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# 2 GPIV

## 2.1 Starting up

Gpiv may be launched in different ways. In case it needs to trigger the lasers and camera, the RTAI and gpivtrig Linux kernel modules will have to be loaded (and unloaded after closing Gpiv). The gpiv_control script (from the gpivtrig package, which also includes the gpivtrig module) might be used: "gpiv_control "gpiv [OPTION1] ... [IMAGE1] ..."". Gpiv_control has to be run with root privileges. In case no trigering is used or if the modules have already been loaded in the kernel, starting the application is straightforward with: "gpiv [OPTION1] ... [IMAGE1] ...". If the modules have not been loaded in the kernel, a warning message will be displayed and the trigger services will be disabled.
The Gpiv console consists a menu bar, a tool-bar, process toggle-buttons, a tabulator and a data buffer list (Figure 2.1). At the bottom of the console you can find an application bar that displays information of the highlighted item as well as a progress bar that displays the progress of the running process.
Gpiv reads its default program parameters from ~/.gnome2/gpiv following the GNOME mechanism. These parameters are defined frome the Settings->Preferences from the console menu's and may be overruled by command line keys for the current session. (Invoke "gpiv --help" or "man gpiv" for information about the command line options.) Apart from the Gpiv parameter settings, there are also variables to ease the use of the program, which can not be defined by command line keys. These variables are stored from previous sessions (like the last displayed tabulator, image base-names during recording or the last selected image-name during loading with File->Open). The PIV process variables that are used for recording, interrogation, validation and post-processing are read from ~/.gpivrc or from the system-wide available gpiv.conf (mostly installed at /etc/ under Unix/Linux) respectively. These process variables are shared with the programs from the Gpivtools package.

Figure 2.1 Gpiv console with image recording tabulator. This tab may (partly) be absent, depending on the configuration options during the building of the program

## 2.2 Menu and toolbar

The menu bar consists general tasks for Gpiv, like file-handling, preferences and help menus. Underlined characters represent the ALT short-hand key for launching the menus.

The "File" menu contains "open", "save", "save as", "close" for reading, storing, and closing data and "exit" for closing the application. For reading and saving images and data, Gpiv uses the Gnome Virtual File System (GVFS). This allows you to load data from an other system (server) you have access to, like ftp or ssh. Loading data from a server is done by typing Ctr+L when the filebrowser is open and typing, for example:
ssh:///my_other_account@another_system:image.png
or from Nautilus (see below).

The native image format for Gpiv is the Portable Network Graphics (PNG) format. Image data may also be read to or stored from raw binary data (name.r) that is accompanied by an ASCII header file (name.h) or HDF5 (name.gpi). Images of formats that use lossless compression (tif, gif, pgm, bmp) are converted to PNG during the loading to guarantee the storage of all header information. To save disk space, the original image will be deleted. In case of cross-correlation, it is expected that the second frame is attached to the first image frame. This may be performed manually with gpiv_combing from the Gpivtools package.

The maximum image dimensions that may be used are defined in gpiv_gtk.h by IMAGE_WIDTH_MAX and IMAGE_HEIGHT_MAX or by the options --enable-img-width and --enable-img-hight of the ./configure script. The maximum image dimensions can not be changed during execution of Gpiv. In case the image dimensions are larger, ./configure will have to be executed (or gpiv_gtk modified) and Gpiv will have to be recompiled. In case IMAGE_WIDTH_MAX and IMAGE_HEIGHT_MAX will have to be redefined, it is recommended to set them at the minimum needed values in order to save RAM memory usage.
After loading, the file basename is displayed in the buffer list and the complete image name is displayed in the "Image Info" tabulator of the console. A display window (or viewer) is launched that shows the image together with the interrogation area's and its name is displayed in the application bar of the viewer as well (Figure 2.2.

