# dials.create_profile_model¶

## Introduction¶

This program computes the profile model from the input reflections. It then saves a modified experiments.json file with the additional profile model information. Usually this is performed during integration; however, on some occasions it may be desirable to compute the profile model independantly.

Examples:

```
dials.create_profile_model experiments.json reflections.pickle
```

## Basic parameters¶

```
output = experiments_with_profile_model.json
profile {
algorithm = gaussian_rs *gaussian_rs
gaussian_rs {
scan_varying = False
min_spots {
overall = 50
per_degree = 20
}
sigma_m_algorithm = basic *extended
parameters {
sigma_b = None
sigma_m = None
}
filter {
min_zeta = 0.05
}
fitting {
scan_step = 5
grid_size = 5
threshold = 0.02
grid_method = single *regular_grid circular_grid spherical_grid
fit_method = *reciprocal_space detector_space
detector_space {
deconvolution = False
}
}
}
gaussian_rs {
scan_varying = False
min_spots {
overall = 50
per_degree = 20
}
sigma_m_algorithm = basic *extended
parameters {
sigma_b = None
sigma_m = None
}
filter {
min_zeta = 0.05
}
fitting {
scan_step = 5
grid_size = 5
threshold = 0.02
grid_method = single *regular_grid circular_grid spherical_grid
fit_method = *reciprocal_space detector_space
detector_space {
deconvolution = False
}
}
}
}
prediction {
d_min = None
d_max = None
margin = 1
force_static = False
padding = 1.0
}
```

## Full parameter definitions¶

```
subtract_background = False
.help = "Subtract background from pixel data before computing profile"
.type = bool
.expert_level = 2
output = experiments_with_profile_model.json
.help = "The filename for the experiments"
.type = str
profile
.help = "
T h e i n t e r f a c e d e f i n i t i o n f o r a "
"p r o f i l e m o d e l .
"
{
algorithm = gaussian_rs *gaussian_rs
.help = "The choice of algorithm"
.type = choice
gaussian_rs
.help = "An extension class implementing a reciprocal space gaussian"
"profile model."
{
scan_varying = False
.help = "Calculate a scan varying model"
.type = bool
min_spots
.help = "if (total_reflections > overall or reflections_per_degree >"
"per_degree) then do the profile modelling."
{
overall = 50
.help = "The minimum number of spots needed to do the profile"
"modelling"
.type = int(value_min=0)
per_degree = 20
.help = "The minimum number of spots needed to do the profile"
"modelling"
.type = int(value_min=0)
}
sigma_m_algorithm = basic *extended
.help = "The algorithm to compute mosaicity"
.type = choice
parameters {
sigma_b = None
.help = "Override the sigma_b value (degrees)"
.type = float(value_min=0)
sigma_m = None
.help = "Override the sigma_m value (degrees)"
.type = float(value_min=0)
}
filter {
min_zeta = 0.05
.help = "Filter reflections by min zeta"
.type = float
}
fitting {
scan_step = 5
.help = "Space between profiles in degrees"
.type = float
grid_size = 5
.help = "The size of the profile grid."
.type = int
threshold = 0.02
.help = "The threshold to use in reference profile"
.type = float
grid_method = single *regular_grid circular_grid spherical_grid
.help = "Select the profile grid method"
.type = choice
fit_method = *reciprocal_space detector_space
.help = "The fitting method"
.type = choice
detector_space {
deconvolution = False
.help = "Do deconvolution in detector space"
.type = bool
}
}
}
gaussian_rs
.help = "An extension class implementing a reciprocal space gaussian"
"profile model."
{
scan_varying = False
.help = "Calculate a scan varying model"
.type = bool
min_spots
.help = "if (total_reflections > overall or reflections_per_degree >"
"per_degree) then do the profile modelling."
{
overall = 50
.help = "The minimum number of spots needed to do the profile"
"modelling"
.type = int(value_min=0)
per_degree = 20
.help = "The minimum number of spots needed to do the profile"
"modelling"
.type = int(value_min=0)
}
sigma_m_algorithm = basic *extended
.help = "The algorithm to compute mosaicity"
.type = choice
parameters {
sigma_b = None
.help = "Override the sigma_b value (degrees)"
.type = float(value_min=0)
sigma_m = None
.help = "Override the sigma_m value (degrees)"
.type = float(value_min=0)
}
filter {
min_zeta = 0.05
.help = "Filter reflections by min zeta"
.type = float
}
fitting {
scan_step = 5
.help = "Space between profiles in degrees"
.type = float
grid_size = 5
.help = "The size of the profile grid."
.type = int
threshold = 0.02
.help = "The threshold to use in reference profile"
.type = float
grid_method = single *regular_grid circular_grid spherical_grid
.help = "Select the profile grid method"
.type = choice
fit_method = *reciprocal_space detector_space
.help = "The fitting method"
.type = choice
detector_space {
deconvolution = False
.help = "Do deconvolution in detector space"
.type = bool
}
}
}
}
prediction {
d_min = None
.help = "The maximum resolution limit"
.type = float
d_max = None
.help = "The minimum resolution limit"
.type = float
margin = 1
.help = "The margin to use to scan varying prediction"
.type = int
force_static = False
.help = "For scan-varying prediction force scan-static prediction"
.type = bool
padding = 1.0
.help = "The padding in degrees"
.type = float(value_min=0)
}
```