User Manual (Version 1.5)

Chapter 1: Getting started
Chapter 2: Main user interface
Chapter 3: Files window
Chapter 4: Settings window
Chapter 5: Signals module
Chapter 6: K-values module (HFD only)
Chapter 7: Sap flux density module (HFD and TDP)
Chapter 8: Sap velocity module (HRM only)
Chapter 9: Dynagage calculation module (Dynagage only)
Chapter 10: Sap flow rate module
Chapter 11: Visualise module
Chapter 12: Graph properties and navigation
Chapter 13: Tools

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 analyse the data.

Supported sensors

This version of Sap Flow Tool supports 6 sap flow measurement devices:

  1. HRM: Sap Velocity Probe (SVP): first generation HRM (Heat Ratio Method) sap flow sensor.
  2. HRM: HRM Sap Flow Meter (HRM-SFM): second generation HRM (Heat Ratio Method) sap flow sensor.
  3. HFD: Heat Field Deformation sensor.
  4. HFD: HFM Sap Flow Meter (HFD-SFM): second generation HFD (Heat Field Deformation) sap flow sensor.
  5. TDP: Thermal Dissipation Probe: Granier type sapflow sensors.
  6. Dynagage: Dynamax Dynagage heat balance sap flow sensors.

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

Sap Flow Tool is also able to visualise data from any other ICT International or non-ICT International sensor!

Chapter 2
Main user interface

This chapter introduces the main user interface of the Sap Flow Tool. More specifics about each part of the interface will be given in subsequent chapters.
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:

Data Analysis modules HFD

HRM:

Data Analysis modules HRM

Non-sap flow sensors:

Data Analysis modules other

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 and TDP), sap velocity calculation (HRM only), Dynagage calculations (Dynagage only), sap flow rate calculation and custom data visualisation. 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

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 files: Add one or more data files to the current SFT project.
    • Save: Save the current SFT project.
    • Save As: Save the current SFT project under a different name.
    • Exit: Close the application.

  • Account menu
    • Log in: Log in with your Sap Flow Tool account email address and password.
    • Log out: Log out.
    • Work offline: Work offline (requires a registered USB copy protection dongle).
    • Create account: Create a new Sap Flow Tool account.
    • Change password: Change your Sap Flow Tool password.
    • Forgot password: Start the password recovery process.
    • Dongle info: Info on the USB copy protection dongles attached to the system.

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

  • Export menu (single sensor selected in the Files window)
    • Signals: Export the (cleaned up) signals to a .csv file.
    • K-values: (HFD only) Export the K-values to a .csv file.
    • Uncorrected velocities: (HRM only) Export the calculated uncorrected sap velocities of an HRM sensor measuring raw temperatures to a .csv file.
    • Calculations: Export all calculations 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, .tiff or .bmp image.
    • Current graph data: Export the current graph data as .txt files for further processing. If the curves have different timelines, multiple files will be created.

  • Export menu (multiple sensors selected in the Files window)
    • Batch export signals: Export the (cleaned up) signals for all the selected sensors to .csv files.
    • Merge signals: (identical sensors only) Merge the signals of the selected sensors and export them as a .csv file.
    • Batch export uncorrected velocities: (HRM only) Export the calculated uncorrected sap velocities of all the selected HRM sensors measuring raw temperatures to .csv files.
    • Batch export K-values: (HFD only) Export the K-values of all the selected HFD sensors to .csv files.
    • Batch export calculations: Export the calculations for all the selected sensors to .csv files.
    • Batch export daily flows: Export the daily total sap flows for all the selected sensors to .csv files.
    • Current graph: Export the current graph as a .jpg, .tiff or .bmp image.
    • Current graph data: Export the current graph data as .txt files for further processing. If the curves have different timelines, multiple files will be created.

  • 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.
    • License: Display the Sap Flow Tool end-user license.
    • Check for updates at startup: Check this item if you want to check for new versions every time the application starts.
    • Check for updates: Check for updates now.
    • 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.

Attach / detach window

Preferences dialog

Global preferences for graph properties and units can be changed in the preferences dialog. Access it through the menu: File > Preferences... (Windows) and Sap Flow Tool > Preferences... (Mac).

