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Tina5/tina-tools/docs/help/imcalc_tool.hlp

1 Imcalc Tool 2 ----------- 3 4 Install imcalc Tv's for data display (see main tinatool Help or User Guide). 5 Data is stored in the main tinatool image stack structure which is accessed 6 via "push" and "pop" buttons from the file i/o tools. 7 8 The calculator supports several image types; unsigned char, integer, floating 9 point and double precision complex. The functions decribed below will cast 10 image types according to the minimum requirment for numerical stability. 11 12 Image type. 13 14 This menu displays the resulting image type after all data manipulations and 15 image creation processes. Selecting the appropriate image type will force the 16 image to that storage representation. False binary (actually stored as unsigned 17 char) and pointer types are also indicated. 18 Casting to a type ptr (pointer) will extract those points on the image which 19 are above IP(thresh) and less than no more than IP(connect) of its neighbours. 20 Casting to type int will force a 16 bit represenation although 32 bit integers 21 are generated from integer arithmetic. 22 23 Graphical Facilities. 24 25 By installing the graph Tv a range of graph plotting facilities become available. 26 All graphs are redrawn after each image processing function to allow monitoring 27 of each stage in calculation, selecting Imcalc Mice (grey) will turn this off. 28 All zero's are suppressed. 29 30 Selecting Imcalc Mice (prof) the following functions; 31 32 Left mouse button. Rubber band straight line. Grey levels along selected along 33 trajectory displayed on release. 34 Middle mouse button. Rubber band circle Grey levels along circular boundary 35 displayed on release. 36 37 Selecting Imcalc Mice (hist) produces the following functions; 38 39 Left mouse button. Rubber band straight line. Grey levels along selected along 40 trajectory histogrammed on release. 41 Middle mouse button. Rubber band circle Grey levels within circular boundary 42 histogrammed on release. 43 Right mouse button. Rubber band region of interest. Contents histogrammed on 44 release. 45 46 Binary segmetation. 47 48 Selecting Imcalc Mice (conn) enables selection of regions using local connectivity 49 defined as any 4 way adjacent non zero data. The "undo" facility will delete the 50 most recent edit. 51 52 Left Mouse. Add all pixels connected to those within the selected ROI on release. 53 Middle Mouse. Delete pixels along drag path (for building connectivity breaks). 54 Right Mouse. Construct a complex image mask from the set of selected pixels. 55 56 The resulting complex mask image can be modified with the selection of extra 57 connected regions or cast in order to recover the binary mask and original 58 data. 59 60 Image Processing Functions. 61 62 Undo - reverse the most recent process. 63 Info - print the image dimesions to the main tinatool window. 64 Imcalc Params - control parameters IP(-). 65 66 Stack manipulation. 67 68 C - remove top image (TOS) from stack. 69 CA - remove all images from stack. 70 store - save TOS in the storage register. 71 fetch - retrieve image from the storage register. 72 dup - duplicate TOS. 73 flp - flip TOS with next image on stack (NOS). 74 roi - edit TOS to selected roi. 75 76 Basic Image Manipulation. 77 78 scale - change normalisation of TOS to 0-IP(scale) default 255.0 79 yrat - change vertical aspect ratio of TOS by IP(const) using linear 80 interpolation. 81 xrat - change horizontal aspect ratio of TOS by IP(const) using linear 82 interpolation. 83 smpl - resample TOS by factor IP(const) using quadratic interpolation. 84 shift - shift the co-ordinates of TOS by IP(sx,sy). 85 bshift - barrel shift TOS by IP(sx,sy). 86 87 Baic Algebra 88 89 + - add TOS to NOS. 90 - - subtract NOS from TOS. 91 * - multiply TOS and NOS. 92 / - divide TOS by NOS minimum division value limited to IP(const). 93 -1* - negate TOS. 94 +k - add IP(const) to TOS. 95 k* - multiply TOS by IP(const). 96 97 Transendental Algebra. 98 99 sqrt - take square-root of TOS image with sign preserved. 100 csqrt - complex square_root of TOS. 101 sqr - take square of TOS image. 