Send a matrix as a proc argument in Chapel - chapel

I'm getting an error when I try to send a matrix into a proc. I'm pretty sure I'm doing something very wrong, can't figure it out.
use LinearAlgebra;
proc main() {
var A = Matrix(
[0.0, 0.8, 1.1, 0.0, 2.0]
,[0.8, 0.0, 1.3, 1.0, 0.0]
,[1.1, 1.3, 0.0, 0.5, 1.7]
,[0.0, 1.0, 0.5, 0.0, 1.5]
,[2.0, 0.0, 1.7, 1.5, 0.0]
);
check_dims(A);
}
proc check_dims(A: Matrix) {
var t: bool = false;
if (A.domain.dim(1) == A.domain.dim(2)){
t = true;
}
return t;
}
Gives me
mad.chpl:3: In function 'main':
mad.chpl:14: error: unresolved call 'check_dims([domain(2,int(64),false)] real(64))'
mad.chpl:17: note: candidates are: check_dims(A: Matrix)
I'm using chpl Version 1.15.0

Linear algebra objects (like matrices and vectors) are represented as arrays in Chapel. Therefore, changing Matrix (a type that does not exist) to [] (the syntax for array-type) should work as expected:
use LinearAlgebra;
proc main() {
var A = Matrix(
[0.0, 0.8, 1.1, 0.0, 2.0]
,[0.8, 0.0, 1.3, 1.0, 0.0]
,[1.1, 1.3, 0.0, 0.5, 1.7]
,[0.0, 1.0, 0.5, 0.0, 1.5]
,[2.0, 0.0, 1.7, 1.5, 0.0]
);
check_dims(A);
}
proc check_dims(A: []) {
var t: bool = false;
// method is dim()
if (A.domain.dim(1) == A.domain.dim(2)){
t = true;
}
return t;
}

Related

Segfault in Tranposed matrix multiplication with .eval() with Eigen 3 library

I added two .eval() just in case. I got no compilation error, and no run time warning. Just segfault.
Thanks for helping me to fix this.
Test:
#include <Eigen/Eigen>
#include <iostream>
using namespace Eigen;
int main() {
Matrix<float, Dynamic, Dynamic> mat_b;
Matrix<float, Dynamic, Dynamic> mat_c;
mat_b << 1.0, 0.0, 0.5, 0.5,
0.0, 1.0, 0.5, 0.5,
1.0, 0.0, 1.0, 0.0,
0.0, 1.0, 0.0, 1.0;
mat_c << 0.0, 0.0, 0.0, 0.0, 1.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 1.0,
1.0, 0.0, 1.0, 0.0, 0.0, 0.0,
1.0, 0.0, 0.0, 1.0, 0.0, 0.0;
std::cout << (mat_b.transpose().eval() * mat_c).eval() << "\n";
}
Result:
Segmentation fault (core dumped)
As stated in documentatipon
The comma initializer
Eigen offers a comma initializer syntax which allows the user to easily set all the coefficients of a matrix, vector or array. Simply list the coefficients, starting at the top-left corner and moving from left to right and from the top to the bottom. The size of the object needs to be specified beforehand. If you list too few or too many coefficients, Eigen will complain.
emphasis is mine. If you expect that Matrix ctor would deduce size from your formatting, that simply not possible in C++. Looks like you created 16x1 and 24x1 matrix and then try to multiply 1x16 (transposed first one) to 24x1 which is not legal.

VTK volume rendering of mammography

I am working on vtk volume rendering of mammography. I have a 50 DICOM slices in folder to construct volume. Here I need to give vtkColorTransferFunction and vtkPiecewiseFunction to set RGB color and scalar opacity.
I am not getting exact values of color and opacity with respect to mammo images (breast images). I need values for color and opacity with respect to breast x-ray images.
Any suggestions will be helpful.
vtkGPUVolumeRayCastMapper *volumeGPUmapper =
vtkGPUVolumeRayCastMapper::New();
volumeGPUmapper->SetInputConnection(clip->GetOutputPort());
// RGB and alpha funcions
double skinOnBlueMap[28][5] =
{
{0, 0.987853825092316, 1.0, 1.0, 0.9},
{10000, 0.987853825092316, 1.0, 1.0, 0.9},
{20000, 0.987853825092316, 1.0, 1.0, 1.0},
{30000, 0.987853825092316, 1.0, 1.0, 1.0},
{40000, 0.0, 0.0, 0.0, 1.0},
{50000, 1.0, 0.0, 0.0, 1.0},
{60000, 1.0, 0.999206542968750, 0.0, 1.0},
{70000, 1.0, 1.0, 1.0, 1.0}
};
vtkSmartPointer<vtkPiecewiseFunction> alphaChannelFunc = vtkSmartPointer<vtkPiecewiseFunction>::New();
vtkSmartPointer<vtkColorTransferFunction> colorFunc = vtkSmartPointer<vtkColorTransferFunction>::New();
for(int i = 0; i < sizeof(skinOnBlueMap)/(5*sizeof(double)); i++)
{
colorFunc->AddRGBPoint(skinOnBlueMap[i][0], skinOnBlueMap[i][1], skinOnBlueMap[i][2], skinOnBlueMap[i][3]);
alphaChannelFunc->AddPoint(skinOnBlueMap[i][0], skinOnBlueMap[i][4]);
}
vtkSmartPointer<vtkVolumeProperty> volumeProperty = vtkSmartPointer<vtkVolumeProperty>::New();
volumeProperty->SetColor(colorFunc);
volumeProperty->SetInterpolationTypeToLinear();
volumeProperty->SetScalarOpacity(alphaChannelFunc);
vtkSmartPointer<vtkVolume> VTKvolume = vtkSmartPointer<vtkVolume>::New();
VTKvolume->SetMapper(volumeGPUmapper);
VTKvolume->SetProperty(volumeProperty);
Those scalar values seem strange to me. It could be the reason your results don't look correct. But to be sure we need the image stack and rendered result.
The scalar values are not even inside the range of the unsigned short type, that is generally used for the voxels.

