POL5788 fix FP bug observed on Centrin dataset (PolusAI#282)

Author: friskluft

src/nyx/environment.cpp

@@ -194,7 +194,7 @@ void Environment::show_cmdline_help()
 void Environment::show_summary(const std::string& head, const std::string& tail)
 {
 	std::cout << head;
-	std::cout << "Available memory: " << Nyxus::virguler(get_ram_limit()) << " bytes\n\n";
+	std::cout << "Available memory: " << Nyxus::virguler_ulong(get_ram_limit()) << " bytes\n\n";
 	std::cout << "Work plan:\n"
 		<< "\tdimensionality: " << dim() << "\n"
 		<< "\tlabels\t" << labels_dir << "\n"

src/nyx/gpucache.cpp

@@ -493,7 +493,7 @@ namespace NyxusGpu
 		size_t amt = 0; 
 		OK(gpu_get_free_mem(amt));
 
-		VERBOSLVL1(std::cout << "GPU RAM amt = " << Nyxus::virguler(amt) << "\n");
+		VERBOSLVL1(std::cout << "GPU RAM amt = " << Nyxus::virguler_ulong(amt) << "\n");
 
 		int n_gabFilters = n_gabor_filters + 1;		// '+1': an extra filter for the baseline signal
 
@@ -508,16 +508,16 @@ namespace NyxusGpu
 			roi_kontur_cloud_len, 
 			n_rois, roi_w, roi_h, n_gabFilters, gabor_ker_side);
 
-		VERBOSLVL1(std::cout << "szb for " << Nyxus::virguler(n_rois) << " ROIs (ideal ROI px:" << Nyxus::virguler(roi_cloud_len) << ", ideal contour px:" << Nyxus::virguler(roi_kontur_cloud_len) << ") = " << Nyxus::virguler(szb) << "\n");
+		VERBOSLVL1(std::cout << "szb for " << Nyxus::virguler_ulong(n_rois) << " ROIs (ideal ROI px:" << Nyxus::virguler_ulong(roi_cloud_len) << ", ideal contour px:" << Nyxus::virguler_ulong(roi_kontur_cloud_len) << ") = " << Nyxus::virguler_ulong(szb) << "\n");
 
 		batch_len = n_rois;
 		size_t critAmt = amt * 0.75; // 75% GPU RAM as critical RAM
 
-		VERBOSLVL1(std::cout << "critical GPU RAM amt = " << Nyxus::virguler(critAmt) << "\n");
+		VERBOSLVL1(std::cout << "critical GPU RAM amt = " << Nyxus::virguler_ulong(critAmt) << "\n");
 
 		if (critAmt < szb)
 		{
-			VERBOSLVL1(std::cout << "Need to split " << Nyxus::virguler(n_rois)  << " ROIs into batches \n");
+			VERBOSLVL1(std::cout << "Need to split " << Nyxus::virguler_ulong(n_rois)  << " ROIs into batches \n");
 
 			size_t try_nrois = 0;
 			for (try_nrois = n_rois; try_nrois>=0; try_nrois--)

src/nyx/grayscale_tiff.h

@@ -2,13 +2,13 @@
 #include "abs_tile_loader.h"
 
 #ifdef __APPLE__
-#define uint64 uint64_hack_
-#define int64 int64_hack_
-#include <tiffio.h>
-#undef uint64
-#undef int64
+    #define uint64 uint64_hack_
+    #define int64 int64_hack_
+    #include <tiffio.h>
+    #undef uint64
+    #undef int64
 #else
-#include <tiffio.h>
+    #include <tiffio.h>
 #endif
 #include <cstring>
 #include <sstream>

src/nyx/helpers/helpers.h

@@ -410,7 +410,7 @@ namespace Nyxus
 		return { smallest, largest };
 	}
 
-	inline std::string virguler (size_t x)
+	inline std::string virguler_ulong (size_t x)
 	{
 		const char SEP = ',';
 
@@ -437,6 +437,23 @@ namespace Nyxus
 		return s2;
 	}
 
+	inline std::string virguler_real (double x)
+	{
+		// integer part
+		size_t y = (size_t)x;
+
+		// fractional part ("123.4567" -> "4567")
+		double f = x - (int)x;
+		std::string s = x < 0.0 ? "-" : "";
+		std::string frac = std::to_string(f);
+		if (frac.length()>=1)
+			frac = frac.erase(0, 1);
+		
+		// all together
+		s += virguler_ulong(y) + frac;
+		return s;
+	}
+
 	template <typename T>
 	inline std::string virguler (const std::vector<T> & x)
 	{