Figure 2.2 Buffer display containing image, Interrogation Area contours and data

Saving the image and data is done in PNG, raw binary or HDF5 format, depending on the program settings or start-up keys (--hdf and --hdf_img). Image data may also be loaded from the Gnome filemanager NAUTILUS with the "open with.." popup menu or by "drag and drop" of the selected images into the buffer list in case Gpiv has already been launched. Typing Ctr+L or from the Go->Location... menu of Nautilus, the filemanager can be connected to another system or server by using GVFS.

The settings menu contains the menus "gpiv buttons" and "tabulator" to (un)display these parts of the console and "preferences" for defining all Gpiv settings. Closing the "preferences" menu with "OK" stores the settings for future sessions. "Apply" only affects the current session. When settings for the buffer display have been changed, they will be broadcasted to all display windows when "OK" or "Apply" are pressed. "Cancel" closes the preferences window without action. Some parameter settings (image width and image height) need to restart Gpiv. You will be acknowledged in that case.

The "help" menu contains "show tooltips" for obtaining additional help. Tooltips are small windows that pop up when an item is highlighted and contain more extended information about the item than can be displayed in the short line of the application bar. The "manual" menu shows this document. "About" gives short info concerning this application.

The toolbar is a quick way for opening / saving / closing images and data, executing / stopping processes that are enabled by the process toggle buttons, which are found below the toolbar, for closing buffers and for exiting the program.

## 2.3 Process toggle-buttons

The process toggle-buttons may be switched on in order to define a chain of processes (pipeline). These processes include recording, image processing, image PIV interrogation, validation and post-processes of the PIV estimators. The parameter settings of the processes are defined in the tabulators of the Gpiv console. The pipeline process is invoked by the "Execute" button on the toolbar and, eventually, interrupted by the "Stop" button.

## 2.4 Buffer list and display window

The buffer list shows a number and the file basename (i.e. the filename without directory name and extension) of the loaded images. Images may be loaded directly into the buffer list by means of "drag and drop" from the Gnome file-manager NAUTILUS. A single buffer may be selected by pointing to it and left mouse clicking. Several buffers may be selected by clicking the first and last buffer while holding the "Shift" key. The execution of processes will than be performed on every selected buffer. The selected buffers will be closed following the Window manager protocol (mostly by pressing Ctrl-W).

For each buffer, a display window is launched that contains the image, squared frames that represent the contours of interrogation areas during the initial and the final step of an iterative interrogation process, a vector field representing the PIV estimators and solid, coloured, squares expressing the magnitudes of derived scalars obtained from the PIV estimators by post processing. The interrogation areas are highlighted when the pointer moves over them. At the bottom of the display window an application bar shows information concerning the data. If displaying of interrogation area frames is disabled, image intensities are shown. Else, the centre point of the highlighted interrogation area and, eventually, values of the PIV estimators and its derived quantities are shown. If the settings of Interrogation Areas are changed or, for some other reason not in accordance with the settings the PIV data have been generated, the PIV values will not be displayed. The same information is displayed in the application bar of the Gpiv console as well. A menubar at the top of the window shows options for changing the settings for the displaying of the data in the individual buffer window. When clicking the right mouse button when pointing within the display, a menu pops up with identic functions as the menubar. Zooming and moving (paning) the image and data may also be performed by the mouse scroll button and moving the pointer (when mouse select is set to "None" in the console) while pressing the left mouse button. In case the display settings will have to be adjusted for all open buffers, change the settings from the Settings->Preferences menu in the Gpiv console. Then, the new settings will be updated to all buffer windows when "Apply" or "OK" is pressed.

## 2.5 Tabulator

The tabulator contains pages with parameter settings and buttons to invoke the processes for image recording, information, processing and interrogation, PIV-data validation and post-processing. Some of these pages may be missing, depending on the options during the compilation of the program.

