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The Bump Modifier is designed to add individual bumpy extrusions to a mesh. Position, orientation and detailed shape of the bump can be controlled. ​ To add a Bump Modifier to the Modifier Stack, click on the Add Modifier button (the + sign under the Modifier Stack) and select Bump. ​ The modifier appears at the end of the stack. It is important to note that the detailed effect of the modifier may depend on the position within the stack. Therefore experiment how it interacts with other modifiers before or after in the list. ​ Different properties of the Bump Modifier is controlled in different places. ​ The Control Panel under the Modifier Stack has several check marks: ​ Enable: Enable or disable the Bump Modifier ​ Symmetric: By default the bump will be cylindrically symmetric around its direction axis that can be seen when the Widget is on. Then the check mark is on. When the Symmetric flag is off, then the bump will be infinite in one direction and controllable in the other. ​ Radial: When the Radial flag is checked, then the bump will be applied radially from the coordinate center of the Widget. Otherwise it is parallel to the directional axis (pink) of the the Widget starting in the plane that contains its coordinate center. Widget: Posititon & Orientation The position and orientation are controlled with the Widget. The numerical control panel for the Widget can be opened by clicking on the Widget button in the Control Panel. Alternatively, use the interactive Widget controls on the left side of the 3-D views. As usual, during interactive control use the x, y and z keys to restrict moving and rotating actions to a particular axis. Magnitude: Shape & Size The shape and size of the bump are controlled from the Magnitude Graph that is accessed in the Control Panel under the Modifier Stack. ​ The Magnitude Graph works the same way as other graphs in Shape. For details see the user manual entry for Graphs . ​ The shape of the bump is set using an Analytic function or a Point graph, where the "x" is the distance from the local coordinate system (widget axis) is cylindrical coordinates. For the "symmetric", i.e. cylindrically symmetric case, the values at negative x are ignored. ​ By default the shape of the bump is set to a Gaussian function. ​ The overall size of the bump can additionally be controlled using the f0 parameter in the top left corner. Magnitude: Change the bump structure The detailed shape of the bump can be arbitrarily complex. This can be achieved by changing the Analytic function as shown in the examples on the right. Alternatively, for even more arbitrary complexity use the Point function by clicking on the Function drop-down list. Edit the Point function following the instructions in on the Graphs page . ​ Mesh resolution: Note that the application of the Bump Modifier may lead to poor mesh resolution in the bump. Currently the mesh resolution can not be improved locally. Therefore, if necessary, the overall mesh resolution can be increased by increasing the number of Segments in the Primitive tab of the object. Modifiers: Bump

Top of Page Overview General Considerations Computing Power Batch Processing Typical Modeling Applications Morpho-kinematic Modeling Photo-realistic Models 3-D Hydrodynamics Exoplanet transits Schematic illustrations Basic Workflow Need a new ShapeX feature? . Overview General Considerations Overview Your first question is likely to be: Is Shape suitable for my modeling problem? ​ Here is a short summary of the types of problems that have been worked on with Shape and others for which we know that the software can be used. We shall also discuss the limitations that might prevent your problem to be attacked with Shape. General considerations: ​ Polygon meshes: Polygon mesh objects are the most basic building blocks in Shape. The software generates them in a similar way as common 3-D animation programs such as the open-source Blender and many other commercial packages. However, these programs have been designed to model mostly opaque objects that surround us and hence compute their visual appearance according to the color assigned to their surface as a function of position and the lighting conditions. Only exceptionally volumetric effects are computed for clouds, fire or other phenomena that are not opaque. ​ In astronomy and astrophysics almost everything is about gas and dust clouds that are at least partially transparent. Real surfaces are very rare and can be found only on rocky planets and other solid bodies. Some stars can be considered to have "surfaces" since the transition from the optically thin to thick regimes is very small compared to their size. ​ The polygon meshes in Shape are therefore mainly used as containers of gaseous or dusty volumes, which are then assigned physical properties as a function of position within that volume rather than on the surface. Computing Power Batch Processing Computing Power: ​ An old saying claims: "There is no such thing as too much computing power." ​ This is also true for Shape applications that wish to push the limits of what is possible. But for many scientific applications today´s power of almost any laptop suffices. Since Shape is a highly interactive software, for your own comfort and an effective workflow make sure to use a mouse instead of just the mouse-pad. More sophisticated devices such as graphics tablets are of additional benefit for some applications. ​ Most processes in Shape make use of parallel computing on multi-core CPUs. Especially the rendering processes and hydrodynamic simulations benefit from many-core CPUs and multi-threading. ​ While the benefit of parallel computing mainly lies in reducing the time required for a computation, memory influences the spatial resolution that can be achieved in a rendering or hydrodynamic simulation. So, if you have ambitions to produce high resolution photo-realistic visualization and animations, then you might want to use a high-end workstation. Individual images can be rendered at high resolution with a special HD renderer that does not require a lot of memory. It does, however, have to do the full rendering process for each image. When you only need to change the camera view point for an animation or time series, other renderers only need to redo the last rendering step, because they keep the pre-processing information in memory, thereby speeding up the process. Batch processing can, at this time, not be done, e.g. as background processes on servers or supercomputers. This is a project for a future version. Typical modeling applications for astrophysics ​ Morpho-kinematic modeling The original design purpose of Shape was the modeling of the 3-D morphology of nebulae using as additional constraint the kinematics observed in spatially resolved high resolution spectroscopic data. As the structure becomes more and more complex, the traditional approach of direct coding of the volumetric density or emissivity as well as velocity distributions becomes impractical. Therefore the technology of interactive polygon mesh construction as volume containers was adapted to astrophysical needs from conventional 3-D modeling in Computer Graphics. ​ This type of modeling is still the flagship application of Shape. The user builds a 3-D volume distribution of density or emissivity, assigns a velocity field and then produces images, position-velocity diagrams and/or channel maps. ​ This is the main approach for modeling the structure and kinematics of circumstellar gas, be it expanding or rotating, such as in planetary nebulae, supernovae or proto-planetary disks. An extension of this methodology is the application of carbon-monoxide (CO) radiation transfer using the ShapeMol module. This is useful to model high-resolution observations with the ALMA or other radio interferometers. A large number of scientific papers contains models of this type and can be referred to as examples. See the list of publications with Shape and Shape models. Morpho-kinematic Modeling Typical Modeling Applications Photo-realistic Models Beyond scientific application ShapeX can be applied to