6. The SIPGI graphical interface

The graphical interface is designed to quickly and easily browse the data at the various stages of the data reduction and to execute and check the various reduction steps. It is entirely written in Python to simplify the handling of graphical elements and to take advantage of the object-oriented programming capabilities offered by this language.

Fig. 6.1 shows the layout of the graphical interface as it appears before ingesting raw data. It is organized in three main operational area, highlighted by the three colored boxes: the starting and setting area (red box in Fig. 6.1), the data manager area (blue box in Fig. 6.1), and the reduction and analysis area (green box in Fig. 6.1).

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Fig. 6.1 The SIPGI layout at first run

6.1. The Starting and Setting Area

In the upper left region of the graphical interface (box A in Fig. 6.1) there is the Staring and Setting Area. It includes four menus, namely SIPGI, Workspace, Project, Parameters which control the main setting of the software plus the Help menu.

In the SIPGI menu the user has to set some general preferences as:

  • the First Alternative FITS viewer to visualize data with a user defined tool. The user can set a tool name (that will be shown on the launch button in the Analysis Utilities menu) and select the tool executable. On OSX an Application can be directly set as the executable (i.e. /Applications/SAOImage.app)

  • the Second Alternative FITS viewer. Similarly to the first one, the user can define a second viewer.

  • the log level. There are six different log levels from Off, i.e. SIPGI does not provide any message during the execution of different reduction steps, to Debug the most detailed log level. A good compromise between information provided and verbosity is log level Info;

  • Rescan the project directories at project loading. Activating this option, SIPGI rescans the Project directories at each start.

In the Workspace menu the user can:

  • manage the creation of a new Workspace clicking on the option New;

  • have information on the Workspace that is shown in the data manager area clicking the option Info;

  • delete the Workspace that is shown in the data manager area clicking the option Delete.

The Project menu is similar to the Workspace one. Here the user:

  • manage the creation of a new Project clicking on the option New.

  • have info on the Project that is shown in the data manager area clicking the option Info;

  • delete the Project that is shown in the data manager area clicking the option Delete. With the option Delete, the user can no longer work on his/her data within SIPGI, but the copy of the raw data created by the built-in data organizer (and possibly all the data products of reduction process) are still on the user disk in the Project directory;

  • delete the Project that is shown in the data manager area and the files from the Project directory clicking the option Delete All Data.

    Note

    The option Delete All Data removes both the Project and the copy of the data and products from the disk. If no copy of the reduction products (including final ones) has been made, all will be lost!

The Parameters Files menu allows the user to set the input parameters of any reduction recipes. The detailed behavior of each recipe is controlled via a set of parameters that are read in by the recipe at the beginning of its execution. SIPGI provides a default value for each parameter tuned on the reduction of LBT MODS and LUCI spectra. Default values change on the basis of the instrument.

Clicking on Parameters Files the list of the recipes appears. Clicking on one recipe, a panel with all its parameters is shown (see Fig. 6.2). Each entry has a brief description on the right side. Moving the mouse on the description, a more detailed description appears. Once all the changes have been done, the user can decide among different options with the buttons at the bottom:

  • Run: it directly runs the recipe from the panel, but does not save the changes for next interactions;

  • Save: it saves the changes but does not run the code;

  • Save and Run: it saves the changes and runs the code;

  • Reset: it sets the parameters values to their default values;

  • Cancel: it closes the windows.

Any time the user saves the changes, they are valid throughout all of the Workspace.

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Fig. 6.2 The figures shows a Parameters File example. Each parameter is followed by a short description. Some parameters have a long description as shown by the yellow box. The long description can be visualized going with the mouse on the short description.

The Help menu shows this manual within the browser.

The View Logs button opens the log panel.

The Exit button closes SIPGI.

6.2. The Data Manager Area

In the data manager area (box B in Fig. 6.1) the user can control the data at different levels, from the ingestion of raw data in a new Project, to the selection of specific input to reduction recipes.

The data manager area is characterized by four buttons at its bottom, namely Import, Rescan, Unclassified, Custom Auxiliary Files, which control the ingestion of the data and the auxiliary files.

The Import button allows the user to put raw files under the SIPGI control. Once the user has created a new Workspace and a new Project, he/she has to import raw data in the SIPGI project, i.e. raw data must be processed by the built-in data organizer. At the end of this process, the user will find data organized in different Datasets in the central panel of the data manager. Concurrently, the user will find a copy of the raw files, organized in the SIPGI scheme, in the Project directory specified at the moment of the creation of a new Project.

The Unclassified button allows the user to see the list of raw files not imported by SIPGI. If some raw files do not have the appropriate entries in all of the keywords necessary to SIPGI (see Appendix B: keywords necessary to SIPGI to import and categorize raw data), the pipeline does not import them since it misses information to categorize and classify them. Similarly, SIPGI does not import those data for which it does not find the appropriate auxiliary files.

The Rescan button allows the user to import new files in SIPGI format in the current Project. This button is mostly for support purposes, i.e. it allows user to upload in SIPGI products produced by the Help Desk.

