VisIVOServer 2.1 User Guide Introduction
Contents
1. this is a commented line this is a commented line a An example of this file is the following for the pointproperty filter op pointproperty a valid filter code memsizelimit 30 this is a commented line resolution 16 16 16 points X Y Z field mass append true periodic true outcol NewColName out outFilename this is a commented line help true this is a commented line file inputFile bin NOTE 1 The parameterFile must contain the options with the same names reported in the following as options 2 Options with one or more parameters must be all specified after the sign in the same line ex field x Y Z 3 Options that do not require parameters must be given with true keyword ex append true VisIVO Filters Add Identifier This filter adds a new column with a sequence of Ids in the input data table Usage VisIVOFilters op addId outcol col_name start start_number help file inputFile bin Example VisIVOFilters op addId outcol PtId file inputFile bin The command produces a new column named PtId a sequence of tags starting from 0 Note start Starting Id Default value is 0 Only an int value can be given outcol Column name of the new id column Default name is Id file Input table filename VisIVO Filters AHFstep This filter executes the serial version of Amiga Halofinder v0 0 271 See t2. ngp The NGP algorithm is adopted out Name of the new table Default name is given gridOrigin It specifies the coordinates of the lower left corner of the grid Default values are assumed from the box of inputFile bin box It specifies the length of a box Default values is assumed from the box of inputFile bin if the gridSpacing option is not given gridSpacing It specifies the length of each cell dimension in the arbitrary unit This parameter is ignored if the box option is given Default values are assumed from the box of the inputFile bin periodic applies a periodical boundary condition file Input table filename VisIVO Filters Poca This operation creates a set of points and a volume starting from a VBT file that contains x y on four logical planes muon track reconstruction The z value on each plane is given as parametric value Usage VisIVOFilters op poca resolution x_res y_res z_res dimvox voxel_size trackplanedist distance innerdist distance outpoints points bin outvol vol bin help file inputFile bin Example 30 VisIVOFilters op poca resolution 600 300 300 dimvox 10 outpoins points outvol vol bin file inputFile bin Produces a points file VBT with scatter points inside the volume of reference a 60x30x30 and a multi volume The input file is a VBT with 10 columns that represent Event number X_A Y_B X_C Y_D X_E Y_F X_G Y_H 8 values coordinates in cm
3. field obsolete list Valid columns names of the input table delete Produces the output table excluding only field listed in the field option out Output table filename Default name is given file Input table filename VisIVO Filters Select Rows This operation creates a new table setting limits on one or more fields of a data table Optionally it creates a list of elements satisfying the requested condition Usage VisIVOFilters op selfield limits filename_limits operator AND OR outlist list_filename format uns int ascii out filename_out bin help file inputFile bin Example VisIVOFilters op selfield limits limitsfile txt operator AND out filename_out bin file inputFile bin 33 The limitsfile txt file must have the following structure A valid column name and an interval indicating the extraction limits X 20 0 30 0 Y 10 0 20 0 Z 0 0 10 0 The command produces a new table filename_out bin and filename_out bin head that contains all the data points of the inputFile table all columns will be reported where X 20 0 30 0 AND Y 10 0 20 0 AND Z 0 0 10 0 The unlimited word can be used to indicate the infinite value Note limits A file that has three columns a valid column name and an interval indicating the extraction limits operator Limits on all fields listed in limits option file are combined by default with logic AND operator If this option is given with O
4. out filename_out bin help file inputFile bin Example VisIVOFilters op swap override file inputFile bin data are swapped and overwritten Note override The same input table is swapped Data are overwritten out Name of the new table Default name is given Ignored if override is specified file Input table filename VisIVO Filters VBT2AHF This operation creates an Amiga halofinder v0 0 271 data file format serila version from six columns of a VisIVO table typically a snapshot of a cosmological simulation This operation needs some important parameters that must be given in an external parameter file It must contain the following data space separated np int number of elements 38 box double box size mass_frac double mass of each element vel_fact float factor to transform velocity field in Km sec omegaO lambda0O omegab gamma H_frac T_initial z_initial z_current double cosmological parameters numberOfTimesteps int header string header identifier Parameter file example 8000000 70 2 6773e 09 150 2 14e 1 7 42e 1 0 044 1 666 7 19e 1 1 e3 50 0 2 500 32ml_z0 2 More details on this parameter on the Amiga HF documentation Note for AMIGA HF users No DONT_KIK_ME EQ_MOT2 ART ISOLATED ISOLATED_P XDOT are included in this filter NOTE The filters is available only if the AHF option is used when compiling VisIVO Usage VisIVOFilters op v
5. NOTE The filters is available only if the AHF option is used when compiling VisIVO Usage VisIVOFilters op ahfhalolist field col_name multilist in_mutlist_File out out_multilist_file help file inputFile bin Example VisIVOFilters op ahfhalolist field Id multilist input AHF_particles out my_multilist Ist file sub_AHF_halos bin The command produces the my_multilist st file that has similar structure to the AHF_particles file produced by Amiga Note field Column name Default name is Id multilist Ascii filename with a multilist 12 out Output ascii filename with the extracted multilist file Input table filename VisIVO Filters Append Tables This operation creates e new table appending data from a list of existing tables Append Filter can append up to 100 tables with the same number of Columns Usage VisIVOFilters op append _ out filename_out bin help filelist table_list txt Example VisIVOFilters op append out out_table bin filelist tab_list txt tab_list txt is a file that contains a list of valid table names The bin extension is automatically added if the listed filename does not contain it home user tab1 bin home user tab2 bin home user otherDirectory tabN bin The filter produces a new table out_table bin and out_table bin head The column names are copied from the first table An error is given if tables contain different numbers of
6. an ASCII table of a selected field of the first number of rows or of all rows Show Volume writes on an output ascii file the volume cells and their values that satisfy given limits Sigma Contours creates a new table where one or more fields of a data table have values within N sigma contours Statistic creates and plots an histogram of a scalar field of a data table Split Table splits an existing table into two or more tables Swap swaps a table from big endian to little endian and viceversa VBT2AHF converts a table into the Amiga Halo Finder data file format Visual creates a randomized new table from an input table listing tables and columns with equal data size to be used with VisIVOViewer Write VOTable creates a VOTable using schema 1 2 from an input VBT NOTE from the subversion 1 1 VisIVOFilters incapsulate the Amiga Halo Finder code v0 0 271 serial version only It also includes the vbt2ahf filter that converts a VBT into the amiga data file format This data format can be used to execute the filter AHFstep or externally to execute the Amiga code VisIVO Filter on gLite systems VisIVO may be compiled on a gLite system In this case the option GLITE must be given to compile the tool The main purpose is to read a VBT from catalogue and or create a modified VBT in the catalogue When running on gLite system the option VO is to specify the virtual organization VO name 2 the input VBT file to be imported ca
