What's new file for Jaques: 6/10 - mean relation in histograms added and made it accesible on the command line in the variables meanx and meanh - added div V and density slopes as derived quantities. These are the first examples of doing derivatives without actually setting ghostzones. More such derived fields may be useful. div B, etc. - added start-vm.sh script that starts up Jacques using the virtual machine not requiring an idl license. 12/09 - cumulative histograms and options to log or not log the histogram - support voronoi densities for the gadget files these are crazy slow for any sizeable dataset so there is a goto, skip_voronoi in read_gadget_file you hve to uncomment for this to be used. - Ctrl+f will now only look for the maximum in the box inside the view this way it is easy to roughly zoom in on an object by hand and then central on the maximum value of the variable selected (Can't believe I've not always done this ...) 11/09 - Plot molecular line emission for C18O, NH3, NH2+ Other molecules can be done (but are unlikely thick) using the routines in projection_with_absorption/krumholz/ - Animations now work also without first reading all the files. Just load a data set and hit Ctrl+A. It will then find the next file, redraw, and continue until it cannot find another file. To interrupt, just type c or C on the command line. This also works for Gadget data. - Jacques now is also a friend of Gadget. I support reading binary snapshots and basically read all the data into memory an construct derived fields. So this may get prohbitive for very large data sets. At the same time one can display the particle data now in both the "Variable" tab as well as the data tab. In the Variable tab it will draw squares with the size of the sph softening length divided by the integer particle size selected in the particle tab. A value of 2 for the size works well. For dark matter data only the particle tab should work (and has not been tested). - Added another script in the scripts directory that makes a movie of whatever one just plotted but centers it on a particle of specified ID. to try this do .r follow_particle_movie.pro and edit the file in the scripts directory to use the particle ID you desire - Added Pressure as a derived field (about time ...) No units yet... 10/09 - Added a watch for next output function. Use Ctrl+Shift+W to activate. This will look for a new data dump in the current directory. If it is found it'll redraw the plot you have. Type c or C on the command line to get rid of it and make Jacques behave normally again. - Added rudimentary support to read SPH particles from Gadget. Now all files that start with snapshot_ are interpreted as SPH data and all data is read in. Only one file at a time can be used. However, the Ctrl+N and Ctrl+Shift+N shortcuts to the next and previous timesteps works. Use only the particle and the histogram tabs with these data. 09/09 Keyboard Ctrl+Shift+R shortcut to cycle through rendering (interpolation options) Also support overrding which particle fields to take log of or not. (Ctrl+L) 07/09 A few more derived fields added. Added suport to plot 1D data fields. Just go to the histogram tab select x on the first drop down list and say density on the second. Hit Ctrl+D and voila, 1D plot .. Added a way to overide the default logging behavior. I.e. say you want to see the density on a linear scale just do Ctrl+L and it'll bring up a window for you to select whether you do or not want the variable selected. You have to quite the window before continuing. 05/09 Cleaned up a number of things. More intuitive data loading to SDVision. Press the load data button then F1 to visualize. Particles work correctly even when a very small region was selected for volume rendering etc. Better integration with iTools (Ctrl+i) short cut allows one to create publication ready oputput. Ctrl+Shift+i gives basic statistic about currently loaded file. Virtual machine suport works again. The image buttons (top right) are different containers now to keep images. Switch to another number and draw different things. You can come back and look at previous images. This help to compare different quantities. Right mouse click now cycles through the slice axes and the middle mouse click now recenters the view on that point. Fixed a bug where a colormap change was not noticed by joint histograms. Projections are also interpolated now and work similar to slices. Another rendering option added that draws a single colored point in the available cell centers. The zoom pick option again now draws a rectangle (hopefully on all platforms) helping one see which region one picks. 