produce photo-realistic visualizations of a variety of nebulas, stars, galaxies and other types of objects. This type of application often requires a mixture of various modeling techniques, using polygon meshes, particles and hydrodynamics. Since high spatial resolution and substantial model complexity is likely to be required for this type of application, substantially more computing power and processing time might be necessary compared to more basic applications. More detailed information and examples of photo-realistic models, in particular with mixed techniques that include polygon mesh and hydrodynamics can be found in Steffen & Koning (2017) . Photo-realistic Models 3-D Hydrodynamics 3-D hydrodynamics The Hydro Module in Shape allows the simulation of basic astrophysical hydrodynamic phenomena at moderate spatial resolution (depending on the computing power in terms of CPU cores and RAM) solving the basic hydrodynamics equations. A simple radiative cooling scheme is included designed for fast computation above 10000 Kelvin. The details of the numerical scheme have been described in Steffen et al. (2013) . The novel feature of the hydrodynamics in ShapeX is that the user does not require programming the initial conditions. For this task the interactive 3-D polygon modeling interface is applied. The full integration of the hydrodynamic module in ShapeX allows a highly flexible analysis of the simulations and mixture with other modeling techniques. This yields very realistic visualizations for scientific and outreach applications. ​ If you have been using a hydrodynamics code that is not part of Shape and find that your visualization and analysis software does not meet your needs consider Shape for it. You can import data from hydrodynamic simulations and use Shape to generate spectral kinematic output (P-V diagrams, channel maps) and images for any viewing angle. It is also possible complement your model with additional features constructed with Shape´s polygon mesh techniques for scientific modeling or illustration, and much more. Exoplanet transits Exoplanet transit lightcurves The lightcurves of exoplanets are a rich research field for which Shape is very well suited using its animation module for setting up the orbital motion, the rotation of the star with star spots and limb darkening or brightening. Shape can not reconstruct the systems parameters automatically from data, but the user can construct not only the time series of a single transit, but automatically vary a number of parameters and setups that allow the construction of a catalog of transit lightcurves and corresponding videos that shows the transit together with the lightcurve. In addition to the scientific value, the movies can be of use for outreach and press release illustrations. Schematic illustrations Schematic 3-D model illustrations ​ The 3-D polygon mesh models can be used for schematic illustrations of model ideas, even if you are not interested in a physical model. For papers and presentations such models can not only be static illustrations, but as interactive demonstrations or movies they can be powerful tools to convince an audience of one´s ideas. Need a new ShapeX feature? Basic workflow: Interactively add the geometric elements of your object in the form of primitive polygon meshes (Primitives) that you can access at the top menu bar of the 3-D Module. These meshes will serve to encase the volumes that will constitute the different parts of the model. Then you modify the simple structure of the Primitives using what we call Modifiers, which give the objects new geometric structure and physical properties as a function of position in space. Using the Physics Module, you then assign the material and radiation properties to the meshes. Finally, the model is rendered with the Render Module and some of the observational properties can be displayed with the (Channel) Maps and Graph Modules, where the observational data can be included and compared with the model results. If the results are not satisfactory, the model will be adjusted until a satisfactory match is found between observations and model. Need a new Shape feature? ​ Don´t hesitate to contact us , we might be able to help either by finding a solution with the current software or implement a new feature for you, thereby helping other potential users with similar applications. Basic Workflow

The Shear Modifier changes the distance of the mesh vertices perpendicular to a chosen axis (default: local z-axis) along another axis. The orientation of the shear axis and direction of the shear can be changed by changing the values in the Axis boxes. Choose a value of 1.0 to select a particular axis (setting the others to 0.0). Intermediate value result in an intermediate axis. A better way to set the reference axis is using the Widget. The Magnitude dialog allows you to define the squeeze amount as an Analytic Function of position along the reference axis. You can also use a Point graph where you can generate an arbitrary function by manually placing points and setting the spline interpolation. To do this, select Point from the Function drop-down list under the graph. The example graph on the right shows the way it was done for the example mesh displayed below. Modifiers: Shear

Modules: Hydrodynamics Overview Hydrodynamic simulations are an important area of astrophysics. Shape is the first astrophysical tool to introduce an interactive mesh-based setup for such simulations without the need of programming or scripting by the user. Furthermore the results of the simulations can be directly incorporated in mesh-based renderings without the need of external software. From the hydrodynamics, just like any other mesh model, can be used to generate spectral information. Filtering using the Filter Module allows you to extract regions with particular properties based on the filter settings. Exporting of the hydrodynamic simulation data allows later incorporation of the data or parts of them into a completely different rendering project. ​ The simulations in Shape are always intrinsically 3D on a uniform cartesian grid. The numerical algorithm in Shape was selected to run relatively fast in 3D with a minimum of variables to keep memory usage as low as possible, while still allowing to simulate the basic astrophysical phenomenology such as shocks and radiative cooling above a temperature of 10^4 K, typical to photoionized nebulae. ​ The details of the numerical scheme used for the hydrodynamics, its limitations and example applications are described in the following research article: W. Steffen, N. Koning, et al., 2013, MNRAS, 436, 470–478 It is recommended to use numerical hydrodynamics tools in Shape or any other application only with sufficient understanding of the the possibilities and limitations of such tools. This module in Shape was made to make access to numerical hydrodynamics easier, but if you do not have insight into the potential artifacts the numerical schemes produce, especially at low spatial resolution, it is recommended to seek the assistance of someone who does. General Workflow ​ The workflow involves three overall steps: First, you set up the elements of the simulation in the 3D Module. Second, the flow parameters are set up in the Hydro Module. The simulation is started and previewed here, too. Rendering and analysis is then done as usual in the Render Module vía a dummy rendering object that is set up in the 3D Module. See below for more details on how to set up a simulation in the 3D Module. User Interface ​ ​ The user interface of the Hydro Module consists of three main parts: The visual preview panels, the menu bar at the top and the parameter panel on the right. From the drop-down list at the top of the parameter panel you have access to four sub-panels: General, Flow, Boundaries and Camera. Menu Bar ​ ​ ​ Calculate : The Calculate Button starts a hydrodynamic simulation. Preview : The Preview Button visualizes the initial setup of the simulation in the preview windows, where you can inspect the distribution of density, speed, temperature and pressure. Add : Add a new windows. You can add several new