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//////////////////////////////////////////////////////////////////////////// // // File name: SegmentationAndAnalysisOfCells.cpp // Location: See Matrox Example Launcher in the MIL Control Center // // // Synopsis: This program shows how to use the blob reconstruction operation // to segment objects using an hysteresis thresholding technique. // - the image is filtered to remove the noise // - the reconstruction from seed operation is used to perform a robust // segmentation of the objects // - blob features are calculated to select specific cells // // Copyright (C) Matrox Electronic Systems Ltd., 1992-2016. // All Rights Reserved //////////////////////////////////////////////////////////////////////////// #include <mil.h> // Target MIL image file specifications. #define IMAGE_FILE M_IMAGE_PATH MIL_TEXT("/BlobAnalysis/ElongatedCells.mim") #define PIXEL_SIZE_X 0.15 // 1 pixel size x = 0.15 mm #define PIXEL_SIZE_Y 0.17 // 1 pixel size y = 0.17 mm #define LOW_THRESHOLD_VALUE 165L #define HIGH_THRESHOLD_VALUE 230L #define MINIMUM_AREA 4.59 // mm^2 #define MAXIMUM_AREA 10.2 // mm^2 #define MINIMUM_FERET_ELONGATION 2.00 int MosMain(void) { MIL_ID MilApplication, // Application identifier. MilSystem, // System identifier. MilDisplay, // Display identifier. MilImage, // Image buffer identifier. MilImageToDisplay, // Image to display identifier. MilGraphicList, // Graphic list identifier. MilDestImage, // Image buffer identifier. MilBinLowImage, // Binary image buffer identifier. MilBinHighImage, // Binary image buffer identifier. MilBinImage, // Binary image buffer identifier. MilBlobResult, // Blob result buffer identifier. MilBlobContext; // Context identifier. MIL_INT SizeX, // Size X of the source buffer. SizeY, // Size Y of the source buffer. NumberOfBlobs; // Number of blobs. MIL_DOUBLE *AreaArray, // Blob areas. *CogXArray, // Blob centers of gravity X. *CogYArray, // Blob centers of gravity Y. *ElongationArray; // Blob elongations. MIL_INT i; // Allocations. MappAllocDefault(M_DEFAULT, &MilApplication, &MilSystem, M_NULL, M_NULL, M_NULL); MdispAlloc(MilSystem, M_DEFAULT, MIL_TEXT("M_DEFAULT"), M_WINDOWED, &MilDisplay); // Restore source image into image buffer. MbufRestore(IMAGE_FILE, MilSystem, &MilImage); // Allocate processing image buffers MbufInquire(MilImage, M_SIZE_X, &SizeX); MbufInquire(MilImage, M_SIZE_Y, &SizeY); MbufAlloc2d(MilSystem, SizeX, SizeY, 8+M_UNSIGNED, M_IMAGE+M_PROC, &MilDestImage); MbufAlloc2d(MilSystem, SizeX, SizeY, 1+M_UNSIGNED, M_IMAGE+M_PROC, &MilBinLowImage); MbufAlloc2d(MilSystem, SizeX, SizeY, 1+M_UNSIGNED, M_IMAGE+M_PROC, &MilBinHighImage); MbufAlloc2d(MilSystem, SizeX, SizeY, 1+M_UNSIGNED, M_IMAGE+M_PROC, &MilBinImage); // Allocate image to be displayed MbufAllocColor(MilSystem, 3, SizeX, SizeY, 8+M_UNSIGNED, M_IMAGE+M_PROC+M_DISP, &MilImageToDisplay); MbufCopy(MilImage, MilImageToDisplay); // Allocate a graphic list and associate it to the display. MgraAllocList(MilSystem, M_DEFAULT, &MilGraphicList); MdispControl(MilDisplay, M_ASSOCIATED_GRAPHIC_LIST_ID, MilGraphicList); // Display the buffer. MdispSelect(MilDisplay, MilImageToDisplay); MosPrintf(MIL_TEXT("\nOBJECT ANALYSIS USING BLOB RECONSTRUCTION\n")); MosPrintf(MIL_TEXT("-----------------------------------------\n\n")); MosPrintf(MIL_TEXT("This program identifies the isolated cells in an image.