Graph properties

  • Graph title: Font size for all graph titles.
  • X-axis: Font size of the X-axis title and labels (numbers).
  • 1st Y-axis: Font size of the first Y-axis (left) title and labels (numbers).
  • 2nd Y-axis: Font size of the second Y-axis (right) title and labels (numbers).

The default graph properties will only be applied to all new graphs and projects. You can push the 'Apply to all graphs' button to apply the current settings to all the graphs of the current project.

Preferences graph properties

Units

  • Velocities: Preferred unit for velocities like heat pulse and sap velocities.
  • Flux densities: Preferred unit for flux densities like the sap flux density.
  • Flow rates: Preferred unit for flow rates like the sap flow rate.
  • Volumes: Preferred unit for volumes like the cumulated and daily sap flow volume.

The selected units will affect all calculated values for velocities, flux densities, flow rates and volumes. Exported data will also use these units.

Please note that changing units doesn't automatically change graph axis autoscaling and graph curve filter properties for graphs in the Visualise module. You might need to change these properties manually to match the changed units.

Preferences units

Chapter 3
Files window

Add and remove data files to and from the current project.
Switch between different sensors.
Quick view graph to quickly inspect the project data.
Files window

Adding files

  • In order to add a data file to the project, click the "Add a new data file" button on the button bar. Next, select the file you want to add from the file selection dialog.
  • Multiple files can also be added simultaneously by selecting them from the file selection dialog.
  • Files can also be added by dragging them into the files list.
  • ICT International data files always have an ".csv" extension. If you want to add non-ICT International data files, please make sure their extension is ".txt".

Removing, renaming, inspecting and reordering files

  • Remove a file from the project by selecting it in the tree and clicking the "Remove from project" button on the button bar. Files will NOT be removed from the file system.
  • Files can be renamed by selecting them in the tree and clicking the "Rename file" button on the button bar. This will also rename the file on the file system.
  • Data files can be opened in a text editor by selecting them in the tree and clicking the "Open data file in text editor" button on the button bar. Currently loaded data will not be reloaded automatically.
  • The files order in the list can be modified by clicking the "Move up" and "Move down" buttons on the button bar.

Browsing the files tree

  • Each loaded file will show up in the files tree with its filename at the first tree level. Hovering over a filename will show the complete path for that file.
  • For each ICT International file, a list of available sensors is shown on the level just below the file name. Switching between sensors is achieved by clicking on the respective sensor name. Below the sensor level, all calculated values are available in a hierarchical structure. Sensor and wood properties need to be set for each individual sensor.
  • For some sensors an "Additional data from file" item is available which will show data columns that have been loaded from the data file but have not been calculated by Sap Flow Tool.
  • Non-ICT International files only show a list of data columns on the level just below the file name (no sensor level).

Working with non-ICT International data files

  • If you want to add non-ICT International data files, please make sure their extension is ".txt".
  • Once an non-ICT International data file has been added to the project, a file settings dialog box will open. Use this dialog box to change the file import settings: e.g. the delimiter, decimal separator, date/time format and header configuration. A preview area shows how the data file will be processed.
  • Non-ICT data file settings can be altered by selecting the file from the tree and clicking the "Change non-ICT data file settings" button on the button bar. This will open up the file settings dialog box.
Non-ICT International data file settings

Quick view graph

Quick view graph
  • The Quick view graph can be enabled or disabled by clicking the "Quick view graph" button on the button bar. This will allow visualising any selected item from the Files window tree.
  • Leaving the Quick view graph open allows to quickly switch between items.

Chapter 4
Settings window

Control which data will be used for analysis.
Set sensor and wood properties.

Data settings

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

As of Sap Flow Tool 1.3 data analysis periods are no longer supported. If you want to apply different sensor and/or wood properties to different parts of your data, it is recommended you split up the data file into several files. This can be achieved by using "Remove data" filters in the Signals module and exporting the signals. The signals can then be (automatically) reimported and be given different wood and/or sensor properties. Finally, the calculated sap flows can be merged again in the Visualise module.

Wood and sensor properties

Wood properties

Wood dimensions

Wood dimensions can be fixed for the entire data set or changing based on diameters loaded from a file.

