Topics covered in this section:
- Trial Management
- Trial Manager Main Window
- Manage Trials
- Manage Traits
- Manage Tags
- KDXplore - KDSmart Data Exchange
- KDSmart/KDXplore - CSV Import File Formats
- Visualisation Tools
The initial Trial Manager window shows the Trials stored in the local KDXplore database along with Traits and Tags for the selected Trial.
The next three annotated examples show the Trial Manager with the Trials tab, Traits and Tags tabs selected highlighting the main window areas.
The main sections of the Trial Manager window highlighted above are:
- Trials tab which has been selected.
- Trials panel which lists the Trials available within KDXplore’s database that can be selected.
- Trial Details panel which displays Trial details for the Trial selected.
- Uses Traits panel which lists the Traits associated with the selected Trial.
- Measurements panel which lists the measurements in the trial by the source.
Selecting the Traits tab will display the following window:
The main sections of the Trial Manager window Traits tab highlighted above are:
- Traits tab which has been selected.
- Traits panel lists the Traits and Trait Bundles available in KDXplore/KDDart.
- Used by Trials panel lists all of the trials that contain the selected trait.
- Details panel lists the details of the currently selected trait.
Selecting the Tags tab will display the following window:
The main sections of the Trial Manager window Tags tab highlighted above are:
- Tags tab which has been selected.
- Tags panel lists the Tags and Tag Bundles available in KDXplore/KDDart.
- Details panel lists the details of the elected Tag.
The following illustration shows section A from above where Trials are displayed and selected.
Trials that are imported into the KDXplore Trial Manager can be grouped by related characteristics. Grouping and filtering makes it easier to quickly locate the required Trial(s) when many Trials are in KDXplore, or when logged into a KDDart database. Trial groups can be displayed based on trial type, KDDart URL, organism, and planting year. To view a trial group, the user will need to:
|1||Select the Group By drop-down menu at which will display the available grouping options.|
|2||Select a grouping option e.g. Trial Planting Year. Once this is selected, the system will display the trial group that has been. It will always display All Trials by default.|
|3||Once a trial grouping is selected, it can be changed by repeating the steps above and choosing another trial grouping.|
- Demonstrates the selection of the 2018 trial year grouping which is opened and the All Trials group which is collapsed.
- Is the filter option which displays a text field below the button for entry of desired Trial Name text.
Functionality to create new types of trial groups will be added in future versions.
In Trial Manager, the Trial tab is the default/home view which displays all the information regarding the Trials currently stored in KDXplore. All trials in KDXplore’s offline database are displayed here.
- Trial Details - All trials in KDXplore’s offline database are displayed here. This displays the information regarding the trial. To edit Trials, either select a Trial by double-clicking it or by selecting the Edit Current Trial button at . By selecting either of the two buttons at the bottom of this panel at , both plot attributes, and trial attributes can be visualised. To quickly edit in Trial Details, double-click in the values column to change values.
- Uses Traits - This area displays the Traits that are currently active for the selected Trial. These Traits are ordered by the user for preference during scoring in KDSmart. Traits can added or removed from Trials by selecting the ‘+’ or ‘-‘ symbols at the top of this panel.
- Measurements by Source - This area displays the phenotypic datasets for the selected Trial and how populated (in percent) each dataset is. Datasets can be created from this panel. Datasets can also be created for a list of specific Traits to send to KDSmart for scoring. The source of each set of measurements (e.g. phone 1) can be viewed from this panel also.
KDXplore can import CSV and Excel XLS or XLSX files easily using drag and drop. For information on file import formats please see the “KDSmart/KDXplore - CSV Import File Formats” help page. Although .CSV files can be easily imported given almost any column format.
Trials can be imported from various sources and in different formats. One of the easiest ways is to import a .CSV file which is outlined below:
|1||Select the Add Trials button at and select the Load From CSV option. This will bring up the Import Trials window at .|
|2||Either drag and drop a .CSV file into the window, or select the Browse button located at .|
|3||Select the Add Device button at to link any connected devices to import data (this is optional).|
|4||Change the Trial Name and Operator if necessary. The Traits that are contained in this file will also be listed in the window. Selecting a Trait by right-clicking it will allow the user to choose import options for that particular Trait i.e. Don’t Import|
|5||Select the Import button at to save the preferences and import the trial.|
Whilst this covered the import of a .CSV file, the same process applies for a .XLS or .XLSX file except the user must choose the Load From XLS option after choosing to add Trial.
