User Manual (Version 1.2.2)

Chapter 1
Getting started

Load a sample SFT (Sap Flow Tool) project

In order to explore Sap Flow Tool it is recommended that you load one of the sample SFT project files. The Sap Flow Tool samples can be found in the 'Sap Flow Tool/samples' folder which was created in your "My Documents" folder during installation.

1. File > Open... (or press Ctrl-O).
2. Navigate to the "Sap Flow Tool/samples" folder in your home directory.
3. Select one of the ".sft" sample files.
4. Click Open.

Create a new SFT project

If you already have a data file, you can start analyzing it with Sap Flow Tool by creating a new SFT project.

1. File > New... (or press Ctrl-N).
2. Specify the SFT project file name.
3. Add data files in the Files window or use the File > Add data file... menu item.
4. Select the data file.
5. Click Open.
6. Select a sensor in the Files window to analyze the data.

Supported sensors

Sap Flow Tool 1.2 supports 3 sap flow measurement devices:

1. HRM: Sap Velocity Probe (SVP): first generation HRM (Heat Ratio Method) sap flow sensor.
2. HRM: Sap Flow Meter (SFM): second generation HRM (Heat Ratio Method) sap flow sensor.
3. HFD: Heat Field Deformation sensor.

More information about these devices can be found on the ICT-International website.

Chapter 2
Main user interface

Main window

The Main window is the central window of Sap Flow Tool. From here you get access to the data and the calculations in a structured way. The menu bar also provides access to file operations, view management, data export, tools and online help.

Data Analysis modules

HFD:

HRM:

The data analysis performed by the Sap Flow Tool software is split up into several steps: raw signal visualisation, K-value calculation (HFD only), sap flux density calculation (HFD only), sap velocity calculation (HRM only) and sap flow rate calculation. Each of these steps is represented by its own "Module". Switching modules can be achieved by clicking the appropriate button on the button bar.

Menu bar

• File menu
• New: Create a new SFT project.
• Open: Open an existing SFT project.
• Recent: Provides access to the most recently opened SFT projects.
• Add data file...: Add a data file to the current SFT project.
• Open data file in Notepad: Open an existing date file in Notepad for editing. Currently loaded data will not be reloaded automatically.
• Save: Save the current SFT project.
• Save As: Save the current SFT project under a different name.
• Exit: Close the application.


• View menu
• Files: Show/hide the Files window.
• Settings: Show/hide the Settings window.
• Context: Show/hide the Context window.


• Export menu
• Signals: Export the (cleaned up) signals for the active period to a .csv file.
• Calculations: Export the calculations for the active period to a .csv file.
• K-values: (HFD only) Export the K-values for the active period to a .csv file.
• Daily flows: Export the daily total sap flows to a .csv file.
• Current graph: Export the current graph as a .jpg image.


• Tools menu
• Stitch files: Stitch together several data files.


• Help menu
• User manual: Shows the Sap Flow Tool user manual.
• Changelog: Opens a detailed history of changes made to Sap Flow Tool.
• Dongle info: Info on the USB copy protection dongles attached to the system.
• Dongle update: Update an attached USB copy protection dongle.
• About: Information about Sap Flow Tool.

Files, Settings and Context windows

The Files window allows adding multiple data files to the current SFT project and switching between the sensors. The Settings window provides access to data and sensor properties. The Context window provides context specific properties of the currently selected module of the Main window. Switching to a different module causes its properties to be shown automatically in the Context window.

These windows can be detached from the Main window by clicking on their title bars and dragging them out of the Main window. Dragging a detached window onto the Main window allows reattaching it. The windows can be organized as tabs or in a vertically layout. Using the "View" menu, a closed window can be shown again or a visible window hidden.

Chapter 3
Files window

Press the "Add..." button to add a new data file to the project. Once loaded, data files are listed without extensions (hover above the file to get the full file name). For each file, a list of valid available sensors is shown. Switching between sensors is achieved by clicking on the respective sensor name. Sensor and wood properties need to be set for each individual sensor.

Data files can be removed from the project by selecting the data file name and pressing the "Remove" button.

Chapter 4
Settings window

Data settings

Tree / plant info

Information about the tree or plant the currently selected sensor is installed on. A general description field is also provided for more detailed descriptions about sensor placement, etc..

Data analysis periods

Data analysis periods can be defined to only analyse a subset of the entire data file. The first period listed is the complete data set (this period cannot be removed). Additional data analysis periods can be created by pressing the "Add..." button and selecting the start and end date/time in the dialog box. A data analysis period can be removed by selecting the period and clicking the "Remove" button.