windows to the preview visualization area. This allows you to simultaneously supervise the evolution of different physical quantities or look at them from different viewing angles or filter conditions. Refresh : Refresh all views to the current state of the hydro simulation. Cascade & Tile : Select how to arrange multiple preview windows. They can also me manually arrange by clicking on the top bar and drag them around. Preview Preview : Each of the preview windows gets a new icon on the menu bar. Change the name in the camera parameters panel on the right to suitably represent the content of the window. Save & Load: Save or load the complete state of the hydrodynamic simulation for the current timestep. This allows you to stop the simulation at this time and restart the simulation where you left off after loading the data back with the Open button. The Open button opens the file dialog to select the previously saved file. Loading a file also allows you to use the result in a different project and render it with a different mesh based scene. After loading a data set click the Preview button on the Menu bar to see the simulation preview. How to set up a hydrodynamic simulation in the 3D Module ​ Numbers that you need to start: The physical size of the computational domain in units of meters. Approximate densities (in particles/m^3) of background and active objects Initial velocities in km/s (in the 3D Module), which are then converted automatically to m/s in the Hydro Module and later back to km/s in the Render Module. Filters in the 3D Module require km/s, whereas those in the Hydro Module require m/s. The timescale on which the simulation is likely to finish in seconds (note that 1 year is approximately p x10^7 sec, which easy to remember) . Setup Render Module ​ The first thing to do is to set the Scene Size and Resolution in the Render Module . ​ Scene Size: The physical size from center to edge of the whole computing domain in meters (you may have to choose the correct units in the Units Tab of the Render Module). ​ Resolution: The voxel resolution for the rendering. This does not need to be the same as the hydro simulation resolution with is set in the Hydro Module. ​ ​ Setup 3D Module ​ Hydro Type: Each mesh object in the 3D Module has to be assigned a Hydro Type in the Hydro tab on the right. ​ Background: The computing domain can not have any region that is completely empty. Therefore there has to be exactly one object with the type Background. The mesh of the background object has to enclose the full domain. Best to use a cube object with the size of the domain or larger. The background distribution of physical properties such as density or temperature may or may not be uniform as needed. ​ Initialize: Object that receive all their properties at the beginning of the simulation and change only passively as a consequence of the simulation receive the hydro type Initialize. These could, for instance, be clumps or rings of high density gas. ​ Boundary: Objects that are updated at every timestep or have to remain the same during the simulation are of type Boundary, since they act like a boundary condition. These could be stellar winds or jet that have to inject gas in a controlled, possibly time-variable manner. Variability is controlled in the Animation Module. Modifiers ​ All hydro objects need to have at least one set of modifiers that describe their physical properties. These can either be [Density, Temperature, Velocity] or [Density, Pressure, Velocity] . Density, Temperature and Pressure must not be zero at any position in the domain otherwise the simulation will proceed only for a limited time or crash immediately. The Velocity may of course be zero. ​ Other modifiers may be added as usual to control the shape, orientation and animation of the objects. Any of the modifiers may be animation including those for the physical properties. ​ To some extent Boundary objects can be interactively moved around with the cursor or by changing numerical parameters while the simulation is running . Set up Hydro Module ​ General Tab ​ Grid Size: The number of cells in each direction of the cubic simulation domain. It is the same in all three dimensions. Note that the computational time and memory required for a simulation strongly depend on the Grid Size. While memory increases with the power of three , the required time increases as the fourth power of this grid size, not third power. This is so, because for smaller cells in the same physical domain the time step is also smaller. Therefore to reach the same final time, more time steps are necessary. So, ramp up this number from below, say starting at 64 and monitor memory and computing time as you increase the resolution. The numbers may be any number, no need to be multiples of 2. ​ End time step: The number of time steps to be executed before the simulation is automatically stopped, unless the End Time is reach first. ​ End time: The physical time in seconds after which the simulation shall be stopped automatically, unless the End Time Step is reach first. ​ Resume: If a simulation as stopped or has been loaded from file, enable the Resume flag to continue the simulation. Click the Calculate Button on the Menu Bar to start resuming the computation. ​ Animate: If Boundary Type objects in the 3D module vary in time in their properties, geometry or position/orientation via the Animation Module, then the Animate flag must be on for this time variability to take effect. ​ Pause: Set this flag to temporarily pause the simulation. This can be useful to save the current state to file or generate a rendering of it in the Render Module. To continue the simulation remove the flag. ​ Filters: For visualization purposes various filters can be selected from the drop-down list that select certain regions according to their physical properties. The filters themselves are set in the Filters Module. Note that SI units are used, including m/s for speed (in the 3D and Render Module the speed it in km/s, so different filters are required for the same filter range). You may combine more than one filter. Flow Tab ​ Courant #: The Courant number is a number that controls the stability of the solution of the numerical differential equations of fluid dynamics. This so called CFL condition expresses that the distance that any information travels during the timestep length within the mesh must be lower than the distance between mesh elements. In other words, information from a given cell or mesh element must propagate only to its immediate neighbors. The number should be less than 1, recommended to be less than 0.5, depending on the particular conditions, incl. the strength of the cooling. Note that making the Courant # smaller, also decreases the time step and hence increases the total computing time. ​ Gamma: The adiabatic index of the gas in the equation of state. For monoatomic gas the value is 5/3 (1.66). ​ Eta: The numerical viscosity coefficient. This exchanges some fraction of the conserved physical quantities between neighboring cells and helps to maintain stability. The cost for the stability is diffusion, i.e. for instance high-density regions expand into low-density ones without the need of a pressure gradient. So, the value should be as small as possible, e.g. 1e-4 or smaller. High contrast regions are particularly affected. ​ T0: The minimum temperature in Kelvin to be maintained if cooling becomes too strong within a timestep and would reduce the temperature below zero. For photoionized regions this value may be set to values of order 1e4 K. Otherwise to a reasonable lower value​ that represents physically plausible low values. ​ Cooling: Enable or disable explicit cooling. See the paper by Steffen et al., (2013) for details. ​ Cooling factor: Apply this factor to the explicit cooling calculation. Boundaries Tab ​ For each side of the cubic domain the boundary condition may be set to Outflow or Reflection . If your simulation is symmetric with respect to a certain plain, then this plane could be one of the boundaries and then a setting of Reflection can be used. Most other applications will have an Outflow condition