Once a Trial has been imported it will appear in the list in the Trial Details panel. Trials can also be imported from KDDart by selecting Load From Database and from connected KDSmart devices through the Load From Tablet Data option when selecting the Add Trials button.
KDXplore can also import Trials from the KDDart Database. To be able to do this, you must first be logged into KDDart. To see how to log into KDDart, follow the next set of instructions. If you are already logged in, then skip to the next part.
|1.||Select the File button at the and then choose the connect option.|
|2.||The KDDart Login window will then appear as at . Enter your username and password and then select the Login button to log into the KDDart Database.|
Logging into KDDart allows the user to easily import Trials with the relevant Traits and Tags attached. The following instructions will demonstrate how to import a Trial from the Database:
¶ Step Action 1 Select the icon at and choose the Load from Database option to open the Database Import window as seen in the image above. 2 Choose an attribute to search for such as the one at . This example is a location attribute that will only display the Trials that take place at Roseworthy. 3 Select the Find Trials button to search for the Trials. If no attributes were selected, then all Trials in the Database are presented. 4 The search results will then be displayed (such as in the following image). Choose a Trial (or multiple Trials) such as the one in and then select the Download Trials button at to complete the import.
Below is an animation that demonstrates the above instructions:
Trials can also be exported so that it can be used on other devices. The exported files can be either a zip file, .CSV, or can be exported through KDXchange. It can also include media such as photographs. The following image and instructions detail how to export a Trial in the .CSV format.
To export a Trial, follow the steps below:
|1||To export a Trial in KDXplore select a Trial such as the Trial at .|
|2||In the Measurements by Source panel, select the column of the dataset for export such as the column at .|
|3||By then selecting the Export Sampled or Traits for Trial button at , a dialog will open asking details for export as in .|
|4||Trial Manager will choose a file destination, but to change it, select the Browse button at and then choose a folder in which to export to.|
|5||Choose the Output Options which will determine the format of the export (KDX, Zip, or CSV).|
|6||Choosing the Include Media Files option will include any photos that were taken with the samples.|
|7||Select either the Close, Export, or Export and Close options to finish the export.|
The Trial Manager module has the function to manage Traits that are available to use within Trials.
Actions available include:
- Adding new Traits;
- Removing a Trait (that is not used by any Trial);
- Editing Trait details;
- Viewing Trait information, e.g. Trait validation rules; and
- Organising them, e.g. using Trait Bundles.
The instructions below demonstrate accessing Traits via the Traits tab and provide an explanation of the available information:
|1||In the Trial Manager module, select the Traits tab at to display the Trait information panels.|
|2||Traits that are currently in KDXplore can be seen here. Selecting a trait such as the Trait at will display information about the selected Trait in the Details panel at . All information about a Trait is shown here including: Trait Name, Datatype, Validation Rule and Barcode.|
|3||In the Used by Trials panel, the Trials that are in KDXplore that are currently using the selected Trait will appear. For the example, only one Trial is using that Trait and it displays the Name, Acronym, and Planting Date of the Trial.|
Users can add new Traits which can then be added to Trials. These new Traits provide users the flexibility the add Traits after a Trial has been created, e.g. adapting a previously used Trial for a new experiment.
The following image and instructions demonstrate how to add new Traits.
New Traits can be added by:
|1||Select the Add Traits button at to create a new Trait. This will bring up the Edit Trait Properties at .|
|2||Within the Edit Trait Properties window are the key Trait fields. Enter the details of the Trait. More information on traits can be found below.|
|3||Select the Save button to save the new Trait and the Trait will be displayed in the Traits window.|
In order to add a new Trait, all of the following details must be entered:
|Trait Name||The name for the new Trait. Must be unique and short because it is displayed in the Scoring screen and there may be limited screen space on smaller devices.|
|Alias||An alternative name for the Trait. This can be something shorter than the Trait name and is optional.|
|Level||This will define the Trait as one that is relevant on the Plot or Sub-Plot level.|
|Description||This is an optional longer explanation of the Trait to assist in data entry.|
|Unit||The unit of measurement in which the Trait can be scored by e.g. centimetres so that a plant leaf can be measured|
|Validation Rule||The Validation rule optionally restricts the values being entered. The nature of the rule is dependent upon the selection of Data Type and can include a minimum and maximum value.|
|Add Traits to Bundle||Checkboxes that allow the user to add the new Trait to existing Trait Bundles.|
The Calc datatype for Trait’s will allow a Traits value to be derived from other Trait data that is available e.g. the user can create a Calc Trait called PLANT_AREA which is equal to PLANT_WIDTH x PLANT_HEIGHT.
