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Merge 827e494 into 5c27616
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@dagewa
dagewa authored Aug 4, 2023
2 parents 5c27616 + 827e494 commit fb30aa9
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Showing 9 changed files with 164 additions and 25 deletions.
1 change: 1 addition & 0 deletions newsfragments/647.feature
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@@ -0,0 +1 @@
The ``Beam`` model now has a ``probe`` value to keep track of the type of radiation.
4 changes: 4 additions & 0 deletions src/dxtbx/dxtbx_model_ext.pyi
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Expand Up @@ -22,6 +22,8 @@ from scitbx.array_family import shared as flex_shared
# Attempt to use the stub typing for flex-inheritance
from scitbx.array_family.flex import FlexPlain

from dxtbx_model_ext import Probe # type: ignore

# TypeVar for the set of Experiment models that can be joint-accepted
# - profile, imageset and scalingmodel are handled as 'object'
TExperimentModel = TypeVar(
Expand Down Expand Up @@ -113,6 +115,8 @@ class Beam(BeamBase):
@staticmethod
def from_dict(data: Dict) -> Beam: ...
def to_dict(self) -> Dict: ...
@staticmethod
def get_probe_from_name(name: str) -> Probe: ...

class PolychromaticBeam(Beam):
@overload
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2 changes: 2 additions & 0 deletions src/dxtbx/format/FormatGatanDM4.py
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Expand Up @@ -21,6 +21,7 @@
)
from dxtbx.format.Format import Format
from dxtbx.format.FormatMultiImage import FormatMultiImage
from dxtbx.model.beam import Probe


def read_tag(f, byteorder):
Expand Down Expand Up @@ -358,6 +359,7 @@ def _beam(self):
wavelength=wavelength,
polarization=(0, 1, 0),
polarization_fraction=0.5,
probe=Probe.electron,
)

def _scan(self):
Expand Down
2 changes: 2 additions & 0 deletions src/dxtbx/format/FormatMRC.py
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Expand Up @@ -19,6 +19,7 @@
from dxtbx.format.Format import Format
from dxtbx.format.FormatMultiImage import FormatMultiImage
from dxtbx.model import ScanFactory
from dxtbx.model.beam import Probe

logger = logging.getLogger("dials")

Expand Down Expand Up @@ -226,6 +227,7 @@ def _beam(self):
wavelength=wavelength,
polarization=(0, 1, 0),
polarization_fraction=0.5,
probe=Probe.electron,
)


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2 changes: 2 additions & 0 deletions src/dxtbx/format/FormatSMVTimePix_SU.py
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Expand Up @@ -12,6 +12,7 @@
from scitbx import matrix

from dxtbx.format.FormatSMV import FormatSMV
from dxtbx.model.beam import Probe

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from dxtbx.model.detector import Detector


Expand Down Expand Up @@ -76,6 +77,7 @@ def _beam(self):
wavelength=wavelength,
polarization=(0, 1, 0),
polarization_fraction=0.5,
probe=Probe.electron,
)

def _scan(self):
Expand Down
90 changes: 78 additions & 12 deletions src/dxtbx/model/beam.h
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Expand Up @@ -13,6 +13,7 @@

#include <iostream>
#include <cmath>
#include <string>
#include <scitbx/vec3.h>
#include <scitbx/array_family/shared.h>
#include <scitbx/array_family/simple_io.h>
Expand All @@ -24,6 +25,9 @@ namespace dxtbx { namespace model {

using scitbx::vec3;

// probe type enumeration
enum Probe { xray = 1, electron = 2, neutron = 3 };

/** Base class for beam objects */
class BeamBase {
public:
Expand All @@ -44,6 +48,8 @@ namespace dxtbx { namespace model {
virtual std::size_t get_num_scan_points() const = 0;
virtual scitbx::af::shared<vec3<double> > get_s0_at_scan_points() const = 0;
virtual vec3<double> get_s0_at_scan_point(std::size_t index) const = 0;
virtual Probe get_probe() const = 0;
virtual std::string get_probe_name() const = 0;

