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Detailed runtime measurements in ImagePyramidAccess object
1 parent cc563ac commit 6ea984d

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2 files changed

+34
-6
lines changed

2 files changed

+34
-6
lines changed

‎source/FAST/Data/Access/ImagePyramidAccess.cpp‎

Lines changed: 28 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -85,7 +85,7 @@ std::unique_ptr<uchar[]> ImagePyramidAccess::getPatchDataChar(int level, int x,
8585
(y - (y/tileHeight)*tileHeight) + height <= tileHeight
8686
) {
8787
// We only need to read 1 tile
88-
mRuntimeManager->startRegularTimer("simple");
88+
mRuntimeManager->startRegularTimer("simple_crop");
8989
auto tileData = std::make_unique<uchar[]>(tileWidth*tileHeight*bytesPerPixel);
9090
{
9191
// From TIFFReadTile documentation: Return the data for the tile containing the specified coordinates.
@@ -124,7 +124,7 @@ std::unique_ptr<uchar[]> ImagePyramidAccess::getPatchDataChar(int level, int x,
124124
}
125125
}
126126
mRuntimeManager->stopRegularTimer("Crop tile");
127-
mRuntimeManager->stopRegularTimer("simple");
127+
mRuntimeManager->stopRegularTimer("simple_crop");
128128
} else {
129129
mRuntimeManager->startRegularTimer("full");
130130
// Create buffer to contain all tiles
@@ -220,7 +220,9 @@ std::unique_ptr<uchar[]> ImagePyramidAccess::getPatchDataChar(int level, int x,
220220
}
221221
} else if(m_fileHandle != nullptr) {
222222
int scale = (float)m_image->getFullWidth()/levelWidth;
223+
mRuntimeManager->startRegularTimer("openslide_read_region");
223224
openslide_read_region(m_fileHandle, (uint32_t*)data.get(), x * scale, y * scale, level, width, height);
225+
mRuntimeManager->stopRegularTimer("openslide_read_region");
224226
}
225227

226228
return data;
@@ -253,7 +255,9 @@ std::shared_ptr<Image> ImagePyramidAccess::getPatchAsImage(int level, int offset
253255
case TYPE_UINT8:
254256
{
255257
auto data = getPatchData<uchar>(level, offsetX, offsetY, width, height);
258+
mRuntimeManager->startRegularTimer("create_image_object");
256259
image = Image::create(width, height, m_image->getDataType(), m_image->getNrOfChannels(), std::move(data));
260+
mRuntimeManager->stopRegularTimer("create_image_object");
257261
}
258262
break;
259263
case TYPE_UINT16:
@@ -294,12 +298,14 @@ std::shared_ptr<Image> ImagePyramidAccess::getPatchAsImage(int level, int offset
294298
SceneGraph::setParentNode(image, std::dynamic_pointer_cast<SpatialDataObject>(m_image));
295299

296300
if(m_fileHandle != nullptr && convertToRGB) {
301+
mRuntimeManager->startRegularTimer("convert_to_rgb");
297302
// Data is stored as BGRA, need to delete alpha channel and reverse it
298303
auto channelConverter = ImageChannelConverter::New();
299304
channelConverter->setChannelsToRemove(false, false, false, true);
300305
channelConverter->setReverseChannels(true);
301306
channelConverter->setInputData(image);
302307
image = channelConverter->updateAndGetOutputData<Image>();
308+
mRuntimeManager->stopRegularTimer("convert_to_rgb");
303309
}
304310
return image;
305311
}
@@ -368,10 +374,14 @@ uint32_t ImagePyramidAccess::writeTileToTIFF(int level, int x, int y, Image::poi
368374
if(m_image->getCompression() == ImageCompression::NEURAL_NETWORK) {
369375
return writeTileToTIFFNeuralNetwork(level, x, y, image);
370376
} else if(m_image->getCompression() == ImageCompression::JPEGXL) {
377+
mRuntimeManager->startRegularTimer("get_image_access_for_writing");
371378
auto access = image->getImageAccess(ACCESS_READ);
379+
mRuntimeManager->stopRegularTimer("get_image_access_for_writing");
372380
return writeTileToTIFFJPEGXL(level, x, y, (uchar*)access->get());
373381
} else if(m_image->getCompression() == ImageCompression::JPEG) {
382+
mRuntimeManager->startRegularTimer("get_image_access_for_writing");
374383
auto access = image->getImageAccess(ACCESS_READ);
384+
mRuntimeManager->stopRegularTimer("get_image_access_for_writing");
375385
return writeTileToTIFFJPEG(level, x, y, (uchar*)access->get());
376386
} else {
377387
auto access = image->getImageAccess(ACCESS_READ);
@@ -390,28 +400,36 @@ uint32_t ImagePyramidAccess::writeTileToTIFF(int level, int x, int y, uchar *dat
390400

