doc/C/gpiv.html

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   8 <P>
   9 <A NAME="gpiv.html"> <H1>2 GPIV</H1></A>
  10
  11 <A NAME="sect2.1"><H2>2.1 Starting up</H2></A>
  12
  13 Gpiv may be launched in different ways. In case it needs to trigger
  14 the lasers and camera, the RTAI and gpivtrig Linux kernel modules will
  15 have to be loaded (and unloaded after closing Gpiv). The gpiv_control
  16 script (from the gpivtrig package, which also includes the gpivtrig
  17 module) might be used: "gpiv_control <b>"</b>gpiv [OPTION1]
  18 ... [IMAGE1] ...<b>"</b>". Gpiv_control has to be run with root
  19 privileges. In case no trigering is used or if the modules have
  20 already been loaded in the kernel, starting the application is
  21 straightforward with: "gpiv [OPTION1] ... [IMAGE1] ...". If the
  22 modules have not been loaded in the kernel, a warning message will be
  23 displayed and the trigger services will be disabled.
  24 <br>
  25
  26 The Gpiv console consists a menu bar, a tool-bar, process
  27 toggle-buttons, a tabulator and a data buffer list (<a
  28 href="#fig2.1">Figure 2.1</A>). At the bottom of the console you can
  29 find an application bar that displays information of the highlighted
  30 item as well as a progress bar that displays the progress of the
  31 running process.
  32 <br>
  33
  34 Gpiv reads its default program parameters from ~/.gnome2/gpiv
  35 following the GNOME mechanism. These parameters are defined frome the
  36 Settings->Preferences from the console menu's and may be overruled by
  37 command line keys for the current session. (Invoke "gpiv --help" or
  38 "man gpiv" for information about the command line options.) Apart from
  39 the Gpiv parameter settings, there are also variables to ease the use
  40 of the program, which can not be defined by command line keys. These
  41 variables are stored from previous sessions (like the last displayed
  42 tabulator, image base-names during recording or the last selected
  43 image-name during loading with File->Open). The PIV process variables
  44 that are used for recording, interrogation, validation and
  45 post-processing are read from ~/.gpivrc or from the system-wide
  46 available gpiv.conf (mostly installed at /etc/ under Unix/Linux)
  47 respectively. These process variables are shared with the programs
  48 from the Gpivtools package.
  49 <br>
  50
  51 <P>
  52 <IMG SRC = "figures/gpiv-fig_console_record.png"><br> <A NAME="fig2.1"
  53 id="fig2.1">Figure 2.1 Gpiv console with image recording
  54 tabulator. This tab may (partly) be absent, depending on the
  55 configuration options during the building of the program</A>
  56 <P>
  57 <P>
  58
  59 <A NAME="sect2.2"><H2>2.2 Menu and toolbar</H2></A>
  60
  61 The menu bar consists general tasks for Gpiv, like file-handling,
  62 preferences and help menus. Underlined characters represent the ALT
  63 short-hand key for launching the menus.
  64 <P>
  65
  66 The "File" menu contains "open", "save", "save as", "close" for
  67 reading, storing, and closing data and "exit" for closing the
  68 application. For reading and saving images and data, Gpiv uses the
  69 Gnome Virtual File System (GVFS). This allows you to load data from an
  70 other system (server) you have access to, like ftp or ssh. Loading
  71 data from a server is done by typing Ctr+L when the filebrowser
  72 is open and typing, for example:
  73 <br>
  74 ssh:///my_other_account@another_system:image.png
  75 <br>
  76 or from Nautilus (see below).
  77 <P>
  78
  79 The native image format for Gpiv is the Portable Network Graphics
  80 (PNG) format. Image data may also be read to or stored from raw binary
  81 data (name.<strong>r</strong>) that is accompanied by an ASCII header
  82 file (name.<strong>h)</strong> or HDF5
  83 (name.<strong>gpi</strong>). Images of formats that use lossless
  84 compression (tif, gif, pgm, bmp) are converted to PNG during the
  85 loading to guarantee the storage of all header information. To save
  86 disk space, the original image will be deleted. In case of
  87 cross-correlation, it is expected that the second frame is attached to
  88 the first image frame. This may be performed manually with
  89 <strong>gpiv_combing</strong> from the Gpivtools package.
  90
  91 <P>
  92 The maximum image dimensions that may be used are defined in
  93 gpiv_gtk.h by IMAGE_WIDTH_MAX and IMAGE_HEIGHT_MAX or by the options
  94 --enable-img-width and --enable-img-hight of the ./configure script.