04/09 Added an exporter for particles in a format that Ralf Kaehlers renderer can read. If you have the particle tab open and are looking at particles and noe to Ctrl+Shift+e to export to amira it'll recognize you want to export particles. All the types that are selected will be exported (you can also downsample). Whatever particle variable is selected will be used as the fourth column in the output files (after x y z) and hence available for rendering. 04/09 - Number of bug fixes. - Ctrl+n and Ctrl+N now also will try to guess the name of the next .hierarchy file. I.e. if you have one snapshot loaded and you want to jump to the next one you only have to hit Ctrl+n to get it. To go back in time just use Ctrl+Shift+n = Ctrl+N. - Ctrl+F12 makes window bigger and Ctrl+F11 makes it smaller. - New button 'g' in the interpolation row on the left frame allows to draw a slice with grid lines overlayed. 12/08 - Added suport for opening multiple windows. Just hit Ctrl+W to open new windows. Jaques will save and restore the necessary state variables to disk (to conserve memory) and you should be able to manipulate date in all the windows simultaneously. This canNOT yet support doing animations in the background. Sorry. However, it is quite useful when comparing different runs or different quantities. - Added support for personal preferences ~/.jaquesrc There is an example in jaquesrc in this directory so you do not have to like mine ;-) - volume quantities can also show cgs units 10/08 Added first parts of particle support for SDvision when working with Jaques.... First Draw the particles in jaques. (this reads the data) Then start SDVisions with Ctrl+Shift+V Then you seee a reader window on the left. Just hit the "Load Data" button at the bottom left. Then F1 as usual gives the list of fields one can use. If you're at the topgrid scale the units between 3D volume data and the particle position seems correct. It doesn't work for different scales than topgrid yet. This can't do that much yet but is perhaps already useful for some users. 05/08 New features to export data to partiview. So far we can export the amrboxes and particle data into partiview readable files. The export routines are in the File menu. You have the choice to either output only the current timestep or all loaded timesteps of a data set. Exporting AMR boxes, what now? Once you have written a .amrbox file you can read it in partiview's commandline with add box ./path/myfile.amrbox A useful command is gobox box# in partiview which centers the view on that box. So say gobox 112 goes to the grid number 112. The other feature is to write .speck files from the particle data. Only the particles selected in the particle tab are written. I.e. if you use Every = 10 or so you can reduce the # of particles in the file and use Type to select which particles you want to export. The .speck file can be then read in to partiview using read ./path/myfile.speck There is also a parti.cf file in this directory which sets up the point sizes and luminosty etc. You most likely have to adapt this to your situation and data btu should be a decent start. If you use parti.cf you can just start partiview with partiview ./parti.cf It reads the point data and uses a star texture for them. 05/08 A number of bug fixes recently introduced... New feature2: - In histogram mode it now reads only the region that would be gridded to a uniform cube when one does Ctrl+D. However, with Ctrl+Shift+D all grids are read to make the histograms. This makes it faster to explore what the histograms look like before using all available data for it. - One can now plot the radius and x,y,z volume and mass as fields. This is useful sometimes. 04/08 Added a whole new histogram facility. This works on particles as well as grid quantities. This make the IMF and pdf fixes of the past superfluous and unsupported. The interface can display one and two D histograms, recognize the units, and allow arbritary weighting fields. Ctrl+H toggles to and from the histogram mode. The minimum and maximum values are there for convencience but should normally not be needed. - Replaced droplists by combobox widgets. Tabbing (i.e. using your keyboard to navigate the widget is much better supported. No mouse is needed now for most things. - Made the weighting field in Projections general. One now can use any field as weight when doing projections. The interpolation buttons do not affect projections anymore. - Incorporated SDvision to be able to interact with Jaques http://irfu.cea.fr/Projets/COAST/visu.htm SDvision does very nice job visualizing unigrid data of scalar and vector quantities. It also provides a particle interface. Jaques so far