|1||By selecting the Calc datatype from the drop-down menu at , a second expression panel can be seen in area .|
|2||Here an expression can be entered representing the derived value. Taking the example used previously, PLANT_AREA* would be: PLANT_WIDTH(asterisk)PLANT_HEIGHT. Traits can be typed, or selected from the Traits panel at .|
|3||The new Calc Trait can also be added to bundles in .|
Any details of a Trait can be edited if the user wants to change the characteristics of the Trait.
To edit Traits, the user must unlock the option. This can be done by selecting the Editing Locked option at in the image above. Trait editing is automatically locked so that details of Traits that are in use by Trials are not changed.
|1||Select a Trait by double-clicking it. This will bring up the Edit Trait Properties Window as shown at .|
|2||Make the desired changes to the Trait and then select the Save option at .|
It is best practice to lock Trait editing when finished editing Traits.
The KDXplore Trial Manager module has the ability to import Traits from external sources. Traits can be imported from either KDDart or a CSV file.
For Trait and Trial file format information please refer to the “KDSmart/KDXplore - CSV Import File Formats” help page.
The Trial Manager module allows for the creation of Bundles which are groups of traits that share a common theme. Adding traits to a bundle allows for easier visibility and management of related traits and custom bundles can be created by the user.
All traits will be automatically allocated to a bundle named All Traits. To create a new bundle, the user can:
|1||Select the Add Trait button at . It will give you the option of choosing to create a new Trait or bundle. Choose the Add Trait Bundle option.|
|2||The Add/Edit Trait Bundle window at will open and there will be a list of available traits. If a required Trait is not available, the bundle can still be created and then edited later. Choose the Trait required and select the Add Trait arrow at to add the selected trait to the new bundle. Multiple Traits can be selected at once by shift+clicking or ctrl+clicking (on Windows).|
|3||The Filter function at allows for Traits to be searched by Trait names and Traits can be added from the search results.|
|4||Pick a name for the bundle and enter it into the right panel . After adding Traits and entering a name, the bundle can be saved.|
Traits can exist in more than one bundle
Once a bundle has been created, it can also be edited to remove or add more traits, or to change the name of the bundle:
|1||Select the bundle to be edited.|
|2||Select the Edit Bundle button at on the toolbar. This will open the Add/Edit Trait Bundle window and traits can be added as were previously done. If more traits were added to the trial then they will now appear in the left panel and can be selected.|
|3||To remove a trait, select the trait to be removed in the right panel and select the Remove From Bundle button at .|
The All Traits bundle cannot be edited or removed.
A bundle can also be removed from the list of bundles and deleted:
|1||Select the bundle to be removed.|
|2||Then the Remove traits icon can be selected. If you have selected a bundle there will be the option to Delete Trait Bundle.|
|3||Once this option is selected, a window will open to confirm the removal of the selected bundle.|
Once a bundle is removed, it cannot be restored.
This is a common help topic for both KDXplore and KDSmart.
There are several methods of moving data into and out of KDSmart which can be found on the Data - Import, Export, Backup page. This topic focuses on using KDXplore with KDSmart, which provides more time saving and productivity benefits for the user. Previously, inbuilt software called KDXchange was used to exchange data between KDXplore and KDSmart. Both applications have recently been updated to include integration with Google Drive which requires much less effort in setup and whilst an internet connection is required, both devices do not need to be on the same WiFi network. Google Drive is now the recommended method, however there may still be a need to use KDXchange so both methods are outlined here.
The following sections outline the steps required for exchanging data between KDSmart and KDXplore:
- Setup - Connecting KDXplore to KDSmart Devices; and
- Transfer - Moving data (Trials, Traits and Tags) between KDSmart and KDXplore.
