v1.0.0-rc.137 (#46)

This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.

* jfjoch_broker: Better track time for each operation in the processing stack
* jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress)
* jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress)
* jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0)

Reviewed-on: #46

image_analysis/spot_finding/StrongPixelSet.cpp

@@ -15,6 +15,7 @@ StrongPixelSet::StrongPixelSet() : strong_pixel_count(0) {
 
 void StrongPixelSet::AddStrongPixel(uint16_t col, uint16_t line, int32_t photons) {
     pixels.push_back(strong_pixel{.col = col, .line = line, .counts = photons});
+    ++strong_pixel_count;
 }
 
 bool is_far_enough(strong_pixel pixel0, strong_pixel pixel1) {
@@ -22,29 +23,25 @@ bool is_far_enough(strong_pixel pixel0, strong_pixel pixel1) {
 }
 
 bool is_adjacent(strong_pixel pixel0, strong_pixel pixel1) {
-    return (fabs(pixel0.line - pixel1.line) <= 1) and
-           (fabs(pixel0.col - pixel1.col) <= 1);
+    auto line_diff = pixel0.line - pixel1.line;
+    auto col_diff = pixel0.col - pixel1.col;
+    return line_diff <= 1 && line_diff >= -1 && col_diff <= 1 && col_diff >= -1;
 }
 
-uint16_t StrongPixelSet::find_root(uint16_t e) {
-    uint16_t r = e;
-    //assert(r < L.size());
-    while (L[r] != r) {
+uint32_t StrongPixelSet::find_root(uint32_t e) {
+    uint32_t r = e;
+    while (L[r] != r)
         r = L[r];
-        //assert(r < L.size());
-    }
     return r;
 }
 
-uint16_t StrongPixelSet::make_union(uint16_t e1, uint16_t e2) {
-    uint16_t e;
+uint32_t StrongPixelSet::make_union(uint32_t e1, uint32_t e2) {
+    uint32_t e;
     if (e1 < e2) {
         e = e1;
-        //assert(e2 < L.size());
         L[e2] = e;
     } else {
         e = e2;
-        //assert(e1 < L.size());
         L[e1] = e;
     }
     return e;
@@ -56,11 +53,11 @@ std::vector<DiffractionSpot> StrongPixelSet::sparseccl() {
     unsigned int labels = 0;
 
     // first scan: pixel association
-    uint16_t start_j = 0;
-    for (uint16_t i = 0; i < pixels.size(); ++i) {
+    uint32_t start_j = 0;
+    for (uint32_t i = 0; i < pixels.size(); ++i) {
         L[i] = i;
-        uint16_t ai = i;
-        for (uint16_t j = start_j; j < i; ++j) {
+        uint32_t ai = i;
+        for (uint32_t j = start_j; j < i; ++j) {
             if (is_adjacent(pixels[i], pixels[j])) {
                 ai = make_union(ai, find_root(j));
             } else if (is_far_enough(pixels[j], pixels[i])) {
@@ -70,7 +67,7 @@ std::vector<DiffractionSpot> StrongPixelSet::sparseccl() {
     }
 
     // second scan: transitive closure
-    for (unsigned int i = 0; i < L.size(); ++i) {
+    for (uint32_t i = 0; i < L.size(); ++i) {
         if (L[i] == i) {
             L[i] = labels++;
         } else {
@@ -80,7 +77,7 @@ std::vector<DiffractionSpot> StrongPixelSet::sparseccl() {
 
     std::vector<DiffractionSpot> spots(labels);
 
-    for (unsigned int i = 0; i < L.size(); i++)
+    for (uint32_t i = 0; i < L.size(); i++)
         spots[L[i]].AddPixel(pixels[i].col, pixels[i].line, pixels[i].counts);
 
     return spots;
@@ -88,7 +85,8 @@ std::vector<DiffractionSpot> StrongPixelSet::sparseccl() {
 
 
 void StrongPixelSet::FindSpotsImage(const SpotFindingSettings &settings, std::vector<DiffractionSpot> &spots) {
-    if (!pixels.empty()) {
+    // Avoid spot finding, when more than 65536 strong pixel count (will be super slow)
+    if (!pixels.empty() && (strong_pixel_count < UINT16_MAX)) {
         for (const auto &spot: sparseccl()) {
             if ((spot.PixelCount() <= settings.max_pix_per_spot)
                 && (spot.PixelCount() >= settings.min_pix_per_spot)) {
@@ -100,7 +98,8 @@ void StrongPixelSet::FindSpotsImage(const SpotFindingSettings &settings, std::ve
 
 void StrongPixelSet::FindSpots(const DiffractionExperiment &experiment, const SpotFindingSettings &settings,
                                std::vector<DiffractionSpot> &spots, uint16_t module_number) {
-    if (!pixels.empty()) {
+    // Avoid spot finding, when more than 65536 strong pixel count (will be super slow)
+    if (!pixels.empty() && (strong_pixel_count < UINT16_MAX)) {
         for (const auto &spot: sparseccl()) {
             if ((spot.PixelCount() <= settings.max_pix_per_spot)
                 && (spot.PixelCount() >= settings.min_pix_per_spot)) {
@@ -114,13 +113,14 @@ void StrongPixelSet::FindSpots(const DiffractionExperiment &experiment, const Sp
 
 void StrongPixelSet::ReadFPGAOutput(const DiffractionExperiment & experiment,
                                     const DeviceOutput &output) {
-    strong_pixel_count += output.spot_finding_result.strong_pixel_count;
-
     // Too many strong pixels will kill performance in data processing, so protection is needed
     // Also if there are no strong pixels, there is no point in looking for them
     if ((output.spot_finding_result.strong_pixel_count == 0) ||
-        (output.spot_finding_result.strong_pixel_count > max_strong_pixel_per_module))
+        (output.spot_finding_result.strong_pixel_count > max_strong_pixel_per_module)) {
+        // If max strong pixel per module condition kicks-in, still report correct strong pixel count
+        strong_pixel_count = output.spot_finding_result.strong_pixel_count;
         return;
+    }
 
     auto pixel_depth = experiment.GetByteDepthImage();
     auto out_ptr = (uint32_t *) output.spot_finding_result.strong_pixel;