7. and radius will have the value inva ue otherwise outvalue Usage VisIVOFilters op include center x_coord y_coord z_coord radius radius field x_col y_col z_col append out filename_out bin outcol col_name outvalue outvalue invalue invalue help file inputFile bin Example VisIVOFilters op iinclude center 1 0 1 0 1 0 radius 1 0 field X Y Z append outcol INOUT help file inputFile bin This command creates a new column in the input table Points inside the sphere center and radius are given will have the default inva ue equal to 1 0 Points outside the sphere will have the default outva ue equal to 0 0 Note center Coordinates of the sphere center radius Radius of the sphere field Three valid columns names Default values are the first three columns append No new table will be created The original table will have the new field out Name of the new table Default name is given Ignored if append is specified outcol Column name of the new field outvalue Value given to points outside the sphere Default value is 0 invalue Value given to points inside the sphere Default value is 1 file Input table filename 23 VisIVO Filters Mathematical Operations It is based on Function parser for C v2 83 by Warp http iki fi warp FunctionParser with some minor modifications The filter creates a new field in a data table as the result of a mathematical
8. at the planes of the system Pulse energy in GeV C The filter gives the track Id and the Energy of each points X Y Z This is the output of the Importer muportal It produces two tables points bin and vol bin containing The points of the POCA algorithm and angles 7 fields event number X Y and Z theta theta square energy A multi volume 7 volumes with cell resolution dimvox on each directiom Each voxel contatins quantities of all scattering points inside the voxel sum of the theta scattering angle sum of theta square theta square average sigma error and number of scatter points Note resolution 3D mesh size in cm Default value 600 300 300 dimvox Cubic voxel dimension in cm Default value 10 trackplanedist Distance in cm between planes 1 2 and planes 3 4 Default value 100 innerdist Distance in cm between planes 3 4 Default value 300 outpoints Name of the new table containing poca points outvol Name of the new table containing volumes file Input table filename VisIVO Filters Point Property This operation assigns a property to each data point on the table The operation performs the following 1 It creates a temporary volume using a field distribution CIC algorithm on a regular mesh The temporary file will have the filename given in out option _tempPDOp bin or _tempPDOp bin and it is automatically cleaned by the operation itself 2 It computes with the same C
9. information Option can be given to provide the NO number In this case the multi list file must not contain this informations but it is a multi list each list must contain NO elements If the onelist option is given the multi list file is only a sequence of rows to be extracted Multi list ascii file example 10 lt Number of lists must not be given if the numberlists option is specified 50 lt Number of elements of the first list must not be given if the listelemnts option is specified 1 lt Sequence of rows 50 forming the list 7 273 1005 23 35 lt Number of elements of the second list 2 lt Sequence of rows 35 forming the list 1006 145 15 Operation not allowed on volumes Usage 17 VisIVOFilters op extractlist multilist filename_list binaryint asciilist numberlists nl listelements nO onelist out filename_out bin help file inputFile bin Example VisIVOFilters op extractlist multilist mylist txt asciilist out list_extract bin file inputFile bin The multilist txt file has the following structure Number NL of lists NL sequences of 1 Number NO of elements in the list 2 NO element ids numbers of rows Multi list ascci file example 10 lt Number of lists NL 50 lt Number of elements NO of the first list 1 lt Sequence of rows NO 50 forming the list 35 lt Number of elements NO of the second list 2 lt Sequence of rows NO 35 for
10. operation fixes to a threshold column values included in an interval Usage VisIVOFilters op cut field columns_list limits filename_limits threshold value operator AND OR out filename_out bin help file inputFile bin Example VisIVOFilters op cut field A B C limits limitsfile txt operator AND out filename_out bin threshold 1 0 file inputFile bin The limitsfile txt file must have the following structure A valid column name and an interval indicating the extraction limits 15 X 20 0 30 0 Y 10 0 20 0 Z 0 0 10 0 The command produces a new table filename_out bin and filename_out bin head that contains all the data points and columns of the inputFile table In any row where X 20 0 30 0 AND Y 10 0 20 0 AND Z 0 0 10 0 the fields A B and C will be changed with the threshold value 1 0 Other fields will not be changed The unlimited word can be used to indicate the infinite value Note field it is a valid columns name list to be reported in the new table Default all columns will be reported limits A file that has three columns a valid column name and an interval indicating the extraction limits threshold Value to be used to cut data Default value is 0 0 operator Limits on all fields listed in the imits option file are combined by default with logic AND operator If this option is given with the OR value the field limits are combined with logic OR operator out Out
11. the new field Default options a new table with only the new field is produced outcol Column name of the new field out Name of the new table Default name is given Ignored if append is specified file Input table filename 24 As reported in the Function parser library function string is very similar to the C syntax Arithmetic float expressions can be created from float literals variables or functions using the following operators in this order of precedence 0 A unit A B A IA A B A B A B A B A B A amp B A B A B A B A lt B expressions in parentheses first a unit multiplier if one has been added exponentiation A raised to the power B unary minus unary logical not result is 1 if int A is 0 else 0 multiplication division and modulo addition and subtraction A lt B A gt B A gt B comparison between A and B result is either 0 or 1 result is 1 if int A and int B differ from 0 else 0 result is 1 if int A or int B differ from 0 else O Since the unary minus has higher precedence than any other operator for example the following expression is valid x y The comparison operators use an epsilon value so expressions which may differ in very least significant digits should work correctly For example 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 1 should always return 1 and the same comparison done with gt or lt should always return 0 Without epsilon this comparison p
