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OpenAPI: Add spot finding enable/disable option

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This commit is contained in:
leonarski_f
2024-04-08 20:56:53 +02:00
parent c1e046b90d
commit 9cff0dc6f7
11 changed files with 70 additions and 31 deletions
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4
broker/JFJochBrokerHttp.cpp
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@@ -19,7 +19,8 @@ inline SpotFindingSettings Convert(const org::openapitools::server::model::Spot_
ret.max_pix_per_spot = input.getMaxPixPerSpot();
ret.high_resolution_limit = input.getHighResolutionLimit();
ret.low_resolution_limit = input.getLowResolutionLimit();
ret.preview_indexed_only = input.previewIndexedOnlyIsSet() ? input.isPreviewIndexedOnly() : false;
ret.preview_indexed_only = input.isPreviewIndexedOnly();
ret.enable = input.isEnable();
return ret;
}
@@ -32,6 +33,7 @@ inline org::openapitools::server::model::Spot_finding_settings Convert(const Spo
ret.setHighResolutionLimit(input.high_resolution_limit);
ret.setLowResolutionLimit(input.low_resolution_limit);
ret.setPreviewIndexedOnly(input.preview_indexed_only);
ret.setEnable(input.enable);
return ret;
}

16
broker/gen/model/Spot_finding_settings.cpp
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@@ -21,6 +21,7 @@ namespace org::openapitools::server::model
Spot_finding_settings::Spot_finding_settings()
{
m_Enable = true;
m_Signal_to_noise_threshold = 0.0f;
m_Photon_count_threshold = 0L;
m_Min_pix_per_spot = 0L;
@@ -51,7 +52,7 @@ bool Spot_finding_settings::validate(std::stringstream& msg, const std::string&
bool success = true;
const std::string _pathPrefix = pathPrefix.empty() ? "Spot_finding_settings" : pathPrefix;
/* Signal_to_noise_threshold */ {
const float& value = m_Signal_to_noise_threshold;
@@ -116,6 +117,9 @@ bool Spot_finding_settings::operator==(const Spot_finding_settings& rhs) const
return
(isEnable() == rhs.isEnable())
&&
(getSignalToNoiseThreshold() == rhs.getSignalToNoiseThreshold())
&&
@@ -148,6 +152,7 @@ bool Spot_finding_settings::operator!=(const Spot_finding_settings& rhs) const
void to_json(nlohmann::json& j, const Spot_finding_settings& o)
{
j = nlohmann::json();
j["enable"] = o.m_Enable;
j["signal_to_noise_threshold"] = o.m_Signal_to_noise_threshold;
j["photon_count_threshold"] = o.m_Photon_count_threshold;
j["min_pix_per_spot"] = o.m_Min_pix_per_spot;
@@ -161,6 +166,7 @@ void to_json(nlohmann::json& j, const Spot_finding_settings& o)
void from_json(const nlohmann::json& j, Spot_finding_settings& o)
{
j.at("enable").get_to(o.m_Enable);
j.at("signal_to_noise_threshold").get_to(o.m_Signal_to_noise_threshold);
j.at("photon_count_threshold").get_to(o.m_Photon_count_threshold);
j.at("min_pix_per_spot").get_to(o.m_Min_pix_per_spot);
@@ -175,6 +181,14 @@ void from_json(const nlohmann::json& j, Spot_finding_settings& o)
}
bool Spot_finding_settings::isEnable() const
{
return m_Enable;
}
void Spot_finding_settings::setEnable(bool const value)
{
m_Enable = value;
}
float Spot_finding_settings::getSignalToNoiseThreshold() const
{
return m_Signal_to_noise_threshold;

7
broker/gen/model/Spot_finding_settings.h
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@@ -57,6 +57,11 @@ public:
/////////////////////////////////////////////
/// Spot_finding_settings members
/// <summary>
///
/// </summary>
bool isEnable() const;
void setEnable(bool const value);
/// <summary>
///
/// </summary>
@@ -98,6 +103,8 @@ public:
friend void to_json(nlohmann::json& j, const Spot_finding_settings& o);
friend void from_json(const nlohmann::json& j, Spot_finding_settings& o);
protected:
bool m_Enable;
float m_Signal_to_noise_threshold;
int64_t m_Photon_count_threshold;

4
broker/jfjoch_api.yaml
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@@ -311,6 +311,7 @@ components:
spot_finding_settings:
type: object
required:
- enable
- signal_to_noise_threshold
- photon_count_threshold
- max_pix_per_spot
@@ -318,6 +319,9 @@ components:
- high_resolution_limit
- low_resolution_limit
properties:
enable:
type: boolean
default: true
signal_to_noise_threshold:
type: number
format: float

8
broker/redoc-static.html
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File diff suppressed because one or more lines are too long

9
common/DiffractionExperiment.cpp
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@@ -665,14 +665,7 @@ void DiffractionExperiment::CheckDataProcessingSettings(const SpotFindingSetting
}
SpotFindingSettings DiffractionExperiment::DefaultDataProcessingSettings() {
SpotFindingSettings ret{};
ret.signal_to_noise_threshold = 3;
ret.photon_count_threshold = 16;
ret.min_pix_per_spot = 2;
ret.max_pix_per_spot = 50;
ret.low_resolution_limit = 20.0;
ret.high_resolution_limit = 2.5;
return ret;
return {};
}
void DiffractionExperiment::FillMessage(StartMessage &message) const {