everywhere. ​ The difference between the two conditions is only how the velocity components of the second to last cell is copied to the last cell. For the Outflow condition the component perpendicular to the boundary is copied as it is, whereas in the Reflection it is inverted. Camera Tab ​ Controls the camera viewpoint and physical variable to be visualized in each preview window. Click on the preview window for which the parameters shall be shown and set. ​ Name: Set the name of the preview window. It is convenient to set it similar to the physical variable to be displayed or some other name that somehow identifies the content. Variable: Select the physical variable to be visualized in the preview window. Note: When you move the cursor over the preview window a value for the physical quantity at the cursor position is shown in the top-left corner of the preview window. This is the integrated value along the line of sight. To see the local value use the Render Slice functionality (see below) to extract a single slice. Then the value shown represents the local value of the variable. ​ Enable: Enable or disable this camera. ​ Ortho: Enable or disable orthographic projection for this camera. Image: Edit the image display parameters for this camera. ​ X Y Z pos: Set the camera position. The X Y positions are currently not functional. When the Ortho mode is disabled, the Z position in terms of the size of the domain (=1) changes the distance of the camera. ​ X Y Z rot: Set the rotation angles of the camera per axis in degrees. The X & Y rotation can also be changed interactively by dragging the mouse over the preview window with the left button pressed. If the resolution of the simulation is small enough for your system, the preview responds interactively at a reasonable framerate. The interactive preview is rendered on the CPU and is therefore efficient only for relatively small resolutions. Render Slice ​ In the Camera Tab you can scroll down to find the Render Slice controls. They allow you to display slices of the full simulation domain to closely inspect particular regions. The slices go along the coordinate axes. The initial position in terms of cell number are set with the sliders labeled X0, Y0, Z0, while the width of the slices are dX, dY, dZ. If you click on the slider handle a number field hopes that allows you to numerically set the value. ​ It is convenient to set the Z width of the slices to 1 and the position to the middle. Then by enabling and disabling the Render Slice with the Enable flag, one can quickly change to a visualization that allows one to read off particular values in the preview window. As mentioned above the local value is only displayed in the preview window, if the width of the slice is set to 1. Otherwise the value shown for the cursor position is the integrated value along the line of sight, where each cell counts with a distance step of 1. For instance, if the integrated value along z is 200 and the domain resolution is 100, then the average local value is 2 along the line of sight at the position of the cursor. ​ Output In the Camera Tab you can scroll down to find the Output​ section. When enabled it will output the full state of the simulation every dSteps timesteps. Choose a location on the filesystem afer opening the Directory selection dialog by clicking on the folder button. Make sure it is a location with sufficient disk space to accommodate the amount of data that will be saved. Status At the bottom of the Parameters Panel on the right there are three values updated at every timestep of a simulation. They help to judge the current status and rate of progress of the simulation. It show the current total Time in seconds, the current timestep dTime and the number of Step s computed so far. Considering the ratio between the total time and the timestep is very large, then the simulation will be progressing very slowly. This could be a hint to regionally problematic physical values.

Quick links Modules: Overview Downloads Modifiers: ​ Boost Bump Density Displacement GeoRotation ​ ​ Image Displacement Image Texture PA/Inc Rotation Pressure Projection ​ ​ Random Rotation Shear Shell Size Spiral ​ ​ Squeeze Squish Stretch Taper Temperature Texture Displacem. ​ ​ Translation Twist Universal Velocity Warp Key sub-systems: Overview

Shape The interactive 3-D astrophysical laboratory Images inspire us. Images lead to ideas. Shape was made as a tool to test astrophysical inspiration. Play True or False. By finding out whether an idea works or not, either way, we deliver new insight into nature for ourselves and others. That is why with Shape we make 3-D images of the universe...and more... ​ Shape responds to your scientific creativity for morpho-kinematic modeling or spectral radiation transfer calculations. Create schematic educational visualizations or even photo-realistic images of astronomical objects. ​ Our Introduction and Overview gives you more information about what you can do with Shape. ​ UPDATE REQUIRED (January 21, 2022) Due to a bug in some renders after camera rotation, an update is needed. Please go to the DOWNLOADS for a link to the patch and instructions. SBa Galaxy This 3-D volumetric galaxy model was created in ShapeX based on a detailed analysis of an actual galaxy image. The Orion Nebula This volumetric 3-D model of the Orion Nebula was created using pure polygon mesh and path objects with radiation transfer computation for the scattering and absorption by the dust from the central illuminating stars. Proto-planetary disk with jet. The dusty disk of this proto-planetary object has an enriched structure using noise-textures added to a relatively low-resolution hydrodynamic simulation from the Hydro Module. The disk and jet were then separated using filters and assigned different emission (jet) and dust scattering (disk) properties. Ring Nebula For the creation of this planetary nebula the application of image texture mapping along the line of sight allowed to include details of the dusty globules at precisely the right projected positions in the nebula. The environment of Eta Carinae This is the complex mesh structure that Mehner et al. (2016) used to model the fast expanding gaseous environment of the massive Eta Carinae stellar binary system. Eta Carinae Homunculus model This simple bipolar model of the dusty Homunculus around Eta Carinae demonstrates the multi-wavelength modeling capabilities with ShapeX. From left to right the wavelength range of the rendering moves from the optical to the infrared. About Shape was created by Wolfgang Steffen and Nico Koning. Shape is free software supported by the Institute of Astronomy, UNAM. Legal and Privacy Information Home: Homepage_about User Guide Index Introduction Learn about the possibilities and limitations of astrophysical modeling and visualization in Shape. What types of physical models can be done. Whether you pursue research or outreach, find out what you can do and what you need to learn to successfully apply Shape in your field. Overview A quick tour is given through the integrated modules of Shape is given. We briefly describe how they work individually and how the general workflow brings everything together via interactive input but no need for a single line of coding from the user. Modules The modular design of Shape allows the user to concentrate on the job at hand. The desktop and the main toolbar are the hubs to get you around. In this section we describe the functionality of each of the modules, so you can quickly decide which one will be needed for your project. Goto Introduction Goto Overview Goto Modules Data Preparation Images, spatially resolved spectra and other data can be displayed as direct background references to build your models. Such data images need to be prepared carefully and correctly imported into Shape. In this section we describe how such data images can be prepared and set up in Shape. Goto Data Preparation Coordinate Systems Detailed knowledge of the various coordinate systems is necessary to correctly modeling in Shape. This is particularly true when kinematic are to be modeled. Here is a description of the coordinate systems in different contexts of the available tools. Goto Coordinate Systems Radiation Transfer Mathematical and physical details about the radiation transfer on the Cartesian grid in Shape are described. The physics and approximations for the calculations of scattering on dust particles are also layed out. Radiation Transfer Home: Service Home: Contact