12. values are assumed from the box of inputFile bin gridSpacing It specifies the length of each cell dimension in arbitrary unit This parameter is ignored if the box option is given Default values are assumed from the box of inputFile bin box It specifies the length of a box Default value is assumed from the box of inputFile bin if the gridSpacing option is not given periodic applies a periodical boundary condition file Input table filename with point distribution VisIVO Filters Interpolate This operation creates new tables from two existing data tables mainly used to produce intermediate frames of a dynamical evolution Usage VisIVOFilters op interpolate field columns_name numbin numberbin periodic interval from to out filename_out help infiles file_start bin file_end bin Example VisIVOFilters op interpolate field X Y Z numbin 20 periodic out mysequence infiles start bin end bin This command produces new tables mysequence_0O bin mysequence_1 bin mysequence_19 bin and the header files having only the three fields X Y and Z This Filter creates a file in the same directory of the out file VSInterpolatefilelist_time txt that lists all names on created files where time is the current time Limits The infiles tables must have the listed columns in the field option in the same corresponding order If Y is the second column of the start bin file the end bin file mu
13. 46 Floor of A Returns the largest integer less than A Rounds down to the next lower integer If int A differs from 0 the return value of this function is B else C Only the parameter which needs to be evaluated is evaluated the other parameter is skipped this makes it safe to use eval in them Rounds A to the closest integer 0 5 is rounded to 1 Natural base e logarithm of A Base 10 logarithm of A If A gt B the result is A else B If A lt B the result is A else B Secant of A equivalent to 1 cos A Sine of A Returns the sine of the angle A where A is measured in radians Same as sin but for hyperbolic sine Square root of A Returns the value whose square is A Tangent of A Returns the tangent of the angle A where A is measured in radians Same as tan but for hyperbolic tangent Examples of function string 1 2 x 1 sin sqrt x 2 y 2 sqrt XCoord xXCoord YCoord YCoord VisIVO Filters Merge Tables This operation creates a new table from two or more existing data tables Up to 100 tables can be merged Volumes can be merged but they must have the same geometry Usage VisIVOFilters op merge size HUGE SMALLEST pad value out filename_out bin help filelist table_param txt Example 26 VisIVOFilters op merge out out_table_file bin filelist tab_selection_file txt the tab_selection_file txt is a file that contain a list of tables and valid columns Wildc
14. IC algorithm the property for each data point considering the cells where the point is spread on the volume 3 It saves the property in a new table or adds the field to the original input table This operation cannot be applied to volumes Usage 31 VisIVOFilters op pointproperty resolution x_res y_res z_res points x_col y_col z_col field column_name constant value append out filename_out bin outcol col_name periodic help file inputFile bin Example VisIVOFilters op pointproperty resolution 16 16 16 points X Y Z field Mass append outcol distribute file inputFile bin The filter distributes the Mass field of points X Y Z and it produces a temporary volume Then it calculates a new field that for each X Y Z point representing the weight value of the nearest mesh cells where the point is distributed using the same CIC algorithm Note resolution 3D mesh size points Columns to be assumed for points coordinates field valid columns name list to be distributed in the grid constant Assign a constant value to all points to be distributed in the grid Ignored if field option is given Default value is a 1 0 for all points append the input table will contain the new field out Name of the new table Default name is given ignored if append is given outcol New field column name periodic applies a periodical boundary condition file Input table filename V
15. In the example shown in section 2 1 all X values then all Y values and so on Note n1 represents the number of columns fields in the VBT e g 6 n2 represents the number of elements of each field in the VBT e g 262144 GeoX GeoY GeoZ represent the number of the volumetric cells in each dimension of the mesh size used only for Volumes e g 64 64 64 DX DY DZ represent the size of each cell used only for Volumes e g 1 0 1 0 1 0 VisIVOServer VisIVO Filters VisIVO Filters are programs that convert data from an original data table internal data format table into a new one or can create a Volume from a table Filters are directly applied by the user using VisIVO Server Website the web procedure directly calls the filters when applicable GENERAL SYNTAX VisIVOFilters help produces a general help VisIVOFilters op operation help produces the help of a specific operation VisIVOFilters op operation lt options gt file InputFile runs the operation VisIVOFilters parameterFile runs the operation with options specified in the parameterFile Where requested the InputFile is a valid table Binary Internal data format In this case the InputFile bin and InputFile bin head must exist GLOBAL OPTIONS The following option can be given on any filter operation memsizelimit percentage_value This option reduces the memory request of the percentage value given with this option Depending on the spe
16. OFilters op extraction geometry geometry txt out pos_extracted bin file inputFile bin The geometry txt file must have four rows and two columns The first three rows have a valid column name and a value that indicates the extraction coordinates X 20 0 Y 20 0 Z 20 0 CORNER 10 0 The command produces a new table pos_extracted bin and pos_extracted bin head that contain all data points of the inputFile table all columns will be reported that are included in the box having the lower corner at X 20 0 Y 20 0 and Z 20 0 and size 10 0 Note geometry is a file name that contains three valid column names and a value for each column The fourth field means the extraction mode and the sub volume size RADIUS a sphere centered in the given values will be extracted CORNER a rectangular region having the lower corner at the given values will be extracted BOX a rectangular region centered in the given values will be extracted 19 Examples X 25 0 Y 25 0 Z 25 0 RADIUS 5 0 or X 25 0 Y 25 0 Z 25 0 BOX 5 0 or X 0 0 Y 0 0 Z 0 0 CORNER 10 0 out Name of the new table Default name is given file Input table filename VisIVO Filters Extract Subvolume This operation extract a table which is a sub volume from the original volume Usage VisIVOFilters op extractsubvolume _ startingcell X Y Z resolution x_res y_res z_res field column_names out filename_out bin help file inputFile bin Exam
17. R value the field limits are combined with logic OR operator out Output table filename Default name is given outlist Output list filename containing the numer of the element satisfying the requested condition Default name is given format Data format in the outlist filename Default value unsigned long long int file Input table filename VisIVO Filters Show Table This operation produces an ASCII table of the selected field of the first number of rows or of all rows Usage VisIVOFilters op showtable field column_name numrows num_of_rows rangerows fromRow toRow width format_width precision format_precision out filename_out txt help file inputFile bin Example VisIVOFilters op showtable field X Y Z numrows 100 out filename_out txt file inputFile bin produces an ascii file filename_out txt that contains the first 100 data points of the X Y and Z fields of the inputFile table Note field Valid columns names Default value of ALL columns will be reported 34 numrows Number of Rows in the Ascii output file Default value is equal to the number of Rows of the input table rangerows Rows range of the inputFile that will be reported in the ascii output file Default range is equal to all the rows of the input table It is ignored if numrows is specified width Field width in the ascii output file Default value is given Anyway a blank space is left between two co