Wood and sensor properties

Wood properties

Wood dimensions

• Stem circumference (cm): Circumference of the stem (including bark) at the location of sensor installation.
• Stem diameter (cm): Diameter of the stem (including bark).
• Bark thickness (cm): Thickness of the bark.
• Xylem radius (cm): Radius of the xylem (heartwood and sapwood).
• Sap wood depth (cm): Depth of the sap wood.
• Beyond last thermistor: Options related to what to do with the sapwood beyond the last thermistor (that is still in the sapwood).
• Linear decrease: Linearly decrease the flux density (HFD) or sap velocity (HRM) such that it reaches 0 at the heartwood boundary.
• Hold value: Keep the value of the flux density (HFD) or sap velocity (HRM) of the last sapwood thermistor position until the heartwood boundary is reached.

Thermal diffusivity

• Value (cm² s–¹): Thermal diffusivity of wet wood.
• Advanced calculation: Whether to use the advanced thermal diffusivity calculation (see below) or the above mentioned value.
• Sapwood fresh weight (g): Weight of a fresh sapwood sample.
• Sapwood dry weight (g): Weight of an oven-dried sapwood sample.
• Sapwood fresh volume (cm³): Volume of a fresh sapwood sample.

The advanced thermal diffusivity (cm² s–¹) calculation of based on the method described by Burgess et al. (2001) which makes use of the weight and volume of a fresh sapwood sample and the oven-dried weight of that sample. For information on this calculation please refer to e.g.:

• Burgess S.S.O., Adams M.A., Turner N.C., Beverly C.R., Ong C.K., Khan A.A.H. and Bleby T.M. (2001) An Improved Heat Pulse Method to Measure Low and Reverse Rates of Sap Flow in Woody Plants. Tree Physiology, 21, 589-598.

HFD sensor properties

• Axial distance (cm): Distance from the heater to the axial needle.
• Tangential distance (cm): Distance from the heater to the tangential needle.
• Thermistor distance (cm): Distance between the thermistors in the sensor.
• First thermistor depth (cm): Depth (below the bark) of the first thermistor.

HRM sensor properties

• Probe spacing (cm): Distance between the heater and the probe needles.
• Thermistor distance (cm): Distance between the thermistors in the sensor.
• First thermistor depth (cm): Depth (below the bark) of the first thermistor.
• Wound diameter (cm): Diameter of the wound caused by drilling.

Chapter 5
Signals module

Raw signal visualisation

In the Signals module the raw symmetric and asymmetric signals are visualised for HFD and the raw heat pulse velocities for HRM. Clicking the "Symmetric" and "Asymmetric" buttons allows switching between both signal types (HFD only). For SFM raw temperatures "Downstream" and "Upstream" buttons allow switching between the downstream and upstream temperature measurements.

Removing or fixing bad measurement data

Sap Flow Tool includes several data filters that allow fixing bad measurement data. Using following procedure to apply a data filter:

1. Make sure the bad data is visible on the graph (zooming into the correct region might be required).
2. Click on the "Mark area to filter" button in the graph toolbar.
3. Click and drag on the graph to mark the affected area.
4. In the dialog box, select the type of filter that should be applied (see below).
5. Click "Ok".
6. Repeat the procedure or click the "Zoom" button in the graph toolbar to stop marking data.

Depending on the type of bad data, several options are available:

• Remove data:
• All values: The selected data will be removed completely for all positions. This action will affect the heat pulse velocity signal (HRM), both upstream and downstream raw temperature signals (HRM) or both symmetric and asymmetric signals (HFD).
• Values above: All data from all positions above the specified value will be removed from the selection. For HFD and raw temperatures HRM the comparison is only performed for the signal type on which the filter is applied: e.g. symmetric/asymmetric or downstream/upstream. If data is removed from one signal type, data at the corresponding time instances of the other type is also removed.
• Values below: All data from all positions below the specified value will be removed from the selection. For HFD and raw temperatures HRM the comparison is only performed for the signal type on which the filter is applied: e.g. symmetric/asymmetric or downstream/upstream. If data is removed from one signal type, data at the corresponding time instances of the other type is also removed.


• Time interpolate:
• All values: The data for the selected positions will be replaced by a linear interpolation between the values just before and just after the selected period.
• Values above: For the selected positions, data above the specified value will be interpolated between data below the specified value. Note that interpolation is not possible when the selected period starts or ends with a value above the threshold. In that case, just remove the data.
• Values below: For the selected positions, data below the specified value will be interpolated between data above the specified value. Note that interpolation is not possible when the selected period starts or ends with a value below the threshold. In that case, just remove the data.