virtual void set_direction(vec3<double> direction) = 0;
virtual void set_wavelength(double wavelength) = 0;
Expand All @@ -59,6 +65,7 @@ namespace dxtbx { namespace model {
virtual void set_transmission(double transmission) = 0;
virtual void set_s0_at_scan_points(
const scitbx::af::const_ref<vec3<double> > &s0) = 0;
virtual void set_probe(Probe probe) = 0;

virtual void reset_scan_points() = 0;
virtual bool is_similar_to(const BeamBase &rhs,
Expand All @@ -82,7 +89,8 @@ namespace dxtbx { namespace model {
polarization_normal_(0.0, 1.0, 0.0),
polarization_fraction_(0.999),
flux_(0),
transmission_(1.0) {}
transmission_(1.0),
probe_(Probe::xray) {}

/**
* @param s0 The incident beam vector.
Expand All @@ -93,7 +101,8 @@ namespace dxtbx { namespace model {
polarization_normal_(0.0, 1.0, 0.0),
polarization_fraction_(0.999),
flux_(0),
transmission_(1.0) {
transmission_(1.0),
probe_(Probe::xray) {
DXTBX_ASSERT(s0.length() > 0);
wavelength_ = 1.0 / s0.length();
direction_ = -s0.normalize();
Expand All @@ -110,7 +119,8 @@ namespace dxtbx { namespace model {
polarization_normal_(0.0, 1.0, 0.0),
polarization_fraction_(0.999),
flux_(0),
transmission_(1.0) {
transmission_(1.0),
probe_(Probe::xray) {
DXTBX_ASSERT(direction.length() > 0);
direction_ = direction.normalize();
}
Expand All @@ -126,7 +136,8 @@ namespace dxtbx { namespace model {
polarization_normal_(0.0, 1.0, 0.0),
polarization_fraction_(0.999),
flux_(0),
transmission_(1.0) {
transmission_(1.0),
probe_(Probe::xray) {
DXTBX_ASSERT(s0.length() > 0);
wavelength_ = 1.0 / s0.length();
direction_ = -s0.normalize();
Expand All @@ -148,7 +159,8 @@ namespace dxtbx { namespace model {
polarization_normal_(0.0, 1.0, 0.0),
polarization_fraction_(0.999),
flux_(0),
transmission_(1.0) {
transmission_(1.0),
probe_(Probe::xray) {
DXTBX_ASSERT(direction.length() > 0);
direction_ = direction.normalize();
}
Expand All @@ -162,6 +174,7 @@ namespace dxtbx { namespace model {
* @param polarization_fraction The polarization fraction
* @param flux The beam flux
* @param transmission The beam transmission
* @param probe The probe value
*/
Beam(vec3<double> direction,
double wavelength,
Expand All @@ -170,14 +183,16 @@ namespace dxtbx { namespace model {
vec3<double> polarization_normal,
double polarization_fraction,
double flux,
double transmission)
double transmission,
Probe probe)
: wavelength_(wavelength),
divergence_(divergence),
sigma_divergence_(sigma_divergence),
polarization_normal_(polarization_normal),
polarization_fraction_(polarization_fraction),
flux_(flux),
transmission_(transmission) {
transmission_(transmission),
probe_(probe) {
DXTBX_ASSERT(direction.length() > 0);
direction_ = direction.normalize();
}
Expand Down Expand Up @@ -289,6 +304,44 @@ namespace dxtbx { namespace model {
return s0_at_scan_points_[index];
}

Probe get_probe() const {
return probe_;
}

std::string get_probe_name() const {
// Return a name that matches NeXus definitions from
// https://manual.nexusformat.org/classes/base_classes/NXsource.html
switch (probe_) {
case xray:
return std::string("x-ray");
case electron:
return std::string("electron");
case neutron:
return std::string("neutron");
default:
DXTBX_ERROR("Unknown probe type");
}
}

static Probe get_probe_from_name(const std::string probe) {
// Return a Probe matched to NeXus definitions from
// https://manual.nexusformat.org/classes/base_classes/NXsource.html

if (probe == "x-ray") {
return Probe::xray;
} else if (probe == "electron") {
return Probe::electron;
} else if (probe == "neutron") {
return Probe::neutron;
}

