User Guide for bean (1D and 2D data processing) G. Hoffmann-Schulz, M. Fromme Version 7 July 2018 2 User Guide for bean bean (BEnsc ANalysis) is dedicated to the analysis of experimental data gathered at BENSC. A detailed description of the program concepts is given elsewhere *. bean is written by means of the PV-WAVE (Visual Numerics) command language Version 11.0 bean can be executed on any UNIX computer (Linux) within the Helmholtz-Berlin intranet. The data may reside on any computer accessible via NFS. A Windows version is available, with a detailed description at: https://www.helmholtz-berlin.de/zentrum/locations/it/software/auswert/exaus_de.html For downloading the bean Windows version, including the BEAN_WIN32.pdf and all needed files, call the following web address: https://www.helmholtz-berlin.de/media/media/angebote/it/auswertesoftware/bean.zip The BENSC guests may obtain ** bean software in conjunction with a PV-WAVE license in order to use this program at their home institute. This program is suited as well for the analysis of one-dimensional data of arbitrary scalar value type as for image processing and analysis of two-dimensional data. bean treats these data as workspaces. A workspace comprises: one-dimensional data: x array of values, generally like TTHS y array of intensities, dy array of statistical errors,... or two-dimensional data: 2D array of intensities and meta data: time of measurement, title strings, and more parameters of physical nature. Workspaces may be read from data files of various formats, like ASCII files, HDF/NEXUS formatted files, and CARESS experimental data files. A file may contain one data set or maybe more of them. The workspaces have default names like E61477_000 for the first spectrum from data file E61477.dat. Workspaces may be used as objects for arithmetic operations (+ - * /....) and methods (merge, fit,..). The two dimensional data may be read of various formats, like PCBAS Image, Fit2D Image, Fuji Image, HDF Image, DC 8 Bit data, DC 24 Bit data, SANS data ASCII intensities, XYZ ASCII, and CARESS files. bean is easy and intuitive to use. The bean graphical user interface (GUI) has a strong resemblance to windows programs in the commercial domain. __________________________________________________________________________ * M. Fromme1, G. Hoffmann-Schulz1, E. Litvinenko2, and P. Ziem1, ”BEAN - A New Standard Program for Data Analysis at BER-II”, IEEE. Trans. Nucl. Sci., 47-2, 272 (2000) 1Helmholtz- Zentrum Berlin, Lise Meitner Campus , 2Frank Laboratory of Neutron Physics, JINR, 141980 Dubna, Russia ** To get the PV-WAVE Software see at Appendix B. 3 The bean GUI comprises: • the bean Spectrum Processing window for data visualization and manipulation • the bean 2D Spectrum Processing window for two dimensional data image processing and analysis • the bean Select window for workspace (WS) selection • the bean Command Manager window for commands input • the bean Fit Dialog window • the bean Peak Analysis window • modal dialog windows like the File Selection window • pop up - menu windows • The Other View for pure data display, like waterfall plot, for 2D, like surface, contour, shadow surface, color image and projection windows A typical data analysis session 1. Read from single or multiple files to workspace(s). 2. Display a workspace or multiple workspaces. (bean Spectrum Processing window, or The Other View window for waterfall plots) 3. Correct erroneous data interactively (cutting ranges on display, eliminating spikes). 4. Merge workspaces. 5. Identify the background (fit/function) and subtract the background from workspaces. 6. fitting of data (Gauss or Lorentz fit function). 7. Save workspaces after data reduction for further processing. First steps Use Linux PC or a PC with MS Windows and XWin32/ VncViewer. Login to a UNIX computer at the Helmholtz-Berlin domain like, dinux6(Linux), dinux7(Linux). Set the display environment variable to your X terminal, if that has not been done automatically. setenv DISPLAY name/address: 0.0 Start bean from the command shell bean The main window bean Spectrum Processing with a smiling ‘Mr. Bean’, and Workspace Selection window (bean Select) appear. 4 The bean Spectrum Processing window This main window is used to initiate the various stages of data analysis and display. You start a session by reading a data file, like shown here. The file menu (pop up window) has been selected by clicking on the File button item of the main menu bar. Within the Read sub menu the Caress data type has been selected. In this special case the input file has several data sets. Hence the 4 parts of file data become separate workspaces (E64968_000,.._001, .._002, .._003). After reading the total input file the last data set is displayed in the main drawing area. The current cursor position is indicated below the plot at the left side. The current workspace name shows up in the middle. At the right side the interaction mode, Zoom, Fit Peak or Points, is displayed. In the following a short description of the pop up menus is given which can be invoked pressing the buttons of the bean main menu bar. Hint: The size of the bean Spectrum Processing window can be changed by selecting the ^ symbol or at each position at the frame of the window. 