  95 The maximum image dimensions can not be changed during execution of
  96 Gpiv. In case the image dimensions are larger, ./configure will have
  97 to be executed (or gpiv_gtk modified) and Gpiv will have to be
  98 recompiled. In case IMAGE_WIDTH_MAX and IMAGE_HEIGHT_MAX will have to
  99 be redefined, it is recommended to set them at the minimum needed
 100 values in order to save RAM memory usage.
 101 <br>
 102 After loading, the file basename is displayed in the buffer list and
 103 the complete image name is displayed in the "Image Info" tabulator of
 104 the console.  A display window (or viewer) is launched that shows the
 105 image together with the interrogation area's and its name is displayed
 106 in the application bar of the viewer as well (<a
 107 href="#fig2.2">Figure 2.2</a>.
 108
 109 <P>
 110 <IMG SRC = "figures/gpiv-fig_display.png"><br>
 111 <A NAME="fig2.2" id="fig2.2">Figure 2.2 Buffer display
 112 containing image, Interrogation Area contours and data</A>
 113 <P>
 114 <P>
 115
 116 <P>
 117 Saving the image and data is done in PNG, raw binary or HDF5 format,
 118 depending on the program settings or start-up keys (--hdf and
 119 --hdf_img). Image data may also be loaded from the Gnome filemanager
 120 NAUTILUS with the "open with.." popup menu or by "drag and drop" of
 121 the selected images into the buffer list in case Gpiv has already been
 122 launched. Typing Ctr+L or from the Go->Location... menu of Nautilus, the
 123 filemanager can be connected to another system or server by using GVFS.
 124
 125 <P>
 126 The settings menu contains the menus "gpiv buttons" and "tabulator" to
 127 (un)display these parts of the console and "preferences" for defining
 128 all Gpiv settings. Closing the "preferences" menu with "OK" stores the
 129 settings for future sessions. "Apply" only affects the current
 130 session. When settings for the buffer display have been changed, they
 131 will be broadcasted to all display windows when "OK" or "Apply" are
 132 pressed. "Cancel" closes the preferences window without action. Some
 133 parameter settings (image width and image height) need to restart
 134 Gpiv. You will be acknowledged in that case.
 135 <P>
 136 The "help" menu contains "show tooltips" for obtaining additional
 137 help. Tooltips are small windows that pop up when an item is
 138 highlighted and contain more extended information about the item than
 139 can be displayed in the short line of the application bar. The "manual"
 140 menu shows this document. "About" gives short info concerning this
 141 application.
 142
 143 <P>
 144 The toolbar is a quick way for opening / saving / closing images and
 145 data, executing / stopping processes that are enabled by the process
 146 toggle buttons, which are found below the toolbar, for closing
 147 buffers and for exiting the program.
 148
 149
 150
 151 <A NAME="sect2.3"><H2>2.3 Process toggle-buttons</H2></A>
 152
 153 The process toggle-buttons may be switched on in order to define a
 154 chain of processes (pipeline). These processes include recording,
 155 image processing, image PIV interrogation, validation and
 156 post-processes of the PIV estimators. The parameter settings of the
 157 processes are defined in the tabulators of the Gpiv console. The
 158 pipeline process is invoked by the "Execute" button on the toolbar
 159 and, eventually, interrupted by the "Stop" button.