only supports scalar and vector quantities and not the particles. This GREATLY expands the capability of jaques. Press Ctrl+Shift+V to start SDvision. Next (or before) load a data set in jaques. Now navigate in jaques to the point and scale for the data-set of interest. Now in the SDvision window press Ctrl+J (import from jaques). If you're in jaques' 'Variable' tab it will take the selected scalar quantity grid it to a uniform grid and load it into SDvision. However, if you're in jaques' 'Vector' tab it will read the vector field, i.e. velocity or B-field and pass that to SDvision. In SDvision hit F1 to generate diffferent types of plots from your data. In particular try the streamlines of vector data and the volume rendering of scalar data. The default cube size jaques will grid to is 256^3. To change this go to View/Isosurface and look at the bottom left for Cube dim & Smoothing options. Even 512^3 cubed works well on a laptop with a decent graphics card. 04/08 Added a function to display the IMF of a bunch of particles. First select the particle interface. Select "particle mass" or "particle mass density" depending on your format. Choose physical units (Ctrl+U) to get it in solar mass Draw (Ctrl+D) now at the command line type > imf You should see a histogram in a separate window. on the command line the variables x and v now contain the log of the bin locations and the number of particles per bin. This gives you more control over plotting it yourself. you can also choose your own min and max values and desired number of bins pro imf, min=mind, max=maxd, binsize=binsize, nbins=nbins 03/08 Added some new features for particle support. A number of bug fixes as well ... - Added derived field particle massdensity which multiplies the field particle mass wit the the cell volume its found in. This gives the correct particle density projection for most enzo simulations where the aprticles masses in fact are written as densities rather than real masses. - Allow now to select particles by type that are to be plotted - Cleaned up interface using a tab widget 03/08 Added construct_projection_with_absorption.pro Ctrl+G This renderes the data from the back to the image plane. This allows to include absorption in the rendering step. 03/08 Added rudimentary support of units for Jaques. Use Ctrl+U to toggle this behavior. As you add new derived quantities also check the get_units.pro routine to see how to add units with labels. Also added improved particle support. There is a size slider that changes the convolution of a 2d histogram of particle positions or particle attributes. This gives a quick impression of DM projections, e.g. When the particle menu is visible and you press Ctrl+Shift+D the aprticle positions are masked and the projection is display as a simple way of showing both. This will not work well for all types of data, though. 12/07 (jwise) Jaques can now take the current movie data loaded into memory and create an HDF5 index file that is readable by Amira. This new option is under Tools / Export to Amira (Ctrl+Shift+E). 12/07 - Full movie data support added. It recognizes all timesteps and can animte them. - GRID CHARTS show the PROJECTED GRIDS - Animation also can ANIMATE GRID CHARTS. Simply first draw a grid chart: Ctrl+Shift+B and the start the animation Ctrl+Shift+A. Same concept as choosing between slices and projections for your movies. The GRID CHARTS also have a COLOR MAP now and give their time etc. Makes for nicer animations. - Jaques now has somewhat better PARTICLE SUPPORT. You can add derived quantities (see the particle v^2 example) Color them by different properties etc. Access (toggle) the particle interface with Ctrl+P If you now hit Ctrl+D it'll display particle things as long as the particle interface is open. - The velocity and vector interface does now know whether it has to read data or not so the old READ button is gone. Also to plot the standard vector plot simply hit Ctrl+D. - Added a SAVE STATE FEATURE. This is particularly useful if it took a long time to construct the grid hierarchy (say you were reading lots of movie data) or the particles took forever to load, just hit Ctrl+Shift+S and save the current state to a file. Next time you start jaques (even on a different computer you can read that .sav file back in and continue where you left things off. 12/07 Jaques now read the latest version of the movie data format. It can only display topgrid time steps so far. This discovered a bug in the movie format ... Thanks John for all the help on this one! I also added an astep variable. So in animation you can type first on the command line: idl> astep = 4 Will only use every fourth file. astep = 1 is the default. 