This action will be applied to the heat pulse velocity signal (HRM) or to the currently active signal type: symmetric/asymmetric (HFD) or downstream/upstream (HRM).


• Position interpolate: (HFD only)
The data of the selected position will be replaced by the linear interpolated/extrapolated value of two adjacent positions. This action will be applied to the currently active signal type: symmetric or asymmetric.


• Linear transform:
The data of the selected positions will be replaced by a linear transformation of the original data. Two parameters control the transformation: a multiplier and an offset. The transformed data is calculated according to: Transformed = Original * Multiplier + Offset. This data filter is specifically useful for data that needs to be shifted and stretched vertically. This action will be applied to the heat pulse velocity signal (HRM) or to the currently active signal type: symmetric or asymmetric (HFD).

Once a data filter is created, it will be added to the list of the Context window. Data filters are applied to the data in the order in which they appear in the list. Data filters can be moved up or down the list by selecting a data filter and pressing the "Move up" and "Move down" buttons. Properties of the data filters can be altered using the "Modify filter" button. Keeping the cursor above a data filter in the list will show a tooltip describing the data filter properties: e.g. affected positions. Selecting a data filter will highlight the area for that filter on the graph, clicking it a second time removes the highlighted area.

Note that data is never removed from the data file. The original data for a certain data filter can be restored by clicking the "Remove filter" button below the list of data filters.

Chapter 6
K-values module (HFD only)

Obtaining K-values

In order to calculate sap flow from the HFD sensor data, K-values need to be obtained for each thermistor position. The K-values are determined by plotting the difference between the symmetric and the asymmetric signal (S-A) and the asymmetric signal (A) with respect to the ratio of the symmetric and the asymmetric signal (S/A). This data is shown in the graph of the K-values analysis part of the K-values module. The K-value is found by extrapolating the data points to y-axis passing through S/A=0 (indicated by red dots on the graph). The K-value represents the temperature difference at the point of zero sap flow.

• K-values based on:
• Entire Period: K-values are calculated based on all the data from the selected data analysis period combined. The K-values obtained as such (for each position), will be used to calculate the sap flow for the entire period.
• Moving window: For each day, K-values are obtained based on data of the current day and a certain number of past days. If a window of 1 is specified, only the data of the current day is used.


• Window size (days): Specify the size of the moving window. Only available when "Moving window" is selected above.
• Day: Select the day for which to view and analyse the data. The date range for the used data is shown between brackets. Only available when "Moving window" is selected above.


• Position: Select the thermistor position for which to view and analyse the data.


• Type: Select how the K-values will be obtained.
• Automatic: This is the default setting. Using this option, K-values are calculated using a adaptive regression algorithm that will automatically determine the optimal portion of the data needed for the regression.
• From regression: When the "Automatic" setting is unable to obtain a valid K-value user intervention will be needed. Move the red vertical markers to select the portion of data to use for the regression.
• Manual: When the "From regression" setting does not allow to select a valid K-value, a value can be entered manually or obtained by moving the red horizontal markers.


• S/A vs. S-A value: K-value obtained from the S/A versus S-A data.


• S/A vs. A value: K-value obtained from the S/A versus A data.


• Average value: Average of the two K-values (S/A vs. S-A and S/A vs. A value). This value will be used for calculating sap flow for the selected position.


• Value: Only available when setting K-values manually.

Visualising the K-values

Clicking the "Visualise K-values" button shows the calculated K-values for each position as a function of time. Only when "Single days" is selected in the Context window, will the K-values change over time. Use this to quickly scan the K-values for possible abnormalities due to the automatic K-value calculation (visible as spikes on the lines). Closer inspection and manual K-value determination might be needed for these days.

Chapter 7
Sap flux density module (HFD only)

Sap flux density calculations

Sap flux densities are calculated for each positions according to following equation:

or for reverse flow situations:

where Qi is the sap flux density (cm³ cm–² h–¹) at position i, 3600 (s–¹) a factor to convert seconds into hours, D the thermal diffusivity (cm² s–¹), Zax the axial distance(cm), Ztg the tangential distance (cm), Lsw the sapwood depth (cm), K the K-value (°C) and Symmetric (°C) and Asymmetric (°C) the measured symmetric and asymmetric signals.

By default the reverse flow equation is used when the Symmetric signal is negative. This threshold value, however, can be changed in the HFD formula switching box of the Context window.

