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Jungfraujoch/common/Coord.cpp
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leonarski_f 680c36c20d
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v1.0.0-rc.166 (#76)
* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands.
* `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion.
* Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants.
* `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing.
* A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed.
* `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing.
* Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences.
* The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to.
* The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after.
* The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution.
* `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have.
* Twinning is no longer reported when the L-test contradicts it.
* The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's.
* `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots.
* The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area.

Reviewed-on: #76
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-09-02 21:17:31 +02:00

260 lines
6.7 KiB
C++

// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochMath.h"
#include <cmath>
#include "Coord.h"
#include "JFJochException.h"
Coord::Coord() {
x = 0.0; y = 0.0; z = 0.0;
}
Coord::Coord(const float in[3]) {
x = in[0];
y = in[1];
z = in[2];
}
Coord::Coord(float in_x, float in_y, float in_z) {
x = in_x;
y = in_y;
z = in_z;
}
Coord Coord::operator+(const Coord &in) const {
return Coord(this->x+in.x, this->y+in.y, this->z+in.z);
}
Coord Coord::operator-(const Coord &in) const {
return Coord(this->x-in.x, this->y-in.y, this->z-in.z);
}
Coord Coord::operator*(float in) const {
return Coord(this->x*in, this->y*in, this->z*in);
}
Coord Coord::operator/(float in) const {
return Coord(this->x/in, this->y/in, this->z/in);
};
Coord Coord::operator-() const {
return Coord(- this->x, -this->y, -this->z);
}
Coord& Coord::operator+=(const Coord &in) {
this->x += in.x;
this->y += in.y;
this->z += in.z;
return *this;
}
Coord& Coord::operator-=(const Coord &in) {
this->x -= in.x;
this->y -= in.y;
this->z -= in.z;
return *this;
}
Coord& Coord::operator*=(float in) {
this->x *= in;
this->y *= in;
this->z *= in;
return *this;
}
Coord& Coord::operator/=(float in) {
this->x /= in;
this->y /= in;
this->z /= in;
return *this;
}
Coord Coord::operator%(const Coord &in) const {
return Coord(this->y * in.z - this->z * in.y,
this->z * in.x - this->x * in.z,
this->x * in.y - this->y * in.x);
}; // Cross product
float Coord::operator*(const Coord &in) const {
return this->x * in.x + this->y * in.y + this->z * in.z;
};
bool Coord::operator==(const Coord &other) const {
if ((this->x == other.x) && (this->y == other.y) && (this->z == other.z))
return true;
else
return false;
}
float Coord::Length() const {
return sqrt(this->x*this->x + this->y*this->y + this->z*this->z);
}
Coord Coord::Normalize() const {
float len = Length();
if (len < 1e-12)
return Coord(0,0,0);
return Coord(this->x/len, this->y/len, this->z/len);
}
Coord operator*(float in1, const Coord& in2) {
return in2 * in1;
}
const float& Coord::operator[](int64_t val) const {
switch (val) {
case 0:
return x;
case 1:
return y;
case 2:
return z;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Coord index must be in range 0-2");
}
}
float& Coord::operator[](int64_t val) {
switch (val) {
case 0:
return x;
case 1:
return y;
case 2:
return z;
default:
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Coord index must be in range 0-2");
}
}
std::ostream &operator<<( std::ostream &output, const Coord &in ) {
output << in.x << " " << in.y << " " << in.z;
return output;
}
float angle_deg(const Coord &c1, const Coord &c2) {
float cos_ang = c1 * c2 / (c1.Length() * c2.Length());
const float epsilon = 1e-5f;
if (cos_ang > 1.0f && cos_ang < 1.0f + epsilon)
cos_ang = 1.0f;
else if (cos_ang < -1.0f && cos_ang > -1.0f - epsilon)
cos_ang = -1.0f;
return acosf(cos_ang) * (180.0f / static_cast<float>(PI));
}
void Coord::swap(Coord &other) noexcept {
std::swap(x, other.x);
std::swap(y, other.y);
std::swap(z, other.z);
}
RotMatrix::RotMatrix() {
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++)
v[i][j] = (i == j) ? 1 : 0;
}
};
RotMatrix::RotMatrix(float alpha, const Coord &dir) {
float c = cosf(alpha);
float s = sinf(alpha);
float t = 1.0f - c;
Coord n = dir.Normalize();
v[0][0] = t * n.x * n.x + c;
v[0][1] = t * n.x * n.y - s * n.z;
v[0][2] = t * n.x * n.z + s * n.y;
v[1][0] = t * n.x * n.y + s * n.z;
v[1][1] = t * n.y * n.y + c;
v[1][2] = t * n.y * n.z - s * n.x;
v[2][0] = t * n.x * n.z - s * n.y;
v[2][1] = t * n.y * n.z + s * n.x;
v[2][2] = t * n.z * n.z + c;
}
RotMatrix::RotMatrix(const Coord &col0, const Coord &col1, const Coord &col2) {
for (int i = 0; i < 3; i++) {
v[i][0] = col0[i];
v[i][1] = col1[i];
v[i][2] = col2[i];
}
}
Coord RotMatrix::Column(int64_t i) const {
return {v[0][i], v[1][i], v[2][i]};
}
Coord RotMatrix::operator*(const Coord &in) const {
return {
v[0][0] * in.x + v[0][1] * in.y + v[0][2] * in.z,
v[1][0] * in.x + v[1][1] * in.y + v[1][2] * in.z,
v[2][0] * in.x + v[2][1] * in.y + v[2][2] * in.z
};
}
RotMatrix RotMatrix::operator*(const RotMatrix &other) const {
RotMatrix result;
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
result.v[i][j] = v[i][0] * other.v[0][j] +
v[i][1] * other.v[1][j] +
v[i][2] * other.v[2][j];
}
}
return result;
}
RotMatrix RotMatrix::transpose() const {
RotMatrix result;
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
result.v[i][j] = v[j][i];
}
}
return result;
}
RotMatrix RotMatrix::invert() const {
RotMatrix result;
float det = v[0][0] * (v[1][1] * v[2][2] - v[1][2] * v[2][1])
- v[0][1] * (v[1][0] * v[2][2] - v[1][2] * v[2][0])
+ v[0][2] * (v[1][0] * v[2][1] - v[1][1] * v[2][0]);
if (det == 0)
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
"Singular matrix, cannot invert");
float invDet = 1.0f / det;
result.v[0][0] = (v[1][1] * v[2][2] - v[1][2] * v[2][1]) * invDet;
result.v[0][1] = (v[0][2] * v[2][1] - v[0][1] * v[2][2]) * invDet;
result.v[0][2] = (v[0][1] * v[1][2] - v[0][2] * v[1][1]) * invDet;
result.v[1][0] = (v[1][2] * v[2][0] - v[1][0] * v[2][2]) * invDet;
result.v[1][1] = (v[0][0] * v[2][2] - v[0][2] * v[2][0]) * invDet;
result.v[1][2] = (v[0][2] * v[1][0] - v[0][0] * v[1][2]) * invDet;
result.v[2][0] = (v[1][0] * v[2][1] - v[1][1] * v[2][0]) * invDet;
result.v[2][1] = (v[0][1] * v[2][0] - v[0][0] * v[2][1]) * invDet;
result.v[2][2] = (v[0][0] * v[1][1] - v[0][1] * v[1][0]) * invDet;
return result;
}
RotMatrix RotMatrix::operator!() const {
return invert();
}
std::vector<float> RotMatrix::arr() const {
std::vector<float> ret;
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
ret.push_back(v[i][j]);
}
}
return ret;
}