### 2.5.1 Record

The most left tabulator 'Record' (Figure 2.1) contains all settings for the triggering of the lasers the camera. This tabulator may only show the widgets for triggering or camera or may be completely absent. This is defined by the compilation options of the program. Triggering is performed by a Linux kernel module from the Gpivtrig software package which sends its trigger pulses over the parallel port. It uses the RealTimeLinux Application Interface (RTAI), which is a real time micro kernel to perform processes at accurate timings, independently of the computing load of the system.
The base-name of the images to be recorded are defined in the entry. The last 5 names that have been used during the actual or previous Gpiv sessions are stored. The name may be extended with the current date and time.
Different timing schedules may be used. For PIV, "Indefinite", "Duration" and "Double exposure" are most relevant. "Indefinite" will continue until "stop timings" button (or "Stop" button from the main tool bar of the application) is pressed. The images are displayed and updated in frame buffer #0. This setting is convenient for pointing, adjusting and focussing the camera. For the other timing settings, images are stored in subsequent buffers, starting at #0. A maximum of GPIV_NIMG_MAX (defined in gpiv.h of Libgpiv and currently set to fourty) buffers may be retrieved. Duration will only send a limited amount of trigger pulses as defined in "frames (N)".
TODO "Interrupt" ...
"Increment dt" will increase the timing of pulses to the lasers as defined in "inc. dt (ms).,
TODO "double exposure" ...
"Dt" represents the time beween two laser pulses of an image-pair.
The camera uses the IEEE1394 (Firewire), IIDC-compliant protocol. The "Node.." menu selects the camera if different cameras are connected to the computer. All other menu-options and settings that belong to the selected camera are updated and enabled / disabled automatically. "Format .., selects the image format, "... fps" the frame rate, TRIGGER MODE ...", "Exp", "Iris", "Shut", "Gain", "Temp", "Zoom" "Pan" and "Tilt" are obvious. Enabling "RTAI trigerring" will use the application's trigger system. If "record" and "stop record" are pressed, the recording of images and the triggering is started and stopped.

### 2.5.2 Image

The 'Image' (Figure 2.3) tab displays information of the image. Some settings, like image file name, correlation type, image dimensions and image colour depth are only displayed for informative purposes and can not be changed. The image filename is determined during recording or loading the image. The image dimensions, correlatation type and colour depth may be modified from the Gpiv settings or from the command line keys. During loading of an image it is checked whether the image header info is in agreement with these settings.

Figure 2.3 GPIV console with image information tabulator

Time scaling, spatial scaling, the positions of row #0 and column #0 (related to a typical location in the experiment) are identic as in the Post processing tabulator. These parameters are used for scaling and positioning the PIV data.
Spatial scaling may be determined interactively by pointing a ruler in a image. The number of pixels that are spanned by the imaged ruler may be obtained in arbitrary, horizontal or vertical direction by activating the subsequent radio buttons. Entering the viewer, then, will change the pointer image to cross-hair. Pressing and holding the left pointer button within the image starts drawing a straight line and shows the pointer position in the application bar. By releasing the pointer button, the straight line disappears, the span length is written to the "span" entry and the "spatial scale" entry is updated for the new value. When pointing in arbitrary direction, Pythagoras' rule is applied for calculating the correct spanned length by the ruler image. The length of the ruler that has been spanned, expressed in mm, will have to be specified manually. Changing this value will automatically update the "spatial scale" value, as well. If "span" or "length" are not changed, the spatial scale setting, like all other image header information and process settings, is read from the system wide gpiv.conf or from ~/.gpivrc during launching Gpiv.
The items Creation Date, Author, Usertext, Copyright, Software, Source, Warning, Disclaimer and "Comment" are typical header text, often recognised, for example, in PNG formatted images.

### 2.5.3 Process

The 'Process' tab (Figure 2.4)shows the settings for some image processing that are often used for PIV.

Figure 2.4 Gpiv console with the Image processing tabulator

An image process is enabled by clicking the check button. A variable is set in the spinner. As a sequence of image processing steps is non-linear, the order of the processes do matter. Therefore, a step number indicates when the process will be invoked. These numbers are automatically set when enabling the process. Disabling an individual process will re-adjust the step numbering of other enabled processes.