12/07 Now includes some features of oJaques. Only the the get 3d data methdod is tested so far. More to come ... oj->g3d(data_fields=df) Everytime now jaques reads a hierarchy file it also defines an OJ object called oj. This is in the common block and hence accesible from the command line. E.g. da = oj->g3d(data_fields=["Density", list_str[var_index]]) will read the Density and the currently selected data field in jaques. The returned variable da is a structure with this form: threeD = {threeD, $ min_level: 0B, $ max_level: 0B, $ Np_total: 0L, $ N_dfields: 0B, $ LEFT_EDGE: [0.D, 0.D, 0.D], $ RIGHT_EDGE: [1.D, 1.D, 1.D], $ DATA_FIELDS: STRARR(100), $ XP: PTR_NEW(), $ ; x coord pointer YP: PTR_NEW(), $ ZP: PTR_NEW(), $ DP: PTRARR(100), $ ; data pointer LP: PTR_NEW(), $ ; level pointer dxl: DBLARR(100) } ; dx of level so *da.dp[0] would be the Density data for every unique 3D grid cell. The associated, e.g. cell volumes are ( da.dxl[*da.lp] )^3 humane.pro uses this to give you powerful access to your data. Say you just loaded a hierarchy file. Now type idl> humane at the commandline. (Do not try this on very large data) Now you have all the following variables defined in global address space x, y, z, dx, d, v, vol, mass, radius Where d is the log10 of density and v is the data values of the selected field in the jaques droplist (the same that would display would you draw a slice). So say if you had selected temperature than v would be the log10 of it. So to get the mass averaged temperature in the volume: tmav = total(10^v*mass)/total(mass) the volume: tvav = total(10^v)/total(vol) Now lets plot the density pdf: idl> pdf, d and the joint density-temperature pdf idl> pdf2d oh and the temperature vs radius idl> pdf2d, x=radius, y=v show the refinement regions: idl> plot, x, dx, /ylog, psym=3 This combination now should make it more convenient to do rapid data exploration using the jaques command line. 11/07 Now support much larger and prettier images and .eps output. - In options menu you can now adjust the image size. So you can now produce say 3000x3000 e.g. for a 10 by 10" image at 300dpi. Jaques can also make much nicer production quality plots now. Use Ctrl+I to send the current image to the idl ITool iimage and have a colorbar and access to nice fonts etc. ITools also can then export a .eps file with cmyk color model that APJ and printers in general prefer. Using also the new higher resolution images shoud make for quite pretty posters. 11/07 Supports simple movies - In Tools menu "Animate" or keybd shortcut: Ctrl+A This will first delete all files "frame*" in the log directory And then go through all files in the file list and do either a slice or projection depending on what was the last image created before the start of the animation. You probably want to keep the "View/Change Min and Max" dialog open to make sure the minimum values and maximum values used for the frames are always the same. To cancel the process type "c" or "C" in the command line window. The frames can be combined with e.g. ffmpeg -r 3 -qscale 3 -i frame%05d.jpg movie.avi Which works well for playback with Apple QuicktimePlayer and ffplay 8/07 Jaques 1.0 email to tabel @ stanford.edu - You can now use IDL without a full IDL license and start in virtual machine mode using the command line idl -vm=TOOLS/SAV/jaques.sav This is a big advantage on laptops etc. if your're not editing the source anyway. - by default Jaques logs all images you make as jpeg files in ~/tmp/ if you have that directory. to change the lcoation or this behavior edit first.com - Jaques is now using true color images (24 bit deep) Noticable change when you do interpolated pictures. - this makes the dump_jpeg now work correctly too. ( Ctrl+S (snapshot) - Jaques now uses the start and count features of HDF routines slices are much faster now. - rewrite of read routines makes it easy to add your own variables look at TOOLS/get_data and follow the examples to define a a new scalar variables on the grid from existing data fields - supports HDF5 packed format 6/07: Jaques 0.99: - Supportig lists of files now. In the Open File dialog you can select a directory and jaques will make a list of all .hierarchy files in it and its subdirecotries. So if you pick your home directory you will get all .hierarchy of all your sims. Any file with one hierarchy file per line and a file extension .mhierarchy can be loaded through the regular open dialog in the file menu. e.g.: this line will create a text file with the different hierarchy files listed: ls -x ~jwise/storage1/SimB-LW20/*003[567].dir/*.hierarchy > jwise-SimB-LW20.mhierarchy /u/ki/jwise/storage1/SimB-LW20/output_0035.dir/output_0035.hierarchy /u/ki/jwise/storage1/SimB-LW20/output_0036.dir/output_0036.hierarchy /u/ki/jwise/storage1/SimB-LW20/output_0037.dir/output_0037.hierarchy use this generally to creat such directory files in a space you can read: ls -x ~/mycooldata/*/*.hierarchy > ~/mycooldata.mhierarchy This makes it much easier to navigate when you have many simulations and also will eventually lead to rudimentary animation ... As you load regular .hierarchy files they are added to this file list to allow you to easily navigate between multiple data sets. So if you already looked at a data dump in the current session you can check this list to easily go back to that data dump. Also use these for a list of one or more data dumps per simualtion you have stored.Once you selected the data dump in this list it automatically sets the data directory. This makes it easy to find other data dumps for the selected simulation e.g. myruns.mhierarchy: ~tabel/runs/FirstStar/output_0049.hierarchy ~tabel/runs/SecondStar/output_0042.hierarchy ~tabel/runs/FirstGalaxy/output_0041.hierarchy ~tabel/runs/FirstGalaxyCluster/output_0009.hierarchy could be a useful file. Also note in the Tools menu bar there is a 'Clear File List' item that will reset the file list. Use Ctrl+N to go to the next data file and Ctrl+Shift+N to go back one data file in your list.This help in looking at the time evolution of your data. Ctrl+Shift+S: Saves the current file list to a .mhierarchy file for later use. - Right clicking on the draw window uses that point as center. I.e. when you zoom in further or out that point will be the center, as well as when you change slice orientations. - Projections: Use the menu button in view or hit Ctrl_Shift+D to get whole projections. These are done through the entire box no matter how far you have zoomed in. For projections the interp/wieght button group at the left specifies whether the projected quantity will be not weighted, weighted by density, or by denisty^2 - Fast Mode: Hit Ctrl+M to toggle between 3 modes: Fine/Faster/Fastest: plot grids that have cell size that will show up as one/two/four pixel, - Changes to interface. All Draw, Refresh, Vector etc.are in the menu bar and as such have access to keyboard shortcuts: Ctrl+D = Draw Ctrl+Shift+D = Draw projection Ctrl+R = Refresh Ctrl+F = find max from finest levels Ctrl+Shift+F = find max from all levels Ctrl+C = Colormap Ctrl+V = vector fields Ctrl+Q = quit Ctrl+O = open Ctrl+Z = zoom in by 10 Ctrl+Shift+Z = zoom in by 2 Ctrl+X = zoom out by 10 Ctrl+Shift+X= zoom out by 2 (there are a few more. You can sse in the menu items) - Added Save as jpeg (Ctrl+S) which still has problems on some X-servers (your milage may vary greatly) - Support for very simple contour plots. First draw an image and then select contour plot from the View menu (Ctrl+Shift+C). - Understands particles and can overplot their positions - Greatly increased speed in reading initial hierarchy file and parsing. - Support for magnetic fields: Bx, By, Bz fields are not "log-ed" B^2 added to list of variables Field-lines (see also vector fields) - Added a relativistic gamma field which gets computed on the fly. This is support for renzo - 2D data sets work also when z is selected as the slicing plane (will be automated for next release) - It does streamlines now. In the vector draw menu use lineplot to plot streamlines (or field lines for B) Click the "Normal" Button to normalize the vectors so only the directions are plotted. If you click it again it changes to raw data signaling that it is plotting the original data again. - Bug fix: Variable DropList now adjust with new data sets being read. Thanks to John Wise for some of the added features like contour plots and particle plotting 2/00: Jaques 0.2r1 - This new version does not have some of the old bugs but surely some brand-new ones. bug reports to tabel@cfa.harvard.edu are very welcome. - Interpolation methods and also the no interpolation routine should be more stable now. Min Max values etc ... - you have now control over the min and max values to be plotted: just click on the button called 'MI MA' a small widget appears with the current min and max values. You can modify those and check the button 'static'. From then on these min max values will not be changed even if you create a new slice. Just click on the new REFRESH button to see the modified image. - Image rendering modified: if you click on the different interpolation buttons just the image will be re-rendered. I.e. data does not have to be read again. -> much faster ! - CHANGE: the FindMax button now sets the center and slice value to the point it