Difference between revisions of "PlugIn Algorithm Median (con't, part 3)"

Latest revision as of 14:55, 16 February 2012

804 if (numberOfSlices > 1) { //3D image update progressBar
</font></div>

805 // do a progress bar update

806 progressBar.setValue(Math.round

807 (( ( (float)(currentSlice*iterations pass)/

808 (iterations*numberOfSlices))* 100)));

809 }

810 }

811 for ( i = 0; i < imageSliceLength && !threadStopped; i ){

812 if (numberOfSlices == 1) { // 2D image update progressBar

813 if (i%mod == 0 && pBarVisible == true) {

814 progressBar.setValue(Math.round

815 ( ( (float)( (pass*imageSliceLength) i)

816 /(iterations*(imageSliceLength -1))*100)) );

817 }

818 }

819 if (entireImage == true || mask.get(a) ) {

820 // Median stuff here

821 row = i/width;

822 col = i%width;

823 if ( (row < upperBound) || (row > lowerBound) ) {

824 destBuffer[a] = srcBuffer[a]; // row too far up or down--out of

825 // bounds

826 }

827 else if ((col < leftBound) || (col > rightBound)) {

828 destBuffer[a] = srcBuffer[a]; // column too far left or right-

829 // -out of bounds

830 }

831

|- |

832 else { // in bounds

833 maskedList = getNeighborList(a, srcBuffer, true);

834 // verify that this element is an outlier

835 if (stdDevLimit == 0.0) { // anything is an outlier

836 shellSort(maskedList);

837 destBuffer[a] = median(maskedList);

838 }

839 else { // look for outlierness

840 average = mean(maskedList);

841 sigma = standardDeviation(maskedList, average);

842 if ((maskedList[kCenter] > (average stdDevLimit*sigma)) ||

843 (maskedList[kCenter] < (average - stdDevLimit*sigma))) {

844 shellSort(maskedList);

845 destBuffer[a] = median(maskedList);

846 }

847 else { // if element was not an outlier, pixel is fine.

848 destBuffer[a] = srcBuffer[a];

849 }

850 }

851 }

852 }

853 else { // not part of the VOI so just copy this into the destination

854 buffer.

855 destBuffer[a] = srcBuffer[a];

856 }

857 a ; // address the next data element from the bufferStartingPoint

858 }

859 }

860

861 // now set up for the repeat for multiple iterations.

862 // But only bother with copying over if there are more iterations.

863 if (pass < iterations - 1) {

864 tempBuffer = destBuffer; // swap dest & src buffers

865 destBuffer = srcBuffer;

866 srcBuffer = tempBuffer;

867 }

868 }

869 // destBuffer should now be copied over for the size of imageSliceLength.

870 // You may return.

871

872 }

873

874 /**

875 * Filter a 3D image with a 3D kernel. Allows median filtering to include the

876 * picture elements at greater depths than only the current slice.

877 * <p><em>Note that this volume filter will correctly filter color images on all

878 * bands (aRGB) because the neighbor list is correct (see getNeighborList()).

879 * This means, however, it will not selectivly filter any bands (one may not

880 * filter only the Red channel, for instance), and will also filter all alpha

881 * values as well. Of course, progress bar updates will not include any

882 * color information. For these reasons it a useable, but limited color

883 * filter.</em>

884 * @param srcBuffer Source image.

885 * @param destBuffer Destination image.

|- |

886 * @see volumeColorFilter

887 * @see getNeighborList

888 *

889 */

890 // some code has been left in to allow this method to properly filter

891 // color images, although the other method is included.

892

893 private void volumeFilter(float srcBuffer[], float destBuffer[]) {

894 int i, pass; // counting the current element

895 int row, // ease of reading to find the row, column and slice

896 column, // (all starting at 0) associated with the current element

897 slice; // [(0,0,0) starts at the closest upper-left corner]

898 int imageSliceLength = srcImage.getSliceSize() * valuesPerPixel;

899 int imageLength = imageSliceLength * numberOfSlices;

900 int kCenter = maskCenter;

901 int width = srcImage.getExtents()[0]; // width of slice in number of pixels

902 int height = srcImage.getExtents()[1]; // height of slice in number of pixels

903 int sliceWidth = width*valuesPerPixel; // width of slice in number of intensity

904 // values (as in colors per pixel (1 for

905 // mono, 4 for color))

906 float tempBuffer[];

907

908 float average; // arithmetic mean

909 float sigma; // standard deviation

910

911 float maskedList[]; // list of buffer-values that were showing inside the

912 // mask these bounds "frame" the interior of the slice which may be filtered

913 // (&adjusted); image outside the frame may not

914 int leftBound, rightBound, // bounds on the column

915 upperBound, lowerBound, // bounds on the row

916 aheadBound, behindBound; // bounds on the slice

917 // (a note on orientation: object front is facing in the same direction as

918 // viewer, thus ahead of viewer is into monitor, behind is out of monitor and

919 // a more positive number of slices is farther forward.)

920 upperBound = halfK;

921 lowerBound = height - halfK -1;

922 behindBound = halfK;

923 aheadBound = numberOfSlices - halfK - 1;

924 // we may say that each column is a pixel intensity: mono images have 1 per

925 // pixel, 4 in color;

926 // these calculations are done separately for color & mono images in

927 // sliceFilter().

928 leftBound = halfK * valuesPerPixel;

929 rightBound = sliceWidth - valuesPerPixel*halfK - 1; // in color: (4*width - 4*halfK

930 // - 1); mono: (width -

931 // halfK - 1)

932 int mod = (imageLength)/100; // mod is 1 percent of length of slice * the number

933 // of slices.

934

935 BitSet mask = srcImage.generateVOIMask();

936 for (pass = 0; pass < iterations && !threadStopped; pass ) {

937 if (pBarVisible == true) {

938 progressBar.setMessage("Filtering image (pass " String.valueOf(pass 1) " of "

939 iterations ") ...");

940 }

941

|- |

942 for ( i = 0; i < imageLength && !threadStopped; i ){

943 if (i%mod == 0 && pBarVisible == true) {

944 progressBar.setValue(Math.round

945 ( ( (float)( (pass*imageLength) i)/(iterations*(imageLength-1))*100)) );

946 }

947

948 if (entireImage == true || mask.get(i/valuesPerPixel) ) {

949 // Median stuff here

950 slice = i/imageSliceLength;

951 row = (i%imageSliceLength)/sliceWidth;

952 column = i%sliceWidth;

953

954 if ( (row < upperBound) || (row > lowerBound) ) {

955 destBuffer[i] = srcBuffer[i]; // row too far up or down--out of

956 // bounds

957 }

958 else if ((column < leftBound) || (column > rightBound)) {

959 destBuffer[i] = srcBuffer[i]; // column too far left or right--out

960 // of bounds

961 }

962 else if ((slice < behindBound) || (slice > aheadBound)) {

963 destBuffer[i] = srcBuffer[i]; // slice too far ahead or behind--out

964 // of bounds

965 }

966 else { // in bounds

967 maskedList = getNeighborList(i, srcBuffer, false);

968 // verify that this element is an outlier

969 if (stdDevLimit == 0.0) { // anything is an outlier

970 shellSort(maskedList);

971 destBuffer[i] = median(maskedList);

972 }

973 else { // look for outlierness

974 average = mean(maskedList);

975 sigma = standardDeviation(maskedList, average);

976 if ((maskedList[kCenter] > (average stdDevLimit*sigma)) ||

977 (maskedList[kCenter] < (average - stdDevLimit*sigma))) {

978 shellSort(maskedList);

979 destBuffer[i] = median(maskedList);

980 }

981 else { // if element was not an outlier, pixel is fine.

982 destBuffer[i] = srcBuffer[i];

983 }

984 }

985 }

986 }

987 else { // not part of the VOI so just copy this

988 // into the destination buffer.

989 destBuffer[i] = srcBuffer[i];

990 }

991 }

992 // now set up for the repeat for multiple iterations.

993 // But only bother with copying over if there are more iterations.

994 if (pass < iterations - 1) {

995 tempBuffer = destBuffer; // swap src & dest buffer

996 destBuffer = srcBuffer;

997 srcBuffer = tempBuffer;

998 }

|- |

999 }

1000 }

1001 /**

1002 * Filter a Color 3D image with a 3D kernel. Allows median filtering to

1003 * include the picture elements at greater depths than only the current

1004 * slice. This method allows selected band filtering, and does not filter

1005 * the alpha band.

1006 * @param srcBuffer Source image.

1007 * @param destBuffer Destination image.