How can I check if the first 15 relevant digits in double values are the same in Boost Test framework?

I tried to use what seems to be designed for the job: BOOST_CHECK_CLOSE, so I have the following test:
BOOST_AUTO_TEST_CASE( MultivariateNormalDensityTest )
{
double TOLLERANCE=1e-14;
Eigen::Vector3d mu(0.0, 1.0, 2.0);
Eigen::Matrix3d sigma;
sigma << 2.0, 1.0, 0.5,
1.0, 2.3, 0.7,
0.5, 0.7, 1.7;
MultivariateNormalDensity<3> mnd(mu, sigma);
BOOST_CHECK_CLOSE(0.027671392189542814988, mnd(Eigen::Vector3d(0.0, 1.0, 2.0)), TOLLERANCE);
BOOST_CHECK_CLOSE(0.0027063822550173750707, mnd(Eigen::Vector3d(2.0, 1.0, 0.5)), TOLLERANCE);
BOOST_CHECK_CLOSE(0.024708597088231143424, mnd(Eigen::Vector3d(0.5, 1.5, 2.5)), TOLLERANCE);
BOOST_CHECK_CLOSE(0.026554587643995836849, mnd(Eigen::Vector3d(-0.3, 0.6, 1.8)), TOLLERANCE);
//examples calculated using R
}
However, the first check fails with the error:
/home/ga1009/PhD/cpp/grzesLib/test/multivariatenormaltests.cpp(36): error in "MultivariateNormalDensityTest": difference{3.76141e-14%} between 0.027671392189542814988{0.027671392189542815} and mnd(Eigen::Vector3d(0.0, 1.0, 2.0)){0.027671392189542805} exceeds 1e-14%
When I do the math I get:
(0.027671392189542815-0.027671392189542805)/0.027671392189542805=0.00000000000000036138406
which is less than 1e-14. What am I doing wrong here?
The tolerance is specified as a percentage, you're off by 100. Fix:
double TOLERANCE=1e-12; // Percent