5 The bean main menu bar • File Quick Read Reading of workspaces with the file browser may be time consuming, if directories have many file entries. Read (Browser) HDF (Hierarchical Data File) CARESS Several CARESS data files, with the same prefix name and a range of consecutive file numbers like the 10 files e614961.dat to e614970.dat, can be read separately, as sum, or merged to one workspace. If polarization modules are set, they can be read separately or Pol to one workspace. Modal dialog windows do these selections. If the number of scan steps > 1, they can be read Read 1D->2D to one workspace and the data are displayed at bean 2D Spectrum Processing window. Include the CARESS file an array (ADET) detector data, an input data window Filename Range Selection window comes to alive. (See next page for detailed information.) These files can be read as Integration ADET. (see also Menu Option ADET options ) At reading ADET data an integration of data is executed. Additional: set Calibration to On/Off and/or set Integration and merge to On/Off at the same time: Means two input modes can be used, an ADET data is read to merge ADET data(2D) and to integrate data(1D). If integration is set, additional a MSK workspace is defined. XYDY ASCII ASCII data with either one (y), two (x,y), or three (x,y,dy) columns of data can be read. 2D ASCII Several ASCII 2D data with the same prefix name and a range of consecutive file numbers like the 10 files E662840_D2_003 to E662840_D2_009, can be read. Options (see Menu Option) load used file ~/.bean After data input the workspace names are listed at the bean Select window. Preview (Browser) The contents of a data file (HDF, NeXus, CARESS) is listed on a text window with the options Save, Print, Dismiss and Read to input the data file as simple/one File or comfortable. Save (Browser) Data, workspaces, options, or input points may be stored as HDF, (xy) ASCII, (xydy) ASCII , Full ASCII (completed workspace) or Options data files. Quick Save Saving of workspaces with the file browser may be time consuming. The directory name may be text edited and has a default from the option file. Default Printer A printer name can be chosen as default printer, or the postscript file mode can be selected. Print The current plot, Main View or other View, can be printed on the selected printer. Exit bean will be terminated. 6 Filename Range Selection window Directory: The current directory path of the Caress data file. Filenname part: The current file name. Generally the type of Caress data: par example: e From file number: The beginning number of range value. To (max. 931604): The digit of last reading file. The max. information informed about the last of possible setting entry. The first entry is like the same at the 'From file number' entry. Now the user can be set a number in a valid range. Extension: The extension of the Data files. par example: .dat Read separate: For each scan step and each detector of each Caress data files separated workspaces will be defined. par example: E931476_D1_000 Read + sum: Summation to one workspace. Read + merge: The data files can be read to one merged workspace in each case. Read + merge: The data files can be read to merged worspaces, each include data of the (same patern, DET) separated detector data. par example: E931477_D1 to E931477_D8 Integration ADET: Include the Caress files an array (ADET data), an integration is executed (Def. ADET Options) after reading. The options of the integration can be set or changed at menu Options/ ADET Options. For each file a nnn_DEQ or nnn_NEQ or nnn_CNE or nnn_EQ or nnn_NEQ (depending of the integration type) and a nn_MSK workspace will be defined. Read meta data: The Caress file will be read to a workspace, which includes (only meta) only the meta data. The workspace is defined as nnn_ALLMETA. par example: E931477_ALLMETA After reading a Tab Info window (Column Selection) comes to alive. The user can select single meta data to get a table of separated values. 7 Additional some modes can be set at the same time: Calibration ON/OFF: The current calibration path must be set at the Options/Edit Options. In case of ON three modes are available to set calibration files: I) Select one date of calibration file list: If calibration files with the following file name notations are exist, an option list with the current dates is defined.