src/nyx/phase1.cpp

@@ -118,84 +118,6 @@ namespace Nyxus
 		return true;
 	}
 
-	//
-	// whole-slide 2D case
-	//
-	bool gather_wholeslide_metrics (const std::string& intens_fpath, ImageLoader& L, LR & roi)
-	{
-		PixIntens minI = std::numeric_limits<PixIntens>::max(), 
-			maxI = std::numeric_limits<PixIntens>::min();
-		AABB a;
-
-		int lvl = 0, // Pyramid level
-			lyr = 0; //	Layer
-
-		// Read the tiff. The image loader is put in the open state in processDataset()
-		size_t nth = L.get_num_tiles_hor(),
-			ntv = L.get_num_tiles_vert(),
-			fw = L.get_tile_width(),
-			th = L.get_tile_height(),
-			tw = L.get_tile_width(),
-			tileSize = L.get_tile_size(),
-			fullwidth = L.get_full_width(),
-			fullheight = L.get_full_height();
-
-		int cnt = 1;
-		for (unsigned int row = 0; row < nth; row++)
-			for (unsigned int col = 0; col < ntv; col++)
-			{
-				// Fetch the tile 
-				bool ok = L.load_tile(row, col);
-				if (!ok)
-				{
-					std::string erm = "Error fetching tile row:" + std::to_string(row) + " col:" + std::to_string(col) + " from " + intens_fpath;
-					#ifdef WITH_PYTHON_H
-						throw erm;
-					#endif	
-					std::cerr << erm << "\n";
-					return false;
-				}
-
-				// Get ahold of tile's pixel buffer
-				const std::vector<uint32_t>& dataI = L.get_int_tile_buffer();
-
-				// Iterate pixels
-				for (size_t i = 0; i < tileSize; i++)
-				{
-					int y = row * th + i / tw,
-						x = col * tw + i % tw;
-
-					// Skip tile buffer pixels beyond the image's bounds
-					if (x >= fullwidth || y >= fullheight)
-						continue;
-
-					// Update whole slide's vROI metrics
-					PixIntens I = dataI[i];
-					minI = std::min (minI, I);
-					maxI = std::max (maxI, I);
-				}
-
-#ifdef WITH_PYTHON_H
-				if (PyErr_CheckSignals() != 0)
-					throw pybind11::error_already_set();
-#endif
-
-				// Show progress info
-				VERBOSLVL2(
-					if (cnt++ % 4 == 0)
-						std::cout << "\t" << int((row * nth + col) * 100 / float(nth * ntv) * 100) / 100. << "%\t" << uniqueLabels.size() << " ROIs" << "\n";
-				);
-			}
-
-		// Per-ROI 
-		roi.aux_area = fullwidth * fullheight;
-		roi.aux_min = minI;
-		roi.aux_max = maxI;
-		roi.aabb.init_from_widthheight (fullwidth, fullheight);
-
-		return true;
-	}
-
 	//
 	// segmented 2.5D case (aka layoutA, collections of 2D slice images e.g. blah_z1_blah.ome.tif, blah_z2_blah.ome.tif, ..., blah_z500_blah.ome.tif)
 	// prerequisite: 'theImLoader' needs to be pre-opened !

src/nyx/raw_format.h

@@ -8,12 +8,14 @@ class RawFormatLoader
 public:
 
     RawFormatLoader (const std::string_view & name, const std::string & filePath)
-        : infostring_(name), filePath_(filePath) {}
+        : infostring_(name), filePath_(filePath), fp_pixels_(false) {}
 
     virtual ~RawFormatLoader() = default;
 
     std::string get_infostring() { return infostring_; }
 
+    bool get_fp_pixels() { return fp_pixels_; }
+
     virtual void loadTileFromFile (
         size_t indexRowGlobalTile,
         size_t indexColGlobalTile,
@@ -62,6 +64,10 @@ class RawFormatLoader
         return (size_t)std::ceil((double)(fullDepth(level)) / tileDepth(level));
     }
 
+protected:
+
+    bool fp_pixels_;
+
 private:
 
     std::string infostring_, filePath_;

src/nyx/raw_image_loader.cpp

@@ -259,9 +259,15 @@ size_t RawImageLoader::get_full_height()
 
 std::string RawImageLoader::get_slide_descr()
 {
-	std::string rv = intFL->get_infostring() + " (int) ";
+	std::string rv = get_fp_phys_pixvoxels() ? "R-" : "N-";
+	rv += intFL->get_infostring() + " I ";
 	if (segFL != nullptr)
-		rv += segFL->get_infostring() + " (seg) ";
+		rv += segFL->get_infostring() + " M ";
 	return rv;
 }
 
+bool RawImageLoader::get_fp_phys_pixvoxels()
+{
+	return intFL->get_fp_pixels();
+}
+

src/nyx/raw_image_loader.h

@@ -31,6 +31,7 @@ class RawImageLoader
 	size_t get_full_width();
 	size_t get_full_height();
 	std::string get_slide_descr();
+	bool get_fp_phys_pixvoxels();
 
 private:
 

src/nyx/raw_omezarr.h

@@ -50,9 +50,9 @@ class RawOmezarrLoader: public RawFormatLoader
         else if (dtype_str == "<i2") { data_format_ = 6; } //int16_t
         else if (dtype_str == "<i4") { data_format_ = 7; } //int32_t
         else if (dtype_str == "<i8") { data_format_ = 8; } //int64_t
-        else if (dtype_str == "<f2") { data_format_ = 9; } //float
-        else if (dtype_str == "<f4") { data_format_ = 9; } //float
-        else if (dtype_str == "<f8") { data_format_ = 10; } //double
+        else if (dtype_str == "<f2") { data_format_ = 9; fp_pixels_ = true; } //float
+        else if (dtype_str == "<f4") { data_format_ = 9; fp_pixels_ = true; } //float
+        else if (dtype_str == "<f8") { data_format_ = 10; fp_pixels_ = true; } //double
         else { data_format_ = 2; } //uint16_t
 
         // allocate the buffer

src/nyx/raw_tiff.h

@@ -117,6 +117,8 @@ class RawTiffTileLoader : public RawFormatLoader
                 }
                 break;
             case 3:
+                this->fp_pixels_ = true;
+
                 switch (bitsPerSample_) 
                 {
                 case 8:
@@ -381,6 +383,8 @@ class RawTiffStripLoader : public RawFormatLoader
                 }
                 break;
             case 3:
+                this->fp_pixels_ = true;
+
                 switch (bitsPerSample_)
                 {
                 case 8: