inspire A Users Guide integrated Software Platform for Interactive REview Version Mar. 2018

Transcription

1 inspire integrated Software Platform for Interactive REview A Users Guide Version Mar CTBTO/ IDC Division/ Software Applications Section

2 Document Version History: Version Date Author Comments / main reason(s) for baseline changes Abdelhakim Gheddou, Radionuclide Officer, Software Integration Unit, Software Applications Section, International Data Centre Division CTBTO Preparatory Commission Tel.: (+43 1) Abdelhakim.Gheddou@ctbto.org First version for training and testing purposes. Implemented functionality: betagamma coincidence Noble Gas Abdelhakim Gheddou Added sections for two new features: - Energy calibration check and update; - Isotope removal. Updated sections: - Sample metrics flag panel; - Spectrum display window; - Analysis results Abdelhakim Gheddou Removed ABGAM related sections. Refactored the structure. Added sections for two new features: - Data assignment; - Revoking a sample release. Page 2 of 23

3 Table of Content 1. Introduction Login to the database Analysis Workflow Options for spectrum selection Using the assignment queue Browsing from the database Data Assignment Loading a specific spectrum Interactive Analysis Features Spectrum Information QC Flags panel Spectrum display Analysis Results Calibration window Removing a false detection Reprocessing window Sample Spectrum Release Release Options Revoking a Release List of Figures Figure 1: Database connection window... 5 Figure 2: Sample assignment queue... 6 Figure 3: Analysis workflow toolbar... 6 Figure 4: Data selection from assignment queue... 7 Figure 5: Data selection window... 8 Figure 6: Spectra assignment feature... 9 Figure 7: Loading sample_id Figure 8: Spectrum information panel Figure 9: Quality check panel MDC of Xe-133 and SOH flag Figure 10: Beta-gamma coincidence histogram Figure 11: NCC analysis results Figure 12: Gamma and beta energy calibration window Figure 13: Analysis results before isotope removal Figure 14: Analysis results after isotope removal Figure 15: Categorization summary after isotope removal Figure 16: Data reprocessing window Figure 17: General comment editor Figure 18: Spectrum release window Figure 19: Spectrum revoke window Page 3 of 23

4 1. INTRODUCTION The CTBTO International Data Centre is in the process of developing a new software application for Radionuclide data analysis. The new tool is baptized inspire, an acronym for integrated Software Platform for Interactive REview. The aim is to complete the migration to open source of the radionuclide software in use at the IDC within the operational interactive review raw spectral data from the International Monitoring System (IMS). Both particulates stations and Noble Gas systems are handled by inspire. The tool is intended for the interactive review of automatic processing results as generated by automatic software applications of the Radionuclide pipeline. inspire is a python language/ Qt framework as a widget toolkit based license-free application. It runs on Linux Operating System under the standard configuration IDC environment (file system structure and database schema of the Radionuclide pipeline). inspire provides relevant features and dedicated functionalities to Analysts to check the data quality, perform the standard interactive review and introduce necessary corrections to automatic processing results as appropriate. In addition to sample spectra analysis, the GUI is also used to interactively check all auxiliary spectral data (gas and detector backgrounds, Quality Control, calibration, blank and spike spectra). inspire software allows assignment of spectra to individual users with required roles and permissions as configured in the database. Interactive changes are only allowed when the spectrum is assigned to the current user. The current User s Guide provides a functional description of inspire software application. This first version 1.0.0, dedicated to beta-gamma coincidence based Noble gas data, is mainly intended for testing and training purposes. Page 4 of 23

5 2. LOGIN TO THE DATABASE Upon launching inspire application by invoking run_inspire in the command prompt), the user is prompted for the login (DB account username & password) as shown in Figure 1. Alternatively, the database connection window is also brought up via the menu item DB connection of the File menu. Figure 1: Database connection window By default the software will automatically select the database pertaining to the LAN from which the software was started by the user. Login : 1. Enter your username and password in the Edit fields next to Username and Password. 2. Then click on the button Login to proceed with the login. In the same window the user can also Logout. This can be useful in the rare event that switching the logged in user is needed (if a new session with different account is to be started). Page 5 of 23