Overview ​ The mesh objects serve as containers of density and limit the volume where the density of an object is placed in space. The density modifier controls the density distribution within the volume fixed by the mesh container. ​ Several other modifiers work in exactly the same way as the density modifier and are therefore not treated separately. These include the temperature and the pressure modifiers . ​ In addition to the common parameters for naming and enabling modifiers, the density modifier has the following parameters: ​ f0: factor that scales the density that is otherwise controlled by the 3-D distribution defined in the Magnitude graph (see below). It is actually part of the Magnitude graph, but because of its frequency of use it is also exposed at this level of the panel. ​ Sigma: currently not in use ​ Operation : This is a drop-down list with the options: Replace, Add and Scale . These are the operations that will be used to determine how this density modifier affects a possibly existing sequence of density modifiers further up in the modifier stack. Replace mode: The first density modifier should be used in Replace mode . If there is a density modifier further down in the stack in Replace mode, then all previous density modifiers have no effect and only this one and those further down in the stack are used. ​ Add mode: the density of this modifier is added to whatever is the result of the previous density modifiers in the stack. ​ Scale mode: the density of this modifier is added to whatever is the result of the previous density modifiers in the stack. ​ In the example on the right there are three renderings of the same geometrical object with density modifiers as shown in the stack above the rendered images. The first image has a density with a point graph that changes as a function of the z-coordinate in cylindrical coordinates. See the graph below the rendered images and note that the Coordinates have been set to Cylindrical. This density modifier is label Ladder Strungs. It is located at the top of the modifier stack and is in Replace mode . ​ The second density modifier is labeled Global Decay and is in Scale mode retaining the default Spherical Coordinate system (see the second modifier graph under the rendered images). It scales the density that results from the first modifier with a normalized Gaussian as a function of distance. ​ In the final example, a Texture was included in the first density modifier. The texture scales this modifiers with the three-dimensional procedural texture of which a slice is shown below. How textures work in more detail is explained in the corresponding section of this manual on Textures. Modifiers: Density (Temperature, Pressure)

Modules In this section we give an overview of the functionality of the different modules and provide links to more detailed information on how to use them and their subsystems. Click on the Module Icon to the left of the description for more information and access to video tutorials on the module. 3-D Module ​ ​ In the 3-D Module the geometric and most other properties of a model are set up interactively. Description Render Module This module takes care of the rendering of image and position-velocity diagrams and a number of settings for other render options. Description Physics Module Radiation transport properties such as emissivity, absorption or scattering are set up as materials (species) in the Physics Module. Description Desktop Module ​ ​ The Desktop Module is your hub to all the other modules, project files, ShapeX configuration and more. Description Video Tutorial Math Module The Math Module allows you to set up variables and relations between them that can then be used throughout Shape as "global variables". Description Modifier Module The Modifier Module lists all modifier that are currently in use and allows you to change parameters of a selection of modifiers simultaneously. Description Maps Module The Maps Module displays channels maps of the 3-D model. The number and velocity range between the first and last channel can be set up. Description Animation Module Most parameters in Shape can be animated over time. This can be used to generate time variation of the models either for scientific modeling of time varying phenomena or for visualization purposes. Description Filter Module Filters for various physical quantities can be defined here. They can then be applied to objects in the 3-D Module. Description Movie Module In the Movie Module one or more animation sequences can be concatenated to a movie and exported for viewing with an external movie player. Description Export Module The Export Module exports the 3-D model into various output formats that can then be used as data for external use. Description Hydrodynamics Module Shape is the first astrophysical tool to introduce an interactive mesh-based setup for such simulations without the need of programming or scripting by the user. Description

The Shell Modifier converts a normal mesh into a shell with user defined thickness. ​ The shell thickness can be set as a function of distance in the Magnitude dialog. Note that the shell can be generated outwards (positive) or inwards (negative) of the original mesh by changing the sign of the magnitude. Currently the magnitude can only be changed as a function of distance from the world coordinate center. This might change in future releases. The magnitude dialog allows you to define the thickness as an Analytic Function of distance or use a graph where you can generate an arbitrary function by manually placing points and setting the spline interpolation. The graph on the right shows the way it was done in this example. Note that only the newly generated mesh is affected by the shell modifier. ​ In the three pictures above the mesh is shown for three different settings. The first one on the left has both parts of the shell enabled. For the second one, the Outer geo flag was disabled. Therefore only the original object mesh remains. On the right, however, the Inner geo flag was disabled. Then the new shell mesh is left. Now the rendered volume fill out the whole space within the outer mesh of what was a shell. Note that the position in the Modifier Stack is important. If a Shell Modifier is placed at the end of the stack, the result will be a shell thickness that conforms to the Magnitude graph. However, if another geometry operator, such as a Bump Modifier or a Squish Modifier is placed below the Shell Modifier, then the final thickness may strongly different from that set up in the Shell Modifier. Caution: If the original mesh is locally complex and the thickness similar or larger than the local curvature, then the newly created mesh for the shell may self-overlap. This can lead to undesirable results. Make sure the thickness of the shell is compatible with the complexity of the mesh. Sometimes applying the shell in the opposite direction by inverting the magnitude of the thickness solves or reduces this potential problem. Modifiers: Shell