### 2.5.4 Interrogation

The 'Interrogation' tab (Figure 2.5a, b)show all the settings for interrogation an image (pair).

Figure 2.5a Gpiv console with Interrogation tabulator, upper part

Figure 2.5b Gpiv console with Interrogation tabulator, lower part

- The upper-left corner of the image represents pixel # (0,0). The starting point (first col/row) and the end-point (last col/row) of the image to be interrogated may be defined in the entry-fields as well as a global pre-shift in horizontal (pre-shift col) and vertical (pre-shift row). The first column and row, as defined in the entry's will always be included in the interrogations. The last column/row of the image to be analyzed depends on Interrogation Area sizes and shifts, but will never exceed the last column/row as defined in the entry-fields.

- The size of the interrogation area's (I.A.) and adjacent shift, expressed in image pixels, may be defined by entry's (for arbitrary dimensions) or by radio-buttons (which is convenient for power of 2 dimensions) in 'Int. Size 1', 'Int. Size 2' and 'Shift'. The size of the second I.A. has to be equal or larger than the first one in order to perform adaptive dimensions during an iterative interrogation process. Some of the settings in the entries and of the radio buttons, then, may be disabled for manipulation or its value to be entered may be limited. In case adaptive dimensions of the I.A.'s is applied, zero offsetting is enabled and the grid of the nodes at which estimators are calculated, is adapted during each iteration. This will often increase computation speed and the stability of the calculation. Starting by a course grid with I.A. dimensions of 'Int. Size 2' and 50% overlap. During each iteration, the sizes of the I.A.'s and adjacent shifts are halved until 'Int. Size 1' and adjacent shifts as defined in 'Shift' have been reached. The new estimators at the finer grid, used as local pre-shift values for zero offsetting, are obtained from the previous interrogation at a courser grid by linear or, if possible (i.e. an internal node) bi-linear interpolation. Finally, an additional interrogation, then, should guarantee an optimum estimator.

If the settings of I.A.'s are changed after aninterrogation, the PIV values will not be displayed when moving the pointer over the data.

#### Mouse select

- "None": disables mouse activity within the viewer window.
- "Area": entering a viewer window, holding the left mouse button and moving the mouse creates a rectangular frame that defines the area to be interrogated. This is an alternative for using the entries "first/last col/row". The entry values will be updated automatically.
- "Vert. line": a vertical line in the image may be defined at which a single column of interrogation areas are to be drawn. Interrogation of the line has to be performed by clicking the "piv" button at the bottom of the "Evaluation" tabulator or by enabling the "piv" process button and pressing the "Execute" button on the toolbar.
- "Hor. line": a horizontal line in the image may be defined at which a single row of interrogation areas are to be drawn.Interrogation of the line has to be performed by clicking the "piv" button at the bottom of the "Evaluation" tabulator or by enabling the "piv" process button and pressing the "Execute" button on the toolbar.

#### Sub-pixel Interpolation

Selects an interpolation scheme for estimating the correlation peak at sub-pixel level.

#### Peak #

Normally the highest correlation peak is used (or the second highest in case of auto-correlation, which is done automatically if auto-correlation has been enabled). An erroneous velocity vector, though, might be caused by a high noise peak in the correlation function that overwhelms the 'true' particle displacement peak. Searching the second or third highest peak may result in a correct estimation.

#### Interrogation scheme

Image deformation uses all estimators of the entire displacement field to deform the image towards the moment in-between the two images have been recorded. The deformed and shifted Interrogation Areas are obtained by interpolation of the image data with a fith order B-spline interpolation routine [1].

In case zero offset (at an integer number of pixels) is enabled, i.e. a second interrogation is performed with a pre-shift of the local estimator, the new correlation peak is found between -1 and +1 pixels. The 'classic' forward interrogation scheme or a central differential scheme may be used. Interrogation following the central differential scheme is done by displacing the interrogation area of the first image with half the magnitude of the pre-shift value in negative direction and displacing the interrogation area of the second image in positive direction (of identic, integer magnitude).