 160
 161
 162 <A NAME="sect2.4"><H2>2.4 Buffer list and display window</H2></A>
 163
 164 The buffer list shows a number and the file basename (i.e. the
 165 filename without directory name and extension) of the loaded
 166 images. Images may be loaded directly into the buffer list by means of
 167 "drag and drop" from the Gnome file-manager NAUTILUS. A single buffer
 168 may be selected by pointing to it and left mouse clicking. Several
 169 buffers may be selected by clicking the first and last buffer while
 170 holding the "Shift" key. The execution of processes will than
 171 be performed on every selected buffer. The selected buffers will be
 172 closed following the Window manager protocol (mostly by pressing
 173 Ctrl-W).
 174
 175 <P>
 176 For each buffer, a display window is launched that contains the image,
 177 squared frames that represent the contours of interrogation areas
 178 during the initial and the final step of an iterative interrogation
 179 process, a vector field representing the PIV estimators and solid,
 180 coloured, squares expressing the magnitudes of derived scalars
 181 obtained from the PIV estimators by post processing. The interrogation
 182 areas are highlighted when the pointer moves over them. At the bottom
 183 of the display window an application bar shows information concerning
 184 the data. If displaying of interrogation area frames is disabled,
 185 image intensities are shown. Else, the centre point of the highlighted
 186 interrogation area and, eventually, values of the PIV estimators and
 187 its derived quantities are shown. If the settings of Interrogation
 188 Areas are changed or, for some other reason not in accordance with the
 189 settings the PIV data have been generated, the PIV values will not be
 190 displayed. The same information is displayed in the application bar of
 191 the Gpiv console as well. A menubar at the top of the window shows
 192 options for changing the settings for the displaying of the data in the
 193 individual buffer window. When clicking the right mouse button when
 194 pointing within the display, a menu pops up with identic functions as
 195 the menubar.  Zooming and moving (paning) the image and data may also
 196 be performed by the mouse scroll button and moving the pointer (when
 197 mouse select is set to "None" in the console) while pressing the left
 198 mouse button. In case the display settings will have to be adjusted
 199 for all open buffers, change the settings from the
 200 Settings->Preferences menu in the Gpiv console. Then, the new settings
 201 will be updated to all buffer windows when "Apply" or "OK" is pressed.
 202
 203
 204 <A NAME="sect2.5"><H2>2.5 Tabulator</H2></A>
 205
 206 The tabulator contains pages with parameter settings and buttons to
 207 invoke the processes for image recording, information, processing and
 208 interrogation, PIV-data validation and post-processing. Some of these
 209 pages may be missing, depending on the options during the compilation
 210 of the program.
 211
 212 <A NAME="sect2.5.1"><H3>2.5.1 Record</H3></A>
 213
 214 The most left tabulator 'Record' (<a href="#fig2.1">Figure 2.1</A>)
 215 contains all settings for the triggering of the lasers the
 216 camera. This tabulator may only show the widgets for triggering or
 217 camera or may be completely absent. This is defined by the compilation
 218 options of the program. Triggering is performed by a Linux kernel
 219 module from the Gpivtrig software package which sends its trigger
 220 pulses over the parallel port. It uses the RealTimeLinux Application
 221 Interface (<a href="http://www.rtai.org">RTAI</a>), which is a real
 222 time micro kernel to perform processes at accurate timings,
 223 independently of the computing load of the system. <br>
 224
 225 The base-name of the images to be recorded are defined in the
 226 entry. The last 5 names that have been used during the actual or
 227 previous Gpiv sessions are stored. The name may be extended with the
 228 current date and time.
 229 <br>
 230
 231 Different timing schedules may be used. For PIV, "Indefinite", "Duration"
 232 and "Double exposure" are most relevant. "Indefinite" will continue until
 233 "stop timings" button (or "Stop" button from the main tool bar of the
 234 application) is pressed. The images are displayed and updated in frame
 235 buffer #0. This setting is convenient for pointing, adjusting and
 236 focussing the camera. For the other timing settings, images are stored
 237 in subsequent buffers, starting at #0. A maximum of GPIV_NIMG_MAX
 238 (defined in gpiv.h of Libgpiv and currently set to fourty) buffers
 239 may be retrieved. Duration will only send a limited amount of trigger
 240 pulses as defined in "frames (N)".
 241 <br>
 242
 243 TODO "Interrupt" ...
 244 <br>
 245
 246 "Increment dt" will increase the timing of pulses to the lasers as
 247 defined in "inc. dt (ms).,
 248 <br>
 249
 250 TODO "double exposure" ...
 251 <br>
 252
 253 "Dt" represents the time beween two laser pulses of an image-pair.
 254 <br><br>
 255
 256 The camera uses the IEEE1394 (Firewire), IIDC-compliant protocol. The
 257 "Node.." menu selects the camera if different cameras are connected to
 258 the computer. All other menu-options and settings that belong to the
 259 selected camera are updated and enabled / disabled
 260 automatically. "Format .., selects the image format, "... fps" the
 261 frame rate, TRIGGER MODE ...", "Exp", "Iris", "Shut", "Gain", "Temp",
 262 "Zoom" "Pan" and "Tilt" are obvious.
 263
 264 Enabling "RTAI trigerring" will use the application's trigger
 265 system. If "record" and "stop record" are pressed, the recording of
 266 images and the triggering is started and stopped.