Maps Module Overview ​ Channel maps are spectroscopic images, where the image contains only emission from a certain small range of wavelength or line-of-sight velocity. They are typical for spectroscopic radio observations, but have come into more frequent use also in the optical and infrared spectral ranges. Usually they are presented in an array of many channel maps representing the complete spectral range that has been observed. The full set of spectral data is often referred to as a data cube, since the image can be arranged as slices of a cube. The Maps Module is divided in three main sections. The dominant region is the display of the channel maps. Above the maps is the main menu and to the right are the parameter tabs. There are three tabs for General parameters, those for an individual selected Channel and for the Output of the channel images (maps). General Workflow: In the General Parameters tab the minimum (initial) and maximum (final) velocities are applied. These are then divided in a number of channels that is the product of the number of channels in rows and columns. To set up this grid of channel maps click on the "Re-grid" button in the main menu and confirm. This generates the grid of image windows. Now render by clicking on the Render Button in the Render Module or press Ctrl-S. Parameter Panels: General: Render: This flag controls whether the channel maps are rendered at all. Make sure to have the tick mark set when using the Map Module. ​ Initial vel: The smallest velocity to be included (can be negative). This is the center velocity of the first channel map (top left in the grid). Final vel: The highest velocity to be included. This is the center velocity of the last channel map (bottom right in the grid). ​ Delta (D) : This is the width of the velocity channels. If set to zero, then the width is calculated from the difference between the final and initial velocity divided by the number of channels. If set manually, then the channels may be narrower than that or wider, in which case they overlap. The intensity taken into account is constant over the interval, which may or may no be the case for the actual observations. ​ Rows & Columns: The number of rows and columns that the channel map grid shall have. The total number of channels is then the product of rows and columns. ​ Transparency: The transparency of the rendered foreground image. It can be changed with the slider to transition between rendered and observed background image. This helps to compare the model with observations. ​ Light Echo: This function is deprecated. ​ Difference: Show the difference image subtracting the observed image from the rendered model image. ​ Export: Export the rendered image in ASCII format for further external processing. ​ Channel: ​ Select a particular channel by clicking on the image in the grid view of the channel maps. The selected channel is highlighted by a thin red line. The Channel parameter panel on the right then displays the settings of that particular channel. To view the image of this channel by itself at a larger scale, click on the "Expand" icon in the main menu of the Map Module. Vel (km/s): The velocity center of this channel. ​ D vel (km/s): The full width of the velocity channel. Image: A reference or observed image can be loaded to be compared with the observation. One can transition between the rendered model and the reference image by changing the Transparency in a numerical way (see below) or using the Transparency slider in the General parameter panel (see above). The reference image can be placed and processed using similar attributes as those used in the Selected Window section of the Render Module. Please see the pages on "Data Preparation " and the Render Module for more details on how to use the Location parameters and the image Modifiers. ​ Output: ​ The output parameters control the appearance and labeling of the grid image output using the Save Grid or Save Images button in the Main Menu of the Map Module. An example grid output is shown on the right. CrossHairs: Mark the center of each channel with a cross. ​ Labels: Label each channel with its central velocity. Color: The color for the labels. Change the color by clicking on the colored squared. A dialog opens to let you select a different color. Menu bar: ​ Re-grid: After you adjusted the General Parameters for the grid of channel maps, the Re-grid button sets up the grid using these parameters. When you change the General Parameters use this button again to apply these parameters. ​ Insert: Individual channels can be inserted before the currently selected channel. Note that this channel does not change the parameters of the pre-existing channel and is therefore not part of the regular sequence that was established using the Re-grid button. This new channel needs to be set up individually in the Channel parameter panel. Delete: Delete the currently selected channel. ​ Save grid & Save images: save the grid of image or individual channel images. Se the section on Output above for details. ​ Palette: Opens the image adjustment dialog for the channel maps. Here you can adjust brightness, scaling, and add other image modifiers. Note that the Gaussian Blur modifier handles the resolution of the maps. This is currently disconnected from the Seeing parameter in the Render Module and needs to be adjusted separately. In the Maps Module it works in terms of pixels, so it is depends on the resolution. This feature will be improved in a future release. ​ Properties: Opens the Properties dialog for the detailed appearance of the grid coordinates, tick marks, fonts and colors. Load obs: Load observed or reference images to the background of the grid. Here you can load a sequence of multiple images to fill all the channels. Select multiple image in the directory dialog that opens by clicking on the first of the sequence and then Shift-click on the last. Reference images for individual channels can be loaded or changed with the corresponding Image load button in the Channel properties panel. ​ Expand: Expands the selected individual channel image to full size of the image grid area for a detailed view. Clicking the same button again restores the full grid. ​ ​

Top of Page Basic Workflow Overview 3-D view ports Menu Bar Primitives Objects, Tools & Lights tabs Transform tools 3-D Module Basic Workflow Basic workflow: Interactively add the geometric elements of your object in the form of primitive polygon meshes (Primitives) that you can access at the top menu bar of the 3-D Module. These meshes will serve to encase the volumes that will constitute the different parts of the model. Then you modify the simple structure of the Primitives using what we call Modifiers, which give the objects new geometric structure and physical properties as a function of position in space. Using the Physics Module, you then assign the material and radiation properties to the meshes. Finally, the model is rendered with the Render Module and some of the observational properties can be displayed with the (Channel) Maps and Graph Modules, where the observational data can be included and compared with the model results. If the results are not satisfactory, the model will be adjusted until a satisfactory match is found between observations and model. Overview of the 3D Module : The purpose of the 3D Module is to set up your model interactively. This module is divided in several sections, the interactive 3-D view ports , the Menu Bar at the top, Objects, Tools & Lights tabs on the right and Transform Tools on the left. ​ 3-D view ports: By default there are four view ports that can simultaneously show you the same number of different views of your mesh model. Several of these camera views are aligned with the coordinate axes (initial defaults: Front, Right). The Free-Form view can be changed arbitrarily using mouse input after selecting the Camera > Orbit tool from the Transform Tools to the left of the 3-D view ports (see Transform Tools for details). A special view port is the Render view, since it represents the view that will be used for rendering in the Render Module. This view can be controlled interactively with the Mouse in the same way as the Free-Form view, but also numerically with Image and Camera parameters in the Render Module. ​ Right-click menu: When you right-click on the area of a 3-D viewport, a menu opens that allows you to set a number of properties of this particular view. Camera: Select a different camera view for this viewport. Save Image: Save the mesh images of the viewports. It saves the image of all viewports in one image. If you want to save only a single view, then use the Maximize command from the right-click menu to open a single view in the 3-D view space (to go back to the four viewports, right-click again and select Restore). Make sure to provide a filename with a valid image extension. Most common image formats are supported, such