DXTBX_ERROR("Unknown probe " + probe);
}

void set_probe(Probe probe) {
probe_ = probe;
}

void reset_scan_points() {
s0_at_scan_points_.clear();
}
Expand Down Expand Up @@ -324,7 +377,8 @@ namespace dxtbx { namespace model {
angle_safe(polarization_normal_, rhs.get_polarization_normal()))
<= eps
&& std::abs(polarization_fraction_ - rhs.get_polarization_fraction())
<= eps;
<= eps
&& (probe_ == rhs.get_probe());
}

virtual bool is_similar_to(const BeamBase &rhs,
Expand Down Expand Up @@ -361,7 +415,8 @@ namespace dxtbx { namespace model {
angle_safe(polarization_normal_, rhs.get_polarization_normal()))
<= polarization_normal_tolerance
&& std::abs(polarization_fraction_ - rhs.get_polarization_fraction())
<= polarization_fraction_tolerance;
<= polarization_fraction_tolerance
&& (probe_ == rhs.get_probe());
}

bool operator!=(const BeamBase &rhs) const {
Expand All @@ -383,6 +438,7 @@ namespace dxtbx { namespace model {
double polarization_fraction_;
double flux_;
double transmission_;
Probe probe_;

private:
double wavelength_;
Expand All @@ -392,6 +448,7 @@ namespace dxtbx { namespace model {
/** Print beam information */
inline std::ostream &operator<<(std::ostream &os, const Beam &b) {
os << "Beam:\n";
os << " probe: " << b.get_probe_name() << "\n";
os << " wavelength: " << b.get_wavelength() << "\n";
os << " sample to source direction : "
<< b.get_sample_to_source_direction().const_ref() << "\n";
Expand All @@ -415,6 +472,7 @@ namespace dxtbx { namespace model {
set_polarization_fraction(0.5);
set_flux(0);
set_transmission(1.0);
set_probe(Probe::xray);
}

/**
Expand All @@ -429,6 +487,7 @@ namespace dxtbx { namespace model {
set_polarization_fraction(0.5);
set_flux(0);
set_transmission(1.0);
set_probe(Probe::xray);
}

/**
Expand All @@ -447,6 +506,7 @@ namespace dxtbx { namespace model {
set_polarization_fraction(0.5);
set_flux(0);
set_transmission(1.0);
set_probe(Probe::xray);
}

/**
Expand All @@ -457,14 +517,16 @@ namespace dxtbx { namespace model {
* @param polarization_fraction The polarization fraction
* @param flux The beam flux
* @param transmission The beam transmission
* @param probe The probe value
*/
PolychromaticBeam(vec3<double> direction,
double divergence,
double sigma_divergence,
vec3<double> polarization_normal,
double polarization_fraction,
double flux,
double transmission) {
double transmission,
Probe probe) {
DXTBX_ASSERT(direction.length() > 0);
direction_ = direction.normalize();
set_divergence(divergence);
Expand All @@ -473,6 +535,7 @@ namespace dxtbx { namespace model {
set_polarization_fraction(polarization_fraction);
set_flux(flux);
set_transmission(transmission);
set_probe(probe);
}

double get_wavelength() const {
Expand Down Expand Up @@ -527,7 +590,8 @@ namespace dxtbx { namespace model {
angle_safe(polarization_normal_, rhs.get_polarization_normal()))
<= eps
&& std::abs(polarization_fraction_ - rhs.get_polarization_fraction())
<= eps;
<= eps
&& (probe_ == rhs.get_probe());
}

bool is_similar_to(const BeamBase &rhs,
Expand All @@ -551,13 +615,15 @@ namespace dxtbx { namespace model {
angle_safe(polarization_normal_, rhs.get_polarization_normal()))
<= polarization_normal_tolerance
&& std::abs(polarization_fraction_ - rhs.get_polarization_fraction())
<= polarization_fraction_tolerance;
<= polarization_fraction_tolerance
&& (probe_ == rhs.get_probe());
}
};

/** Print beam information */
inline std::ostream &operator<<(std::ostream &os, const PolychromaticBeam &b) {
os << "Beam:\n";
os << " probe: " << b.get_probe_name() << "\n";
os << " sample to source direction : "
<< b.get_sample_to_source_direction().const_ref() << "\n";
os << " divergence: " << b.get_divergence() << "\n";
Expand Down
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