FileStorage for OpenCV Python API

I'm currently using FileStorage class for storing matrices XML/YAML using OpenCV C++ API.
However, I have to write a Python Script that reads those XML/YAML files.
I'm looking for existing OpenCV Python API that can read the XML/YAML files generated by OpenCV C++ API
You can use PyYAML to parse the YAML file.
Since PyYAML doesn't understand OpenCV data types, you need to specify a constructor for each OpenCV data type that you are trying to load. For example:
import yaml
def opencv_matrix(loader, node):
mapping = loader.construct_mapping(node, deep=True)
mat = np.array(mapping["data"])
mat.resize(mapping["rows"], mapping["cols"])
return mat
yaml.add_constructor(u"tag:yaml.org,2002:opencv-matrix", opencv_matrix)
Once you've done that, loading the yaml file is simple:
with open(file_name) as fin:
result = yaml.load(fin.read())
Result will be a dict, where the keys are the names of whatever you saved in the YAML.
Using the FileStorage functions available in OpenCV 3.2, I've used this with success:
import cv2
fs = cv2.FileStorage("calibration.xml", cv2.FILE_STORAGE_READ)
fn = fs.getNode("Camera_Matrix")
print (fn.mat())
In addition to #misha's response, OpenCV YAML's are somewhat incompatible with Python.
Few reasons for incompatibility are:
Yaml created by OpenCV doesn't have a space after ":". Whereas Python requires it. [Ex: It should be a: 2, and not a:2 for Python]
First line of YAML file created by OpenCV is wrong. Either convert "%YAML:1.0" to "%YAML 1.0". Or skip the first line while reading.
The following function takes care of providing that:
import yaml
import re
def readYAMLFile(fileName):
ret = {}
skip_lines=1 # Skip the first line which says "%YAML:1.0". Or replace it with "%YAML 1.0"
with open(scoreFileName) as fin:
for i in range(skip_lines):
fin.readline()
yamlFileOut = fin.read()
myRe = re.compile(r":([^ ])") # Add space after ":", if it doesn't exist. Python yaml requirement
yamlFileOut = myRe.sub(r': \1', yamlFileOut)
ret = yaml.load(yamlFileOut)
return ret
outDict = readYAMLFile("file.yaml")
NOTE: Above response is applicable only for yaml's. XML's have their own share of problems, something I haven't explored completely.
I wrote a small snippet to read and write FileStorage-compatible YAMLs in Python:
# A yaml constructor is for loading from a yaml node.
# This is taken from #misha 's answer: http://stackoverflow.com/a/15942429
def opencv_matrix_constructor(loader, node):
mapping = loader.construct_mapping(node, deep=True)
mat = np.array(mapping["data"])
mat.resize(mapping["rows"], mapping["cols"])
return mat
yaml.add_constructor(u"tag:yaml.org,2002:opencv-matrix", opencv_matrix_constructor)
# A yaml representer is for dumping structs into a yaml node.
# So for an opencv_matrix type (to be compatible with c++'s FileStorage) we save the rows, cols, type and flattened-data
def opencv_matrix_representer(dumper, mat):
mapping = {'rows': mat.shape[0], 'cols': mat.shape[1], 'dt': 'd', 'data': mat.reshape(-1).tolist()}
return dumper.represent_mapping(u"tag:yaml.org,2002:opencv-matrix", mapping)
yaml.add_representer(np.ndarray, opencv_matrix_representer)
#examples
with open('output.yaml', 'w') as f:
yaml.dump({"a matrix": np.zeros((10,10)), "another_one": np.zeros((2,4))}, f)
with open('output.yaml', 'r') as f:
print yaml.load(f)
To improve on the previous answer by #Roy_Shilkrot I added support for numpy vectors as well as matrices:
# A yaml constructor is for loading from a yaml node.
# This is taken from #misha 's answer: http://stackoverflow.com/a/15942429
def opencv_matrix_constructor(loader, node):
mapping = loader.construct_mapping(node, deep=True)
mat = np.array(mapping["data"])
if mapping["cols"] > 1:
mat.resize(mapping["rows"], mapping["cols"])
else:
mat.resize(mapping["rows"], )
return mat
yaml.add_constructor(u"tag:yaml.org,2002:opencv-matrix", opencv_matrix_constructor)
# A yaml representer is for dumping structs into a yaml node.
# So for an opencv_matrix type (to be compatible with c++'s FileStorage) we save the rows, cols, type and flattened-data
def opencv_matrix_representer(dumper, mat):
if mat.ndim > 1:
mapping = {'rows': mat.shape[0], 'cols': mat.shape[1], 'dt': 'd', 'data': mat.reshape(-1).tolist()}
else:
mapping = {'rows': mat.shape[0], 'cols': 1, 'dt': 'd', 'data': mat.tolist()}
return dumper.represent_mapping(u"tag:yaml.org,2002:opencv-matrix", mapping)
yaml.add_representer(np.ndarray, opencv_matrix_representer)
Example:
with open('output.yaml', 'w') as f:
yaml.dump({"a matrix": np.zeros((10,10)), "another_one": np.zeros((5,))}, f)
with open('output.yaml', 'r') as f:
print yaml.load(f)
Output:
a matrix: !!opencv-matrix
cols: 10
data: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0]
dt: d
rows: 10
another_one: !!opencv-matrix
cols: 1
data: [0.0, 0.0, 0.0, 0.0, 0.0]
dt: d
rows: 5
Though I could not control the order of rows, cols, dt, data.
pip install opencv-contrib-python for video support to install specific version use pip install opencv-contrib-python