6 Upon successful login, the data loading window is brought up, with the assignment queue as default. Figure 2: Sample assignment queue 3. ANALYSIS WORKFLOW inspire GUI software provides workflow for review of samples. There are workflow buttons on the top of inspire GUI which reflect the high level steps in a sample review process: Load Data, Quality Check, Review, Reprocess, and Release. The workflow guides the user to perform the analysis in sequence: quality check after loading a sample, to perform the review, reprocess as appropriate and release the sample. Figure 3: Analysis workflow toolbar The workflow offers the steps Review and Reprocess as the next steps in the workflow. The workflow is not enforced. The user can choose to use the workflow buttons or ignore them and e.g. load a different spectrum. Page 6 of 23

7 4. OPTIONS FOR SPECTRUM SELECTION Three possibilities are available for selecting a spectrum to load: (a) from the sample assignment queue, (b) using the selection window to browse the database using relevant filters (c) by entering a valid sample identification (SID) number 4.1. USING THE ASSIGNMENT QUEUE Automatic assignment of spectra to individual analysts (users) can be performed in the automatic processing pipeline. Furthermore, spectra can also be (re)assigned either externally or via inspire related link. The user can display spectra that are previously assigned to him or her by selecting the tabulation Assignment Queue under Load Data frame or by clicking the submenu item Assignment Queue under the menu item Load Data. This results in a display of samples that are assigned to the current user (Analyst) as in Figure 4, below. Figure 4: Data selection from assignment queue The display window provides information related to the following sub-set of spectrum identification parameters: - Sample type - Data type - Spectrum qualifier (Qualifier) - Spectrum status in the workflow (Status) - Station code (Station) - Detector code (Detector) - Sample collection stop (Collect stop) - Sample collection, in days (Smp Time (d)) - Spectrum acquisition start timestamp (Acq Start) - Spectrum acquisition time, in hours (Acq Time (h)) - Sample identification number (SID) - Sample category (Category) Page 7 of 23

8 Assigned spectra can be sorted out in different possible ways by cliquing on header items of the grid. Note both ascending and descending modes are available. To load a spectrum from the queue: 1) Select the corresponding row in the list, 2) Then, press the button Load BROWSING FROM THE DATABASE Activating the Select Data sub-menu item of the Load Data menu or selecting the tabulation Select Data under Load Data frame brings up the selection facility window as shown in Figure 5, below. Notes on Figure 5: Figure 5: Data selection window The following filtering parameters can be used according to individual cases of selection criteria: - Sample type: Particulates, Noble Gas beta-gamma or HPGe Noble Gas. - Data type: individual data type or all available data_types (sample, blank, calibration, detector background, gas background, quality control, spike, all). - Spectrum qualifier: PREliminary spectra, FULL spectra or both. - Spectrum analysis status: individual status or All. - Station code: individual station or all available stations. - Detector code: individual detector or all available detectors. - Timeframe (From To) of sample collection stop or spectrum acquisition start (depending on data type). In addition, the checkbox Only assigned to me can be optionally activated (default: deactivated). Page 8 of 23

9 When the selection parameters are set as appropriate, the search is activated by pressing the button Query. The list of spectra matching the pre-selected filters will then be displayed with relevant information DATA ASSIGNMENT The Sample operation window offers a feature for (re)assigning spectral data (to current or other user), using the following steps: - mark the sample(s) to (re)assign by ticking the corresponding check box widget in the last column (as in Figure 5, above); - select the (new) assignee; - press the button Assign. The new assignee of the spectra in focus will then be shown in the corresponding column (as in Figure 6, below). Figure 6: Spectra assignment feature Page 9 of 23

10 4.4. LOADING A SPECIFIC SPECTRUM If the spectrum identification number of the spectrum of interest is known, the best option is to use the sub-menu item Load Sample_ID of the Load Data menu or select the tabulation Load Sample_ID under Load Data. This brings up the dialog window (Figure 7) with a text field where the sample_id of interest can be entered. The spectrum can then be loaded just by clicking on the Load button. Figure 7: Loading sample_id Page 10 of 23

