Add image quality features #216

JesseMckinzie · 2024-04-23T13:49:33Z

Add features for calculation image quality from https://github.com/hamshkhawar/image-tools/tree/quality/polus-image-quality-plugin

sameeul · 2024-04-29T12:56:42Z

CMakeLists.txt

@@ -258,7 +263,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
 	find_package(Threads QUIET)
 	if (Threads_FOUND)
 		if (CMAKE_USE_PTHREADS_INIT)
-			SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+			SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -g")


Why are we adding debug flag here?

sameeul · 2024-04-29T13:22:03Z

src/nyx/helpers/helpers.h

+	}
+
+
+	inline std::vector<int> arrange(int start, int end, int step=1) {


This should be replaced by ~~std::copy~~ std::iota

sameeul · 2024-04-29T13:26:14Z

src/nyx/helpers/helpers.h

+	}
+
+
+	inline std::vector<std::vector<int>> flipud (std::vector<std::vector<int>> vec) {


use std::reverse?

sameeul · 2024-05-21T13:45:02Z

src/nyx/roi_cache.cpp

@@ -91,7 +91,7 @@ std::vector<StatsReal> LR::get_fvals (int fcode)

 void LR::initialize_fvals()
 {
-	fvals.resize ((int)Nyxus::Feature3D::_COUNT_);
+	fvals.resize ((int)Nyxus::FeatureIMQ::_COUNT_);
 	for (auto& valVec : fvals)
 		valVec.push_back(0.0);
 }


I am not sure if this is correct. At a given run, we other either computing 2D or 3D or IMQ features. In that case, should not Nyxus::Feature2D::_COUNT_ be sufficient (at the moment), since that's max number of features we are going to have at a given run?

@friskluft : Your thoughts?

sameeul · 2024-05-21T13:51:02Z

tests/test_all.cc

-
-TEST(TEST_NYXUS, TEST_PARQUET) {
-	test_parquet();
-}



Need to enable these back.

sameeul · 2024-05-21T13:56:42Z

tests/test_feature_calculation.h

+#include "test_data.h"
+#include "test_main_nyxus.h"
+
+// check values of multiple features


These should go inside namespace Nyxus

sameeul · 2024-05-21T13:57:25Z

tests/test_feature_calculation.h

+void test_truth(const std::vector<double> values, const std::vector<double>& truth_values, double frac_tolerance) {
+
+    if (values.size() != truth_values.size()) {
+        FAIL() << "Number of truth values does not match the number of features calculated" << std::endl;
+    }
+
+    for (int i = 0; i < values.size(); ++i) {
+        ASSERT_TRUE(agrees_gt(values[i], truth_values[i], frac_tolerance));
+    }
+}
+
+// check value of single feature
+void test_truth(const std::vector<double> values, double truth_value, double frac_tolerance) {
+    ASSERT_TRUE(agrees_gt(values[0], truth_value, frac_tolerance));
+}
+


If possible, make the two names different, since the action is different.

sameeul · 2024-05-21T14:13:15Z

test.py

+from nyxus import Nyxus 
+
+
+nyx = Nyxus(["FOCUS_SCORE"])
+
+features = nyx.featurize_directory("/Users/mckinziejr/Documents/GitHub/nyxus/data/int", "/Users/mckinziejr/Documents/GitHub/nyxus/data/int")
+
+print(features)


This is probably added by mistake

sameeul · 2024-05-21T14:16:10Z

src/nyx/features/sharpness.h

+#include "../feature_method.h"
+#include "../environment.h"
+
+#define EPSILON 1e-8


There is already an EPSILON variable in Nyxus somwhere. Use a constexpr instead of macro

sameeul · 2024-05-21T20:58:24Z

tests/test_feature_calculation.h

+namespace Nyxus
+{
+    // check value of single feature
+    void test_truth(const std::vector<double> values, double truth_value, double frac_tolerance) {


not performance critical but this function should be like the following:

void test_truth(const double& value, double truth_value, double frac_tolerance){ ASSERT_TRUE(agrees_gt(value, truth_value, frac_tolerance)); }

JesseMckinzie added 27 commits March 26, 2024 10:44

Add FocusScore

f85d60f

Add Power Spectrum Slope calculation

7135975

Update FocusScore

405439b

Add Brisque calculation

0510b82

Update Power Spectrum feature

b39bde9

Update focus score

0341eb4

Add Saturation calculation

03b30ac

Add Sharpness calculation

f8a0cea

Add Brisque calculation

aef3964

Add image quality features

ea9e9bf

Add documentation for image quality features

4e5315d

Add tests for image quality features

fe47ba7

Clean code

5a9498e

Include functional

88d0e2b

Include algorithm

221c693

Update test_all.cc

fb946fb

Freeze arrow version

0d54eb3

Update conda_cpp.txt

8fa28e5

Update tests

652cf80

Fix bug

4d0de13

Disable image quality features for ALL group

1d9e99d

Add _USE_MATH_DEFINES for M_PI on Windows

1acfb5e

Add LocalFocusScore

8078740

Update min and max saturation features

cc71d30

Update sharpness.cpp

4ce0b2a

Update image quality unit tests

ffb205b

Merge branch 'main' into image_quality_v5

120d21e

sameeul reviewed Apr 29, 2024

View reviewed changes

JesseMckinzie added 13 commits May 14, 2024 21:15

Add ImageQuality class

9cf6c7d

Separate image quality from other 2D features

3c5f7d4

Add padding for fft on non power of 2 images

97236dc

Clean image quality code

4817684

Update unit tests for ImageQuality

5e3216a

Update test_nyxus.py

6c32ab0

Update featureset.h

fac02b5

Update LocalFocusScore feature

ad62223

Fix LocalFocusScore

6d085a4

Add single roi mode for image quality featurize montage

3923722

Update ImageQuality tests

9fc3d1a

Update LocalFocusScore test

e63f88a

Update kernel to be c-style array

f196cac

sameeul reviewed May 21, 2024

View reviewed changes

JesseMckinzie added 3 commits May 21, 2024 08:04

Re-enable tests

f516b60

Remove unused function

140c703

Add test functions to Nyxus namespace

ecaf7ba

sameeul reviewed May 21, 2024

View reviewed changes

Delete test.py

7134cc6

sameeul reviewed May 21, 2024

View reviewed changes

JesseMckinzie added 3 commits May 21, 2024 09:23

Update epsilon to constexpr

1effc83

Update fft to take in vector of real numbers and return result in place

a5f0e57

Update power_spectrum.cpp

c0f9190

sameeul reviewed May 21, 2024

View reviewed changes

JesseMckinzie added 2 commits May 22, 2024 07:03

Update test_feature_calculation.h

98b3ef1

Merge branch 'main' into image_quality_v5

0322a6b

sameeul merged commit c2d9431 into PolusAI:main May 23, 2024
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Add image quality features #216

Add image quality features #216

JesseMckinzie commented Apr 23, 2024

sameeul Apr 29, 2024

sameeul Apr 29, 2024 •

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sameeul Apr 29, 2024

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sameeul May 21, 2024

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sameeul May 21, 2024

		}


		inline std::vector<int> arrange(int start, int end, int step=1) {

		}


		inline std::vector<std::vector<int>> flipud (std::vector<std::vector<int>> vec) {

Add image quality features #216

Add image quality features #216

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JesseMckinzie commented Apr 23, 2024

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sameeul Apr 29, 2024 •

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sameeul May 21, 2024 •

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