 267
 268
 269
 270 <A NAME="sect2.5.2"><H3>2.5.2 Image</H3></A>
 271
 272 The 'Image' (<a href="#fig2.3">Figure 2.3</A>) tab displays
 273 information of the image. Some settings, like image file name,
 274 correlation type, image dimensions and image colour depth are only
 275 displayed for informative purposes and can not be changed. The image
 276 filename is determined during recording or loading the image. The
 277 image dimensions, correlatation type and colour depth may be modified
 278 from the Gpiv settings or from the command line keys. During loading
 279 of an image it is checked whether the image header info is in
 280 agreement with these settings.
 281 <P>
 282 <IMG SRC = "figures/gpiv-fig_console_image_info.png"><br> <A NAME="fig2.3"
 283 id="fig2.3"></A>Figure 2.3 GPIV console with image information
 284 tabulator</A>
 285 <P>
 286 <P>
 287
 288 <br>
 289 Time scaling, spatial scaling, the positions of row #0 and column #0
 290 (related to a typical location in the experiment) are identic as in
 291 the Post processing tabulator. These parameters are used for scaling
 292 and positioning the PIV data.
 293
 294 <br>
 295
 296 Spatial scaling may be determined interactively by pointing a ruler in
 297 a image. The number of pixels that are spanned by the imaged ruler may
 298 be obtained in arbitrary, horizontal or vertical direction by
 299 activating the subsequent radio buttons. Entering the viewer, then,
 300 will change the pointer image to cross-hair. Pressing and holding the
 301 left pointer button within the image starts drawing a straight line
 302 and shows the pointer position in the application bar. By releasing
 303 the pointer button, the straight line disappears, the span length is
 304 written to the "span" entry and the "spatial scale" entry is updated
 305 for the new value. When pointing in arbitrary direction, Pythagoras'
 306 rule is applied for calculating the correct spanned length by the
 307 ruler image. The length of the ruler that has been spanned, expressed
 308 in mm, will have to be specified manually. Changing this
 309 value will automatically update the "spatial scale" value, as well. If
 310 "span" or "length" are not changed, the spatial scale setting, like
 311 all other image header information and process settings, is read from
 312 the system wide gpiv.conf or from ~/.gpivrc during launching Gpiv.
 313
 314 <br>
 315 The items Creation Date, Author, Usertext, Copyright, Software,
 316 Source, Warning, Disclaimer and "Comment" are typical header
 317 text, often recognised, for example, in PNG formatted images.
 318
 319
 320
 321 <A NAME="sect2.5.3"><H3>2.5.3 Process</H3></A>
 322
 323 The 'Process' tab (<a href="#fig2.4">Figure 2.4</A>)shows the
 324 settings for some image processing that are often used for PIV.
 325 <P>
 326 <P>
 327 <IMG SRC = "figures/gpiv-fig_console_image_process.png"><br>
 328 <A NAME="fig2.4" id="fig2.4">
 329 Figure 2.4 Gpiv console with the Image processing tabulator</A>
 330 <P>
 331 <P>
 332 An image process is enabled by clicking the check button. A variable
 333 is set in the spinner. As a sequence of image processing steps is
 334 non-linear, the order of the processes do matter. Therefore, a step
 335 number indicates when the process will be invoked. These numbers are
 336 automatically set when enabling the process. Disabling an individual
 337 process will re-adjust the step numbering of other enabled processes.
 338
 339 <A NAME="sect2.5.4"><H3>2.5.4 Interrogation</H3></A>
 340
 341 The 'Interrogation' tab (<a href="#fig2.5a">Figure 2.5a, b</A>)show all the
 342 settings for interrogation an image (pair).
 343 <P>
 344 <P>
 345 <IMG SRC = "figures/gpiv-fig_console_interrogat_upper.png"><br>
 346 <A NAME="fig2.5a" id="fig2.5a">
 347 Figure 2.5a Gpiv console with Interrogation tabulator, upper part</A>
 348 <P>
 349 <IMG SRC = "figures/gpiv-fig_console_interrogat_lower.png"><br>
 350 <A NAME="fig2.5b" id="fig2.5b">
 351 Figure 2.5b Gpiv console with Interrogation tabulator, lower part</A>
 352 <P>
 353 <P>
 354
 355 - The upper-left corner of the image represents pixel # (0,0). The
 356 starting point (first col/row) and the end-point (last col/row) of the
 357 image to be interrogated may be defined in the entry-fields as well as
 358 a global pre-shift in horizontal (pre-shift col) and vertical
 359 (pre-shift row). The first column and row, as defined in the entry's will
 360 always be included in the interrogations. The last column/row of the image
 361 to be analyzed depends on Interrogation Area sizes and shifts, but
 362 will never exceed the last column/row as defined in the
 363 entry-fields.