18. VisIVOServer 2 1 User Guide Introduction Authors Becciani U Bandieramonte M Costa A Krokos M Massimino P VisIVO Server is a suite of software tools for creating customized views of 3D renderings from astrophysical data tables These tools are founded on the VisIVO Desktop functionality visivo oact inaf it and support the most popular Linux based platforms e g www ubuntu com Their defining characteristic is that no fixed limits are prescribed regarding the dimensionality of data tables input for processing thus supporting very large scale datasets VisIVO Server websites are currently hosted by the University of Portsmouth UK visivo port ac uk the INAF Astrophysical Observatory of Catania Italy visivo oact inaf it and in the near future by CINECA Italy visivo cineca it These web sites offer data management functionality for registered users datasets can be uploaded for temporary storage and processing for a period of up to two months The sites can also be utilized through anonymous access in which case datasets can be uploaded and stored for a maximum of four days to maximize available resources a limited dimensionality is only supported Assuming that datasets are uploaded users are typically presented with tree like structures for easy data navigation containing pointers to files tables volumes as well as visuals Files point to single or possibly several for distributed datasets astrophysical data tab
19. ard means all the columns of the given table tab1 bin Col_1 tab1i bin Col_2 tab5 bin Col_x tab4 bin This command produces a new table filename_out bin and filename_out bin head having columns Col_1 and Col_2 from tab1i bin Col_x from tab5 bin and all the columns of tab4 bin Note size SMALLEST default option Produce a new table having the size of the smallest table HUGE produces a new table having the size of the greatest table pad Pads the table rows of the smallest table with the given value if HUGE size is used Default value is 0 out Name of the new table Default name is given filelist obsolete file Input filename containing the table list VisIVO Filters Module This operation creates a new table or a new field computing the module of three fields of the input data table Usage VisIVOFilters op module field parameters append outcol colname out filename_out bin help file inputFile bin Example VisIVOFilters op module field Vx Vy Vz outcol Module append file inputFile bin This command appends a new field named Module to the inputFile bin file that represents the module of the fields Vx Vy and Vz sqrt Vx42 Vy 2 Vz 2 27 Note field Three valid columns name lists used to compute the module append No new table will be created The original table will have the new field Default options a new table with only the new field is produced outcol C
20. bt2ahf field columns_name par parfile out filename_out help file inputFile bin Example VisIVOFilters op vbt2ahf field X Y Z Vx Vy Vz par myFile par out outFile amg help file input bin produces yhe outFile amg file from X Y Z Vx Vy Vz fields of input bin file and considering the parameter file data Note field a valid list of columns names Default names X Y Z Vx Vy Vz are considered par A valid input parameter file out is the output amiga data format file Default name is given file Input table Typically a snapshot of a cosmological simulation VisIVO Filters 39 Visual This operation creates an eventually randomized new table from one or more input tables All the input tables must have the same number of rows The new table can be used with VisIVOViewer The operation cannot be applied to volume tables Usage VisIVOFilters op visualop size number_of_elements out filename_out bin help filelist tab_selection_file txt Example VisIVOFilters op visualop out filename_out bin filelist tab_selection_file txt The tab_selection_file txt is a text file that contain a list of tables and valid columns Wildcard x means all columns of the given table tab1 bin Col_1 tab5 bin Col_x tab4 bin bys tab1 bin Col_2 The command produces a new table filename_out bin and filename_out bin head having columns Co _i and Col_2 from tabi bin Col_x from tab5 bin and al
21. cific filter request and on the system where VisIVOFilters runs the allocated memory could exceed the available size and the application could be aborted or can use a significant portion of the system swap area with a dramatic lost of performance This parameter can be given to reduce the allocated space avoiding this effect A Warning message will be given when this option is used The allowed value is a float greater than O and lower than 95 0 NOTE The filters AHFstep AHF Galaxy Extraction AHF Halos List and VBT2AHF are available only if the AHF option is used when compiling VisIVO The following filter operations are available Add Identifier adds a column tag to a table AHFstep runs the serial version of Amiga Halofinder v0 0 271 AHF Galaxy Extraction extracts up to three multi lists from a multi list Designed for particles files of Amiga AHF Halos List extracts a multi list from a multi list Designed for particles files of Amiga Append Tables creates e new table appending data from a list of existing tables Cartesian2polar creates three new fields as the result of the polar transformation Change Column Name changes the column names in a table Coarse Volume produces a coarse sub volume with plane extraction from the original volume Cut sets to a given threshold column values included in a given interval Decimator creates a sub table as a regular subsample from the input table Extract List creates a new table
22. columns Note out Name of the new table Default name is given filelist obslote file An ascii file with a valid list of tables VisIVO Filters Cartesian2polar This operation creates three new fields in a data table as the result of the spherical polar transformation of three existing fields Usage 13 VisIVOFilters op cartesian2polar field X Y Z append outcol rho theta phi out filename_out bin file inputFile bin Example VisIVOFilters op cartesian2polar field X Y Z append file inputFile bin This command appends three new fields to the inputFile bin file that represent s the spherical polar transformation Note field Three valid columns name used as cartesian coordinates append No new table will be created The original table will have new fields Default options a new table with only the new field is produced outcol Column name of the new fields Default names are rho theta and phi out Name of the new table Default name is given Ignored if append is specified file Input table filename VisIVO Filters Change column names This operation changes the column names in an existing table Usage VisIVOFilters op changecolname field column_names newnames new_names help file inputFile bin Example VisIVOFilters op changecolname field X_r Y_r newnames X_n Y_n file inputFile bin This command changes the column names X_r into Xn and Y_r into Y_
23. creation when the input table has s large number of rows 1 Million out Output ascii filename Default name is given file Input table filename 41
24. e multiplied for the cell volume and assigned to the point If the density option is given the cell volume is assumed 1 3 It saves the property in a new table or adds the field to the original input table Usage VisIVOFilters op grid2point points x_col y_col z_col field column_name density append out filename_out bin outcol col_name tsc ngp help volume inputVolmeData bin gridOrigin xgO xg1 xg2 gridSpacing sgO sg1 sg2 box length periodic file inputFile bin Example VisIVOFilters op grid2point points X Y Z field Mass append volume myvolume bin outcol distribute file inputFile bin It adds a new column distribute to the inputFile bin table The filter distributes the Mass field of myvolume bin VBT to the points X Y Z using a CIC algorithm Note points Columns to be assumed for points coordinates field Valid Volume Column Name Default value is the first column name 21 density Cell volume is not considered cell volume 1 append No new table will be created The original table will have the new field out Name of the new table Default name is given Ignored if append is specified outcol Column name of the new field tsc The TSC algorithm is adopted ngp The NGP algorithm is adopted volume Input data volume filename a VisIVO Binary Table gridOrigin It specifies the coordinate of the lower left corner of the grid Default