Fixed wood dimensions

Wood properties
  • 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.
    • Beyond last thermistor

Changing wood dimensions

Follow these steps to load diameters from a file:

  1. Select 'From file' as the Type of the wood dimensions.
  2. Load the stem diameters as a non-ict data file (.txt) in the Files window. Note that the diameters should be in cm. Sap Flow Tool will not convert other units automatically. Also note that the diameters should be the outer stem diameters including the bark.
  3. Then drag the item containing the stem diameters from the Files window to the 'Stem diameter (cm)' field of the Wood properties tab.
Changing wood dimensions

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

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

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.

  • Raw temperature HRM:
    • Prepulse temperature: Algorithm to use to calculate the pre-pulse reference temperature.
      • 30 second average: Average temperature of the 30 seconds preceding the pulse.
      • last 3 seconds average: Average temperature of the last 3 seconds preceding the pulse.
      • slope and intercept: (default) Temperature correction based on the slope and intercept of the pre-pulse temperatures.
    • HPV algorithm: Heat pulse velocity algorithm.
      • HRM: (default) Classical HRM algorithm.
      • HRMX: Export only.
      • MAXMAX: Export only.
      • CHPM: Export only.
      • TMAX: Export only.
      • HRMold: Export only.

TDP sensor properties

TDP sensor properties
  • First thermocouple depth (cm, below bark): Depth (below the bark) of the first thermocouple.
  • Thermocouple distance (cm): Distance between the thermocouples in a needle.
  • Granier scaling coefficient (cm³.cm–².s–¹): Scaling coefficient of the Granier TDP power function.
  • Granier power coefficient (-): Power coefficient of the Granier TDP power function.

  • dTmax settings for each position:
    • Position: Thermocouple position for which the dTmax settings are shown.
    • dTmax type: Specify how the dTmax should be determined
      • Daily maximum: Value determined for each day between the start hour and the start hour of the next day
      • Period maximum: Value determined by the maximum of the entire calculation period.
      • Manual: Manually specified value.
    • dTmax start hour (h in 24h period): Hour at which the dTmax calculation interval starts. Should be taken as the time most closely approaching zero flow conditions.
    • Manual dTmax (mV): Manual dTmax value which will be used for the entire calculation period.

Dynagage sensor properties

Dynagage sensor properties
  • Heater resistance, R (Ohm): Resistance of the Dynagage heating element.
  • Thermocouple spacing, dX (mm): Thermocouple junction spacing.
  • Initial Ksh (W.mV–¹): Initial Ksh value which will be used for the measurements before the time instance at which a value can be determined automatically.
  • Fixed: Use a fixed Ksh value for the entire period.
  • Ksh interval start and stop (in 24h period): Start and stop hour used for automatic Ksh calculation.
  • Minimum flow rate (% of max flow rate so far): Always ensure a minimum flow. Minimum flow = percentage of the maximum flow encountered so far.
  • Low flow detection: Enable low flow detection. Low flow if dT < threshold AND Qf < percentage * Pin. Flow will be set to 0 when low flow is detected.
  • Low flow dT threshold: dT threshold used for low flow detection.
  • Low flow Pin percentage: Pin percentage used for low flow detection.

Chapter 5
Signals module

Visualise the raw signals.
Remove and fix bad measurement data.
Signals module

Raw signal visualisation

In the Signals module the raw symmetric and asymmetric signals are visualised for HFD, the raw heat pulse velocities for HRM, the thermocouple and heater measurements for Dynagage and the probe temperature differences for TDP. Clicking the "Symmetric" and "Asymmetric" buttons allows switching between both signal types (HFD only). For HRM-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 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 mark area to filter 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).

Bad data removal
Caution: Artificial data will be generated when using the data filters (except for "Remove data").

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.

Tip: Once a data set has been cleaned up it can be exported (using the "Export > Signals" menu) to a .csv file for further use in Sap Flow Tool or another application.

Chapter 6
K-values module (HFD only)

K-value data analysis (automatic, regression or manual).
Visualise the K-values as a function of time.

Obtaining K-values

K-value data analysis

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.

Note: The HFD 'K'-value should not be confused with 'k' which is used in many sap flow publications to denote thermal diffusivity. The HFD equations use 'D' for thermal diffusivity.
  • 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.
Tip: Differences between the "S/A vs. S-A" and the "S/A vs. A" K-values might indicate that the needles have not been installed parallel to each other.