Beforehand, a little background information is useful in understanding some of the technicalities before launching into the task.
KDSmart and KDXplore are two flexible applications in the KDDart platform:
KDSmart is used on Android tablets or phones to collect phenotypic data in the field for Trials or Nurseries; and
KDXplore is a multiplatform desktop/laptop application which fullfils several roles including managing data on one or more KDSmart devices.
The following illustration depicts a simple trial data workflow for KDDart, however look to the centre to see KDSmart and KDXplore’s role in the workflow:
Whilst KDSmart can be used on its own using CSV files for data transfer there may be a need to upscale to multiple KDSmart devices and larger trials. Using KDXplore benefits the user by improving data management and handling.
Some of these benefits are:
- Work more efficiently and productively with Trial and Nursery data offline (away from office networks or Internet) using laptop or workstation, not just small screens of tablets or phones;
- Provides visualisation tools to assist with data exploration and review;
- Provides broader toolset coverage of the breeding cycle;
- Enables easier management and data exchange with multiple KDSmart devices;
- Retains data from each individual KDSmart device “download” with TableName/Operator/When details;
- Facilitates uploading data to a KDDart database when possible (i.e. when a connection to the office network/Internet is available);
- Barcode production for printing to use with KDSmart barcode scoring;
- Facilitates improved consistency amongst multiple KDSmart devices with Trait and Tag editing and distribution;
- Viewing Traits used in different Trials; and
- The ability to exchange data whilst on site so that data can be curated as efficiently as possible.
A few setup steps are required, however this has been made as easy as possible. The communication software between KDSmart and KDXplore is referred to as KDXchange.
Google Drive is a quick and easy way of exchanging data between devices and requires little set up time. The example provided will take you from exporting a Scoring Set from KDXplore to Google Drive, importing it into KDSmart, exporting the Scored Data file to Google Drive, and then importing that file into KDXplore for curation.
The process of exchanging data will be described in the following steps:
- Connect to the Internet
- Google Drive Setup
- Transferring Files from KDXplore to Google Drive
- Transferring Files into KDSmart from Google Drive
- Transferring Files from KDSmart to Google Drive
- Transferring Files into KDXplore from Google Drive
Step 1 - Connect to the Internet¶
Google Drive transfers will only work when devices are connected to the internet but they do not have to be connected at the same time. For example, a user on KDXplore may export a Scoring Set to Google Drive which is uploaded to their personal folder, turn off their computer, and then go out into the field and import that Scoring Set into to KDSmart. For users who do not have mobile data on their KDSmart device or are in an area that does not have signal, it will still be necessary to connect to WiFi.
For further information on setting up WiFi please see the Step 1 - Using WiFi section below.
Step 2 - Google Drive Setup¶
As well as having an internet connection, you will need to have a Google account which gives you access to Google Drive. A free account will provide 15gb of space which is more than enough for using with KDXplore and KDSmart. To sign up or access Google Drive see Google Drive.
This link will be usable on KDXplore, Android devices should have a Google Drive application that would usually be already installed by default but can also be found in the Google Play Store.
Step 3 - Transferring Files from KDXplore to Google Drive¶
Once a Trial, Trait or Tag has been created, it needs to be transferred to a KDSmart device for use in the field. The following instructions demonstrate how to transfer Trials (or other data) from KDXplore to Google Drive so that they can be used in KDSmart.
|1.||Ensure that Google Drive is opened in an internet browser and have KDXplore open to prepare for the transfer.|
|2.||Choose a Scoring Set such as the one at and then select the export button at .|
|3.||The Export window will display (as at ) which provides export options. Selecting the Browse button will allow you to choose a location on the computer to save the Scoring Set to. Ensure that the radio button for KDX file is selected so that it is ready to be used in KDSmart.|
|4.||Select either the Export or the Export & Close options within the Export window and the KDX file will be exported to your chosen location. A dialogue will open and ask whether you want to open the containing directory - do this is you want to transfer the file to Google Drive right away.|
Click+Drag the file into the web browser with Google Drive opened and drop it to complete the upload. The file should now appear in Google Drive and there will be a message which confirms that the upload has been completed.
