The method
: To calculate homogeneous (4-point) 3D strains, you need to create a spiral transformation, digitize the frames of interest, and create 3D coordinate data using the PHNew program. Once this is done, the Finite program actually calculates strains. PHNew is also used for non-homogeneous strain (finite element method) analysis to create the coordinate data files needed for Continuity.The digitized data files
: If images are on a video tape, they must be captured and saved as image files on the PC (in TIFF format for example). If they were acquired digitally on the PC, you're ready to digitize!Use PC (Scion) image to digitize both views of spiral image frame and the data frames, and save files as a*.dat and l*.dat as text only.
The digitized files needed are: (1) the AP and LAT views of the spiral, noting any missing beads and the spiral size (large or small). Remember calibration is good for 14 beads max, so you don't need to digitize 20 cal beads. (2) the AP and LAT views of the bead set. You may include any number of "frames" in the digitized file. The bead data files should contain the x-y coordinates of any special beads (apex, base, reference bead, etc.), followed by the regular beads. If they are in "columns", note the number of columns and the number of beads in each column. If they are not in columns (an array for example), note the total number of beads. Each frame must contain the exact same number of beads in the same order. All files should be tab or space delimited text files (2 columns only) without any headers or extra lines.
Notes on choosing biplane x-ray imaging planes
Calculate the 3D coordinate data
: Open Phnew program, then open Setup -> Phantom Size. Set the phantom size used in the experiment. Also, if beads were not digitized on the spiral, enter Bead #'s skipped. If the spiral file already exists, use File -> Spiral Cal file to get the file, then jump to "Digitize AP ..." below. Run Phnew program to create the 3-D spiral file:( a ). File -> Open -> Digilized spiral files (AP then LAT).
( b ). File -> Calculate -> Spiral Transformation .
( c ). File -> Save -> Spiral Calibration File. (save the 3D calibration file such as spiral*.ph )
At this point you have created a spiral transformation. Remember to check the errors to make sure the spiral was digitized properly.
Open Setup -> Data file Setup to enter the number of frames, the number of special points (apex, base, reference and any other " special " points), the number of columns, and how many beads for each column, and run Phnew program to create the CD (x-ray coordinate data), TM (transformation matrix) and CA (cardiac coordinate) data files:
( a ). Open File -> Open -> Digilized data files (AP then LAT).
( b ). Open File -> Calculate -> 3D data coordinates.
( c ). Open File -> Save -> The old CD and TM files. ( save file such as cd*.dat and tm*.dat ).
( d ). Open File -> Save -> X, Y, Z data in columns for all frames. -> Cardiac Coordinates (save the file such as ca*.dat ).
Fitting errors for 3D coordinates are given and should be checked for each frame. Individual point fits can help when coordinates are suspect.
Fitting the coordinate data
: A technique we have used to fit the "raw" data is to fit the coordinate data before any strains are calculated. This can significantly reduce noise, but only works with time series data sets.( a ) Use Sigmaplot program to graph x, y, z coordinates in cardiac coordinates vs. time. Fit cardiac data in x, y, z and obtain " fitted" X-Y-Z values (save the file as cafit*.dat).
( b ). Replace cd*.dat file by cafit*.dat in cd*.dat style, and form a new TM file making the ß rotation matrix = 1, i.e. [ I ]. We use the identity rotation matrix since the data are already in cardiac coordinates, there is no need to rotate them again. Note that the data need not be fitted.
Calculate the strains
: To calculate strains, use the Finite program on PC (usually in the /bin dir). This program requires a CD and TM file, and the files must be in the same directory as the actual program. The CD file contains the x-ray coordinate data for a number of "frames". The TM file contains the transformation matrix for rotation into cardiac coordinates based on the first frame of the CD file. Finite uses the first frame as reference for the strains, and the following frames as deformed. Thus if the CD file contains 4 frames, strains will be calculated for 3 states. The user must enter the 4 points for the calculation; point numbering includes the special points. The output of Finite is in 3 files, including the strains (ST file), the eigenvectors and eignenvalues (principal strains and angles; EV file) and other BS (the properly named BS file).Sample files:
The following sample files are available
aspiral.html digitized spiral file (AP), small spiral, no missing points
lspiral.html digitized spiral file (LAT), small spiral, no missing points
spiralcal.html spiral cal file created with PHNew from above files
apdata.html ap data file with 6 frames; each frame contains 8 points of which 3 are special points (ref, apex, base), then 3 columns with 2,2,1 points in the columns
latdata.html lat data file with 6 frames to match the ap file above
cddata.html x-ray coordinate data (CD) for the 6 frames above
tmdata.html transformation matrix (TM) from above data
strain.html strain (ST) file from Finite containing strains from above CD data file (no fitting)