11 5. INTERACTIVE ANALYSIS FEATURES The main window of inspire (Figures 8, 9 and 10 below) consists of contextually dynamic dock widgets: Spectrum information; Sample metrics; Spectrum display area; Analysis results; Calibration parameters; Data reprocessing; Sample release and product related features; The following sections describe the key panels of the main window SPECTRUM INFORMATION This panel displays detailed information on spectrum identification parameters. These consist of the following items as shown in Figure 8, below: Notes on Figure 8: - Station code; - Detector code; Figure 8: Spectrum information panel - Assignee: Database username of Analyst to whom the spectrum is currently assigned; - Sample_id: spectrum identification number as assigned by the automatic processing pipeline, - Sample type: (NG beta-gamma, NG HPGe; Particulates); - Data type: type of spectral data (S: Sample, B: Blank filter, C: Calibration, D: Detector background, Q: Quality Control, K: spiked sample); - Status: processing status of the spectrum (U: Unprocessed, P: Processed, R: Reviewed, V: Viewed, A: Analyzed by the parsing program but not processed yet or failed the processing, B: marked as Bad, D: marked as Duplicate, H: Hold on for review). - Collection start: date and time of air sampling start; Page 11 of 23

12 - Collection stop: date and time of air sampling stop; - Acquisition start: date and time of spectrum acquisition start; - Acquisition stop: date and time of spectrum acquisition stop; - Auto Category: sample category based on automatic processing results; - Category: (current) sample category based on interactive review of the spectrum QC FLAGS PANEL This panel, as in Figure 9 below, shows Quality Control (QC) flags for FULL sample spectra. These sample metrics measure the spectral data quality from the CTBT verification value point of view. In case the sample reliability is seriously compromised, the sample in question has to be released without category. These are compared to reference thresholds of operational requirements and displayed in color-coded mode for test item pass/fail: - Flag color in green: the parameter is within the limits (PASS), - in red: the parameter value is beyond the required range (FAIL), - and in yellow: the parameters doesn t fulfill certification requirement but still within acceptable range in terms of data value for verification as in IDC review policy; Figure 9: Quality check panel MDC of Xe-133 and SOH flag Clicking on a QC flag button displays related time series over the previous week, as default. The combobox on the top-right side allows the time window to be extended to one month, three months, one year or the whole history in the database. The flag quality for each sample in the history in focus is displayed with corresponding color coding. Page 12 of 23

13 Five sample metrics are currently considered for Noble Gas data: collection time, acquisition time, reporting time, volume of stable xenon, MDC for Xe-133. These quality indicators are materialized as a flagging system on Norfy s dashboard with traffic-lights like color coding (green, yellow, red). The Figure below provides the boundary limits as currently set in IDC review policies for SAUNA systems. Collection Time (h) AcquisitionTime (h) Stable Xenon Volume (ml) MDC for Xe-133 (mbq/m3) Reporting Time (h) The overall flag from SOH data stand point is also integrated into inspire s dashboard. SOH status reflects whether the SOH data quality is reviewed (using ROSS software) or just based on automatic processing (auto_ross). Additional flags as also available on inspire s dashboard are intended for the purposes of investigating special situations. These include: - Sample processing time (at the station). - Whether Gas background data is available for the sample and used by bg_analyze. If Gas background is not present then the software will use the most recent prior gas Background and shows red flag. If no gas background spectrum is found the software generates an error message and terminates. - Whether Detector background is available for the sample and used by bg_analyze. If Detector Background is not present then the software will use a default Detector Background specified in a detector specific database table then generate a warning and continue. A red flag is shown on Norfy s dashboard. - Live acquisition time for Gas background (red if less than 4 hours). - Radon counts in ROI 1 of the Sample. - Air flow of the sampling system (average value) for the sample collection time. Sample volume derived from Air Flow. This rough sample volume might be higher than the effective sample volume as derived from stable Xenon volume (effective air volume, in m3, is obtained by dividing stable xenon volume, in ml, by 0.087). Page 13 of 23