Step 4 - Transferring Files into KDSmart from Google Drive¶
Files that have been uploaded to Google Drive from KDXplore need to be imported into KDSmart. The following steps will demonstrate how to open Google Drive on your device and choose files to be imported into KDSmart.
|1.||Navigate to the Trials screen and select the Import button at .|
|2.||Select an import option - for this tutorial choose the File KDX option at . This will open Google Drive.|
A successful import will result in the following screen. The attachment message indicates that there are no attachments to the Trial.
Step 5 - Transferring Files from KDSmart to Google Drive¶
Once data is collected by scoring with KDSmart, the data will need to be transferred to KDXplore for curation. Step 5 will demonstrate how to transfer scored data for KDXplore using Google Drive.
|1.||On the Trials screen in the above image, ensure that the Scored Trial that you want to transfer is selected and then choose the Options button at and then the Share option at .|
Once the file has been saved, confirmation notifications will be displayed on the device as seen in the below image. This will indicate that the Scored Trials are now stored in Google Drive.
Step 6 - Transferring Files into KDXplore from Google Drive¶
The final step is to load the Scored Trial from Google Drive into KDXplore. This will allow the user to curate and analysing the scored data.
|1.||Ensure that Google Drive is opened. If it is not, then there is a Google Drive button in KDXplore which will open it in a browser. This button is located at in the above image.|
|2.||Choose any file such as the one located at . Right-Click this file and then choose the Download option. This will download the file to the default location for your browser (e.g. The Downloads folder).|
Click+Drag the downloaded file (such as the one in the below image) to the Trials panel in KDXplore. This will display the Load Trial Data window at . The Download button can also be selected to display the Load Trial Data window.
|4.||Select/highlight the file you want to import, select a Source device, and then enter the Name of the Device User.|
Whilst the Google Drive method is now the recommended method for exchanging data between KDXplore and KDSmart, KDXchange is still provided as a backup method for exchanging data.
Connecting Devices has three steps.
Step 1 - Using WiFi¶
KDXplore and KDSmart devices connect and synchronise data using a WiFi network.
The KDSmart device(s) and the KDXplore laptop/PC must be connected and visible to each other on the same network (i.e. same wifi connection). This is a networking requirement and not a limitation of KDSmart/KDXchange.
Depending on the network configuration, there may be times when your PC/Laptop is connected to a wired network (not on WiFi) yet will be able to connect to KDSmart devices on WiFi.
Many organisational IT policies lock computer settings preventing the set up or activation of your own WiFi Hotspot without needing Administrator user access on the computer.
Before traveling to ‘the field’ we suggest you prepare, test and become familiarised with this means of connecting devices. Seek support in your organisation if needed.
If the message above is displayed try the Connect Anyway button, however this may result in mixed success. Only a couple of tries is needed!
In the Field - Your Own WiFi Hotspot¶
When a WiFi network is unavailable at your location, a portable WiFi hotspot can be created on your Laptop (if it has that capability). The connection can then be shared with your other KDSmart devices using KDXchange (see the above tip).
The KDXchange Window¶
The following image displays a section of the KDXchange screen highlighted to show the following areas:
- Connection panel is where the options to connect devices are located. This includes the IP Address where the KDXchange server will be created.
- KDXplore panel links KDXplore from the user’s computer. This means that the list of Trials, Traits, and Tags that are on the user’s version of KDXplore are displayed. The user will need to choose between either the Trials, Traits or Tags to be selected.
- KDSmart Devices is a list of all the KDSmart devices that are connected to KDXchange or are available for connection. The image demonstrates that a device named ‘Galaxy S8+’ from the user named ‘Tester’ is currently connected.
- Device is a panel which displays data from the currently connected KDSmart device.
KDXchange server software in KDXplore and KDSmart enables them to communicate and needs to be kept running on the pc/laptop until any synchronisation tasks between the devices has completed. Also the devices should be kept in close proximity whilst connected. Once tasks have completed the KDXchange server can be stopped.
Step 2 - Prepare KDXplore/KDXchange¶
Step 2 involves preparing KDXplore on the laptop/pc to communicate with KDSmart devices. The following steps must be performed on the laptop/pc:
|2.1 (KDX)||On the Laptop/PC start KDXplore and select the Trial Manager icon.|
|2.2 (KDX)||Select the KDXchange Server icon at top of the Trial Manager window to open KDXchange.|
|2.3 (KDX)||Select the Start button ( or Shift Start to enter address and/or port number) which is located at on the above image.|
|2.4 (KDX)||The Network/IP Address and the Port number need to be confirmed.