1008 * @see volumeFilter

1009 *

1010 */

1011 private void volumeColorFilter(float srcBuffer[], float destBuffer[]) {

1012 int i, pass; // counting the current element

1013 int initialIndex; // reference to the color band being filtered/copied: aRBG:

1014 // 0, 1, 2, 3;

1015 // it is an offset to the identified pixel, or column, of

1016 // the slice

1017 int row, // ease of reading to find the row, column and slice

1018 column, // (all starting at 0) associated with the current element

1019 slice; // [(0,0,0) starts at the closest upper-left corner]

1020 int kCenter = maskCenter;

1021 int width = srcImage.getExtents()[0]; // width of slice in number of pixels

1022 int height = srcImage.getExtents()[1]; // height of slice in number of pixels

1023 int sliceWidth = width*valuesPerPixel; // width of slice in number of

1024 // intensity values (as in colors per

1025 // pixel (1 for mono, 4 for color))

1026 int sliceSize = width * height; // in pixels (or elements)

1027 int imageSliceLength = width * height * valuesPerPixel; // in values-pixels

1028 int imageSize = sliceSize * numberOfSlices; // in pixels (or elements)

1029 int imageLength = imageSliceLength * numberOfSlices; // in (values-pixels)

1030 float tempBuffer[];

1031

1032 float average; // arithmetic mean

1033 float sigma; // standard deviation

1034

1035 float maskedList[]; // list of buffer-values that were showing inside the

1036 // mask

1037 // these bounds "frame" the interior of the slice which may be

1038 // filtered (&adjusted); image outside the frame may not

1039 int leftBound, rightBound, // bounds on the column

1040 upperBound, lowerBound, // bounds on the row

1041 aheadBound, behindBound; // bounds on the slice

1042 // (a note on orientation: object front is facing in the same direction as

1043 // viewer, thus ahead of viewer is into monitor, behind is out of monitor and

1044 // a more positive number of slices is farther forward.)

1045 upperBound = halfK;

1046 lowerBound = height - halfK -1;

1047 behindBound = halfK;

1048 aheadBound = numberOfSlices - halfK - 1;

1049 // we may say that each column is a pixel intensity: mono images have 1 per

1050 // pixel, 4 in color; these calculations are done separately for color &

1051 // mono images in sliceFilter().

1052 leftBound = halfK * valuesPerPixel;

1053 rightBound = sliceWidth - valuesPerPixel*halfK - 1; // in color: (4*width -

1054 // 4*halfK - 1); mono:

1055 // (width - halfK - 1)

|- |

1056 int mod = (imageSize)/100; // mod is 1 percent of length of slice * the number

1057 // of slices.

1058

1059 BitSet mask = srcImage.generateVOIMask();

1060

1061 // copy all alpha values in the image

1062 setCopyColorText("alpha");

1063 for (i = 0; i < imageLength; i =4) {

1064 destBuffer[i] = srcBuffer[i]; // copy alpha;

1065 }

1066

1067 // choose i so the proper colors go alongside the initial index

1068 // so we get the right output statements in the progress bar

1069 // copy only needed RGB values

1070 initialIndex = 0; // start with alpha on each pass (routine moved so we don't

1071 // do it for each pass)

1072 while (initialIndex < 3 && !threadStopped) { // alpha:0, R:1, G:2, B:3. But

1073 // alpha must be copied

1074 initialIndex; // next initial index

1075

1076 if (!rChannel && initialIndex==1) {

1077 // when looking at the image reds but we're not filtering the red

1078 // channel copy all red values

1079 setCopyColorText("red");

1080 for (i = initialIndex; i < imageLength; i =4) {

1081 destBuffer[i] = srcBuffer[i];

1082 }

1083 }

1084 else if (!gChannel && initialIndex==2) { // when looking at the image greens

1085 // but we're not filtering the

1086 // greens channel copy all greens

1087 // values

1088 setCopyColorText("green");

1089 for (i = initialIndex; i < imageLength; i =4) {

1090 destBuffer[i] = srcBuffer[i];

1091 }

1092 }

1093 else if (!bChannel && initialIndex==3) {

1094 // when looking at the image blues but we're not filtering the

1095 // blues channel copy all blue values

1096 setCopyColorText("blue");

1097 for (i = initialIndex; i < imageLength; i =4) {

1098 destBuffer[i] = srcBuffer[i];

1099 }

1100 }

1101 else {

1102 for (pass = 0; pass < iterations && !threadStopped; pass ) {

1103 if (pBarVisible == true) {

1104 if (initialIndex == 1) {

1105 progressBar.setMessage("Filtering red channel (pass "

1106 String.valueOf(pass 1) " of " iterations ") ...");

1107 }

1108 else if (initialIndex == 2) {

1109 progressBar.setMessage("Filtering green channel (pass "

1110 String.valueOf(pass 1) " of " iterations ") ...");

1111 }

1112

|- |

1113 else if (initialIndex == 3) {

1114 progressBar.setMessage("Filtering blue channel (pass "