25. ere only 10 of points that are inside this sphere will be reported in the output VBT 30 0 is the radius of the last sphere The value 0 01 is the percentage of randomization inside this sphere only 1 of points that are inside this sphere will be reported in the output VBT background 0 001 only 1 o9 of points that are outside the last sphere will be reported in the output VBT Note points columns to be assumed for points coordinates pos camera point coordinates Default value is the center of the domain geometry file that contains a radius and a randomization value 1 0 all values included 0 1 means 1 per cent of value included in the layer Each row of this file determine a layer A default geometry is created with three spheres and different levels of randomization depending on the input dataset background a randomization value for points outside the geometry Default value is fixed to have a maximum 100 000 points from input VBT out Name of the new table Default name is given file Input table filename VisIVO Filters Point Distribute This operation creates a volume using a field distribution CIC default or NGP or TSC algorithm on a regular mesh The filter produces by default a density field the field is distributed and divided for the cell volume Usage VisIVOFilters op pointdistribute resolution x_res y_res z_res points x_col y_col z_col field column_names constant value n
26. he Amiga HF documentation for more details NOTE The filters is available only if the AHF option is used when compiling VisIVO Usage VisIVOFilters op AHFstep help input AmigaParameterFile Example VisIVOFilters op AHFstep input myparFile par The command produces the following file prefix halos prefix mass prefix particles prefix profiles prefix substructure 10 containing the halos properties computed by the inputfile Note input A parameter file that has the following fields file with initial conditions filename in the Amiga halo finder data format See vbt2ahf filter prefix for output file names filename prefix number of domain grid cells 1D Nth for domain grid refinement criterion number of particles per cell on the domain grid 0 6 suggested values Nth for refinements refinement criterion number of particles per cell on all refinement grids 0 6 suggested values final redshift unimportant value for AHFStep dump step unimportant value for AHFStep total number of output files unimportant value for AHFStep Example out_8MI_0 3000_amg AMG8ML_out_z0 128 4 OOOO VisIVO Filters AHF Galaxy Extraction This filter is designed for Amiga particles file This file is a multilist of particles in halos The filter extracts particles and creates up to three multi lists It extracts up to three ascii multi lists from a general input ascii multilist following the Ids i
27. ill be saved in the output table But only the corresponding rows for the fie d selected columns are reported out Name of the new table Default name is given file Input table filename VisIVO Filters Statistic This operation produces average min and max value of field and creates an histogram of fields in the input table Usage 36 VisIVOFilters op statistic list columns_name histogram bin range min max out result txt help file inputFile bin Example VisIVOFilters op statistic list X Y histogram 1000 range 10 0 100 0 out result txt file inputFile bin produces min max and average values printed in stdout The command also produces a result txt file that gives the histogram values of X and Y in the range 10 0 100 0 with 1000 bins Note list A valid list of columns name Default value all columns histogram produces an histogram ascii file with a given number of bins If the bins number is not specified the default value is fixed to 10 of the total rows of the input table range produces the results only inside the specified interval out Output ascii filename with histogram file Input table filename An error is given if there are no data in the specified range VisIVO Filters Split Table This operation divides an existing table into two or more tables using a field that will be used to divide the table Usage VisIVOFilters op splittable field colu
28. isIVO Filters Randomizer This operation creates a sub table as a random subsample from the input table Usage VisIVOFilters op randomizer perc percentage field parameters iseed iseed out filename_out bin help file inputFile bin Example VisIVOFilters op randomizer perc 10 0 iseed 1 out filename_out bin file inputFile bin produces a new table filename_out bin and filename_out bin head of 10 percent size of the original inputFile Values are extracted in a random sequence Note perc Percentage from 0 0 to 95 0 of the input file obtained in the output file Note only the first decimal place is considered 32 field obsolete list Valid columns names of the input table Default all columns are included iseed Specifies the seed for the random generation Default value 0 out Output table filename Default name is given file Input table filename VisIVO Filters Select Columns This operation creates e new table using or excluding one or more fields of a data table The default case produces the output table including only listed fields Usage VisIVOFilters op selcolumns field parameters delete out filename_out bin help file inputFile bin Example VisIVOFilters op selcolumns field X Y out filename_out bin file inputFile bin produces a new table filename_out bin and filename_out bin head with only X and Y columns of inputFile Note
29. l the columns of tab4 bin If the row number of the input tables exceeds 8000000 elements the output file will be limited to 8000000 randomized sampled rows The column names in the output table will have the suffix _visual_ where represent the number order listed in the txt file The output VBT will contain the columns of the listed tables in alphabetic order In the above example the header of the VBT if tab4 bin contains two columns A and B and there are 8000000 rows will be float 5 8000000 little Col_1_visual_1 Col_2_visual_5 A_visual_3 B_visual_4 Col_x_visual_2 Note size Number of max rows in the output table Default is the minimum between 8000000 rows and the rows of input tables The input tables must have the same number of rows out Output table filename Default name is given filelist obsolete file Input text file with a list of tables and columns 40 VisIVO Filters Write VOTable This operation produces a VOTable 1 2 with selected field Usage VisIVOFilters op wrvotable field column_name force out filename_out xml help file inputFile bin Example VisIVOFilters op wrvotable field ra dec u out votable_out xml file inputFile bin produces a VOTable votable_out xml that contains data of ra dec and u fields of the inputFile table Note field Valid columns names Default values of ALL columns will be reported force Must be given to force the VOTable