 364 <P>
 365
 366 - The size of the interrogation area's (I.A.) and adjacent shift,
 367 expressed in image pixels, may be defined by entry's (for arbitrary
 368 dimensions) or by radio-buttons (which is convenient for power of 2
 369 dimensions) in 'Int. Size 1', 'Int. Size 2' and 'Shift'. The size of
 370 the second I.A. has to be equal or larger than the first one in order
 371 to perform adaptive dimensions during an iterative interrogation
 372 process. Some of the settings in the entries and of the radio buttons,
 373 then, may be disabled for manipulation or its value to be entered may
 374 be limited. In case adaptive dimensions of the I.A.'s is applied, zero
 375 offsetting is enabled and the grid of the nodes at which estimators
 376 are calculated, is adapted during each iteration. This will often
 377 increase computation speed and the stability of the
 378 calculation. Starting by a course grid with I.A. dimensions of
 379 'Int. Size 2' and 50% overlap. During each iteration, the sizes of the
 380 I.A.'s and adjacent shifts are halved until 'Int. Size 1' and adjacent
 381 shifts as defined in 'Shift' have been reached. The new estimators at
 382 the finer grid, used as local pre-shift values for zero offsetting,
 383 are obtained from the previous interrogation at a courser grid by
 384 linear or, if possible (i.e. an internal node) bi-linear
 385 interpolation. Finally, an additional interrogation, then, should
 386 guarantee an optimum estimator.
 387 <P>
 388 If the settings of I.A.'s are changed after aninterrogation, the PIV
 389 values will not be displayed when moving the pointer over the data.
 390 <P>
 391
 392 <H4>Mouse select</H4>
 393 <ul>
 394 <li>"None": disables mouse activity within the viewer window.
 395
 396 <li>"Area": entering a viewer window, holding the left mouse
 397 button and moving the mouse creates a rectangular frame that defines the area
 398 to be interrogated. This is an alternative for using the entries "first/last
 399 col/row". The entry values will be updated automatically.
 400
 401 <!--
 402 <li>"Single int.": entering a viewer window and clicking the left
 403 mouse button invokes a new interrogation at the highlighted
 404 interrogation area. The actual interrogation takes place after
 405 releasing of the mouse button. The pointer has to be at the identic
 406 interrogation area during pressing and during releasing of the
 407 button. When the pointer has been moved out of the interrogation area
 408 during releasing, nothing will happen and a new interrogation may be
 409 invoked immediately. In case a successfull interrogation has taken
 410 place, the mouse selection will be set to "None" in order to prevent
 411 accidential interrogations. For multiple interrogations, hold down the
 412 shift key during releasing of the mouse button. Other, already
 413 existing estimators will be conserved.
 414
 415 <li>"Single point": entering a viewer window and clicking the left
 416 mouse button invokes a new interrogation at an arbitrary point.  The
 417 mouse selection will be set to "None" in order to prevent accidential
 418 interrogations. For multiple interrogations, hold down the shift key
 419 during releasing of the mouse button. Already existing estimators will
 420 be thrown away!
 421
 422 <li>"Drag int.": entering a viewer window causes to displace (drag)
 423 the highlighted interrogation area. An adjacent interrogation area is
 424 highlighted and dragged in case the pointer is closer to its centre
 425 point. Clicking the right mouse button invokes an interrogation at the
 426 centre point of the (displaced) interrogation area. The actual
 427 interrogation takes place after releasing of the mouse button. The
 428 pointer has to be at the identic interrogation area during pressing
 429 and during releasing of the button. When the pointer has been moved
 430 out of the interrogation area during releasing, nothing will happen
 431 and a new interrogation may be invoked immediately. In case a
 432 successfull interrogation has taken place, the mouse selection will be
 433 set to "None" in order to prevent accidential interrogations. For
 434 multiple interrogations, hold down the shift key during releasing of
 435 the mouse button. Other, already existing estimators will be
 436 conserved.