29
frontend_ui/src/components/DataProcessingSettings.tsx
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@@ -15,6 +15,7 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
interval : NodeJS.Timer | undefined;
state : MyState = {
s: {
enable: true,
photon_count_threshold: 8,
signal_to_noise_threshold: 3.0,
min_pix_per_spot: 2,
@@ -74,6 +75,7 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
}
));
this.putValues();
this.getValues();
}
setMinPixPerSpot = (event: Event, newValue: number | number[]) => {
@@ -86,6 +88,7 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
}
));
this.putValues();
this.getValues();
}
setHighResolutionLimit = (event: Event, newValue: number | number[]) => {
@@ -98,12 +101,23 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
}
));
this.putValues();
this.getValues();
}
enableSpotFindingToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
let x = this.state;
x.s.enable = event.target.checked;
if (!x.s.enable)
x.s.preview_indexed_only = false;
this.putValues2(x);
this.getValues();
}
previewIndexedToggle = (event: React.ChangeEvent<HTMLInputElement>) => {
let x = this.state;
x.s.preview_indexed_only = event.target.checked;
this.putValues2(x);
this.getValues();
}
render() {
@@ -112,32 +126,35 @@ class DataProcessingSettings extends Component<MyProps, MyState> {
<Grid item xs={1}/>
<Grid item xs={10}>
<br/><strong>Data processing parameters</strong><br/><br/>
<br/><strong>Spot finding parameters</strong><br/><br/>
<Switch onChange={this.enableSpotFindingToggle} checked={this.state.s.enable}
disabled={this.state.connection_error}/>
Enable spot finding <br/><br/>
<Typography gutterBottom> Count threshold </Typography>
<Slider disabled={this.state.connection_error}
<Slider disabled={this.state.connection_error || !this.state.s.enable}
value={Number(this.state.s.photon_count_threshold)}
onChange={this.setPhotonCountThreshold}
min={1} max={50} step={1} valueLabelDisplay="auto" />
<br/><Typography> Signal-to-noise threshold </Typography>
<Slider disabled={this.state.connection_error}
<Slider disabled={this.state.connection_error || !this.state.s.enable}
value={Number(this.state.s.signal_to_noise_threshold)}
onChange={this.setSignalToNoiseThreshold}
min={2} max={10} step={0.5} valueLabelDisplay="auto" />
<br/><Typography> Minimum pixel / spot </Typography>
<Slider disabled={this.state.connection_error}
<Slider disabled={this.state.connection_error || !this.state.s.enable}
value={Number(this.state.s.min_pix_per_spot)}
onChange={this.setMinPixPerSpot}
min={1} max={8} step={1} valueLabelDisplay="auto" />
<Typography> High resolution limit [&#8491;] </Typography>
<Slider disabled={this.state.connection_error}
<Slider disabled={this.state.connection_error || !this.state.s.enable}
value={Number(this.state.s.high_resolution_limit)}
onChange={this.setHighResolutionLimit}
min={1} max={5} step={0.2} valueLabelDisplay="auto" />
<br/>
<Switch onChange={this.previewIndexedToggle} checked={this.state.s.preview_indexed_only}
disabled={this.state.connection_error}/>
disabled={this.state.connection_error || !this.state.s.enable}/>
Preview only indexed frames <br/><br/>
</Grid>
<Grid item xs={1}/>

4
frontend_ui/src/openapi/models/dataset_settings.ts
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@@ -49,9 +49,9 @@ export type dataset_settings = {
*/
file_prefix?: string;
/**
* Number of round-robin data files
* Number of files in a single HDF5 data file (0 = write all images to a single data file).
*/
data_file_count?: number;
images_per_file?: number;
space_group_number?: number;
/**
* /entry/sample/name in NXmx

1
frontend_ui/src/openapi/models/spot_finding_settings.ts
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@@ -4,6 +4,7 @@
/* eslint-disable */
export type spot_finding_settings = {
enable: boolean;
signal_to_noise_threshold: number;
photon_count_threshold: number;
min_pix_per_spot: number;

4
image_analysis/MXAnalyzer.cpp
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@@ -17,7 +17,7 @@ MXAnalyzer::MXAnalyzer(const DiffractionExperiment &in_experiment)
}
void MXAnalyzer::ReadFromFPGA(const DeviceOutput *output, const SpotFindingSettings &settings, size_t module_number) {
if (!find_spots)
if (!find_spots || !settings.enable)
return;
StrongPixelSet strong_pixel_set;
strong_pixel_set.ReadFPGAOutput(experiment, *output);
@@ -29,7 +29,7 @@ void MXAnalyzer::ReadFromCPU(const int16_t *image, const SpotFindingSettings &se
return;
std::vector<float> d_map(RAW_MODULE_SIZE);
DeviceOutput output;
DeviceOutput output{};
memcpy(output.pixels, image, RAW_MODULE_SIZE * sizeof(int16_t));
CalcSpotFinderResolutionMap(d_map.data(), experiment, module_number);

15
image_analysis/SpotFindingSettings.h
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@@ -6,13 +6,14 @@
#include <cstdint>
struct SpotFindingSettings {
float signal_to_noise_threshold; // STRONG_PIXEL in XDS
int64_t photon_count_threshold; // Threshold in photon counts
int64_t min_pix_per_spot; // Minimum pixels per spot
int64_t max_pix_per_spot; // Maximum pixels per spot
float high_resolution_limit;
float low_resolution_limit;
bool preview_indexed_only;
bool enable = true;
float signal_to_noise_threshold = 3; // STRONG_PIXEL in XDS
int64_t photon_count_threshold = 10; // Threshold in photon counts
int64_t min_pix_per_spot = 2; // Minimum pixels per spot
int64_t max_pix_per_spot = 50; // Maximum pixels per spot
float high_resolution_limit = 2.5;
float low_resolution_limit = 50.0;
bool preview_indexed_only = false;
};
#endif //JUNGFRAUJOCH_SPOTFINDINGSETTINGS_H