14 5.3. SPECTRUM DISPLAY This view, as in Figure 10 below, shows three different graphical representations of spectral data: - Beta-gamma coincidence histogram with color mapped counts; - Single beta and gamma spectra; - Projected beta and gamma spectra. These display modes are available for sample, gas background, detector background and QC; Notes on Figure 10: Figure 10: Beta-gamma coincidence histogram The upper buttons Sample, GasBackground, DetectorBackground and QualityControl allow displaying related individual data components of the current dataset, as applicable. The upper-right buttons NCC, 2Df allow displaying related ROI limits. The combobox Channel/Energy changes the bottom axis unit. The GUI provides zooming in/out options. Pressing the left mouse button and dragging zooms in to the area of a rectangle you draw. Left clicking steps back to the previous scaling mode. Page 14 of 23

15 brings the histogram back to the default (full scale) mode reapplies pre-zoom in stepwise mode reapplies pre-zoom out in stepwise mode 5.4. ANALYSIS RESULTS This view, as in Figure 11 below, displays analysis results of xenon isotopes Xe-131m, Xe-133, Xe-133m and Xe-135 based on Net Count Calculation (NCC) method. Figure 11: NCC analysis results Notes on Figure 11: The table of the main tabulation Isotope Concentrations shows analysis results based on NCC method. The results include nuclide identification flag (Flag), activity concentration (Conc), uncertainty (Uncert) on activity concentration and Critical Limit (LC). The results are expressed in mbq/m3 (air concentration). The Flag is set to Detected if the isotope is detected (above LC) and to Not present if the isotope is not detected (below LC). Page 15 of 23

16 For more in depth investigation, intermediate analysis results are also available under three secondary tabulations. o ROI counts: the table contains ROI gross count, temporary net count, net count and LC for ROIs 2 to 10. o ROI concentrations: the table contains ROI based activity concentration, MDC and LC for ROIs 2 to CALIBRATION WINDOW inspire offers a Calibration utility for checking gamma and beta energy calibrations. The window contains two tabulations for gamma and beta calibrations. Both tabulations display three plots: - The plot in the left side shows the currently used calibration plot; - The plot in the middle shows test calibration plot, based on selected calibration option from the lower tabulation Reprocess; - The plot in the right side shows shift analysis results (used vs. test calibration). The gamma plots (both Used and Test calibrations) contain annotations of X-rays and gamma energy lines where corresponding QC peaks are expected. The beta-gamma coincidence plots (both Used and Test calibrations) contain annotations of reference line E γ = 662 E β where corresponding QC maximum coincidence counts of Cs-137 scattering are expected. The Figures 12 below illustrate a case where the currently used gamma and beta energy calibrations result in significant shifts. Whereas QC based calibrations would successfully correct the gain shift in both gamma and beta energies. Page 16 of 23

17 Figure 12: Gamma and beta energy calibration window Page 17 of 23

18 5.6. REMOVING A FALSE DETECTION inspire offers a feature for interactively removing a false detection of xenon isotope(s). A false detection can be removed by clicking on the button Remove on the corresponding row in the Isotope Concentrations table under NCC results. The figures below illustrate the steps for removing Xe-135; a) Go to NCC-tables and display Isotope Concentrations. b) Click on the button REMOVE corresponding to Xe-135 row. Figure 13: Analysis results before isotope removal c) Click on Yes in the confirmation message dialog window. Page 18 of 23

19 d) Note that the color of Xe-135 row will turn into grey and the caption of the previously REMOVE button is changed to INSERT. This allows the action to be rolled back as appropriate. Figure 14: Analysis results after isotope removal e) Note that the categorization summary under the tabulation Release Sample will be updated for Xe-135. Figure 15: Categorization summary after isotope removal Note: the isotope removal functionality can only be used within IDC review policies of analysis procedures, if so specified; Page 19 of 23