as .png (recommended), .jpg, .gif, etc. (example: image1.png). The Save Image function is the same as that of the Save button in the 3-D Module´s top menu bar. Saving your viewport images with this function does not include the colored coordinate axes or the viewport labels. To saves these you can make screenshots of these areas. Properties: In this dialog you can set a few parameters for the individual view port. Scene alpha: This parameter changes the transparency of the whole polygon object scene, so a comparison with observations or the rendered scene may be easier with lower alpha values. Background: This setting selects the background image of the scene between None, Observed and Rendered, which enables you to compared the corresponding images with the mesh. Including the Observed data is useful to place and shape mesh objects according to the observations. Note that a direct comparison with observed data makes only sense for the Render image. Sometimes, comparing the observed images with other views might be helpful when checking for symmetry properties. Maximize: For more detailed inspection, this command fills the space of the four viewports with a single one. Restore the four views using the Restore command in the right-click menu. 3-D view ports Overview Menu Bar Menu bar: The Menu Bar of the 3-D Module provides quick access to a number of commands (left section) and the creation of Primitive mesh objects (right section). ​ ​ ​ Save: Save the mesh images of the viewports. It saves the image of all viewports in one image. If you want to save only a single view, then use the Maximize command from the right-click menu to open a single view in the 3-D view space (to go back to the four viewports, right-click again and select Restore). Make sure to provide a filename with a valid image extension. Most common image formats are supported, such as .png (recommended), .jpg, .gif, etc. (example: image1.png). Saving your viewport images with this function does not include the colored coordinate axes or the viewport labels. To saves these you can make screenshots of these areas. Import: This command allows you to import objects from a different project. A file selection dialog opens to select the project from which to import objects. Then a second dialog allows your to select one or more objects (shift-click for selecting multiple objects). Note that it is divided into tabs for different types of objects which have to be imported separately. Options: The Options dialog contains settings for viewing coordinate grids in the 3-D viewports and other options that might be helpful during modeling and for publication of model meshes. Undo: This command opens the Undo Stack utility. It shows recent commands that can be undone and redone. You can select which commands to undo or redo and set the maximum number of commands to be held in the stacks. Additional Undo options exist for example for the Path vertex objects which can be undone with Ctrl-z or redone with Ctrl-y. Primitives: The most important functionality of the menu bar in the 3-D Module is to provide quick access to the creation of various Primitives, i.e. basic geometric mesh objects that can be described with only a few parameters. ​ ​ ​ ​ Create a new primitive object by a first click on the corresponding icon, then click on one of the 3-D viewports and immediate drag the mouse to the right to increase the first parameter of the primitive. When the first size is adequate, click again and drag to the right to increase the second parameter (if necessary). One click and drag to the right for each parameter (sphere has one, cone and plane have two, “cube” has three) of the primitive object and then one more click to finish. Your object appears in the Systems folder of the Objects tab located to the right of the 3-D viewports. By default the names of the objects is PS_#, where # is the number in order of creation. This name can and should be changed to something more descriptive in the General parameters menu of the drop-down list to the right of the Objects folder tree. The detailed properties of the individual objects can be changed after selecting it by clicking on the objects name in the Objects stack, where it will be highlighted and in the 3-D viewports the corresponding mesh will turn white, if the Show status flag in the General properties is activated (this is the default). The Object Properties drop-down list contains five different parameter sections: General, Particles, Modifiers, Primitive and Fields. Click on Object Properties for a link to a more detailed description of its content. Primitives Objects, Tool and Lights tabs: The parameters of objects and different tools can be set in the Parameter Tabs on the right side of the 3-D Module. There are three tabs available for the parameters. Objects: handles the parameters of the objects in the 3-D viewports. Tools: allows access to the parameters of tools such as the Draw Tool or Erase Tool for particles accessed in the corresponding tab on the left of the 3-D Module). The parameters in the Tools tab appear once the tool has been activated. Lights: change the lighting properties of the 3-D viewports by changing the properties of the default Ambient Light or adding, deleting and changing the positions and parameters of other types of light. A more elaborate lighting scheme is often useful to create schematic illustrations using the mesh objects. ​ Objects, Tools & Lights tabs Transform tools: On the left side of the 3-D Module there is a set of tabs with a variety of tools, most of which interactively change the positions and orientations of various types of helper objects: Cameras: change the view points of Render or Free-Form view ports interactively. Systems: change the transform properties of individual objects (Systems) of the scene. Widgets: change the local coordinate system of the selected tool or modifier. Vertices: with these tools individual or a group of vertices of meshes are manipulated for very detailed local changes of the meshes. Particles: draw and erase Particles on and around meshes that serve as supports. This allows very detailed structures to be added to an object than can not be easily generated with meshes or procedural filament tools. The parameters of the Draw and Erase particles tools are set in the Tools tab on the right of the 3-D Module. Transform tools Objects Tree: The objects tree is a hierarchical list of the current objects in the scene. They can be collected in folders and sub-folder. With the tick boxes to the left of each object an object can be switched on or off. Similarly switching on or off a folder does the same for all objects in a folder. ​ New objects are placed in the default "Systems" folder. ​ New folders are created using the "Add new folder" button at the bottom left. Copy objects with the copy-button. The copy is then placed at the bottom of the list in the same folder. Move objects and folders around within the object tree by dragging and dropping. Delete objects and folder with the delete button at the bottom of the panel. ​ The color of the symbol to the left of the object name is the same as the mesh color and helps to identify the object in the 3-D views. If the object is not enabled, the color of the symbol is grey. ​

Render Module Properties Panel: Units Properties Panel: Units ​ Observational astronomers and theorists often work with very different units. This can be accommodated for in Shape by choosing the units that work best with your reference images or target audience. ​ World & Image units: Various units can be selected for the World (Coordinate System) in the 3-D environment and the Images. The appropriate unit is selected from a drop-down menu and by default is set to meters (m). Some of the units are in terms of typical linear and others are in angular sizes. Energy: The energy units refer to the intensity units of the images. In addition to the SI (International System) some of the typical astronomical units are also available. Distance: The units for distances are similar to those for the World & Images, except that the angular units are, of course, not available.