30. les Tables are highly efficient internal VisIVO Server data representations they are typically produced from importing datasets uploaded by users using VisIVO Importer see below Volumes are internal VisIVO Server data representations they are produced either from direct importing of user datasets or by performing operations on already existing tables Visuals are collections of highly customized user produced views of 3D renderings of volumes VisIVO Server consists of three core components VisIVO Importer VisIVO Filter and VisIVO Viewer respectively Their functionality and usage is described in the following sections To create customized views of 3D renderings from astrophysical data tables a two stage process is employed First VisIVO Importer is utilized to convert user datasets into VisIVO Binary Tables VBTs Then VisIVO Viewer is invoked to display customized views of 3D 1 renderings AS an example consider displaying views from only three columns of an astrophysical data table supplied in ascii form say col_1 col_2 and col_3 by using the commands VisIVOImporter fformat ascii UserDataSet txt VisIVOViewer x col_1 y col _2 z col_3 scale glyphs pixel VBT bin VisIVOServer is distributed with GPL V 2 License for NON COMMERCIAL use VisIVOServer is hosted by sourceforge https sourceforge net projects visivoserver and its source code is downloadable via svn svn co https visivoserver svn sourceforge net s
31. ming the list 1006 145 15 The command produces a new table ist_extracted bin and list_extracted bin head that contain all data rows of the inputFile table all columns will be reported that are included in the multi list file Note multilist is the multi list file name binaryint The default multi list file format is binary unsigned long long int If this parameter is specified the file is binary int asciilist The multi list file format is binary If this parameter is specified the file is an ascii text numberlists The multi list file format is just a sequence of nl lists specified in this option Each list starts with the number of elements in the list 18 listelements The multi list file format is just a sequence of nl lists Each list has the same number of nO elements This option requires that the numberlists option is specified otherwise it is ignored onelist If this option is given the multi list file is considered as only one list Each element is the ID of the particle to be extracted The numberlists and listelements options will be ignored out Name of the new table Default name is given file Input table filename VisIVO Filters Extract Subregion This operation creates a new table from a sub box or a sphere Operation not allowed on volumes Usage VisIVOFilters op extraction geometry geometry_file out filename_out bin help file inputFile bin Example VisIV
32. mn volumesplit direction numoftables numberOfTable maxsizetable MaxMbyteSize hugesplit out filename_out bin help file inputFile bin Example VisIVOFilters op splittable field X numoftables 10 out filename_out file inputFile bin This command will compute the X range e g range 0 100 and will produce 10 tables where the X range will be 0 10 10 20 20 30 and so on Note filed A valid column name along which the table will be split Must be given to split a table volumesplit Direction 1 2 or 3 along which the volume will be split Must be given to split a volume numoftables give the number of tables in which the input table will be split It must be greather than 1 37 maxsizetable indicates the maximum size of the split table in MegaBytes VisIVO Filter will compute how many tables will be created This option is ignored if numoftable option is given hugesplit Must be given to force the generation of more than 100 tables from the input table avoiding errors out Output prefix root table filename A suffix _split_ bin is added to each generated table to this prefix Default name is given file Input table filename VisIVO Filters Swap This operation produces the Endianism swap little Endian to big Endian data format and viceversa of a VisIVO Binary Table It can produce a new swapped table or data can be overwritten Usage VisIVOFilters op swap override
33. n a given input table and using the threshold value given in the select value NOTE The filters is available only if the AHF option is used when compiling VisIVO Usage VisIVOFilters op ahfhalogalaxyext field col1 col2 col3 multilist in_mutlist_File threshold value out out_multilist_file help file inputFile bin 11 Example VisIVOFilters op ahfhalogalaxyext field Id1 Id2 Id3 multilist input AHF_particles out my_multilist Ist file sub_AHF_halos bin The lists are extracted my_multilist Ist_Id1_particles where Id1 gt 1 0 my_multilist Ist_Id2_ particles where Id2 gt 1 0 and Idi lt 1 0 my_multilist Ist_Id3_ particles where Id3 gt 1 0 and Idi lt 1 0 Id2 lt 1 0 from input AHF_particles The threshold value 1 0 default can be changed with the specific option Id1 Id2 and Id3 must be valid column name Note field Up to three column names Default name is Id multilist Ascii filename with a multilist threshold Selector value among the three columns Default Value 1 0 out Output ascii root filename with a multilist file Input table filename VisIVO Filters AHF Halos List This filter is designed for Amiga particles file This file is a multi list of particles in halos The filter extract some lists and creates a new multi list It reads a column from an input table with Ids integer positive values that represents the list to be extracted from the input multi list file
34. n be a logical filename Ifn and must start with lfn 3 the output VBT can be local out option or the output Ifn can be given But in any case the out is the local filename where a temporary VBT will be created 4 lfnout is the output logical filename In this case a VBT will be saved in the grid catalogue and deleted from local filesystem 5 the option se is to specify the Storage Element SE The following options can be applied to all filters VO value optional is used to set the virtual organization VO when running on gLite grid It is mandatory when running on gLite using catalogue se value optional is used to set the Storage Element SE when running on gLite grid Default value is DPM_HOST site default storage element lIfnout value optional is used to set the logical filename lfn when running on gLite grid VisIVO Filters ParameterFile All the following listed filters contain the op code and options The code and all the options can be given in a parameterFile Lines starting with are comments An example of this file is the following for the mathop filter op mathop a valid filter code memsizelimit 30 this is a commented line expression myexp txt this is a commented line compute A B C No escape and special lt lt gt gt characters mut be given append true outcol NewColName out outFilename help true file inputFile bin
35. n in the inputFile table Note field Valid columns names newnames Valid new columns names file Input table filename VisIVO Filters 14 Coarse Volume This operation produces a coarse sub volume with plane extraction from the original volume Usage VisIVOFilters op coarsevolume perc percentage newres x_res y_res z_res field column_names out filename_out bin help file inputFile bin Example VisIVOFilters op coarsevolume perc 10 0 field Mass Temperature out subvolume bin file inputFile bin produces a new table subvolume bin and subvolume bin head It is a volume of 10 percent of the original volume If the original volume is a mesh of 320x320x640 the output volume will be 32x32x64 and only the listed fields Mass and Temperature will be considered Planes are extracted from the original volume as a regular distribution from the original mesh Note perc A percentage from 0 0 to 100 0 sub volume_ will be produced Default value produces a sub volume that could be directly uploaded and visualized with VisIVOViewer and VisIVODesktop applications field List of columns contained in the original file Default all columns will be extracted newres A sub volume with new resolution will be produced No default is given This parameter is ignored if perc option is given out Name of the new table Default name is given file Input table filename VisIVO Filters Cut This