The selected Network/IP Address in this example is different to that of another computer. The IP address of the computer running KDXplore (suggested by default), is usually fine but can changed if required.
Select the OK button in the window at to confirm this IP Address.
The Port Number usually should be left at the default setting, however if it is changed, both KDSmart and KDXplore must have the same port number. Once OK has been selected, the window will disappear and the program will start listening for devices which means that it is scanning for available devices on the Wi-Fi network.
Once KDXplore is listening for devices, there will be a message displaying the IP address and port number at in the following image. By selecting the Stop button at , the user can stop KDXplore listening for devices.
Step 3 - Preparing KDSmart Devices For Upload/Download¶
Step 3 involves connecting one or more KDSmart devices via WiFi with KDXplore on the laptop/pc. These ‘connection’ steps are common to both Upload to KDXplore or Download from KDXplore and for Trials, Traits or Tags.
|3.1 (KDX)||Ensure that the KDXchange server is listening for any KDSmart device(s) from the previous Part 2 steps (as demonstrated above).|
A dialogue box will open which will ask for information about the device as seen in the following image:
Once user information has been entered, the device connection is complete. The KDXplore will should look like the following image:
To find information on importing CSV file formats, follow the link to the following KDSmart Help topic CSV Import File Formats which will open in a new tab.
Curation is the aspect of Trial Manager that allows for exploration, visualisation and QC/QA checking of phenotypic data. Entering curation with a new dataset, the aim is to assess data and either accept values from a device as quality information, or to correct values potentially using another data source. This can also be done by editing values manually. The result of curation is phenotypic data that has been pushed to the offline database of KDXplore as known values for the selected Trial and for later export if wished. See below for how to access Curation.
To access Curation:
|1||Curation can be located by entering the Trial tab of Trial manager at .|
|2||Select a Trial by clicking on it to display the Trial information.|
|3||Either double-click on the Trial, or select the Edit Current Trial button at to open the Curation window.|
- Curation Messages panel which displays information and messages about events that are occurring in the Curation window.
- Values panel displays information on selected sample values and allows for the editing of values.
- Plot Info & Traits panel lists all Traits that are in the Trial and contains checkboxes that are used to select Traits that can be used in curation.
- The Curation Samples panel displays all information on the selected Traits and samples within two tables:
The Plot Info & Traits panel lists all Traits that are included in the Trial that is being curated and plot information i.e. Plot numbers. The purpose of this panel is to select Traits and plot information that can be displayed in the Curation Sample panel. The checkboxes allow for quickly changing what is displayed to the user. Any changes to the items selected will be evident in the Curation Messages window. To select items, the user can:
To display any information about plots and Traits:
|1||Select a checkbox to an associated Trait or Plot Info as represented in .|
|2||If it is desirable to choose all traits, then select the Check Traits button at . Plot Info can also be selected by holding down the shift key before selecting the button. Holding down the ctrl key and then selecting the button will result in only Plot Info to be selected.|
|3||The Uncheck All Traits button at will uncheck all Traits that are currently chosen if it is selected. Plot Info will also be selected by holding shift and only Plot Info will be selected if holding ctrl|
|4||By selecting the Check Selected button at will only select Traits that are highlighted.|
|5||The selection of the Data Entry Mode checkbox will allow the user to choose Traits that they can use for the entering of new data.|
|6||Once The desired Traits have been selected, they will appear in the Curation Samples panel.|
Once Traits have been chosen in the Plot Info & Traits panel, they will appear in the Curation Samples panel and are displayed in both the Trait Instances table and the Curation Samples tables.
Curated Values appear in the sample table as Bold.
Missing Values appear as an Empty cell.
The example below demonstrates how to open the Curation Samples panel and how to use different aspects of it:
- Each Trait that appears in the Trait Instances table (such as the EH_CM Trait in ) will correspond to a Trait that is in the Curation Samples panel (as seen in ).
- To present information on a specific Trait in the Curation Samples panel, double-click any trait in the Trait Instances panel.
