2.6. Useful Modules

2.6.1. Introduction

Utility modules are used within each main modules of PyMoDAQ but can also be used as building blocks for custom application. In that sense, all Data Viewers and even DAQ Viewer and DAQ Move can be used as building blocks to control actuators and display datas in a custom application.

2.6.2. Data Viewers

These modules are to be used to display various type of data and helps you manipulate these using scaling, ROI, measurements… They are mostly used within the main modules of PyMoDAQ but can also be used as building blocks for custom application. In that sense, DAQ Viewer and DAQ Move can also be used as building blocks to control actuators and display datas in a custom application. 0D Viewer


Fig. 2.43 0D viewer data display 1D Viewer


Fig. 2.44 1D viewer data display 2D Viewer


Fig. 2.45 2D viewer data display ND Viewer

A ND viewer is a display object that can represent 0D, 1D, 2D, 3D or 4D data. It is a combination of 2 Viewers (up: navigation viewer and bottom: signal viewer, see panels of Fig. 2.46) and use the concept of signal axis and navigation axis. Let’s say you want to represent a previously acquired 2D scan where each of the pixels in the scan is actually data from a camera (2D). It then means that you have 2 navigation axis (the ones of the scan) and two signal axis (the ones of the camera) and 4D data to deal with. The way to plot them is to represent the scan on a navigation 2D viewer where each pixel intensity is the result of the integration of the actual data taken at this pixel (or within a ROI that you can select, see white rectangle on Fig. 2.46 bottom panel). Moving the crosshair on the navigation panel change the display in the signal panel in order to show the data within the pixel pointed by the crosshair.


Fig. 2.46 ND viewer data display

ND viewer is mostly used by the H5Browser (and sometimes by the DAQ_Viewer) to display data saved with PyMoDAQ, a few metadata attributes written in the h5file nodes (see From DAQ_Scan) tells the NDViewer how to display acquired scans. If, for some reasons, you want to display your 4D data in another way (that is changing which dimension is navigation and which is signal), you can press the axes button on the top viewer and change the navigation axes on the popup window it opened.

2.6.3. Module Manager

The module manager is an object used to deal with:

  • Selection of actuators and detectors by a user (and internal facilities to manipulate them, see the API when it will be written…)

  • Synchronize acquisition from selected detectors

  • Synchronize moves from selected actuators

  • Probe as lists all the datas that will be exported by the selected detectors (see Fig. 2.47)

  • Test Actuators positioning. Clicking on test_actuator will let you enter positions for all selected actuators that will be displayed when reached


Fig. 2.47 The Module Manager user interface with selectable detectors and actuators, with probed data feature and actuators testing.

2.6.4. Scanner

The Scanner module is an object dealing with configuration of scan modes and is mainly used by the DAQ_Scan extension. It features a graphical interface, see Fig. 2.49, allowing the configuration of the scan type and all its particular settings. The Scan type sets the type of scan, Scan1D for a scan as a function of only one actuator, Scan2D for a scan as a function of two actuators, Sequential for scans as a function of 1, 2…N actuators and Tabular for a list of points coordinates in any number of actuator phase space. All specific features of these scan types are described below: Scan1D

The possible settings are visible on Fig. 2.48 and described below:

  • scan subtype: either Linear (usual uniform 1D scan), Back to start (the actuator comes back to the initial position after each linear step, for a referenced measurement for instance), Random same as Linear except the predetermined positions are sampled randomly and from version 2.0.1 Adaptive that features no predetermined positions. These will be determined by an algorithm influenced by the signal returned from a detector on the previously sampled positions (see Adaptive)

  • Start: Initial position of the selected actuator (in selected actuator controller unit)

  • Stop: Last position of the scan (in selected actuator controller unit)

  • Step: Step size of the step (in selected actuator controller unit)

For the special case of the Adaptive mode, one more feature is available: the Loss type*. It modifies the algorithm behaviour (see Adaptive)


Fig. 2.48 The Scanner user interface set on a Scan1D scan type and the visible list of scan subtype. Scan2D

The possible settings are visible on Fig. 2.49 and described below:


Fig. 2.49 The Scanner user interface set on a Scan2D scan type and a Spiral scan subtype and its particular settings.

  • Scan subtype: See Fig. 2.50 either linear (scan line by line), linear back and forth (scan line by line but in reverse direction each 2 lines), spiral (start from the center and scan as a spiral), Random (random sampling of the linear case) and Adaptive (see Adaptive)

  • Start, Stop, Step: for each axes (each actuators)

  • Rmax, Rstep, Npts/axis: in case of spiral scan only. Rmax is the maximum radius of the spiral (calculated), and Npts/axis is the number of points for both axis (total number of points is therefore Npts/axis²).