36. nsecutive ascii numbers precision Field precision in the ascii output file Default value is given out Output ascii filename Default name is given file Input table filename VisIVO Filters Show Volume This operation writes on an output ascii file the volume cells and their values that satisfy given limits Usage VisIVOFilters op showvol field column_name limits filename_limits operator AND OR numcells value out filename_out txt help file inputFile bin Example VisIVOFilters op showvol field density mass limits limitsfile txt operator AND out filename_out txt file inputFile bin produces an ascii file that lists all cells where limits are satisfied The limitsfile txt file must have the following structure A valid column name and an interval indicating the extraction limits density 20 0 30 0 mass 10 0 20 0 The keyword unlimited can be used to indicate the infinite value The output ascii file will report on each row the cell X Y and Z and the field value Note field Valid columns names Default value of ALL columns will be reported limits A file that has three columns a valid column name and an interval that indicate the limits operator Limits on all field listed in the imits option file are combined by default with logic AND operator If this option is given with OR value the field limits are combined with logic OR operator numcells Set the maximum numbe
37. odensity tsc ngp out filename_out bin gridOrigin x0 yO z0 box length gridSpacing sgO sg1 sg2 periodic avg help file inputFile bin Example 29 VisIVOFilters op pointdistribute resolution 16 16 16 points X Y Z field Mass Temperature out filename_out bin file inputFile bin It produces a new volume table filename_out bin and filename_out bin head on a 16x16x16 mesh using x y and z as point coordinates The filter distributes the Mass and the Temperature elements of points X Y Z Only the Mass and Temperature fields will be reported in the new table as a density field Note resolution 3D mesh size points Columns to be assumed for points coordinates field valid columns name list to be distributed in the grid constant Assign a constant value to all points to be distributed in the grid Ignored if field option is given Default value is a 1 0 for all points nodensity Overrides the default behaviour The field distribution is not divided for the cell volume avg Distributes the first field on the volume grid and computes the arithmetic average value on each cell of the first field The output volume table will have three fields For each cell there will be the number of total elements in the cell NumberOfElements the sum of total field value fieldSum and the arithmetic average value fieldAvg Only the ngp algorithm will be applied tsc The TSC algorithm is adopted
38. olumn name of the new field out Name of the new table Default name is given Ignored if append is specified file Input table filename VisIVO Filters Multi resolution This operation creates a new VBT as a random subsample from the input table with different resolutions Starting from a fixed position that represent the center of inner sphere concentric spheres are considered Different level of randomization can be given creating more detail table in the inner sphere and lower detail in the outer regions or vice versa The region that is external to the last sphere represents the background Usage VisIVOFilters op mres points x_col y_col z_col pos values geometry layer_file txt background vaule out filename_out bin help file inputFile bin Example VisIVOFilters op mres points X Y Z pos 10 0 10 0 10 0 geometry layer txt background 0 0001 out pos_layer bin file pos bin produces a new table pos_ ayer bin and pos_layer bin head The pos parameter specify the center of the spheres The geometry file ayer txt in this example has the following values 28 5 0 1 0 10 0 0 1 30 0 0 01 5 0 is the radius of the inner sphere The 1 0 is the percentage of randomization inside the inner sphere all points that are inside the inner sphere will be reported in the output VBT 10 0 is the radius of the second sphere The value 0 1 is the percentage of randomization inside this sph
39. operation between the existing fields Usage VisIVOFilters op mathop expression math_expression txt compute lt lt expression gt gt append outcol col_name out filename_out bin help file inputFile bin Example VisIVOFilters op mathop expression my_expression txt outcol SqrMod out SqrModTable bin file inputFile bin my_expression txt is a file that contains only one row with a mathematical expression sqrt VelxX VelX VelY VelY VelZ VelZ being VelX VelY and Ve Z columns name listed in inputFile bin head The command produces a new table SqrModTable bin and SqrModTable bin head with only one column called SqrMod having the same length of the columns of the inputFile bin table Note A new field is produced expression A file with only one row having any valid mathematical expression with Valid Column names Ignored if compute option is given compute A valid mathematical expression with Valid Column names The expression must start with lt lt and finish with gt gt characters It has the priority on the expression option The expression must contain the escape character control for the lt lt and gt gt symbols and the parentheses To evaluate A B C the correct syntax will b compute lt lt A B C gt gt NOTE the lt lt gt gt and escape characters MUST NOT BE GIVEN if the parameter file is used append No new table will be created The original table will have
40. ple VisIVOFilters op extractsubvolume startingcell 8 8 8 field Mass Temperature resolution 16 16 16 out mysubvolume bin file inputFile bin produces a new table volume mysubvolume bin and mysubvolume bin head that is a sub volume of resolution 16x16x16 from the original volume and starting from the cell 8 8 8 of the original mesh Only Mass and Temperature fields will be reported in the new table Note startingcell X Y Z number of the first cell to be extracted O 0 0 is the first cell of the original grid 20 resolution Grid size 3D of the new subgrid field Valid columns name list to be reported in the new table out Name of the new table Default name is given file Input table filename VisIVO Filters Grid2Point This operation distributes a volume property to a point data set on the same computational domain using a field distribution CIC NGP TSC algorithm on a regular mesh CIC is the default adopted algorithm The Cell geometry is considered only to compute the cell volume value in this operation This filter produces a new table or adds a new field to the input table The operation performs the following 1 It loads a volume input volume data table and a table with a point distribution in the same volume 2 It computes using a CIC or NGP or TSC algorithm a value assumed density for each data point considering the cells value where the point is spread The grid points density values ar
