daq_scan_main.rst

Introduction

The dashboard gives you full control for manual adjustments (using the UI) of each actuator, checking their impact on live data from the detectors. Once all is set, one can move to an automated scan using the main control window of the DAQ_Scan, see daq_scan_main.

Main Control Window

The main control window is comprised of various panels to set all parameters and display live data taken during a scan.

Main DAQ_Scan user interface.

• The instrument selection panel allows to quickly select the detectors and the actuators to use for the next scan
• The settings panel is divided in three sections (see settings_paragraph for more details):
  • Scanner settings: select and set the next scan type and values.
  • General settings: options on timing, scan averaging and plotting.
  • Save settings: everything about what should be saved, how and where.
• The Live plots selection panel allows to select which data produced from selected detectors should be rendered live
• The Live Plots panels renders the data as a function of varying parameters as selected in the Live plots selection panel

Scan Flow

Performing a scan is typically done by:

• Selecting which detectors to save data from
• Selecting which actuators will be the scan varying parameters
• Selecting the type of scan (see daq_scan_scanner): 1D, 2D, ... and subtypes
• For a given type and subtype, settings the start, stop, ... of the selected actuators
• Selecting data to be rendered live (none by default)
• Starting the scan

Selecting detectors and actuators

The Instrument selection panel is the user interface of the module manager (see module_manager for details). It allows the user to select the actuators and detectors for the next scan (see list_modules). This interface is also used for the DAQ_Logger extension.

List of declared modules from a preset

Selecting the type of scan

All specifics of the upcoming scan are configured using the scanner_paragrah module interface as seen on scan2D_fig2 in the case of a spiral Scan2D scan configuration.

The Scanner user interface set on a Scan2D scan type and an adaptive scan subtype and its particular settings.

Selecting the data to render live

For a data acquisition system to be efficient, live data must be plotted in order to follow the experiment behaviour and check if something is going wrong or successfully without the need to perform a full data analysis. For this PyMoDAQ live data display will allows the user to select data to be plotted from the selected detectors.

The list of all possible data to be plotted can be obtained by clicking on the button. All data will be classified by dimensionality (0D, 1D). The total dimensionality of the data + the scan dimensions (1 for scan1D and 2 for Scan2D...) should not exceed 2 (this means one cannot plot more complex plots than 2D intensity plots). It also means that you should use ROI to generate lower dimensionality data from your raw data for a proper live plot.

For instance, if the chosen detector is a 1D one, see det1D. Such a detector can generate various type of live data.

An example of a 1D detector having 2 channels. 0D data are generated as well from the integration of channel CH0 within the regions of interest (ROI_00 and ROI_01).

It will export the raw 1D data and the 1D lineouts and integrated 0D data from the declared ROI as shown on det1D_data_probe

An example of all data generated from a 1D detector having 2 channels. 0D data and 1D data are generated as well from the integration of channel CH0 within the regions of interest (ROI_00 and ROI_01).

Given these constraints, one live plot panel will be created by selected data to be rendered with some specificities. One of these is that by default, all 0D data will be grouped on a single viewer panel, as shown on daq_scan_main (this can be changed using the general_settings_daq_scan)

The viewer type will be chosen (Viewer1D or 2D) given the dimensionality of the data to be ploted and the number of selected actuators.

• if the scan is 1D:

  • exported 0D datas will be displayed on a Viewer1D panel as a line as a function of the actuator position, see daq_scan_main.
  • exported 1D datas will be displayed on a Viewer2D panel as color levels as a function of the actuator position, see scan1D_1D.

An example of a detector exporting 1D live data plotted as a function of the actuator position. Channel CH0 is plotted in red while channel CH1 is plotted in green.

• if the scan is 2D:

  • exported 0D datas will be displayed on a Viewer2D panel as a pixel map where each pixel coordinates represents a scan coordinate. The color and intensity of the pixels refer to channels and data values, see scan2D_0D for a linear 2D scan.

An example of a detector exporting 0D live data plotted as a function of the 2 actuators's position. Integrated regions of channel CH0 are plotted in red and green.

So at maximum, 2D dimensionality can be represented. In order to see live data from 2D detectors, one should therefore export lineouts from ROIs or integrate data. All these operations are extremely simple to perform using the ROI features of the data viewers (see data_viewers)

Various settings

Toolbar

The toolbar is comprised of buttons to start and stop a scan as well as quit the application. Some other functionalities can also be triggered with other buttons as described below:

• : will shut down all modules and quit the application (redundant with: File/Quit menu)
• Init. Positions: will move all selected actuators to their initial positions as defined by the currently set scan.
• : will start the currently set scan (first it will set it then start it)
• : stop the currently running scan (in case of a batch of scans, it will skips the current one).
• : when checked, allows currently actuators to be moved by double clicking on a position in the live plots
• : opens the logs in a text editor

Menu Bar Description

There are two entries in the menu bar: File and Settings

The File entry will let you:

• load a previously saved scan file (and keep saving scans on it)
• Save the current file in another filename than the default one
• Load the content of the current file into the H5Browser

The Settings entry will let you:

• display the Navigator see navigator_paragrah
• Display and activate the Scan Batch Manager

Settings

The settings tree as shown on daq_scan_main is actually divided in a few subtrees that contain everything needed to define a given scan, save data and plot live information.

General Settings

The General Settings are comprised of:

• Time Flow
  • Wait time step: extra time the application wait before moving on to the next scan step. Enable rough timing if needed
  • Wait time between: extra time the application wait before starting a detector's grab after the actuators reached their final value.
  • timeout: raise a timeout if one of the scan step (moving or detecting) is taking a longer time than timeout to respond
• Scan options :
  • N average: Select how many scans to average. Save all individual scans.
• Scan options :
  • Get Data probe selected detectors to get info on the data they are generating (including processed data from ROI)
  • Group 0D data: Will group all generated 0D data to be plotted on the same viewer panel (work only for 0D data)
  • Plot 0D shows the list of data that are 0D
  • Plot 1D shows the list of data that are 1D
  • Prepare Viewers generates viewer panels depending on the selected data to be live ploted
  • Plot at each step
    • if checked, update the live plots at each step in the scan
    • if not, display a Refresh plots integer parameter, say T. Will update the live plots every T milliseconds
• Save Settings: See h5saver_settings

Saving: Dataset and scans

DAQ_Scan module will save your data in datasets. Each dataset is a unique h5 file and may contain multiple scans. The idea behind this is to have a unique file for a set of related data (the dataset) together with all the meta information: logger data, module parameters (settings, ROI...) even png screenshots of the various panels.

figure_h5browser_data displays the content of a typical dataset file containing various scans and how each data and metadata is used by the H5Browser_module to display the info to the user.

h5 browser and arrows to explain how each data or metadata is being displayed

The Save Settings (see save_settings_fig) is the user interface of the h5saver_module, it is a general interface to parametrize data saving in the hdf5 file:

Save settings for the DAQ_Scan extension

In order to save correctly your datas, saving modules are to be used, see module_savers.