A linear weight kernel in order to correct for biasing effects that is generated by the estimation of the correlation function.

"Image deformation", "Central differential" and "Zero offset" are iterative processes that continue until the convergence criterium has been reached. The total amount of differences in the estimators between two succesive iteration steps, related to the number of gridpoints, is used as criterium for convergence and amounts to 0.25 pixels (defined by GPIV_EPSI_MIN). The estimators are validated on outliers after each iteration step of the interrogation procedure. Erroneous vectors are subsequently substitued (and re-validated) by the second or third highest correlation peak or by the quantity as specified in "Outliers" in the Validation tabulator.

#### Correlation

In case subsequent recordings have been performed on separate image frames ("Cross") or on one single frame ("Auto"). This option is informative and can not be changed. as it is defined in the header of the image.

The Gauss weigthing check button enables weighting of the Interrogation Area's with a Gaussian function. It is believed that this may improve the PIV analyses as the high-frequency signal generated by the abrupt borders of the I.A. is suppressed.

Symmetric Phase Only filtering (SPOF) is applied to the (2-dimensional) correlation function. Only the phase, but not the amplitude, of the correlation is used to determine the displacement peak. SPOF filtering increases the SNR, by generating a high and narrow displacement peak and low side lobes. It might improve the analysis, especially when there are reflections, from boundaries for example, in one of the images are present [3].

#### Interrogation areas and correlation

The "Monitor" button allows to monitor the interrogation process by visualizing the interrogation areas, the correlation function and the estimated displacement vector. Coloured areas, that are 128x128 pixels in size, are displayed as indication of the dimensions. The interrogation areas and correlation function may be magnified by the "Zoom" entry. The vector length may be adjusted by "Vector scale". By zooming and scaling, the dimensions of the images and the vector may exceed the coloured area's. For that case, only a part of the images and vector is displayed. Monitoring the interrogation process will slightly slow down the calculation speed.
Tip: by enabling "Single Int" of the mouse selection, each interrogation area may be monitored individually, which might often be more convenient than monitoring the interrogation of an entire image.

#### piv

At the bottom of the "Evaluation" tabulator the "piv" button may be invoked to interrogate the image, which is identic as enabling the 'piv' check-button in the process toolbar of the console and pressing the 'Execute' button. The function of this button is similar to that of the command line program rr of the Gpivtools package.

### 2.5.5 Validation

Figure 2.6 Gpiv console with Validation tabulator

#### Disable data

Put PIV data into (in)active state for further processing. At inactive state the vector color will be displayed red.

- "None": disables mouse activity within the viewer window.
- "Enable": puts data in active state by pointing and clicking a single PIV estimator.
- "Disable point": puts data in inactive state by pointing and clicking a single PIV estimator.
- "Enable area": puts a rectangular area containing PIV data in active state. The starting corner of the area (upper-left) is defined by pressing the right mouse button. The opposite corner is defined by moving the mouse with holding the button pressed and releasing it at the location of the opposite corner. A rectangular frame is drawn during the operation.
- "Disable area": puts a rectangular area containing PIV data in inactive state. The starting corner of the area (upper-left) is defined by pressing the right mouse button. The opposite corner is defined by moving the mouse with holding the button pressed and releasing it at the location of the opposite corner. A rectangular frame is drawn during the operation.

#### Histograms

- "residu" displays the (log) inverse histogram of median residus. The critical residu value for accepting/rejecting outliers is determined by the slope of the straight line plotted through the histogram data. The critical value is calculated and displayed in the "Threshold" entry. The function of this process is similar to that of the command line program errvec of the Gpivtools package.
- "sub-pixel" displays a histogram of sub-pixel estimators of the PIV dataset. The function of this process is similar to that of the command line program peaklck of the Gpivtools package.
- The "U-comp" and "V-comp" buttons display the histograms of horizontal and vertical particle displacement estimators. These data may be stored by "Save" in filename.pdf.