102 log - take logarithm of TOS. 103 exp - exponentiate TOS maintaining sign. 104 sin - take trigonometric sine of TOS. 105 asin - take trigonometric inverse sine of TOS. 106 107 Standard Noise and Texture Filters. 108 109 thres - threshold TOS at making all pixels less than IP(thres) zero, operates 110 only on real component of complex images. 111 lsf - linear sequential (exponential) smoothing filter of TOS with decay 112 parameter and up/down left right handedness given by IP(sigma,LR,UD). 113 med - median filter of TOS for 3x3 pixel patch. 114 rank - rank order filtering of TOS with pixel region IP(range) and expected 115 grey level noise level of IP(const). 116 gauss - gaussian filter of TOS with standard deviation and convolution area of 117 IP(sigma,range). 118 tsmooth - local smoothed average of TOS image along direction of minimum 119 gradient. 120 121 Numerical differential functions. 122 123 diffx - numerical aproximation to first derivative of TOS in x using 124 (-1,0,1) filter. 125 diffy - numerical approximation to first derivative of TOS in y. 126 grdsq - sum squared of diffx and diffy of TOS image. 127 lap - sum of the second derivatives in x and y of TOS image. 128 ddn - second order image derivative invariant of TOS image. 129 ddt - second order image derivative invariant of TOS image. 130 crv - curvature of TOS image with IP(Precision). 131 132 Complex Image manipulation. 133 134 xy norm- calculate gain variation across image with smoothness given by IP(sigma) 135 and noise estimate given by IP(const) (see noise below). 136 z norm - calculate the modal grey level ratio between the TOS and NOS (stabilised 137 according to noise estimate IP(const)) and set IP(const) to this value. 138 arg - compute phase of complex TOS image. 139 cis - convert phase back to complex with unit modulus. 140 conj - complex conjugate of complex TOS image. 141 optf - construct optimal smoothed fourier image for deconvolution from TOS 142 image with noise level set by IP(const). 143 144 Fourier and related Functions. 145 146 rmdc - remove dc component of the TOS image. 147 quad - create a double sized image from TOS with 4 fold symmetry. 148 fft - compute fast fourier transform of TOS image. 149 ffti - compute inverse fast fourier transform of TOS image. 150 power - compute power spectrum of TOS fft image. 151 fdx - compute x derivative in the fourier domain of complex TOS image. 152 fdy - compute y derivative in the fourier domain of complex TOS image. 153 154 Miscelaneous. 155 156 erfp - compute the probability of a z score variable centred at IP(thresh). 157 max pos - indicate position of maximum of TOS image. 158 skel - skeletonize a binary image. 159 erode - morphological erosion of TOS image with sphere radius IP(range). 160 dilate - morphological dilation of TOS image with sphere radius IP(range). 161 scat - compute scatter plot from a complex image with axes defined by IP(scale) 162 iscat - locate all data within the current ROI of the scatter plot on original 163 complex image. Return an image with each pixel given by the grey level 164 within the selected ROI. 165 hist - histogram the current image in the selected ROI within the limits 166 IP(thresh)- IP(range) and IP(thresh) + IP(range). Return an image 167 with the frequency of each pixel and set IP(thresh) to the mean and 168 IP(const) equal to the RMS deviation. 169 zpad - zero pad the existing image around the outside by a distance IP(range). 170 noise - set IP(const) to the noise level in the current image, estimated from 171 width of the central peak of the second spatial derivative. 172 window - limit the grey level range of the current image between IP(thresh) and 173 IP(thresh) + IP(const). 174 175 Sequences of button presses and parameter changes can be stored using the 176 Macro facility in the main tool. 177 178 The Create Tool can be used to generate a variety of simple images. For 179 documentation on this and more details regarding the Imcalc Tool see the User 180 Guide. 181 182 183 NAT 14/3/2000. 184 --------------------------------------------------------------------------------

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