D arrays from larger multidimensional variables and create line plots.
Combine two geo-gridded arrays in one plot by differencing, summing or averaging.
Plot lon-lat data on a global or regional map using any of over 100 map projections or make a zonal average line plot.
Overlay continent outlines or masks on lon-lat map plots.
Use any of numerous color tables for the scale colorbar, or apply your own custom ACT, CPT, or RGB color table.
Save plots to disk GIF, JPEG, PNG or TIFF bitmap images or as PDF or PostScript graphics files.
Export lon-lat map plots in KMZ format.
Export animations as AVI or MOV video or as a collection of invididual frame images.
Explore remote THREDDS and OpenDAP catalogs and open datasets served from them.
If you are interested in interactive visualization over web, there are some options such as:
ncWMS: an webmapping server that reads NetCDF data and publish it using Web Mapping Service standard.
GeoServer: another webmapping server that has plugin to read NetCDF data.
Vtk (visualization Toolkit) is a C++ open source 2D and 3D visualization library that I use to visualize radar data in 3D.
Is there a programmatic way to convert two images into an animation sequence (e.g., an animated GIF) like the following example?
This image sequence, taken from a http://memrise.com course, doesn't seem to have manually-edited frames, but seems automatically transformed using some kind shape morphing algorithm. Is there a common term used to describe such an animation or algorithm? Is there a feature in ImageMagick or Photoshop/Gimp that generates such animations, given a pair of images?
Ideally the technique could be scriptable so I could create animations for several pairs of start-end images.
Edit: I have just been told about Gimp's tool under Filters->Animation->Blend, which appears to do the same thing as jQuery morph: each frame i is start + (finish - start)/N*i. In other words, you're transitioning each pixel independently from the start value to the finish value, without any shape morphing. The example gives is more complicated, as it modifies the contours of both images to achieve its compelling effect.
Other examples:
http://static.memrise.com/uploads/mems/32000121024054535.gif
http://static.memrise.com/uploads/mems/225428000121109232837.gif
I have written a tool that doesn't require setting manual keypoints and is not restricted to a domain (like faces). Anyway, the images have to be similar (e.g. two faces or two cars from the same perspective).
https://github.com/kallaballa/Poppy
There is also a web-version created with emscripten.
I generated the above animation using following command line:
poppy flame.png glyph.png flame.png
Although this is an old question, since ImageMagick is mentioned, for anyone who comes here from google it may be worth looking at this imagemagick plugin called shapemorph.
GIMP can't do that directly, but over the years a series of (now poorly maintaind) plug-ins to do that where released by third parties. The keyword for searching for this is "morph" - you should find a bunch of stand alone programs to do that as well, from "gratis" to full fledged Free Software, such as xmorph
Given pairs of vector files (.wmf extension) it is possible to use linear interpolation of shapenodes in Visual Basic for Applications to create frames for GIF animations , though this would take along time to explain. For some examples see
http://www.giless.co.uk/animatorMorphGIFs.htm (it is like a slideshow)
I have made some improvements since then, as well!
Is there any 3D CAD software out there, free-ware, shareware, open-source, or commercial, that uses the simplified instruction set made famous by the Logo Turtle (e.g. FORWARD 100, LEFT 90, etc) as the basis for a scripted 3D CAD application? The scripting approach is simple and easy because the user is always at the location of the "turtle"; the command language is easier for some people to master than the GUI interfaces of many CAD programs.
This would be geared to DIY projects, not sophisticated engineering scenarios. For example, I'd really like to make a 3D rendering of a piping schematic, and it would be really cool to use the Logo-turtle instruction-set to plot out the length and direction of the pipes. FORWARD 100, LEFT 45, FORWARD 25, UP 29, FORWARD 40, etc . Even cooler would be the ability to drop into the emerging design appropriate fittings (elbows, T, Y, couplings,adapters, etc) selected from a Toolbox, and to do things like change pipe diameter on-the-fly.
Anything like this out there?
It's hard to answer a question like this in the negative with absolute assurance, but I believe the answer is no. The reason is that rather than specifying angles to turn right and left, (i.e. one rotational degree of freedom) you'd have to have roll, pitch and yaw (three rotational degrees of freedom). This would make control of a 3d turtle a bit tricky.
Further, a user would probably like to do more than just create lines and (segmented) curves. For instance, it's hard to see how the turtle paradigm would extend to surface modeling.
There are however, free products for intuitive 3d modeling. For instance Autodesk 123D or Google Sketchup.
FMSLogo has commands for 3D drawing, for example: http://fmslogo.sourceforge.net/manual/understand-your-orientation-in-3D.html. It seems that other Logo implementations have something similar as well. But perhaps it's still far away from what #Tim was looking for.
While not Logo-based, one could script something along these lines using OpenSCAD pretty simply.
https://openscad.org/
The problem is that the 3D model gets very complex very quickly and performance bogs down.
Other similar tools include Toolpath Language: https://tplang.org/ which is integrated into the 3D previewer CAMotics: https://camotics.org/
Or, one could just use G-Code and G-Code previewer.