Render Module Properties Panel: Output Properties Panel: Output ​ The Output panel sets the type and file location for the output of the 3-D render cube information from the current scene. This information can then be processed and, with the Export Module, exported to other standard formats for external visualization. Enabled: Enable the output to be executed after the rendering is finished. Slices: When enabled, the output is done in the form of PNG format images slices. Each slice contains RGBA information in the XY-plane of the world coordinate system. Name: This text field takes the name of the output file without an extension. Unless Slices is enabled, the output will be a single file with the extension ILV. The ILV file can be loaded into the Export Module for further processing and output in other formats. Background Image: In this section you can control which the viewing of all the foreground rendered images and the observed background images in all windows. Image: From the drop-down list you can choose which images are used as background or reference image. The initial choice is between Observed and None. If Observed is chosen, the Observed images chosen in the Selected Window panel will be visible as background. If you choose None, then you can click on the button beneath to save in memory the current rendered images as a background or reference. Each image is identified by the time stamp of the moment of click on the save button in this panel. ​ The button labeled "x" allows the user to delete a saved set of rendered reference images from the drop-down list. Transparency: The slider controls the transparency of the foreground rendered image. Moving the slider to the right makes the foreground gradually more transparent, thereby allowing a comparison between the reference image in the background with the foreground.

To see this working, head to your live site. Categories All Posts My Posts Login / Sign up Shape Exchange Forum Get in touch with the Shape user community. Ask questions or reply to those of others. Show your science or fun results. Create New Post General Questions Ask about the science that can be done with Shape. Need help with the modeling strategy? Here is the place to ask. subcategory-list-item.views subcategory-list-item.posts 3 Follow Workflow What is a good way to achieve may goal?Done this, what´s next? Questions on how to get into the flow ... subcategory-list-item.views subcategory-list-item.posts 0 Follow Please, show me how to ... Tutorials and more from you and your peers. subcategory-list-item.views subcategory-list-item.posts 0 Follow 3-D Module Tips and tricks all around the 3-D Module. Did you find a curious way to do something? Share it here. subcategory-list-item.views subcategory-list-item.posts 0 Follow Render Module Having ideas or questions on the Render Module? Something doesn´t look as you expected? Talk or ask about it here. subcategory-list-item.views subcategory-list-item.posts 0 Follow Bug Reports Found something that isn´t right in Shape? Please, report any bugs here. We will check it out and fix it asap. subcategory-list-item.views subcategory-list-item.posts 5 Follow New Posts luisvpar Apr 26, 2023 Problems to install ShapeX in Fedora (RPM based) Bug Reports Hello. I want to report the problems that I have found to install ShapeX in my system: Fedora 37 (x86-64 kernel 6.2.11-300). First problem that I have found is that there is no RPM package provided for ShapeX. Thus, I tried to create a RPM from the DEB package using 'alien'. The RPM was created but several dependencies were not found when I tried to install it ('rpm -i shapex.rpm'): Can't install: does not find libraries: error: Failed dependencies: libavcodec-ffmpeg.so.56()(64bit) is needed by shapex-1.0-2.x86_64 libavcodec-ffmpeg.so.56(LIBAVCODEC_FFMPEG_56)(64bit) is needed by shapex-1.0-2.x86_64 libavcodec.so.53()(64bit) is needed by shapex-1.0-2.x86_64 libavcodec.so.53(LIBAVCODEC_53)(64bit) is needed by shapex-1.0-2.x86_64 libavcodec.so.54()(64bit) is needed by shapex-1.0-2.x86_64 libavcodec.so.54(LIBAVCODEC_54)(64bit) is needed by shapex-1.0-2.x86_64 ... And more related to 'libavcodec (53, 54, 55, 56, 57, 58)', 'libavcodec-ffmpeg (56)', 'libavformat (53, 54, 55, 56, 57, 58)' and 'libavformat-ffmpeg (56)'. I tried to install the 'ffmpeg' and 'ffmepg-libs' packages from RPMFUSION repo. Unfortunately, this did not solve the problem. The 58 ver of 'libavformat' and 'libavcodec' were installed and I even tried to create soft links for the older versions with no luck. I have also tried to install it on a different Fedora 38 (same kernel and also x86-64 based) and I have found the same problem. In this case it was even worse since it was not possible to install the ffmpeg and ffmpeg-libs due to a conflict with 'lbswcale-free' package. I hope this helps and if someone has found a solution please share it. Thanks in advance for your answers and to the developers. Like 0 comments 0 Marco Gómez Jun 07, 2023 ShapeX crashes in MacOS Ventura Bug Reports I am trying to run ShapeX under MacOS Ventura. I downloaded the latest ShapeX_22_06_10 version with the ShapeX_update_X.1.3.0 and whenever I choose 3D rendering the program enters "Not Responding" mode. How can I fix this issue? Like 6 comments 6 vazquez Sep 01, 2022 Hi Nico & Wolfgang, Recently my iMac couldn't read a shp file built in Ubuntu. However, Ubuntu can read my shp files built in iMac. Help pls Bug Reports Like 3 comments 3 Forum - Frameless