1115 String.valueOf(pass 1) " of " iterations ") ...");

1116 }

1117 }

1118 // if we needed to filter the image, we dropped through the

1119 // selection to filter the color given by ints initialIndex

1120 for ( i = initialIndex; i < imageLength && !threadStopped; i =4){

1121 if (i%mod == 0 && pBarVisible == true) {

1122 progressBar.setValue(Math.round

1123 ( ( (float)(iterations*(initialIndex - 1)*imageSize imageSize*pass

1124 i/4)/(3*iterations*(imageSize-1))*100)) );

1125 }

1126

1127 if (entireImage == true || mask.get(i/valuesPerPixel) ) {

1128 // Median stuff here

1129 slice = i/imageSliceLength;

1130 row = (i%imageSliceLength)/sliceWidth;

1131 column = i%sliceWidth;

1132

1133 if ( (row < upperBound) || (row > lowerBound) ) {

1134 destBuffer[i] = srcBuffer[i]; // row too far up or down--out of

1135 // bounds

1136 }

1137 else if ((column < leftBound) || (column > rightBound)) {

1138 destBuffer[i] = srcBuffer[i]; // column too far left or right--

1139 // out of bounds

1140 }

1141 else if ((slice < behindBound) || (slice > aheadBound)) {

1142 destBuffer[i] = srcBuffer[i]; // slice too far ahead or behind--

1143 // out of bounds

1144 }

1145 else { // in bounds

1146 maskedList = getNeighborList(i, srcBuffer, false);

1147 // verify that this element is an outlier

1148 if (stdDevLimit == 0.0) { // anything is an outlier

1149 shellSort(maskedList);

1150 destBuffer[i] = median(maskedList);

1151 }

1152 else { // look for outlierness

1153 average = mean(maskedList);

1154 sigma = standardDeviation(maskedList, average);

1155 if ((maskedList[kCenter] > (average stdDevLimit*sigma)) ||

1156 (maskedList[kCenter] < (average - stdDevLimit*sigma))) {

1157 shellSort(maskedList);

1158 destBuffer[i] = median(maskedList);

1159 }

1160 else { // if element was not an outlier, pixel is fine.

1161 destBuffer[i] = srcBuffer[i];

1162 }

1163 }

1164 }

1165 }

1166

|- |

1167 else { // not part of the VOI so just copy this into the

1168 // destination buffer.

1169 destBuffer[i] = srcBuffer[i];

1170 }

1171 }

1172 // now set up for the repeat for multiple iterations.

1173 // But only bother with copying over if there are more iterations.

1174 if (pass < iterations - 1) {

1175 tempBuffer = destBuffer; // swap src & dest buffer

1176 destBuffer = srcBuffer;

1177 srcBuffer = tempBuffer;

1178 }

1179 }

1180 if (iterations%2 == 0) { // if even number of iterations, then

1181 tempBuffer = destBuffer; // swap src & dest buffer is necessary

1182 destBuffer = srcBuffer; // to keep other colors not-yet-filtered

1183 // from

1184 srcBuffer = tempBuffer; // filtering from the wrong buffer,

1185 // overwriting the real src

1186 }

1187 }

1188 }

1189 }

1190

1191 /**

1192 * Forms kernel. Note that the <bold>kernel</bold> uses the 0th place, unlike the

1193 * kernelMask where counting starts at 1.

1194 *

1195 */

1196 private void makeKernel(){

1197 try {

1198 if (sliceFiltering)

1199 kernel = new byte[kernelSize*kernelSize];

|}

PlugIn Algorithm Median (con't, part 4)