#### Validate on velocity gradient

Calculates velocity gradient over an interrogation area and displays vectors in red color if they exceed the critical value. The critical value is defined in libgpiv/include/gpiv/valid.h: GRADIENT_THRESHOLD and is set to 2 pixels, i.e. identic to the optimum particle image diameter. This quantity is chosen in order to prevent a too wide, or even a splitting up, of the highest correlation peak.

#### Outliers

To set the parameters for testing and substituting on erroneous vectors. The number of the surrounding displacement data of a point under investigation may be defined by "Neighbors". The number represents the two-dimensional array, which is typically 3x3 and may have a maximum of 9x9. The "Data yield" is needed to calculate the threshold value from the residu statistics. This value has to be filled in manually and should be obtained from the mean number of particles within an interrogation area. One way to obtain the particle density, is by enabling the "Monitor" button and "Single int" of the mouse selection in the "Interrogation" tabulator and analyzing some points in the image.

The critical threshold may be filled in manually or may be obtained by invoking "residu" button.

The type of residus may be chosen between "Normalized median", "Median" or "Snr". The normalized median option uses the ratio between the residu (obtained from the actual didplacement and the median displacement from the neighboring data) and between the median residu (resulting from the neighbors). The threshold, then, may be kept at 2 pixels for obtaining a data yield of 90% [2]. This setting should be advantageous if turbulence is heterogeneous within the area of observation. The median option uses the residu between actual data point and the median displacement from its surroundings.

Outliers may be substituted by the local mean value of the surrounding vectors, by the median value of the surrounding vectors or by the displacement from the next highest correlation peak. Unless "Nothing" has been choosen, the data will first be substituted subsequently by a PIV estimator from the next highest correlation peak, the median displacement value, and local mean. If the residu still exceeds the threshold after trying these substitutions, the PIV estimator will be substituted by the preferred option as enabled here.

Finally, the validation on outliers is performed by pressing the "validate on outliers" button or by enabling "validate" in the process toolbar of the Gpiv console and pressing "Execute". Validation is also performed after each step of the interrogation procedure if the Interrogation scheme is set to "Image deformation", "Central differential" or "Zero offset". The function of testing on outliers and substituting is similar to that of the command line program errvec of the Gpivtools package.

### 2.5.6 Post processing

The "Post processing" tab (Figure 2.7) contains tools to apply modifications on PIV estimators and to calculate derived quantities from the PIV estimators.

#### Scaling

- "Spatial scale" is calculated by measuring the number of pixels per mm. The values will have to be set manually or may be obtained interactively from the Image tabulator.
- "time scale" represents the time between two successive image recordings (mostly the separation time between two laser flashes).
- "pos. of col #0": The horizontal location of the image within an experiment is defined by the position of column #0, related to a marker point in the experiment.
- "pos. of row #0": The vertical location of the image within an experiment is defined by the position of column #0, related to a marker point in the experiment. The function of this process is similar to the command line program scale of the Gpivtools package.

Vorticity, shear and normal strain may be derived from the PIV estimators with different numerical schemes; Central differential scheme, Least squares, Richardson and the Circulation method (only for the calculation of vorticity). The function of this process is similar to the command line program vorstra of the Gpivtools package.

Figure 2.7 Gpiv console with Post processing tabulator

#### References

[1] P. Thévenaz, T. Blu, M. Unser, "Interpolation Revisited," IEEE Transactions on Medical Imaging, vol. 19, no. 7, pp. 739-758, July 2000

[2] J. Westerweel, F. Scarano, "Universal outlier detection for PIV data", Exp. in Fluids (2005) 39:1096-1100

[3] M.P. Wernet, "Symmetric phase only filtering: a new paradigm for DPIV data processing", Meas. Sci. Technol (2005), vol 16, pp 601-618

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