20 5.7. REPROCESSING WINDOW inspire supports reprocessing of one or more components of the current data set. This functionality is available via the tab Reprocessing in the spectra dock widget, which allows the user to configure various processing parameters and reprocess. The layout of this tabulation depends on the sample type. Figure 16 corresponds to beta-gamma coincidence based Noble Gas data where the following reprocessing options are provided: Possibility to select the analysis method for reprocessing. Currently NCC method is supported. The user can select one of them or both. Possibility to change the energy calibration used for reprocessing. If this option is used then a new type C calibration directive is created in the database before starting the reprocessing run and the analysis tool will load the new directive for processing. As possible starting points for the new calibration directive the existing calibration candidates can be selected via a combobox for β and γ. Possibility to select the data components which the analysis tool shall process. For NCC the main sample and the QC spectrum will always be processed, but gas background and detector background are optional. Different command line parameters can be configured for the reprocessing run. The resulting command line(s) are displayed and updated according to the user choices. When the Reprocess button is pressed, inspire will first create a new calibration directive if necessary and then the reprocessing tool will be invoked by executing the appropriate command(s). Finally the sample will be reloaded with refreshed results. Figure 16: Data reprocessing window Page 20 of 23

21 6. SAMPLE SPECTRUM RELEASE GENERAL COMMENTS EDITOR The General Comments Editor can be accessed via the Products Tab. It can be used to view and modify any general comments applying to the current sample. The term general in this context means that the comments apply to the whole sample as opposed to isotope comments. Figure 17: General comment editor Notes on Figure 17: The right side table displays already added general comments for the currently selected sample. The table includes the time when the comment was generated and the author of the comment. If the Analyst finds an incorrect comment in the tabular list, the analyst can mark the comment in the table and update or delete the comment as appropriate. The analyst can also add new comments. For convenience the GUI offers several lists of predefined comments applying to samples with specific properties. But the analyst is free to modify the comments and/or write her own general comment. Note that depending on the sample type the list of available predefined comments is updated in contextual mode. Also note that the system automatically generates a comment related to the sample category if the category is above the lowest category (A or 1 depending on the sample type) Page 21 of 23

22 1.1. RELEASE OPTIONS The sample release is accessed via the Products Tabulation. Figure 18: Spectrum release window The release window contains: Sample Category; Isotope category details (detected or not, concentration and uncertainty, LC, abnormal threshold and category); A read-only list of the general comments that were applied to the sample (the general comments can only be modified in the general comments editor see previous section); View ARR (pre)view/ View RRR Three release options are available for sample spectra: A button for Release with category; A button for Release without category; A combobox for changing the sample status to D (duplicate) or B (bad). Available actions here depend on the data type and the status of the sample. Most actions are only available for samples in status P (processed). The Right away to R radio button can be used to release samples skipping the Q (quality check) waiting time. This option is currently disabled. Other spectral data (Detector Background, QC and calibration) can be marked as V (Viewed) as appropriate, which indicates that these are of good quality. Page 22 of 23

23 1.2. REVOKING A RELEASE The revoke functionality is accessible via the Load Data dock widget. The following steps allow Analysts to revoke released sample(s) that are still under status Q: (a) Activate the Sample operation tab under Load data dock widget; (b) Select data type S, spectral qualifier FULL, status Q; (c) Set the time frame to include sample(s) collection stop(s) to be revoked; (d) Tick the check box assigned to me, as appropriate; (e) Press the button Query. The system displays corresponding sample spectra under status Q. (f) In the returned list of sample spectra under status Q, mark the sample(s) to revoke, by ticking the check box in the last column of the grid; (g) Press the button Revoke. Figure 19: Spectrum revoke window The system will bring up a confirmation dialog message (Are you sure you want to revoke the sample(s)?). Upon confirmation, the revoke procedure will be executed. The following changes should occur: - Sample status will be updated from Q back to P; - RRR_html.htm, REVSAMPML.sml (and SSREB_html.htm in case of level C) files will be removed from the temporary location of the file system; - Related database entries in GARDS_PRODUCT will be deleted. Page 23 of 23