391401
uint32_t ImagePyramidAccess::writeTileToTIFFJPEGXL(int level, int x, int y, uchar *data) {
392402
std::lock_guard<std::mutex> lock(m_readMutex);
393-
TIFFSetDirectory(m_tiffHandle, level);
394-
uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
403+
mRuntimeManager->startRegularTimer("jpegxl_compression");
395404
JPEGXLCompression jxl;
396405
std::vector<uchar> compressed;
397406
jxl.compress(data, m_image->getLevelTileWidth(level), m_image->getLevelTileHeight(level), &compressed, m_image->getCompressionQuality());
407+
mRuntimeManager->stopRegularTimer("jpegxl_compression");
408+
mRuntimeManager->startRegularTimer("tiff_write_tile");
409+
TIFFSetDirectory(m_tiffHandle, level);
410+
uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
398411
TIFFSetWriteOffset(m_tiffHandle, 0); // Set write offset to 0, so that we dont appen data
399412
TIFFWriteRawTile(m_tiffHandle, tile_id, (void *) compressed.data(), compressed.size()); // This appends data..
400413
TIFFCheckpointDirectory(m_tiffHandle);
414+
mRuntimeManager->stopRegularTimer("tiff_write_tile");
401415
return tile_id;
402416
}
403417

404418

405419
uint32_t ImagePyramidAccess::writeTileToTIFFJPEG(int level, int x, int y, uchar *data) {
406420
std::lock_guard<std::mutex> lock(m_readMutex);
407-
TIFFSetDirectory(m_tiffHandle, level);
408-
uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
421+
mRuntimeManager->startRegularTimer("jpeg_compression");
409422
JPEGCompression jpeg;
410423
std::vector<uchar> compressed;
411424
jpeg.compress(data, m_image->getLevelTileWidth(level), m_image->getLevelTileHeight(level), &compressed, m_image->getCompressionQuality());
425+
mRuntimeManager->stopRegularTimer("jpeg_compression");
426+
mRuntimeManager->startRegularTimer("tiff_write_tile");
427+
TIFFSetDirectory(m_tiffHandle, level);
428+
uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
412429
TIFFSetWriteOffset(m_tiffHandle, 0); // Set write offset to 0, so that we dont appen data
413430
TIFFWriteRawTile(m_tiffHandle, tile_id, (void *) compressed.data(), compressed.size()); // This appends data..
414431
TIFFCheckpointDirectory(m_tiffHandle);
432+
mRuntimeManager->stopRegularTimer("tiff_write_tile");
415433
return tile_id;
416434
}
417435

@@ -441,6 +459,7 @@ void ImagePyramidAccess::setPatch(int level, int x, int y, Image::pointer patch,
441459
throw Exception("setPatch only available for TIFF backend ImagePyramids");
442460

443461
if(m_image->getLevelTileWidth(level) > patch->getWidth() || m_image->getLevelTileHeight(level) > patch->getHeight()) {
462+
mRuntimeManager->startRegularTimer("padding");
444463
// Padding needed
445464
auto paddedImage = Image::create(m_image->getLevelTileWidth(level), m_image->getLevelTileHeight(level), patch->getDataType(), m_image->getNrOfChannels());
446465
if(m_image->getNrOfChannels() >= 3) {
@@ -458,6 +477,7 @@ void ImagePyramidAccess::setPatch(int level, int x, int y, Image::pointer patch,
458477
device->getCommandQueue().finish();
459478
}
460479
patch = paddedImage;
480+
mRuntimeManager->stopRegularTimer("padding");
461481
}
462482

463483
// Write tile to this level
@@ -675,13 +695,15 @@ void ImagePyramidAccess::setBlankPatch(int level, int x, int y) {
675695
throw Exception("setBlankPatch only available for TIFF backend ImagePyramids");
676696

677697
std::lock_guard<std::mutex> lock(m_readMutex);
698+
mRuntimeManager->startRegularTimer("write_blank_patch");
678699
TIFFSetDirectory(m_tiffHandle, level);
679700
uint32_t tile_id = TIFFComputeTile(m_tiffHandle, x, y, 0, 0);
680701
TIFFSetWriteOffset(m_tiffHandle, 0); // Set write offset to 0, so that we dont appen data
681702
// Writing zero bytes, will produce a warning, thus we write 1 byte
682703
char data = 0;
683704
TIFFWriteRawTile(m_tiffHandle, tile_id, &data, 0);
684705
TIFFCheckpointDirectory(m_tiffHandle);
706+
mRuntimeManager->stopRegularTimer("write_blank_patch");
685707
m_initializedPatchList.insert(std::to_string(level) + "-" + std::to_string(tile_id));
686708

687709
// TODO Propagate or not?

‎source/FAST/Data/Access/ImagePyramidAccess.hpp‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -119,6 +119,12 @@ class FAST_EXPORT ImagePyramidAccess : public Object {
119119
void release();
120120
~ImagePyramidAccess() override;
121121
void setJPEGTables(uint32_t tableCount, void* tableData);
122+
// Deal with SWIG issue:
123+
void enableRuntimeMeasurements() { Object::enableRuntimeMeasurements(); };
124+
void disableRuntimeMeasurements() { Object::disableRuntimeMeasurements(); };
125+
RuntimeMeasurement::pointer getRuntime() { return Object::getRuntime(); };
126+
RuntimeMeasurement::pointer getRuntime(std::string name) { return Object::getRuntime(name); };
127+
RuntimeMeasurementsManager::pointer getAllRuntimes() { return Object::getAllRuntimes(); };
122128
private:
123129
std::unique_ptr<uchar[]> getPatchDataChar(int level, int x, int y, int width, int height);
124130
std::shared_ptr<ImagePyramid> m_image;

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