\n\n")); MosPrintf(MIL_TEXT("Press <Enter> to continue.\n\n")); MosGetch(); // Image noise reduction MimConvolve(MilImage, MilDestImage, M_DERICHE_FILTER(M_SMOOTH, 50)); // Display the result MbufCopy(MilDestImage, MilImageToDisplay); MosPrintf(MIL_TEXT("The image is smoothed to reduce noise.\n\n")); MosPrintf(MIL_TEXT("Press <Enter> to continue.\n\n")); MosGetch(); // Binarize the smoothed image using a low threshold value./ MimBinarize(MilDestImage, MilBinLowImage, M_FIXED+M_GREATER, LOW_THRESHOLD_VALUE, M_NULL); // Binarize the smoothed using a high threshold value. MimBinarize(MilDestImage, MilBinHighImage, M_FIXED+M_GREATER, HIGH_THRESHOLD_VALUE, M_NULL); // Display the binarize results MbufClear(MilImageToDisplay, 0L); MbufClearCond(MilImageToDisplay, 255, 0, 0, MilBinLowImage, M_NOT_EQUAL, 0); MbufClearCond(MilImageToDisplay, 0, 255, 0, MilBinHighImage, M_NOT_EQUAL, 0); MosPrintf(MIL_TEXT("The blobs that are segmented using a low threshold value are displayed in red.\n")); MosPrintf(MIL_TEXT("The cells are well segmented, however there is also the presence noise.\n\n")); MosPrintf(MIL_TEXT("The blobs that are segmented using a high threshold value are displayed in green.\n")); MosPrintf(MIL_TEXT("The cells are well identified, and there is no noise. However the cells are not well\n")); MosPrintf(MIL_TEXT("segmented.\n\n")); MosPrintf(MIL_TEXT("Press <Enter> to continue.\n\n")); MosGetch(); // Reconstruct the blobs from seed MblobReconstruct(MilBinLowImage, MilBinHighImage, MilBinImage, M_RECONSTRUCT_FROM_SEED, M_BINARY); MbufClearCond(MilImageToDisplay, 0, 0, 255, MilBinImage, M_NOT_EQUAL, 0); MosPrintf(MIL_TEXT("The blobs segmented using a low threshold that are touching the blobs segmented\n")); MosPrintf(MIL_TEXT("using a high threshold and displayed in blue.\n\n")); MosPrintf(MIL_TEXT("Press <Enter> to continue.\n\n")); MosGetch(); // Calibrate the binary image to measure the blob features in world units. McalUniform(MilBinImage, 0, 0, PIXEL_SIZE_X, PIXEL_SIZE_Y, 0, M_DEFAULT); // Allocate a blob context. MblobAlloc(MilSystem, M_DEFAULT, M_DEFAULT, &MilBlobContext); // Enable blob features. MblobControl(MilBlobContext, M_CENTER_OF_GRAVITY + M_BINARY, M_ENABLE); MblobControl(MilBlobContext, M_FERETS, M_ENABLE); // Allocate a blob result buffer. MblobAllocResult(MilSystem, M_DEFAULT, M_DEFAULT, &MilBlobResult); // Calculate selected features for each blob. MblobCalculate(MilBlobContext, MilBinImage, M_NULL, MilBlobResult); MblobControl(MilBlobResult, M_INPUT_SELECT_UNITS, M_WORLD); // Display the original image and the blob results MbufCopy(MilImage, MilImageToDisplay); // Display the segmented blobs. MgraColor(M_DEFAULT, M_COLOR_RED); MblobDraw(M_DEFAULT, MilBlobResult, MilGraphicList, M_DRAW_BLOBS, M_DEFAULT, M_DEFAULT); // Exclude the blobs whose the area is outside the expected range of values. MblobSelect(MilBlobResult, M_EXCLUDE, M_AREA, M_OUT_RANGE, MINIMUM_AREA, MAXIMUM_AREA); // Exclude the blobs whose the elongation is less than the minimum expected value. MblobSelect(MilBlobResult, M_EXCLUDE, M_FERET_ELONGATION, M_LESS, MINIMUM_FERET_ELONGATION, M_NULL); // Get the total number of selected blobs. MblobGetResult(MilBlobResult, M_DEFAULT, M_NUMBER + M_TYPE_MIL_INT, &NumberOfBlobs); // Display the selected blobs. MgraColor(M_DEFAULT, M_COLOR_BLUE); MblobDraw(M_DEFAULT, MilBlobResult, MilGraphicList, M_DRAW_BLOBS, M_INCLUDED_BLOBS, M_DEFAULT); MgraColor(M_DEFAULT, M_COLOR_YELLOW); MblobDraw(M_DEFAULT, MilBlobResult, MilGraphicList, M_DRAW_CENTER_OF_GRAVITY, M_INCLUDED_BLOBS, M_DEFAULT); // Set the text's background fill mode and font properties MgraColor(M_DEFAULT, M_COLOR_GREEN); MgraControl(M_DEFAULT, M_BACKGROUND_MODE, M_TRANSPARENT); MgraFont(M_DEFAULT, MIL_FONT_NAME(M_FONT_DEFAULT_TTF)); MgraControl(M_DEFAULT, M_FONT_SIZE, 12); MosPrintf(MIL_TEXT("The reconstructed blobs are analyzed to detect only isolated\n")); MosPrintf(MIL_TEXT("cells (in blue) using their area and elongation measures.\n\n")); if (NumberOfBlobs>0) { MosPrintf(MIL_TEXT("Number of detected cells: %d\n\n"), NumberOfBlobs); AreaArray = new MIL_DOUBLE[NumberOfBlobs]; CogXArray = new MIL_DOUBLE[NumberOfBlobs]; CogYArray = new MIL_DOUBLE[NumberOfBlobs]; ElongationArray = new MIL_DOUBLE[NumberOfBlobs]; // Retrieve the results. MblobControl(MilBlobResult, M_RESULT_OUTPUT_UNITS, M_PIXEL); MblobGetResult(MilBlobResult, M_DEFAULT, M_CENTER_OF_GRAVITY_X + M_BINARY + M_TYPE_MIL_DOUBLE, CogXArray); MblobGetResult(MilBlobResult, M_DEFAULT, M_CENTER_OF_GRAVITY_Y + M_BINARY + M_TYPE_MIL_DOUBLE, CogYArray); MblobControl(MilBlobResult, M_RESULT_OUTPUT_UNITS, M_WORLD); MblobGetResult(MilBlobResult, M_DEFAULT, M_AREA + M_TYPE_MIL_DOUBLE, AreaArray); MblobGetResult(MilBlobResult, M_DEFAULT, M_FERET_ELONGATION + M_TYPE_MIL_DOUBLE, ElongationArray); // Print the results of each blob. MIL_TEXT_CHAR TextIndex[16]; for(i=0; i < NumberOfBlobs; i++) { MosSprintf(TextIndex, 3, MIL_TEXT("%d"), i); MgraText(M_DEFAULT, MilGraphicList, CogXArray[i]+2, CogYArray[i]-14, TextIndex); MosPrintf(MIL_TEXT("Blob #%ld:\t[area = %.2f mm^2] [elongation = %.2f]\n"), i, AreaArray[i], ElongationArray[i]); } // Release allocated arrays delete []AreaArray; delete []CogXArray; delete []CogYArray; delete []ElongationArray; } MosPrintf(MIL_TEXT("Press <Enter> to terminate.\n\n")); MosGetch(); /* Free all allocations. */ MgraFree(MilGraphicList); MblobFree(MilBlobResult); MblobFree(MilBlobContext); MbufFree(MilBinLowImage); MbufFree(MilBinHighImage); MbufFree(MilBinImage); MbufFree(MilDestImage); MbufFree(MilImage); MbufFree(MilImageToDisplay); MdispFree(MilDisplay); MappFreeDefault(MilApplication, MilSystem, M_NULL, M_NULL, M_NULL); return 0; }