 437 /-->
 438
 439 <li>"Vert. line": a vertical line in the image may be defined at which
 440 a single column of interrogation areas are to be drawn. Interrogation
 441 of the line has to be performed by clicking the "piv" button at the
 442 bottom of the "Evaluation" tabulator or by enabling the "piv" process
 443 button and pressing the "Execute" button on the toolbar.
 444
 445 <li>"Hor. line": a horizontal line in the image may be defined at which a
 446 single row of interrogation areas are to be drawn.Interrogation
 447 of the line has to be performed by clicking the "piv" button at the
 448 bottom of the "Evaluation" tabulator or by enabling the "piv" process
 449 button and pressing the "Execute" button on the toolbar.
 450 </ul>
 451
 452
 453
 454 <H4>Sub-pixel Interpolation</H4>
 455
 456 Selects an interpolation scheme for estimating the correlation peak at
 457 sub-pixel level.
 458
 459
 460
 461 <H4>Peak #</H4>
 462
 463 Normally the highest correlation peak is used (or the second highest
 464 in case of auto-correlation, which is done automatically if
 465 auto-correlation has been enabled). An erroneous velocity vector,
 466 though, might be caused by a high noise peak in the correlation
 467 function that overwhelms the 'true' particle displacement
 468 peak. Searching the second or third highest peak may result in a
 469 correct estimation.
 470
 471
 472
 473 <H4>Interrogation scheme</H4>
 474
 475 Image deformation uses all estimators of the entire displacement field
 476 to deform the image towards the moment in-between the two images have
 477 been recorded. The deformed and shifted Interrogation Areas are
 478 obtained by interpolation of the image data with a fith order B-spline
 479 interpolation routine  <a href="#ref1">[1]</a>.
 480 <p>
 481 In case zero offset (at an integer number of pixels) is enabled,
 482 i.e. a second interrogation is performed with a pre-shift of the local
 483 estimator, the new correlation peak is found between -1 and +1
 484 pixels. The 'classic' forward
 485 interrogation scheme or a central differential scheme may be
 486 used. Interrogation following the central differential scheme is done
 487 by displacing the interrogation area of the first image with half the
 488 magnitude of the pre-shift value in negative direction and displacing
 489 the interrogation area of the second image in positive direction (of
 490 identic, integer magnitude).
 491 <p>
 492 A linear weight kernel in order to correct for biasing effects that is
 493 generated by the estimation of the correlation function.
 494 <p>
 495 "Image deformation", "Central differential" and "Zero offset" are
 496 iterative processes that continue until the convergence criterium has
 497 been reached.  The total amount of differences in the estimators
 498 between two succesive iteration steps, related to the number of
 499 gridpoints, is used as criterium for convergence and amounts to 0.25
 500 pixels (defined by GPIV_EPSI_MIN).
 501
 502 The estimators are validated on outliers after each iteration step of the
 503 interrogation procedure. Erroneous vectors are subsequently
 504 substitued (and re-validated) by the second or third highest
 505 correlation peak or by the quantity as specified in "Outliers" in the
 506 Validation tabulator.
 507
 508 <H4>Correlation</H4>
 509
 510 In case subsequent recordings have been performed on separate image
 511 frames ("Cross") or on one single frame ("Auto"). This option is
 512 informative and can not be changed. as it is defined in the
 513 header of the image.
 514 <p>
 515 The Gauss weigthing check button enables weighting of the Interrogation
 516 Area's with a Gaussian function. It is believed that this may improve
 517 the PIV analyses as the high-frequency signal generated by the abrupt
 518 borders of the I.A. is suppressed.
 519 <p>
 520
 521 Symmetric Phase Only filtering (SPOF) is applied to the
 522 (2-dimensional) correlation function. Only the phase, but not the
 523 amplitude, of the correlation is used to determine the displacement
 524 peak. SPOF filtering increases the SNR, by generating a high and
 525 narrow displacement peak and low side lobes. It might improve the
 526 analysis, especially when there are reflections, from boundaries for
 527 example, in one of the images are present <a
 528 href="#ref3">[3]</a>.
 529
 530 <H4>Interrogation areas and correlation</H4>
 531
 532 The "Monitor" button allows to monitor the interrogation process by
 533 visualizing the interrogation areas, the correlation function and the
 534 estimated displacement vector. Coloured areas, that are 128x128 pixels
 535 in size, are displayed as indication of the dimensions. The
 536 interrogation areas and correlation function may be magnified by the
 537 "Zoom" entry. The vector length may be adjusted by "Vector scale". By
 538 zooming and scaling, the dimensions of the images and the vector may
 539 exceed the coloured area's. For that case, only a part of the images
 540 and vector is displayed. Monitoring the interrogation process will
 541 slightly slow down the calculation speed.