found. -Added derived quantitites: PRESSURE, ENTROPY, and tangential velocity ('ANGULAR MOMENTUM') wrt the center. Let me know if you want something else to be included. - velocities are now always shown linear. HINT: If you click on View:Data Parameter File the editor will pop up and display the paraemter file which contains lines like DataLabel[3] = x-velocity #DataCGSConversionFactor[3] = 9.03571e+06 multiplying by this factor gives you the quantitiy in CGS units - Label of the displayed quantitiy is shown in colormap window. Tickmarks are larger. - Color Map legend has now a large font -> easier to read on transparencies. - Refresh button added. This just redraws the image and the color map - Dump Tiff function added for 24 bit true color displays and figures 5/9/99: Jaques.0.1.r3 - INTERPOLATED SLICES: are possible now and smoothing is hence obsolete. Various interpolations are possible. Try for best results. - VELOCITY FILEDS: You can now substract a velocity by simply picking a point in the visualization window. The reset button than allows to restore the original velocities. This is useful in order to visualize the velocities relative to a cetrain point. 4/16/98: Jaques.0.1 - IDL VERSION 5: From now on Jaques will only work with IDL version 5.xx. The few changes needed were due to some naming convention changes in version 5. PICKFILE -> DIALOG_PICKFILE, WIDGET_MESSAGE -> DIALOG_MESSAGE. - PEAKS: the philosophy of Jaques is now to have a bunch of points of interest, so called peaks. These peaks are specified in a file with default extension ".peaks". These files can be created, edited, and read from within Jaques. The file format is very simple. The first three columns specify the x,y, and z coordinate of the peak. Any additional column is not used by Jaques, but can be used to store some values at this peak. Any line containing a # is considered as comment line! - SMOOTHING: Jaques does now adaptive smoothing. The smoothing parameter specifiys over how many cell on a given level of refinement it will perform a boxcar average. Simply set it to 0 to switch of smoothing. - IMAGE STACK: The KEEP button allows to store the current image and the values used to create it in an IMAGE stack. This images can be retrieved again by pressing the buttons on top right of the main widget. Whenever you press the keep button the current image will be stored in image 1 and all other images in the stack will be pushed up by 1. - VELOCITY VECTORS: Jaques now knows to plot the velocity vectors on the given slice. Fromt the View Menu you can activate the widgets for velocity plotting. The read button must be used to read the velocity information. When Jaques constructes the velocity slice it uses the SMOOTHING parameter of the slicer. The plot button is used to display the velocity vectors. Click on the small vertical drawing area to change the color of the vectors. - ISO SURFACES: The iso surface tool can now do shading specified by a light source, or from the values of a different data set. This is I guess the most unstable and least debugged part of the code so far. Furthermore, jaques now can talk to SLICER3 the new iso-surface and slicing tool of IDL version 5. This is much better than IDL's old SLICER. - HDF_SD data: following enzo, Jaques now only supports HDF_SD data and not the old hdf_DSD format. - TOOLS: Now you can acces a text editor and a calculator from within Jaques. Also found in the TOOLS menu is XPALETTE which allows you to modify individual colors in the colormap. This might be useful when creating postscript files etc. - DATA VALUES (POINT OF INTEREST): Clicking on the main drawing window now displays (in the text widget) the x,y,z position, and the data value at that point. Note that the data value is simply taken from scaling the back the displayed color to the data units. Hence, the accuaracy of the information depends on the size of the color table. The string G100L4 indicates that the finest grid the specified point is in has the grid number 100 and level 4 of refinement. - INSIGHT: Jaques now knows how to interact with IDL's insight. Why is this useful? Sending image data to insight allows you to arrange multiple plots on one page, print them, create ".epsf" (encapsulated PS figure) files and do various other tranformations of the images. How do I use insight from within jaques? You can start up insight from the "Tools" menu. The "SNAP" pull down menu will become sensitive and allow you to send the image data of the drawing window and the color map either "separate" or as "combined" data to insight. For what to do with this data please see the idl online user guide and tutorials on insight.