  • Selection: see Scan Selector


Fig. 2.50 The main Scan2D subtypes: Linear, Back and Forth and Spiral. Sequential

The possible settings are visible on Fig. 2.51 and described below:

  • Scan subtype: only linear this means the scan have a sequence of Scan1D of the last specified actuator (on Fig. 2.51, it is Xaxis) for all positions of the last but end actuator (here Yaxis) and so on. So on Fig. 2.51 there will be 11 steps for Xaxis times 11 steps for Yaxis times 10 steps for Theta axis so in total 11x11x10=1210 total steps for this 3 dimensions scan.


If only 1 actuator is selected, then the Sequential scan is identical to the Scan1D scan but where only the linear subtype is available. If 2 actuators are selected, then the Sequential scan is identical to the Scan2D scan but where only the linear subtype is available.


Fig. 2.51 The Scanner user interface set on a Sequential scan type with a sequence of three actuators Tabular

The tabular scan type consists of a list of positions (for each selected actuators). Tabular Linear/Manual case

In the Linear/Manual case, the module will move actuators on each positions and grab datas. On Fig. 2.52, a list of 79 positions has been set. By right clicking on the table, a context manager pops up and gives the possibility to:

  • add one more position in the list

  • remove the selected position

  • clear all the positions

  • load positions from a text file (as many columns as selected actuators with their positions separated by a tab)

  • save the current list of positions in a text file (for later quick loading of positions)

One can also drag and drop elements of the list at a different index in the list.


Fig. 2.52 The Scanner user interface set on a Tabular scan type with a list of points for 2 actuators. A context menu with other options is also visible (right click on the table to show it) Tabular Linear/Polylines case

In the particular case of 2 selected actuators, it could be more interesting to draw the positions for the tabular scan. One possibility is to draw segments on a 2D viewer (see Fig. 2.53) and positions will be points along these segments (it will be a kind of 1D cuts within a 2D phase space). A new setting, Curvilinear step appears. The positions will be points starting from the start of the first segment and then step along them by the value of this setting. That gives, for Fig. 2.53, 40 points defined along the segments.


Fig. 2.53 An example of 1D complex sections selected within a 2D area Tabular Adaptive case

Valid for 1 or 2 selected actuators. The tabular adaptive case will be similar to scan1D adaptive mode, except that one adaptive Scan1D will be done for each segments defined by the list of positions in the table. For instance, Fig. 2.54 shows a list of 4 positions defining 4 segments in a 2D space. The adaptive scan will be done on/along these 4 segments. Positions can be set manually or from a Polylines selection as seen on Fig. 2.53.


Fig. 2.54 The Scanner user interface set on a Tabular scan type with a list of points for 2 actuators. A context menu with other options is also visible (right click on the table to show it) Adaptive

All the adaptive features are using the python-adaptive package (Parallel active learning of mathematical functions, 10.5281/zenodo.1182437). And the reader is invited to explore their tutorials to discover how these algorithms work. In PyMoDAQ the learner1D algorithm is used for the Scan1D and Tabular scan types while the learner2D one is used for Scan2D scan type. Bounds

As a general rule, the adaptive algorithm will need bounds to work with. For Scan1D scan type, these will be defined from the start and stop settings. For Tabular, it is the start and ends of the segments. Finally for Scan2D, it is the: Start Ax 1, Stop Ax 1 and Start Ax 2, Stop Ax 2 that are defining scan bounds. Feedback

The adaptive algorithm will need for each probed positions a feedback value telling it the fitness of the probed points. From these on all previous points, it will determine the best next points to probe. In order to provide such a feedback, on has to choose a signal among all available from the DashBoard detectors. It has to be a Scalar so originate from a 0D detector or integrated ROI from 1D or 2D detectors. The module manager user interface (right most setting tree in the DAQ_Scan module ,see Fig. 2.47) will let you probe available datas exported from currently selected detectors. You can then pick the Data0D one you want to use as the Adaptive feedback. For instance, on Fig. 2.47, three Data0D are available, one from a 0D detector (CH000) and 2 from the Measurements ROIs of a 1D detector. In that case the CH000 data has been selected and will therefore be use as feedback for the Adaptive algorithm. Loss

All the Adaptive options are called Loss on the Scanner UI. These influence the adaptive algorithm, using previously probed positions and their feedback to guess the next point to probe. See the Adaptive documentation on loss to understand all the possibilities. Scan Selector

Scans can be specified manually using the Scanner Settings (explained above). However, in the case of a scan using 2 DAQ_Move modules, it could be more convenient to select an area using a rectangular ROI within a 2D viewer. Various such viewers can be used. For instance, the viewer of a camera (if one think of a camera in a microscope to select an area to cartography) or even the DAQ_Scan 2D viewer. Sometimes it could also be interesting to do linear sections within a 2D phase space (let’s say defined by the ranges of 2 DAQ_Moves). This defines complex tabular type scan within a 2D area, difficult to set manually. Fig. 2.53 displays such sections within the DAQ_Scan viewer where a previous 2D scan has been recorded. The user just have to choose the correct selection mode in the scanner settings, see Fig. 2.55, and select on which 2D viewer to display the ROI (From Module option).