 542
 543 <br>
 544 Tip: by enabling "Single Int" of the mouse selection, each
 545 interrogation area may be monitored individually, which might often be
 546 more convenient than monitoring the interrogation of an entire image.
 547 <P>
 548
 549
 550
 551 <H4>piv</H4>
 552
 553 At the bottom of the "Evaluation" tabulator the "piv" button may be
 554 invoked to interrogate the image, which is identic as enabling the
 555 'piv' check-button in the process toolbar of the console and pressing
 556 the 'Execute' button. The function of this button is similar to that
 557 of the command line program <b>rr</b> of the Gpivtools package.
 558
 559
 560 <A NAME="sect2.5.5"><H3>2.5.5 Validation </H3></A>
 561
 562 <P>
 563 <IMG SRC = "figures/gpiv-fig_console_valid.png"><br>
 564 <A NAME="fig2.6" id="fig2.6">Figure 2.6 Gpiv console with Validation
 565 tabulator</A>
 566
 567
 568
 569 <H4>Disable data</H4>
 570
 571 Put PIV data into  (in)active state for further processing.
 572 At inactive state the vector color will be displayed red.
 573 <ul>
 574 <li>"None": disables mouse activity within the viewer window.
 575
 576 <li>"Enable": puts data in active state by pointing and clicking a
 577 single PIV estimator.
 578
 579 <li>"Disable point": puts data in inactive state by pointing and
 580 clicking a single PIV estimator.
 581
 582 <li>"Enable area": puts a rectangular area containing PIV data in
 583 active state. The starting corner of the area (upper-left) is defined
 584 by pressing the right mouse button. The opposite corner is defined by
 585 moving the mouse with holding the button pressed and releasing it at the
 586 location of the opposite corner. A rectangular frame is drawn during
 587 the operation.
 588
 589 <li>"Disable area": puts a rectangular area containing PIV data in
 590 inactive state. The starting corner of the area (upper-left) is defined
 591 by pressing the right mouse button. The opposite corner is defined by
 592 moving the mouse with holding the button pressed and releasing it at the
 593 location of the opposite corner. A rectangular frame is drawn during
 594 the operation.
 595 </ul>
 596
 597
 598
 599 <H4>Histograms</H4>
 600
 601 <ul>
 602 <li>"residu" displays the (log) inverse histogram of median
 603 residus. The critical residu value for accepting/rejecting outliers is
 604 determined by the slope of the straight line plotted through the
 605 histogram data. The critical value is calculated and displayed in the
 606 "Threshold" entry. The function of this process is similar to that of
 607 the command line program <b>errvec</b> of the Gpivtools package.</li>
 608
 609 <li>"sub-pixel" displays a histogram of sub-pixel estimators of the
 610 PIV dataset. The function of this process is similar to that of the
 611 command line program <b>peaklck</b> of the Gpivtools package.</li>
 612
 613 <li>The "U-comp" and "V-comp" buttons display the histograms of
 614 horizontal and vertical particle displacement estimators. These data
 615 may be stored by "Save" in filename.pdf.</li>
 616
 617
 618 </ul>
 619
 620
 621 <H4>Validate on velocity gradient</H4>
 622
 623 Calculates velocity gradient over an interrogation area and displays
 624 vectors in red color if they exceed the critical value. The critical
 625 value is defined in libgpiv/include/gpiv/valid.h: GRADIENT_THRESHOLD
 626 and is set to 2 pixels, i.e. identic to the optimum particle image
 627 diameter. This quantity is chosen in order to prevent a too wide, or
 628 even a splitting up, of the highest correlation peak.
 629
 630
 631 <H4>Outliers</H4>
 632
 633 To set the parameters for testing and substituting on erroneous
 634 vectors. The number of the surrounding displacement data of a point
 635 under investigation may be defined by "Neighbors". The number
 636 represents the two-dimensional array, which is typically 3x3 and may
 637 have a maximum of 9x9. The "Data yield" is needed to calculate the
 638 threshold value from the residu statistics. This value has to be
 639 filled in manually and should be obtained from the mean number of
 640 particles within an interrogation area. One way to obtain the particle
 641 density, is by enabling the "Monitor" button and "Single int" of the
 642 mouse selection in the "Interrogation" tabulator and analyzing some points
 643 in the image.