The Custom Auxiliary Files button opens the Custom Auxiliary Files Manager. During the reduction, the user can have the necessity to upload a Customized auxiliary file that better matches his/her scientific necessities as, for example, a Spectro-photometric standard at higher resolution or a new Stellar template. In addition the user could desire to reuse a Master File obtained in a old reduction for the reduction of a specific target. Once a new file is uploaded, it will be ingested in SIPGI that can use it for reduction purposes (for more details see the Note).

The central part of the data manager area allows the user to browse within his/her data. The two drop-down menus at the top of the area (see Fig. 6.3) permit to select the Workspace and the Project. Once selected, the Datasets associated to that Project appear in the central part of the data manager area.

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Fig. 6.3 The Figure shows the Workspace and Project drop-down menu and the aspect of the central part of the data manager area once raw files are imported.

Clicking on a specific Dataset, the user will have access to the different Reduction Units (see Fig. 6.4) and consequently to the data contained therein.

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Fig. 6.4 The figure shows the organization of data produced by the built-in data organizer. In particular, it shows (red squares) two Reduction Units collecting the scientific data of the target MyQuasar observed with the mask ID140777 with the G400L-Dual grism and with the G670L-Dual grism. These data are in the Project QSO belonging to the Workspace MODS.

6.2.1. Reduction unit layout

Fig. 6.5 shows the typical aspect of a Reduction Unit. In each Reduction Unit there are three main panels: the frames panel, the master frames panel, and the generic master frames and auxiliary files panel.

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Fig. 6.5 This figure shows the Reduction Unit layout organized in 3 panels: A the frames panel, B the master frames panel, C the generic master frames and auxiliary files panel

6.2.1.1. Frames panel

In the top panel (A in the figure Fig. 6.5) the files of the Reduction Unit are shown. A series of drop down menus allows the user to filter the files in the Reduction Unit according to their file type, observing night, origin, exposure time, dichroic, arm, and in LUCI workspaces also according to readmode, savemode and DIT (these last three info are necessary for the creation of the Master Dark).

6.2.1.2. Master frames panel

In the middle panel (B in the figure Fig. 6.5) all the Master calibration files created in the current Reduction Unit such as Master Flat, Master Lamp, Master Dark, sensitivity function are shown. Every Master calibration file created by the user is visible only in the Reduction Unit where it is created. To make a Master File available to all the Reduction Units of the current Projects, the user must promote it to generic master frame (see Share as auxiliary in the Context menus section)

6.2.1.3. Generic master frames and calibration files

In the bottom panel (C in the figure Fig. 6.5) of a Reduction Unit, SIPGI shows all the auxiliary system and customized files, plus all the Master Files that have been promoted by the user to the generic master frame panel. A set of drop-down menus on top of this panel allows the user to easily select files.

6.2.1.4. Context menus

The panels A and B have 2 context menus to easily handle the reduction unit files.

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Fig. 6.6 The figure shows the context menus available in the panels A and B of the Reduction Unit.

For each file in the panel A, it is possible to select the following actions:

  • Show Header: shows the header of the selected files;

  • Show log extension: displays logs of the reduced frames (present if frames are reduced with the flag DUMP_LOG=True) (see The data reduction recipes);

  • Rename file: renames the single selected file;

  • Rename files block: renames a bunch of selected files, replacing the common part of the file name with something provided by the user;

  • Delete files: deletes selected files;

  • Show the full file path: shows the path on disk of the selected file;

  • Export/Import PAF: this 2 entries allow to share the Paf files between files exporting and importing these values.

  • Show Creation list: shows the list of files used to create the selected combined file or the selected bad pixel image.

Important

If the user wants to delete some files from the Project he/she must use the Delete files option and do not delete them from the Project directory.

The panel B provides the same context menu of panel A plus the entry Share as auxiliary. This entry allows to promote a Master File from the master frame panel to the generic one. This procedure will move the selected file from the middle B panel to the bottom C panel. In this way, the promoted file will be at disposal for every Reduction Unit of the Project.

6.3. The reduction and the analysis area

6.3.1. The Reduction Tab

The Reduction Tab contains two main blocks: in the top one there are the main reduction recipes and in the bottom one are present some utility functions. In each Workspace, only the recipes useful for the reduction of the corresponding instrument are activated. Those non active have light gray color buttons.

The buttons have a quite explanatory name and in the top block they are ordered following the main steps of a standard reduction.

The standard execution of each recipe is quite simple thanks to the file organization. The user must select the input files in the Reduction Unit, optionally the Calibration files and/or the Master File and click the recipe button. Some recipes require input files from different Reduction Units. For this reason their functioning passes through the creation of a input files list. The user can recognize these recipes from the presence of “…” in the button name.

The task performed by each recipe, its inputs and outputs are described in The data reduction recipes.

6.3.2. The Analysis Tab

The Analysis Tab contains a set of utilities to visualize and inspect the results. The input files and functioning are described in The Analysis Utilities.