- The options in area allow the user the choice for displaying sample information;
- Hide Inactive Plots allows for hiding plots which have been marked as inactive.
- Un-Curated will only include samples that have been curated.
- Only Scored displays only samples that have so far been scored.
- The Help button at has a help guide to the Curation Window.
- Values that are in the database have a symbol represented by 3 blue bars (e.g. ). Values from devices are shown with a red corner (if no value has been selected). When there are multiple values from different sources a yellow caution triangle is visible in the top left corner of each cell.
There are some options for Trait samples that are available to the user in the Curation Samples shown at that can be reached by selecting either singular or multiple values, and then right-clicking the values:
- Accept/Supress Values will either accept values as being valid, or supress values that the user deems as invalid. If this option is chosen then a dialogue box requesting information on the reason why it has been either accepted or supressed will appear.
- Activate Plot/Reactivate Plot will deactivate an entire plot e.g. column 6, row 1 at . Note that a deactivated plot will be ‘crossed out’. Deactivated plots can be reactivated by choosing the Activate Plot option.
- Heatmap/Scatter Plot/Box Plot creates a visualisation of the selected data. More will be explained about visualisation in the future.
- Inspect Plot opens the Plot Inspection window.
The Plot Inspection window displays a visualisation of a comparison of selected Traits from selected plots. It is highly customisable, and can be saved as a .PNG file or printed directly from KDXplore. To access the Plot Inspection window, simply righ click a value or mulitple values, and choose the Inspect Plot option.
One of the primary functions of the Trial Management module is to curate data that is collected from the field before it is uploaded to KDDart. Values can be curated in a number of different ways in KDXplore. Once a value is selected, typing a value will immediately fill the cells and this must be confirmed by pressing the Enter key. Values can only be curated to values included by their validation rules, E.g. for EH_CM with a validation rule of (30...200). KDXplore will not let the user choose values that are below 30 or above 200. Simple statistics can be displayed when there are multiple sample sources for the selected measurements. These statistics are displayed in the Trait Values panel.
The most simple way to curate Trial data is to curate a single value. The examples below demonstrates how to curate a single measurement.
Curating a single measurement can be done by:
|1||Select a single measurement such as the one at . This will display the measurment information in the Values panel at .|
|2||Enter the new value into the text-field at . You will be able to see that as you type this value, the corresponding value in the Trait Instances panel will also change in real time.|
|3||It will not be set permanantly until you select the Set Value button at .|
All previous changes and edits are listed in the Values panel as seen below:
If the user would like to make a change to a previous edit, then they can choose that particular section and edit that e.g. If a value is set to missing and then the curation is saves, there is no option to undo the changes in values. In this situation, the user can select the particular edit such as , and then delete the change (at ) which will revert the sample value to its original value.
The Value panel also has the functionality of displaying multiple samples at once. This allows for the selection of multiple samples to curate at once and can make curation of multiple samples easier and more efficient.
In the above image, the user has selected multiple samples in and they are all displaying in the Values panel in . Samples are curated the same as in Single-Selection Curation, however there are additional display options such as the ability to display/not display curated and un-curated values.
Specific Trait instances can be curated across the entire Trial. The below example provides an example of how to access this function.
Navigating to the Sample Data tab of the sample editor panel seen in area , the dataset available for the trial can be seen. By Selecting a dataset that is not the database set such as in , sample measurements for one, or multiple selected Trait instances can be curated for the entire trial. Select the Trait instance or option by using the drop down seen in area .
If changes to samples are made, then they need to be saved which can be done when exiting the Curation window and or by choosing the Save button at the top of the window.
A quick and simple way of curating measurements is by accepting or suppressing values. It will be necessary to accept values if there are measurements from multiple devices in the dataset. The accepting is the choice of one of the values as the correct one and supressing a value marks it as the incorrect value.
This can be done by right-clicking on a sample as in and then either choosing Accept Values(s) like in or Suppress Values(s) as in . This will open a dialog (as seen below) where the sample source can be accepted or supressed. This is where you select a device (or data source) from the drop-down menu.
Accepting a measurement
Supressing a measurement
Values can also be accepted from visualisation tools, as seen below. Specific visualisation tools are covered in the following sections.
if there is no sample source for values the curated values of cells will be changed to MISSING.