 644 <p>
 645
 646 The critical threshold may be filled in manually or may
 647 be obtained by invoking "residu" button.
 648 <p>
 649
 650 The type of residus may be chosen between "Normalized median",
 651 "Median" or "Snr". The normalized median option uses the ratio between
 652 the residu (obtained from the actual didplacement and the median
 653 displacement from the neighboring data) and between the median residu
 654 (resulting from the neighbors). The threshold, then, may be kept at 2
 655 pixels for obtaining a data yield of 90% <a href="#ref2">[2]</a>. This
 656 setting should be advantageous if turbulence is heterogeneous within
 657 the area of observation. The median option uses the residu between
 658 actual data point and the median displacement from its surroundings.
 659 <p>
 660
 661 Outliers may be substituted by the local mean value of the surrounding
 662 vectors, by the median value of the surrounding vectors or by the
 663 displacement from the next highest correlation peak. Unless "Nothing"
 664 has been choosen, the data will first be substituted subsequently by a
 665 PIV estimator from the next highest correlation peak, the median
 666 displacement value, and local mean. If the residu still exceeds the
 667 threshold after trying these substitutions, the PIV estimator will be
 668 substituted by the preferred option as enabled here.
 669 <p>
 670
 671 Finally, the validation on outliers is performed by pressing the
 672 "validate on outliers" button or by enabling "validate" in the process
 673 toolbar of the Gpiv console and pressing "Execute". Validation is also
 674 performed after each step of the interrogation procedure if the
 675 Interrogation scheme is set to "Image deformation", "Central
 676 differential" or "Zero offset". The function of testing on outliers
 677 and substituting is similar to that of the command line program
 678 <b>errvec</b> of the Gpivtools package.
 679
 680 <A NAME="sect2.5.6"><H3>2.5.6 Post processing </H3></A>
 681
 682 The "Post processing" tab (<a href="#fig2.7">Figure 2.7</A>) contains
 683 tools to apply modifications on PIV estimators and to calculate
 684 derived quantities from the PIV estimators.
 685 <P>
 686
 687 <H4>Scaling</H4>
 688
 689 <ul>
 690 <li>"Spatial scale" is calculated by measuring the number of pixels per
 691 mm. The values will have to be set manually or may be obtained interactively
 692 from the <a href="#sect2.5.2">Image</A> tabulator.
 693
 694 <li>"time scale" represents the time between
 695 two successive image recordings (mostly the separation time between
 696 two laser flashes).
 697
 698 <li>"pos. of col #0": The horizontal location of the image within an
 699 experiment is defined by the position of column #0, related to
 700 a marker point in the experiment.
 701
 702 <li>"pos. of row #0": The vertical location of the image within an
 703 experiment is defined by the position of column #0, related to
 704 a marker point in the experiment.
 705
 706 The function of this
 707 process is similar to the command line program <b>scale </b> of the
 708 Gpivtools package.
 709 </ul>
 710 <P>
 711
 712 Vorticity, shear and normal strain may be derived from the PIV
 713 estimators with different numerical schemes; Central differential
 714 scheme, Least squares, Richardson and the Circulation method (only for
 715 the calculation of vorticity). The function of this process is similar
 716 to the command line program <b> vorstra </b> of
 717 the Gpivtools package.
 718
 719 <P>
 720 <IMG SRC = "figures/gpiv-fig_console_post.png"><br>
 721 <A NAME="fig2.7" id="fig2.7">Figure 2.7 Gpiv console with Post processing
 722 tabulator</A>
 723 <P>
 724 <P>
 725 <P>
 726 <H4>References</H4>
 727
 728 <a id="ref1"> [1] P. Thévenaz, T. Blu, M. Unser, "Interpolation
 729 Revisited," IEEE Transactions on Medical Imaging, vol. 19, no. 7,
 730 pp. 739-758, July 2000</a>
 731 <P>
 732 <a id="ref2"> [2] J. Westerweel, F. Scarano, "Universal outlier
 733 detection for PIV data", Exp. in Fluids (2005) 39:1096-1100</a>
 734 <P>
 735 <a id="ref3"> [3] M.P. Wernet, "Symmetric phase only filtering: a new paradigm for DPIV
 736 data processing", Meas. Sci. Technol (2005), vol 16, pp 601-618</a>
 737
 738 <P>
 739 <P>
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