@@ Line 1: / Line 1: @@
 {|
 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (numberOfSlices &gt; 1) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">//</font></span> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">3D image update progressBar</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 805 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">//</font></span> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">do a progress bar update</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 806 progressBar.setValue(Math.round<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 807 (( ( (<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span>)(currentSlice*iterations pass)/<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 808 (iterations*numberOfSlices))* 100)));<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 809 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 810 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 811 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> ( i = 0; i &lt; imageSliceLength &amp;&amp; !threadStopped; i ){<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 812 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (numberOfSlices == 1) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// 2D image update progressBar</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 813 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (i%mod == 0 &amp;&amp; pBarVisible == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span>) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 814 progressBar.setValue(Math.round<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 815 ( ( (<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span>)( (pass*imageSliceLength) i)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 816 /(iterations*(imageSliceLength -1))*100)) );<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 817 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 818 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 819 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (entireImage == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span> || mask.get(a) ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 820 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// Median stuff here</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 821 row = i/width;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 822 col = i%width;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 823 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> ( (row &lt; upperBound) || (row &gt; lowerBound) ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 824 destBuffer[a] = srcBuffer[a]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// row too far up or down--out of</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 825 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 826 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 827 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> ((col &lt; leftBound) || (col &gt; rightBound)) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 828 destBuffer[a] = srcBuffer[a]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// column too far left or right-</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 829 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // -out of </font></span> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 830 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 831 <br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 832 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 833 maskedList = getNeighborList(a, srcBuffer, true);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 834 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// verify that this element is an outlier</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 835 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (stdDevLimit == 0.0) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// anything is an outlier</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 836 shellSort(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 837 destBuffer[a] = median(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 838 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 839 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// look for outlierness</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 840 average = mean(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 841 sigma = standardDeviation(maskedList, average);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 842 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if </font>'''</span>((maskedList[kCenter] &gt; (average stdDevLimit*sigma)) ||<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 843 (maskedList[kCenter] &lt; (average - stdDevLimit*sigma))) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 844 shellSort(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 845 destBuffer[a] = median(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 846 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 847 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// if element was not an outlier, pixel is fine.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 848 destBuffer[a] = srcBuffer[a];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 849 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 850 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 851 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 852 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 853 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// not part of the VOI so just copy this into the destination</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 854 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">buffer.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 855 destBuffer[a] = srcBuffer[a];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 856 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 857 a ; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// address the next data element from the bufferStartingPoint</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 858 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 859 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 860 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 861 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// now set up for the repeat for multiple iterations.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 862 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// But only bother with copying over if there are more iterations.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 863 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (pass &lt; iterations - 1) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 864 tempBuffer = destBuffer; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// swap dest &amp; src buffers</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 865 destBuffer = srcBuffer;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 866 srcBuffer = tempBuffer;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 867 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 868 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 869 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// destBuffer should now be copied over for the size of imageSliceLength. </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 870 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // You may return.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 871 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 872 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 873 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 874 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">/**</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 875 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * Filter a 3D image with a 3D kernel. Allows median filtering to include the</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 876 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * picture elements at greater depths than only the current slice.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 877 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * &lt;p&gt;&lt;em&gt;Note that this volume filter will correctly filter color images on all</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 878 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * bands (aRGB) because the neighbor list is correct (see getNeighborList()). </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 879 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * This means, however, it will not selectivly filter any bands (one may not</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 880 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * filter only the Red channel, for instance), and will also filter all alpha</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 881 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * values as well. Of course, progress bar updates will not include any</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 882 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * color information. For these reasons it a useable, but limited color</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 883 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * filter.&lt;/em&gt;</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 884 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @param srcBuffer Source image.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 885 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @param destBuffer Destination image.</font></span><br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 886 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @see volumeColorFilter</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 887 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @see getNeighborList</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 888 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> *</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 889 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> */</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 890 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // some code has been left in to allow this method to properly filter</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 891 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // color images, although the other method is included.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 892 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 893 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">private void</font>'''</span> volumeFilter(<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> srcBuffer[], <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> destBuffer[]) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 894 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> i, pass; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// counting the current element</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 895 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> row, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// ease of reading to find the row, column and slice</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 896 column, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// (all starting at 0) associated with the current element</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 897 slice; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// [(0,0,0) starts at the closest upper-left corner]</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 898 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int </font>'''</span>imageSliceLength = srcImage.getSliceSize() * valuesPerPixel;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 899 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> imageLength = imageSliceLength * numberOfSlices;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 900 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> kCenter = maskCenter;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 901 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> width = srcImage.getExtents()[0]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// width of slice in number of pixels</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 902 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> height = srcImage.getExtents()[1]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// height of slice in number of pixels</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 903 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> sliceWidth = width*valuesPerPixel; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// width of slice in number of intensity</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 904 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// values (as in colors per pixel (1 for</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 905 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // mono, 4 for color))</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 906 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> tempBuffer[];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 907 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 908 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> average; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// arithmetic mean</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 909 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> sigma; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// standard deviation</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 910 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 911 float maskedList[]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// list of buffer-values that were showing inside the</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 912 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// mask these bounds "frame" the interior of the slice which may be filtered</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 913 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // (&amp;adjusted); image outside the frame may not</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 914 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> leftBound, rightBound, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds on the column</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 915 upperBound, lowerBound, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds on the row</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 916 aheadBound, behindBound; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds on the slice</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 917 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// (a note on orientation: object front is facing in the same direction as</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 918 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // viewer, thus ahead of viewer is into monitor, behind is out of monitor and</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 919 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // a more positive number of slices is farther forward.)</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 920 upperBound = halfK;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 921 lowerBound = height - halfK -1;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 922 behindBound = halfK;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 923 aheadBound = numberOfSlices - halfK - 1;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 924 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// we may say that each column is a pixel intensity: mono images have 1 per</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 925 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // pixel, 4 in color;</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 926 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// these calculations are done separately for color &amp; mono images in</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 927 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // sliceFilter().</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 928 leftBound = halfK * valuesPerPixel;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 929 rightBound = sliceWidth - valuesPerPixel*halfK - 1; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in color:</font></span> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">(4*width - 4*halfK</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 930 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // - 1); mono: (width - </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 931 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // halfK - 1)</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 932 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> mod = (imageLength)/100; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// mod is 1 percent of length of slice * the number </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 933 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // of slices.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 934 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 935 BitSet mask = srcImage.generateVOIMask();<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 936 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">for</font></span> (pass = 0; pass &lt; iterations &amp;&amp; !threadStopped; pass ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 937 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (pBarVisible == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span>) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 938 progressBar.setMessage("Filtering image (pass " String.valueOf(pass 1) " of " <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 939 iterations ") ...");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 940 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 941 <br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 942 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> ( i = 0; i &lt; imageLength &amp;&amp; !threadStopped; i ){<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 943 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if </font>'''</span>(i%mod == 0 &amp;&amp; pBarVisible == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span>) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 944 progressBar.setValue(Math.round<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 945 ( ( (<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span>)( (pass*imageLength) i)/(iterations*(imageLength-1))*100)) );<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 946 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 947 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 948 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (entireImage == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span> || mask.get(i/valuesPerPixel) ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 949 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// Median stuff here</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 950 slice = i/imageSliceLength;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 951 row = (i%imageSliceLength)/sliceWidth;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 952 column = i%sliceWidth;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 953 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 954 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> ( (row &lt; upperBound) || (row &gt; lowerBound) ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 955 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// row too far up or down--out of</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 956 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 957 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 958 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> ((column &lt; leftBound) || (column &gt; rightBound)) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 959 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// column too far left or right--out</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 960 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // of bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 961 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 962 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> ((slice &lt; behindBound) || (slice &gt; aheadBound)) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 963 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// slice too far ahead or behind--out</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 964 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // of bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 965 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 966 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 967 maskedList = getNeighborList(i, srcBuffer, <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">false</font>'''</span>);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 968 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// verify that this element is an outlier</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 969 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (stdDevLimit == 0.0) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// anything is an outlier</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 970 shellSort(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 971 destBuffer[i] = median(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 972 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 973 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { /<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">/ look for outlierness</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 974 average = mean(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 975 sigma = standardDeviation(maskedList, average);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 976 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> ((maskedList[kCenter] &gt; (average stdDevLimit*sigma)) ||<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 977 (maskedList[kCenter] &lt; (average - stdDevLimit*sigma))) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 978 shellSort(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 979 destBuffer[i] = median(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 980 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 981 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// if element was not an outlier, pixel is fine.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 982 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 983 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 984 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 985 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 986 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 987 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// not part of the VOI so just copy this</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 988 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // into the destination buffer.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 989 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 990 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 991 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 992 /<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">/ now set up for the repeat for multiple iterations.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 993 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // But only bother with copying over if there are more iterations.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 994 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (pass &lt; iterations - 1) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 995 tempBuffer = destBuffer; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// swap src &amp; dest buffer</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 996 destBuffer = srcBuffer;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 997 srcBuffer = tempBuffer;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 998 }<br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 999 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1000 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1001 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">/**</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1002 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * Filter a Color 3D image with a 3D kernel. Allows median filtering to</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1003 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * include the picture elements at greater depths than only the current</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1004 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * slice. This method allows selected band filtering, and does not filter</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1005 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * the alpha band.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1006 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @param srcBuffer Source image.