Visualising the K-values

Visualise 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 and TDP)

2D visualisation of sap flux densities as a function of time and depth (radial profile).
3D visualisation of sap flux densities.

HFD sap flux density calculations

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

Flux density equation

or for reverse flow situations:

Reverse flux density equation

where Qi is the sap flux density (cm³ cm–² h–¹) at position i, 3600 (s.h–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.

Note: The HFD 'K'-value should not be confused with 'k' which is used in many sap flow publications to denote thermal diffusivity. The HFD equations use 'D' for thermal diffusivity.

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.

TDP sap flux density calculations

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

Flux density equation

where Qi is the sap flux density (cm³ cm–² h–¹) at position i, 3600 (s.h–¹) a factor to convert seconds into hours, alpha the Granier scaling coefficient (cm³.cm–².s–¹), beta the Granier power coefficient (-), dTmax the maximum temperature difference at zero flow conditions (mV or °C) and dT the temperature difference between both probes (mV or °C).

Sap Flow Tool allows to determine the dTmax value in three ways. (1) by automatically determining the maximum temperature difference for each day. For this option, a starting hour should be entered in the sensor settings. This will define the period corresponding to one day, e.g. from 6 am till 6 am the next day. (2) by automatically determining the maximum temperature difference for the entire period. (3) by specifying the maximum temperature difference manually.

An example TDP calculation is shown in the Sap Flow Tool example 'sample_8_tdp.sft'. Use the sample data file (sample_8_tdp.csv) as a template to import your own data. Rename the data file and replace the sample date, time and temperature difference columns with your own data and import the new file into Sap Flow Tool. Make sure to use a .csv file extension, otherwise the data file will not be recognised as a sap flow sensor data file.

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

  • Granier A. (1987) Evaluation of transpiration in a Douglas-fir stand by means of sap flow measurements. Tree Physiology, 3, 309–20.

2D sap flux density visualisation

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 Animate radial profile 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

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)

2D visualisation of sap velocities as a function of time and depth (radial profile).
3D visualisation of sap velocities.

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:

Raw heat pulse velocity 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:

Flux density equation

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.

Note: The thermal diffusivity constant 'k' should not be confused with the HFD 'K'-value. The HFD equations use 'D' for thermal diffusivity.

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.
Note: The void fraction equation (Eq. 11) in the paper of Burgess et al. contains an error: 'rho_b * 0.6536 + m_c' should be 'rho_b * (0.6536 + m_c)'. Sap Flow Tool uses the correct equation to calculate the void fraction.

2D sap velocity visualisation

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 Animate radial profile 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

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
Dynagage calculation module (Dynagage only)

Visualises the intermediate Dynagage sap flow calculations.

Calculations of Dynagage data are performed according to the method described in the Dynagage installation and operation manual (see reference below).

Intermediate Dynagage calculations are shown on the Dynagage calculations graph. The last curve on the graph called 'Errors' shows the error codes of any problems encountered during the calculations:

  • 0: No error
  • 1: Negative or 'NAN' (not a number) values encountered. These values are replaced by 0 automatically.
  • 2: Low flow detected according to the sensor settings. Values are replaced by 0 automatically.

The Ksh value which will be used for the sap flow calculations ('Ksh in use' curve) can be fixed for the entire period or determined automatically for each measurement day. Automatic determination of the Ksh value works by taking, each day, the average of the calculated Ksh values ('Ksh' curve) from a period determined by a start and stop hour. This start and stop hour should correspond to the period of zero flow conditions, typically at the end of the night.

In situations where zero flow conditions are not present (e.g. in some greenhouse situations), Sap Flow Tool allows to set a minimal flow during the night. This works by incorporating a certain percentage of the maximal flow encountered so far in the Ksh calculations. See reference of Vermeulen and Steppe (2007) for more details about this.

An example Dynagage calculation is shown in the Sap Flow Tool example 'sample_7_dynagage.sft'. Use the sample data file (sample_7_dynagage.csv) as a template to import your own data. Rename the data file and replace the sample date, time and temperature difference columns with your own data and import the new file into Sap Flow Tool. Make sure to use a .csv file extension, otherwise the data file will not be recognised as a sap flow sensor data file.