For more information on the background of these equations please refer to e.g.:

• Nadezhdina N., Cermák J., Gaspárek J., Nadezhdin V. and Prax A. (2006). Vertical and horizontal water redistribution in Norway spruce (Picea abies) roots in the Moravian Upland. Tree Physiology, 26(10), 1277-1288.
• Poyatos R., Cermák J. and Llorens P. (2007). Variation in the radial patterns of sap flux density in pubescent oak (Quercus pubescens) and its implications for tree and stand transpiration measurements. Tree Physiology, 27(4), 537-548.

2D sap flux density visualisation

2D sap flux densities are displayed as a function of time (upper graph) and depth (lower graph). The latter is called the sap flux density radial profile. The radial profile at each time instance can be visualised by moving the red marker line across the upper graph. This causes the corresponding radial profile to be shown in the lower graph. An animation of the radial profile can be initiated by clicking the "Animate radial profile" button from the graph toolbar. To stop the animation, click the button a second time. The animation speed can be controlled from the Context window. Sap wood depth and xylem radius are indicated by red lines on the radial profile graph.

Beside the sap flux densities at each position, the mean sap flux density is also calculated and can be shown by clicking on the "Mean" legend item.

The thermal diffusivity that is used to calculate the sap flux density is shown in the Context window. The K-values used to calculate the sap flux densities are also shown in de Context window depending on which type of K-value calculation method was chosen in the K-values module. Values will be displayed only for the "Entire period" option. If the "Single days" calculation option was chosen, no K-values are displayed since each day is calculated using a different K-value.

3D sap flux density visualisation

A 3D graph of the sap flux densities can be shown by clicking the "3D" button in the Context window. White/red/yellow colours indicate positive flow, green colours represent reverse flow.

The thermal diffusivity that is used to calculate the sap flux density is shown in the Context window. The K-values used to calculate the sap flux densities are also shown in de Context window depending on which type of K-value calculation method was chosen in the K-values module. Values will be displayed only for the "Entire period" option. If the "Single days" calculation option was chosen, no K-values are displayed since each day is calculated using a different K-value.

Chapter 8
Sap velocity module (HRM only)

Heat pulse velocity calculations (based on raw temperatures)

A Sap Flow Meter HRM device is able to record the raw temperatures upstream and downstream from the heater. Based on these measurements, raw heat pulse velocities are calculated using following equation:

where Vhi is the raw heat pulse velocity (cm h–¹) at position i, k the reference thermal diffusivity (0.0025 cm² s–¹), x (0.5 cm) the distance between the heater and the thermistor probes, v1 and v2 the increases in temperature (°C, from the initial temperatures) at equidistant points downstream and upstream from the heater and 3600 a factor to convert seconds to hours.

Sap velocity calculations (based on raw heat pulse velocities)

Both HRM devices can record raw heat pulse velocities. In order to calculate sap velocities from these measured heat pulse velocities, following equation is used:

where Vsi is the sap velocity (cm h–¹) at position i, k the thermal diffusivity (cm² s–¹), 0.0025 the reference thermal diffusivity (cm² s–¹), B the wound correction factor (-), ρb the basic density of wood (sapwood dry weight/sapwood fresh volume, kg m–³), cw the specific heat capacity of the wood matrix (1200 J kg–¹ °C–¹), cs the specific heat capacity of sap (water, 4182 J kg–¹ °C–¹), ρs the density of water (1000 kg m–³), mc the water content of sapwood ((sapwood fresh weight - sapwood dry weight)/sapwood dry weight, kg kg–¹) and Vhi the measured heat pulse velocity (cm h–¹) at position i.

As can be seen from the above equation, sap velocities are calculated from the (corrected) heat pulse velocities using 3 calculation factors. The first factor corrects for thermal diffusivity deviations from the reference value. The second factor corrects for possible wounding caused by sensor installation and operation. Finally the third factor converts heat pulse velocities to sap velocities. The calculation factors used to calculate the sap velocities are shown in de Context window.

For more information on the background of these equations please refer to e.g.:

• Burgess S.S.O., Adams M.A., Turner N.C., Beverly C.R., Ong C.K., Khan A.A.H. and Bleby T.M. (2001) An Improved Heat Pulse Method to Measure Low and Reverse Rates of Sap Flow in Woody Plants. Tree Physiology, 21, 589-598.

2D sap velocity visualisation

2D sap velocities are displayed as a function of time (upper graph) and depth (lower graph). The latter is called the sap velocity radial profile. The radial profile at each time instance can be visualised by moving the red marker line across the upper graph. This causes the corresponding radial profile to be shown in the lower graph. An animation of the radial profile can be initiated by clicking the "Animate radial profile" button from the graph toolbar. To stop the animation, click the button a second time. The animation speed can be controlled from the Context window. Sap wood depth and xylem radius are indicated by red lines on the radial profile graph.

Beside the sap velocity at each position, the mean sap velocity is also calculated and can be shown by clicking on the "Mean" legend item.

The calculation factors used to correct raw heat pulse velocities and convert them to sap velocities are shown in the Context window. The first factor shows the thermal diffusivity as used in the calculations, the second factor shows the wound correction and the third factor is used to convert heat pulse velocities to sap velocities.

3D sap velocity visualisation

A 3D graph of the sap velocities can be shown by clicking the "3D" button in the Context window. White/red/yellow colours indicate positive flow, green colours represent reverse flow.

The calculation factors used to correct raw heat pulse velocities and convert them to sap velocities are shown in the Context window. The first factor shows the thermal diffusivity as used in the calculations, the second factor shows the wound correction and the third factor is used to convert heat pulse velocities to sap velocities.

Chapter 9
Sap flow rate module

Sap flow rate calculations

Sap flow rates for each position are calculated according to following equations:

where Fi is the sap flow rate (cm³ h–¹) in the cross sectional area Ai (cm²) of the wood ring surrounding position i and Qi the sap flux density (cm³ cm–² h–¹) at position i (HFD) or Vsi the sap velocity (cm h–¹) at position i (HRM). The width of each wood ring equals two times the distance between thermistors.

The total flow rate ("Total") is calculated by summing the individual contributions of each wood ring. For the case where the sensor does not cover the entire sap wood depth an estimated flow rate in the remaining part of the sap wood (beyond the sensor) is also calculated (Flow+). Depending on the choice made for the "Beyond last thermistor" property ("Wood properties" of the "Settings window") it will be assumed that the sap flux density (HFD) or sap velocity (HRM) decreases linearly from the border of the wood ring of the last sapwood thermistor position to 0 at the heartwood boundary or that the sap flux density (HFD) or sap velocity (HRM) remains constant until the heartwood boundary. Both values can be added to obtain an estimated total flow rate for the entire sap wood ("Total+"). Cumulated sap volumes (cm³) are also calculated for the "Total" and "Total+" flow rates, "Cumulated" and "Cumulated+" respectively. Beside cumulated sap volumes, also total daily sap flow volumes are calculated ("Daily" and "Daily+").

2D sap flow rate and volume visualisation

The 2D graph of the sap flow rates and sap volumes can be made visible by clicking the "2D" button in the Context window. Sap flow rate values can be read from the left Y-axis while sap volumes (cumulated and daily totals) can be read from the right Y-axis.

3D sap flow rate visualisation

The 3D graph of the sap flow rates can be made visible by clicking the "3D" button in the Context window. White/red/yellow colours indicate positive flow, green colours represent reverse flow.

Chapter 10
Graph properties and navigation

2D graph properties and navigation

Zooming and scrolling:

Zooming in on a graph can be achieved by selecting the "Zoom" button from the graph toolbar, left clicking on the graph and marking the region of interest while keeping the mouse button pressed (a black zoom box will appear). Upon releasing the mouse button, the graph will be zoomed in. This procedure can be repeated several times. While being zoomed in, use the bottom en right scroll bars for further navigation on the graph. Press the middle mouse button or the "Zoom out one step" button from the graph toolbar to zoom out one step. Use the "Esc" key or the "Zoom out full" button from the graph toolbar to zoom out completely.

Zooming in and out of a graph can also be done by means of the scroll wheel on your mouse.

Hiding/showing curves:

The graph legend items can be clicked in order to show or hide certain graph curves.

Properties:

Right mouse clicking on a graph brings up a context menu which leads to the graph properties dialog. Use this dialog to change the appearance of the graph curves, enable/disable the graph grid and enable/disable axis autoscaling. The graph properties can also be accessed using the "Properties" button from the graph toolbar.

3D graph properties and navigation

Rotation and moving

In order to rotate the graph left click on it and move the mouse while keeping the button pressed. The default graph orientation can be restored by clicking the "Default view" button in the Context window. Use the "Top view" button to switch to a surface map view of the graph.

Left clicking the graph while also pressing the "Ctrl" key allows to move the graph left/right and up/down.

Scaling

Axis scaling can be achieved using the "Scale" controls in the Context window. A scale value of 1 represents no scaling, larger values increase the scale factor and smaller value decrease the scale factor.

Chapter 11
Tools

Data file stitching tool.

The data file stitching tool can be accessed through the "Tools > Stitch files" menu and makes it possible to stitch several raw data files together. The resulting file can then be further used in Sap Flow Tool.