How to test multi-parameter formula

I'm refactoring some code that implements a formula and I want to do it test-first, to improve my testing skills, and leave the code covered.
This particular piece of code is a formula that takes 3 parameters and returns a value. I even have some data tables with expected results for different inputs, so in theory, I could jusst type a zillion tests, just changing the input parameters and checking the results against the corresponding expected value.
But I thought there should be a better way to do it, and looking at the docs I've found Value Parameterized Tests.
So, with that I now know how to automatically create the tests for the different inputs.
But how do I get the corresponding expected result to compare it with my calculated one?
The only thing I've been able to come up with is a static lookup table and a static member in the text fixture which is an index to the lookup table and is incremented in each run. Something like this:
#include "gtest/gtest.h"
double MyFormula(double A, double B, double C)
{
return A*B - C*C; // Example. The real one is much more complex
}
class MyTest:public ::testing::TestWithParam<std::tr1::tuple<double, double, double>>
{
protected:
MyTest(){ Index++; }
virtual void SetUp()
{
m_C = std::tr1::get<0>(GetParam());
m_A = std::tr1::get<1>(GetParam());
m_B = std::tr1::get<2>(GetParam());
}
double m_A;
double m_B;
double m_C;
static double ExpectedRes[];
static int Index;
};
int MyTest::Index = -1;
double MyTest::ExpectedRes[] =
{
// C = 1
// B: 1 2 3 4 5 6 7 8 9 10
/*A = 1*/ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0,
/*A = 2*/ 1.0, 3.0, 5.0, 7.0, 9.0, 11.0, 13.0, 15.0, 17.0, 19.0,
/*A = 3*/ 2.0, 5.0, 8.0, 11.0, 14.0, 17.0, 20.0, 23.0, 26.0, 29.0,
// C = 2
// B: 1 2 3 4 5 6 7 8 9 10
/*A = 1*/ -3.0, -2.0, -1.0, 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0,
/*A = 2*/ -2.0, 0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0,
/*A = 3*/ -1.0, 2.0, 5.0, 8.0, 11.0, 14.0, 17.0, 20.0, 23.0, 26.0,
};
TEST_P(MyTest, TestFormula)
{
double res = MyFormula(m_A, m_B, m_C);
ASSERT_EQ(ExpectedRes[Index], res);
}
INSTANTIATE_TEST_CASE_P(TestWithParameters,
MyTest,
testing::Combine( testing::Range(1.0, 3.0), // C
testing::Range(1.0, 4.0), // A
testing::Range(1.0, 11.0) // B
));
Is this a good approach or is there any better way to get the right expected result for each run?
Include the expected result along with the inputs. Instead of a triple of input values, make your test parameter be a 4-tuple.
class MyTest: public ::testing::TestWithParam<
std::tr1::tuple<double, double, double, double>>
{ };
TEST_P(MyTest, TestFormula)
{
double const C = std::tr1::get<0>(GetParam());
double const A = std::tr1::get<1>(GetParam());
double const B = std::tr1::get<2>(GetParam());
double const result = std::tr1::get<3>(GetParam());
ASSERT_EQ(result, MyFormula(A, B, C));
}
The downside is that you won't be able to keep your test parameters concise with testing::Combine. Instead, you can use testing::Values to define each distinct 4-tuple you wish to test. You might hit the argument-count limit for Values, so you can split your instantiations, such as by putting all the C = 1 cases in one and all the C = 2 cases in another.
INSTANTIATE_TEST_CASE_P(
TestWithParametersC1, MyTest, testing::Values(
// C A B
make_tuple( 1.0, 1.0, 1.0, 0.0),
make_tuple( 1.0, 1.0, 2.0, 1.0),
make_tuple( 1.0, 1.0, 3.0, 2.0),
// ...
));
INSTANTIATE_TEST_CASE_P(
TestWithParametersC2, MyTest, testing::Values(
// C A B
make_tuple( 2.0, 1.0, 1.0, -3.0),
make_tuple( 2.0, 1.0, 2.0, -2.0),
make_tuple( 2.0, 1.0, 3.0, -1.0),
// ...
));
Or you can put all the values in an array separate from your instantiation and then use testing::ValuesIn:
std::tr1::tuple<double, double, double, double> const FormulaTable[] = {
// C A B
make_tuple( 1.0, 1.0, 1.0, 0.0),
make_tuple( 1.0, 1.0, 2.0, 1.0),
make_tuple( 1.0, 1.0, 3.0, 2.0),
// ...
make_tuple( 2.0, 1.0, 1.0, -3.0),
make_tuple( 2.0, 1.0, 2.0, -2.0),
make_tuple( 2.0, 1.0, 3.0, -1.0),
// ...
};
INSTANTIATE_TEST_CASE_P(
TestWithParameters, MyTest, ::testing::ValuesIn(FormulaTable));
See hard coding the expected result is like you are limiting again the no of test cases. If you want to get a complete data driven model, I would rather suggest you to read inputs, expected result from a flat file/xml/xls file.
I don't have much experience with unit testing, but as a mathematician, I think there is not a lot more you could do.
If you would know some invariants of your formula, you could test for them, but i think that does only make sense in very few scenarios.
As an example, if you would want to test, if you have correctly implemented the natural exponential function, you could make use of the knowledge, that it's derivative should have the same value as the function itself. You could then calculate a numerical approximation to the derivative for a million points and see if they are close to the actual function value.