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

  • van Bavel M.G., van Bavel C.H.M. (2005). Dynagage installation and operation manual. ftp://ftp.dynamax.com/manuals/Dynagage_Manual.pdf
  • Steinberg S., van Bavel C. and McFarland M. (1989). A gauge to measure mass flow in stems and trunks of woody plants. Journal of the American Society for Horticultural Science, 114, 466–472.
  • Vermeulen K. and Steppe K. (2007). Solutions to Overcome Pitfalls of Two Automated Systems for Direct Measurement of Greenhouse Tomato Water Uptake. HortTechnology, 17, 220–226.

Chapter 10
Sap flow rate module

2D visualisation of sap flow rates and sap flow volumes (cumulated and daily totals).
3D visualisation of sap flow rates.

Sap flow rate calculations

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

Flow rate equation

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 and TDP) 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 and TDP) 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 and TDP) 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 flow volumes (cm³) are also calculated for the "Total" and "Total+" flow rates, "Cumulated" and "Cumulated+" respectively. Beside cumulated sap flow volumes, also total daily sap flow volumes are calculated ("Daily" and "Daily+").

Total, Flow+ and Total+ sap flows

2D sap flow rate and volume visualisation

2D sap flow rate and volume visualisation

The 2D graph of the sap flow rates and sap flow 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 flow volumes (cumulated and daily totals) can be read from the right Y-axis.

3D sap flow rate visualisation

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.

Note: The step-like pattern of the sap flow rates is the result of the assumption that within each sapwood ring the sap flow rate remains constant. Depending on the choice made for the "Beyond last thermistor" property ("Wood properties" of the "Settings window"), the sap flow rate in the sapwood ring beyond the last thermistor will stay constant or decrease to 0.

Chapter 11
Visualise module

Combine data from several sensors.
Visualise non-ICT International data.
Modify graph data through data filters: e.g. remove, interpolate, integrate, moving average, linear transform, ...
Visualise module

Graphs

Working with graphs

  • In order to add a graph to the Visualise module, click the "Add graph" button in the Context window next to the graph list. Next, enter the graph title and an empty graph will be created.
  • Graphs can be renamed by selecting the graph and clicking the "Rename graph" button in the Context window next to the graph list.
  • Switching between graphs can be done by selecting the graph from the graph list in the Context window or by using the tabs below the graphs.
  • Graphs can be removed by selecting the graph and clicking the "Remove graph" button in the Context window next to the graph list.
  • Graph (and curve) properties can be accessed by clicking the "Graph properties" button on the graph button bar or through right clicking the graph and selecting "Properties" from the pop-up menu.

Graph properties

Visualise graph properties
  • Graphs can be given a title which will be shown above the graph.
  • The grid on the graph can be enabled or disabled.
  • Each graph axis (X-axis, 1st Y-axis and 2nd Y-axis) can be configured separately.

Curves

Working with curves

  • Once a graph has been created, curves can be added by dragging items from the Files window to the graph.
  • Multiple curves can be added simultaneously by selecting and dragging multiple items in the Files window and/or selecting and dragging items which have subitems.
  • Curves can be removed by right clicking the curve legend item and selecting "Remove" from the pop-up menu.
  • Curve properties can be accessed by right clicking the curve legend item and selecting "Properties" from the pop-up menu.

Curve properties

Visualise curve properties
  • Curves can be removed by clicking the "Remove curve" button on the button bar.
  • The order in which the curves are shown on the graph can be changed by clicking the "Up" or "Down" buttons on the button bar.
  • Curves can be given a title which will be shown in the graph legend.
  • The data path shows the Files window path of the selected curve.
  • Curves can be merged with other curves on the graph. This causes the merged curves to appear as one curve on the graph.
  • Curves that are merged with other curves can be shown or hidden in the curve list by clicking the "Show/hide merged curves" button on the button bar.

Data filters

Data filters can be used to modify curve data.