Fig. 2.55 In the scanner settings, the selection entry gives the choice between Manual selection of from PolyLines (in the case of 1D scans) or From ROI in the case of 2D scans. Module Manager

This module is made so that selecting actuators and detectors for a given action is made easy. On top of it, there are features to test communication and retrieve infos on exported datas (mandatory fro the adaptive scan mode) or positioning. Internally, it also features a clean way to synchronize detectors and actuators that should be set together within a single action (such as a scan step).


Fig. 2.56 User interface of the module manager listing detectors and actuators that can be selected for a given action.

2.6.5. H5Saver

This module is a help to save data in a hierachical hdf5 binary file through the pytables package. Using the H5Saver object will make sure you can explore your datas with the H5Browser. The object can be used to: punctually save one set of data such as with the DAQ_Viewer (see Single Datas), save multiple acquisition such as with the DAQ_Scan (see From DAQ_Scan) or save on the fly with enlargeable arrays such as the Continuous Saving mode of the DAQ_Viewer.


Fig. 2.57 User interface of the H5Saver module

On the possible saving options, you’ll find (see Fig. 2.57):

  • Save 2D datas and above: if not selected, 2D datas (and above) will not be saved but only lineouts or integrated area (this is only in order to save memory space, but is dangerous as you loose the possibility to get back initial raw data. Save raw datas should be unselected in that case)

  • Save raw datas only: if selected, only data exported form the detector plugins will be saved, not the data generated from ROIs or lineouts.

  • Backend: you can chose among any of the three hdf5 backend (tables is recommended and by default)

  • Show File Content?: if clicked, the H5Browser will open to display content of the current hdf5 file

  • Base path: The folder where all datasets and scans will be saved, for instance: C:\Data

  • Base name: the name given to the scans you are going to do (default is Scan)

  • current Scan: indexed name from base name, for instance: Scan000

  • h5 file: complete path of the current h5 file, for instance: C:\Data\2018\20181226\Dataset_20181226_000\Dataset_20181226_000.h5

  • Compression options: by default data are compressed to mid level * compression library: see pytables package or HDF5 documentation for details * Compression level: integer between 0 (no compression) and 9 (maximum compression)

2.6.6. Preset manager

The Preset manager is an object that helps to generate, modify and save preset configurations of DashBoard. A preset is a set of actuators and detectors represented in a tree like structure, see Fig. 2.58.


Fig. 2.58 An example of a preset creation named preset_adaptive containing 3 DAQ_Move modules and 3 detector modules and just about to select a fourth detector from the list of all available detector plugins.

Each added module load on the fly its settings so that one can set them to our need, for instance COM port selection, channel activation, exposure time… Every time a preset is created, it is then loadable. The init? boolean specifies if the Dashboard should try to initialize the hardware while loading the module in the dashboard.

2.6.7. Overshoot manager

The Overshoot manager is used to configure safety actions (for instance the absolute positioning of one or more actuators, such as a beam block to stop a laser beam) when a detected value (from a running detector module) gets out of range with respect to some predefined bounds, see Fig. 2.59. It is configurable in the framework of the Dashboard module, when actuators and detectors have been activated. A file containing its configuration will be saved (with a name derived from the preset configuration name and will automatically be loaded with its preset if existing on disk)


Fig. 2.59 An example of an overshoot creation named overshoot_default (and corresponding xml file) containing one listening detector and 2 actuators to be activated.

2.6.8. ROI manager

The ROI manager is used to save and load in one click all ROIs or Lineouts defined in the current detector’s viewers, see Fig. 2.60. The file name will be derived from the preset configuration file, so that at start up, it will automatically be loaded, and ROIs and Lineouts will be restored.


Fig. 2.60 An example of ROI manager modification named from the preset preset_adaptive (and corresponding xml file) containing all ROIs and lineouts defined on the detectors’s viewers.

2.6.9. DAQ_Measurement

In construction

2.6.11. Remote Manager

In construction