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1007 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @param destBuffer Destination image.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1008 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * @see volumeFilter</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1009 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> *</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1010 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> */</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1011 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">private void</font>'''</span> volumeColorFilter(<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> srcBuffer[], <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> destBuffer[]) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1012 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> i, pass; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// counting the current element</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1013 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> initialIndex; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // reference to the color band being filtered/copied: aRBG:</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1014 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // 0, 1, 2, 3;</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1015 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// it is an offset to the identified pixel, or column, of</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1016 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // the slice</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1017 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> row, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// ease of reading to find the row, column and slice</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1018 column, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// (all starting at 0) associated with the current element</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1019 slice; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// [(0,0,0) starts at the closest upper-left corner]</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1020 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> kCenter = maskCenter;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1021 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> width = srcImage.getExtents()[0]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// width of slice in number of pixels</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1022 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> height = srcImage.getExtents()[1]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// height of slice in number of pixels</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1023 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> sliceWidth = width*valuesPerPixel; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// width of slice in number of </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1024 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // intensity values (as in colors per</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1025 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // pixel (1 for mono, 4 for color))</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1026 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> sliceSize = width * height; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in pixels (or elements</font></span>)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1027 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> imageSliceLength = width * height * valuesPerPixel; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in values-pixels</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1028 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> imageSize = sliceSize * numberOfSlices; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in pixels (or elements)</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1029 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> imageLength = imageSliceLength * numberOfSlices; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in (values-pixels)</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1030 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> tempBuffer[];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1031 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1032 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> average; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// arithmetic mean</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1033 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> sigma; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// standard deviation</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1034 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1035 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span> maskedList[]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// list of buffer-values that were showing inside the</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1036 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // mask</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1037 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// these bounds "frame" the interior of the slice which may be </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1038 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // filtered (&amp;adjusted); image outside the frame may not</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1039 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> leftBound, rightBound, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds on the column</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1040 upperBound, lowerBound, <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds on the row</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1041 aheadBound, behindBound; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds on the slice</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1042 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // (a note on orientation: object front is facing in the same direction as</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1043 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // viewer, thus ahead of viewer is into monitor, behind is out of monitor and</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1044 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // a more positive number of slices is farther forward.)</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1045 upperBound = halfK;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1046 lowerBound = height - halfK -1;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1047 behindBound = halfK;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1048 aheadBound = numberOfSlices - halfK - 1;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1049 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// we may say that each column is a pixel intensity: mono images have 1 per</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1050 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // pixel, 4 in color; these calculations are done separately for color &amp; </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1051 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // mono images in sliceFilter().</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1052 leftBound = halfK * valuesPerPixel;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1053 rightBound = sliceWidth - valuesPerPixel*halfK - 1; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in color: (4*width - </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1054 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // 4*halfK - 1); mono: </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1055 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // (width - halfK - 1)</font></span><br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1056 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">int</font>'''</span> mod = (imageSize)/100; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// mod is 1 percent of length of slice * the number </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1057 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // of slices.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1058 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1059 BitSet mask = srcImage.generateVOIMask();<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1060 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1061 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// copy all alpha values in the image</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1062 setCopyColorText("alpha");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1063 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> (i = 0; i &lt; imageLength; i =4) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1064 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// copy alpha;</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1065 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1066 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1067 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// choose i so the proper colors go alongside the initial index</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1068 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // so we get the right output statements in the progress bar</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1069 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // copy only needed RGB values</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1070 initialIndex = 0; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// start with alpha on each pass (routine moved so we don't</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1071 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">//</font></span> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">do it for each pass)</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1072 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">while</font>'''</span> (initialIndex &lt; 3 &amp;&amp; !threadStopped) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// alpha:0, R:1, G:2, B:3. But</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1073 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // alpha must be copied</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1074 initialIndex; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// next initial index</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1075 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1076 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (!rChannel &amp;&amp; initialIndex==1) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1077 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// when looking at the image reds but we're not filtering the red</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1078 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // channel copy all red values</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1079 setCopyColorText("red");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1080 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> (i = initialIndex; i &lt; imageLength; i =4) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1081 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1082 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1083 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1084 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> (!gChannel &amp;&amp; initialIndex==2) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// when looking at the image greens</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1085 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // but we're not filtering the</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1086 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // greens channel copy all greens </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1087 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // values</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1088 setCopyColorText("green");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1089 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> (i = initialIndex; i &lt; imageLength; i =4) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1090 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1091 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1092 