Working with data filters

  • A data filter can be added to a graph by clicking the "Mark area" button mark area to filter button on the graph button bar. This will bring up the "Edit data filter" dialog box which can be used to configure the data filter.
  • Data filters can be modified by clicking the "Modify data filter" button in the Context window next to the data filters list.
  • Data filters can be removed by clicking the "Remove data filter" button in the Context window next to the data filters list.
  • The data filter order can be modified by clicking the "Move up" and "Move down" buttons in the Context window next to the data filters list. The data filters will be applied to the data in the order they are listed in the data filters list.
  • The curve filter box above the data filters list in the Context window can be used to filter out all the filters that are being applied to a certain curve. The filter is case sensitive and wildcards (? and *) are allowed.
  • Selecting a filter from the list marks the time period to which this filter is applied on the graph.
  • Hovering the mouse over a filter will show the period and the curves to which the filter is being applied.

Editing data filters

Visualise data filters
  • The beginning and end of the time period to which the filter is applied can be changed.
  • The type of filter can be changed by selecting one from the drop down box.
  • For each filter a short explanation is given together with some filter settings (if applicable).
  • The curves to which the filter will be applied can be selected by activating their respective checkbox.

Available filters

Following filters are available

  • Remove data: This filter removes data from the selected curves between the begin and end date/time.
    • All values: Removes all data.
    • Values above or equal to: Only removes data with values above or equal to a certain value.
    • Values below or equal to: Only removes data with values below or equal to a certain value.

  • Interpolate: This filter linearly interpolates data from the selected curves between the begin and end date/time.
    • All values: Interpolate all data.
    • Above or equal to: Interpolate only data above or equal to a certain value.
    • Below or equal to: Interpolate only data below or equal to a certain value.

  • Linear transform: This filter performs a linear transformation on data from the selected curves between the begin and end date/time. Transformed = Original * Multiplier + Offset.
    • Multiplier: Multiplier of the linear transformation.
    • Offset: Offset of the linear transformation.

  • Integrate: This filter calculates the surface below the curve between each two adjacent data points. The resulting unit is: Y-axis unit * time unit. The time unit can be selected below. E.g. MPa.h for a Y-axis unit in MPa and a time unit in hours.
    • Time unit: Time unit used to express the integral.
    • Allow negative values: Allow negative integrated values in case the data values are negative. Otherwise an absolute value is used.

  • Cumulate: This filter cumulates the data values in time.

  • Sum: This filter calculates the total sum of the data values within a specified time window. E.g. when a 1 day time window is chosen, daily sums are calculated.
    • Time window: Time window over which total sums of the data values are to be calculated.

  • Average: This filter calculates the average of the data values within a specified time window. E.g. when a 1 day time window is chosen, daily averages are calculated.
    • Time window: Time window over which averages of the data values are to be calculated.

  • Moving average: This filter calculates a moving average of the data values within a specified time window. E.g. when a time window of 2 hours is chosen, each data point will be assigned a value equal to the average of the preceding 2 hours of data.
    • Time window: Time window over which the moving average of the data values are to be calculated.

  • Absolute value: This filter returns the absolute value of the data.

Chapter 12
Graph properties and navigation

2D graph properties and navigation

2D graph navigation

Zooming and scrolling:

Zooming in on a graph can be achieved by selecting the "Zoom" button Zoom 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 Zoom out one step from the graph toolbar to zoom out one step. Use the "Esc" key or the "Zoom out full" button Zoom out full 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.

Value inspector:

Clicking the "Value inspector" button on the graph toolbar shows/hides the value inspector slider on the graph. Use the mouse to reposition the slider and read the numerical values of each of the curves below their title on the legend.

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 Graph properties from the graph toolbar.

2D graph properties
Tip: For very large data sets, using the "Thin lines" line style might improve software performance.

3D graph properties and navigation

3D graph properties

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 13
Tools

Data file stitching tool.

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.

Caution: Files should be ordered chronologically and have the same sensors in them (including the order in which the sensors appear in the file)!
Note: Loading a stitched file in Sap Flow Tool will produce a warning due to the presence of several headers in the .csv file. If you want to avoid this message, export the signals back to a .csv file and all excessive headers will be removed.

Legal Notice

Sap Flow Tool is based in part on the work of the Qwt project (http://qwt.sf.net) and the QwtPlot3D project (http://qwtplot3d.sourceforge.net).


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