Any changes made to Trial data in the Curation window will need to be saved to take effect. When sample measurements are curated in KDXplore they do not become the “database” value for that plot until they are saved. Before exiting curation, if changes have been made a dialog will appear confirming exit-without-save. All device measurements will still remain once curation is complete.
Select the Save button at to save the curated values into the KDXplore offline database. Measurements can also be saved by selecting the File option at . The Curation window also displays the amount of changes that have been made in which can inform the user as to whether they need to save or not. The Undo/Redo buttons at allow changes to be undone or redone.
Data from Trials can be exported from KDXplore through the Curation Export function. This allows for data to be more easily curated in the Trial Management module and then exported as a file so that it can be shared with other devices. The image below provides an example of how data might be exported.
Curated data can be exported by:
|1||Select the Export button seen in area . This will open the Export Curated Data window as seen at .|
|2||Either enter a desired file path into the text-field, or select the Choose button in Toto choose a location for the exported data.|
|3||Choose a name for both the X Axis and Y Axis in . The default name for these axes are Column and Row, and by choosing the Use Names From Trial button will allow the user to set their own names for these axes to the exported data.|
Determine the options for:
|5||The area in allows for setting particular values when exporting. The Use/Show Defaults button will set the default value for each field e.g. the Missing Values field will be set to MISSING.|
The ability to display outliers in data measurement will enable the user to determine possibly incorrect or notable measurements. The example below demonstrates how to display outliers for a particular Trait.
This can be done by:
|1||Right-clicking a trait in the Trait Instance table (i.e. ), the option to Show Outliers can be selected from the menu.|
|2||Selecting this will display the values of outliers in a dialogue that is opened at . It will also highlight the outlier measurements in the Curation Samples table and visualisation tools at .|
KDXplore’s Trial Management Module provides users with a variety of data visualisation options.
Visualisations for Trait Instances can be generated from both Trait Instance tables, the Curation Sample table, or from the tool bar at the top of the Curation window. Simply right-click a Trait Instance in the Trait Instance table or a group of samples in the Curation Sample and select the intended action e.g. Heat map. The following examples will detail the steps for creating each type of visualisation.
The Trial Management Module can create a Heat-Map which is a representation of the experiment data that is displayed as varying colours.
To generate a heat map:
|1||First select the Heat Map button at . This will display the Heat Map window at .|
|2||Select both the axes and a value to display. The axes are set to the X and Y axis (which in this case are the Column and Row) by default. Select a trait instance and then the Value button at .|
|3||Once the desired values have been chosen, select the Create Heat Map button at .|
|4||This will display the heat map in a separate window at .|
The Trial Management module also has the function of creating a Scatter Plot to represent experiment data.
To begin creation of a scatter plot:
|1||Select the Scatter Plot button at . This will display the Scatter Plot window at .|
|2||The first checked Trait Instance will be the X-value in the to-be-generated scatter plot. Multiple Trait Instances can be plotted to the same plot by selecting multiple value instances. In the example above, the value EH_CM was chosen first at so it was automatically defined a the X-axis. The next value to be chosen was the PH_CM at .|
|3||Once the desired Traits have been chosen, select the Continue button at . The scatter plot will be generated and displayed as in .|
Another graph that can be created is the Box Plot.
To begin creation of a box plot:
|1||Select the Box Plot button at . This will display the Box Plot window at .|
|2||The first checked Trait Instance will be the X-value in the to-be-generated box plot. Multiple Trait Instances can be plotted to the same plot by selecting multiple value instances. In the example above, the value EH_CM was chosen first at so it was automatically defined a the X-axis. The next value to be chosen was the PH_CM at .|
|3||Once the desired Traits have been chosen, select the Continue button at . The box plot will be generated and displayed as in .|
|4||Outliers, mean and median can all be seen on plot and deactivated using the check boxes at the bottom of the Box Plot window.|
The Field View allows the user to have a top-down view of a grid which represents the plots of the experiment. The following image details steps for opening Field View.
To open the Field View window:
|1||Select the Field View button at and then choose the Field View option. This will open the window at .|
|2||The user can select a Trait Instance to display at .|
|3||By selecting specific plots as in the ones at , the user will be displaying these plots in the Values panel and the Curation Samples table as seen at .|