41. put table filename Default name is given file Input table filename VisIVO Filters Decimator This operation creates a sub table as a regular subsample from the input table Usage VisIVOFilters op decimator skip step out filename_out bin help file inputFile bin Example VisIVOFilters op decimator skip 9 out inputFile_samp bin file inputFile bin produces a new table filename_out bin and filename_out bin head having a 10 percent size of the original inputFile Values are extracted in a regular sequence skipping step element every time The skip value is an integer number gt 1 and represents the number of skipped values In the above example only one element every 10 elements will be reported in the output file The output table must fit the available RAM Note skip Integer representing the skipped values 16 out Name of the new table Default name is given file Input table filename VisIVO Filters Extract List This operation creates a new table from an input table with the elements rows listed in a given multi list file The filter extracts rows from a data table A multi list is given in ascii or binary format unsigned long long int The multi list has the following structure Number NL of lists NL sequences of 1 Number NO of elements in the list 2 NO element ids numbers of rows Option can be given to provide the NL number In this case the multi list file must not contain this
42. r of cells that will be reported in the output out Output ascii filename Default name is given file Input table filename 35 VisIVO Filters Sigma Contours This operation creates a new table where one or more fields of a data table have values within or outside N sigma contours The filter can be applied on fields that have a Gaussian distribution For the selected fields the filter prints in the stdout the average and the sigma values of the distributions Usage VisIVOFilters op sigmacontours nsigma nOfSigma field columns_list allcolumns out filename_out bin help file filename bin Example VisIVOFilters op sigmacontours nsigma 2 field F1 F2 F5 allcolumns out ncontours bin file example bin The command produces a new table where columns F1 F2 and F5 have all of them values included in 2 sigma contours The option al lcolumns creates a new table with all the columns of the input table otherwise only F1 F2 and F5 will be reported in the output table The command also prints in the stdout the average values and the sigma values for F1 F2 and F5 columns nsigma Number of sigma used in the variable selection Default value 1 sigma countour field List of columns that must have values within N sigma contours Default value all the columns in the table lt lt std endl exclude Values outside N sigma contours will be reported allcolumns All columns of the input tables w
43. robably returns the wrong value abs A acos A acosh A asin A asinh A atan A atan2 A B atanh A ceil A cos A cosh A cot A csc A Absolute value of A If A is negative returns A otherwise returns A Arc cosine of A Returns the angle measured in radians whose cosine is A Same as acos but for hyperbolic cosine Arc sine of A Returns the angle measured in radians whose sine is A Same as asin but for hyperbolic sine Arc tangent of A Returns the angle measured in radians whose tangent is A Arc tangent of A B The two main differences to atan is that it will return the right angle depending on the signs of A and B atan can only return values betwen pi 2 and pi 2 and that the return value of pi 2 and pi 2 are possible Same as atan but for hyperbolic tangent Ceiling of A Returns the smallest integer greater than A Rounds up to the next higher integer Cosine of A Returns the cosine of the angle A where A is measured in radians Same as cos but for hyperbolic cosine Cotangent of A equivalent to 1 tan A Cosecant of A equivalent to 1 sin A 25 exp A floor A if A B C int A log A log10 A max A B min A B sec A sin A sinh A sqrt A tan A tanh A Exponential of A Returns the value of e raised to the power A where e is the base of the natural logarithm i e the non repeating value approximately equal to 2 718281828
44. st contain Y as the second column The input tables must have the same number of rows and the interpolated elements are considered in the same order No index is currently supported Note field obsolete list a valid list of columns names that must exist on both input tables Default all columns in infile files are considered 22 numbin is the number of bins between the file_start bin and the file_end bin input files or the interval given in the interval option The default value is 10 The number of created tables is equal to numberbin 1 periodic applies a periodical boundary condition interval VisIVO assumes a distance of 1 0 between the two input frames file_start bin and file_end bin This option produces the intermediate frames tables in a subinterval between the two input frames The value 0 5 is the medium point of the interval If the from value is lower than 0 0 it is considered 0 0 If the to value is lower than 1 0 it is considered 1 0 If the from value is equal to to value the operation is not performed Default value from 0 0 to 1 0 out is the root name of the new tables The default name is given The new name is given by the filename_out bin where is the number of created tables infiles contains the names of the input tables of the interpolation process VisIVO Filters Include This operation produces a new table or adds a new field to the input table Points inside the sphere given with center
45. vnroot visivoserver branches 1 2 visivoserver Disclaimer user data integrity is never warranted VisIVO BINARY TABLE A VisIVO Binary Table VBT is a highly efficient data representation used by VisIVO Server internally A VBT is realized through a header file extension bin head containing all necessary metadata and a raw data file extension bin storing actual data values For example the header may contain information regarding the overall number of fields and number of points for each field for point datasets or the number of cells and relevant mesh sizes for volume datasets The raw data file is typically a sequence of values e g all X followed by all Y values Header The header file contains the following fields float double nl n2 GeoX GeoY GeoZ DX DY DZ little big X Y Z Vx Vy Vz float double is the data type of the storage variables used n1 denotes the number of columns fields in the VBT n2 denotes the number of rows in the VBT GeoX GeoY GeoZ DX DY DZ are employed only if the VBT represents volumetric datasets In that case GeoX GeoY and GeoZ represent the mesh geometry while DX DY and DZ represent the x y and z size of volumetric cells little big denotes the endianism employed in the VBT After this field there exist n1 rows that indicate the VBT columns as positions X Y Z and velocities Vx Vy Vz Raw The binary file is simply a sequence of n1 n2 values
46. with the element of input table listed in a separate file Extract Subregion creates a new table from an input table of a sub box or of a sphere Extract Subvolume produces a table which represents a sub volume from the original volume Grid2Point distributes the values of an input grid to a point distribution in the same domain using the NGP CIC TSC algorithm Interpolate creates new tables from two existing data tables with a linear interpolation Include assigns a different offset value to points inside and or outside a sphere in the domain Math Operations creates a new field in a data table as the result of a mathematical operation between the existing fields Merge Tables creates a new table from two or more existing data tables Module creates a new table field computing the module of three fields of the input table Multi resolution creates a new table using different levels of randomization inside a dataset Poca creates a set of pointsand a volume starting from data plane Support to the Muon portal Project Point Distribute creates a volume using a field distribution CIC NGP TSC algorithm ona regular mesh Point Property assigns a property to each data point on the table Randomizer creates a random subset from the original data table Select Columns creates a new table using one or more columns of a data table Select Rows creates a new table using limits on one or more fields of a data table Show Table produces
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