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1093 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> (!bChannel &amp;&amp; initialIndex==3) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1094 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// when looking at the image blues but we're not filtering the </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1095 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // blues channel copy all blue values</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1096 setCopyColorText("blue");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1097 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> (i = initialIndex; i &lt; imageLength; i =4) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1098 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1099 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1100 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1101 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1102 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> (pass = 0; pass &lt; iterations &amp;&amp; !threadStopped; pass ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1103 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (pBarVisible == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span>) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1104 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> if</font>'''</span> (initialIndex == 1) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1105 progressBar.setMessage("Filtering red channel (pass " <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1106 String.valueOf(pass 1) " of " iterations ") ...");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1107 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1108 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> else if</font>'''</span> (initialIndex == 2) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1109 progressBar.setMessage("Filtering green channel (pass " <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1110 String.valueOf(pass 1) " of " iterations ") ...");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1111 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1112 <br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1113 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> (initialIndex == 3) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1114 progressBar.setMessage("Filtering blue channel (pass " <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1115 String.valueOf(pass 1) " of " iterations ") ...");<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1116 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1117 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1118 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// if we needed to filter the image, we dropped through the </font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1119 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // selection to filter the color given by ints initialIndex</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1120 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">for</font>'''</span> ( i = initialIndex; i &lt; imageLength &amp;&amp; !threadStopped; i =4){<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1121 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (i%mod == 0 &amp;&amp; pBarVisible == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span>) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1122 progressBar.setValue(Math.round<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1123 ( ( (<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">float</font>'''</span>)(iterations*(initialIndex - 1)*imageSize imageSize*pass<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1124 i/4)/(3*iterations*(imageSize-1))*100)) );<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1125 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1126 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1127 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (entireImage == <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">true</font>'''</span> || mask.get(i/valuesPerPixel) ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1128 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// Median stuff here</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1129 slice = i/imageSliceLength;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1130 row = (i%imageSliceLength)/sliceWidth;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1131 column = i%sliceWidth;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1132 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1133 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> ( (row &lt; upperBound) || (row &gt; lowerBound) ) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1134 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// row too far up or down--out of</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1135 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1136 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1137 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> ((column &lt; leftBound) || (column &gt; rightBound)) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1138 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// column too far left or right--</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1139 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // out of bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1140 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1141 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else if</font>'''</span> ((slice &lt; behindBound) || (slice &gt; aheadBound)) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1142 destBuffer[i] = srcBuffer[i]; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// slice too far ahead or behind--</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1143 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // out of bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1144 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1145 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// in bounds</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1146 maskedList = getNeighborList(i, srcBuffer, <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">false</font>'''</span>);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1147 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// verify that this element is an outlier</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1148 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (stdDevLimit == 0.0) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// anything is an outlier</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1149 shellSort(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1150 destBuffer[i] = median(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1151 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1152 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// look for outlierness</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1153 average = mean(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1154 sigma = standardDeviation(maskedList, average);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1155 if ((maskedList[kCenter] &gt; (average stdDevLimit*sigma)) ||<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1156 (maskedList[kCenter] &lt; (average - stdDevLimit*sigma))) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1157 shellSort(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1158 destBuffer[i] = median(maskedList);<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1159 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1160 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// if element was not an outlier, pixel is fine.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1161 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1162 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1163 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1164 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1165 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1166 <br /></font></div> |- | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1167 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">else</font>'''</span> { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// not part of the VOI so just copy this into the</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1168 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // destination buffer.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1169 destBuffer[i] = srcBuffer[i];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1170 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1171 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1172 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// now set up for the repeat for multiple iterations.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1173 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // But only bother with copying over if there are more iterations.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1174 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (pass &lt; iterations - 1) {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1175 tempBuffer = destBuffer; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// swap src &amp; dest buffer</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1176 destBuffer = srcBuffer;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1177 srcBuffer = tempBuffer;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1178 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1179 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1180 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (iterations%2 == 0) { <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// if even number of iterations, then</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1181 tempBuffer = destBuffer; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// swap src &amp; dest buffer is necessary</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1182 destBuffer = srcBuffer; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// to keep other colors not-yet-filtered</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1183 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // from</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1184 srcBuffer = tempBuffer; <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">// filtering from the wrong buffer,</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1185 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> // overwriting the real src</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1186 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1187 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1188 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1189 }<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1190 <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1191 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07">/**</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1192 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * Forms kernel. Note that the &lt;bold&gt;kernel&lt;/bold&gt; uses the 0th place, unlike the</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1193 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> * kernelMask where counting starts at 1.</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1194 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> *</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#00ef07"> 1195 <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#00ef07"> */</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1196 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">private void</font>'''</span> makeKernel(){<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1197 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">try</font>'''</span> {<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1198 <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">if</font>'''</span> (sliceFiltering)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1199 kernel = <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">new byte</font>'''</span>[kernelSize*kernelSize];<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 30pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -30pt; text-transform: none; vertical-align: baseline"><font color="#000000"> |}
+[[PlugIn Algorithm Median (con't, part 4)]]

Difference between revisions of "PlugIn Algorithm Median (con't, part 3)"

Latest revision as of 14:55, 16 February 2012

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