def make_error_model_plots(params, experiments):
"""Generate normal probability plot data."""
data = {}
if experiments[0].scaling_model.error_model:
em = experiments[0].scaling_model.error_model
if em.filtered_Ih_table:
table = em.filtered_Ih_table
data["intensity"] = table.intensities
sigmaprime = calc_sigmaprime(em.parameters, table)
data["delta_hl"] = calc_deltahl(table, table.calc_nh(), sigmaprime)
data["inv_scale"] = table.inverse_scale_factors
data["sigma"] = sigmaprime * data["inv_scale"]
data["binning_info"] = em.binner.binning_info
em.clear_Ih_table()
if params.weighting.error_model.basic.minimisation == "regression":
x, y = calculate_regression_x_y(em.filtered_Ih_table)
data["regression_x"] = x
data["regression_y"] = y
data["model_a"] = em.parameters[0]
data["model_b"] = em.parameters[1]
data["summary"] = str(em)
d = {"error_model_plots": {}, "error_model_summary": "No error model applied"}
if "delta_hl" in data:
d["error_model_plots"].update(normal_probability_plot(data))
d["error_model_plots"].update(
i_over_sig_i_vs_i_plot(data["intensity"], data["sigma"])
)
d["error_model_plots"].update(error_model_variance_plot(data))
if "regression_x" in data:
d["error_model_plots"].update(error_regression_plot(data))
if "summary" in data:
d["error_model_summary"] = data["summary"]
return d
def make_error_model_plots(params, experiments):
"""Generate normal probability plot data."""
d = {
"error_model_plots": {},
"error_model_summary": "No error model applied"
}
error_model_data = [] # a list of dicts of error model data
if experiments[0].scaling_model.error_model:
error_models = [e.scaling_model.error_model for e in experiments]
unique_error_models = OrderedSet(error_models)
if len(unique_error_models) == 1:
d["error_model_summary"] = str(error_models[0])
else:
d["error_model_summary"] = ""
for i, e in enumerate(unique_error_models):
indices = [
str(j + 1) for j, x in enumerate(error_models) if e is x
]
d["error_model_summary"] += (
f"\nError model {i+1}, applied to sweeps {', '.join(indices)}:"
+ str(e))
for em in unique_error_models:
if em.filtered_Ih_table:
data_i = {}
table = em.filtered_Ih_table
data_i["intensity"] = table.intensities
sigmaprime = calc_sigmaprime(em.parameters, table)
data_i["delta_hl"] = calc_deltahl(table, table.calc_nh(),
sigmaprime)
data_i["inv_scale"] = table.inverse_scale_factors
data_i["sigma"] = sigmaprime * data_i["inv_scale"]
data_i["binning_info"] = em.binner.binning_info
em.clear_Ih_table()
if params.weighting.error_model.basic.minimisation == "regression":
x, y = calculate_regression_x_y(em.filtered_Ih_table)
data_i["regression_x"] = x
data_i["regression_y"] = y
data_i["model_a"] = em.parameters[0]
data_i["model_b"] = em.parameters[1]
error_model_data.append(data_i)
if error_model_data:
for i, emd in enumerate(error_model_data):
d["error_model_plots"].update(
normal_probability_plot(emd, label=i + 1))
d["error_model_plots"].update(
i_over_sig_i_vs_i_plot(
flumpy.from_numpy(emd["intensity"]),
flumpy.from_numpy(emd["sigma"]),
label=i + 1,
))
d["error_model_plots"].update(
error_model_variance_plot(emd, label=i + 1))
if "regression_x" in emd:
d["error_model_plots"].update(
error_regression_plot(emd, label=i + 1))
return d
def make_plots(self):
"""Generate normal probability plot data."""
d = {"error_model_plots": {}}
if "delta_hl" in self.data:
d["error_model_plots"].update(normal_probability_plot(self.data))
d["error_model_plots"].update(
i_over_sig_i_vs_i_plot(self.data["intensity"],
self.data["sigma"]))
return d
def make_output(model, params):
"""Get relevant data from the model and make html report."""
if not (params.output.html or params.output.json):
return
data = {}
table = model.filtered_Ih_table
data["intensity"] = table.intensities
sigmaprime = calc_sigmaprime(model.parameters, table)
data["delta_hl"] = calc_deltahl(table, table.calc_nh(), sigmaprime)
data["inv_scale"] = table.inverse_scale_factors
data["sigma"] = sigmaprime * data["inv_scale"]
data["binning_info"] = model.binner.binning_info
d = {"error_model_plots": {}}
d["error_model_plots"].update(normal_probability_plot(data))
d["error_model_plots"].update(
i_over_sig_i_vs_i_plot(data["intensity"], data["sigma"])
)
d["error_model_plots"].update(error_model_variance_plot(data))
if params.basic.minimisation == "regression":
x, y = calculate_regression_x_y(model.filtered_Ih_table)
data["regression_x"] = x
data["regression_y"] = y
data["model_a"] = model.parameters[0]
data["model_b"] = model.parameters[1]
d["error_model_plots"].update(error_regression_plot(data))
if params.output.html:
logger.info("Writing html report to: %s", params.output.html)
loader = ChoiceLoader(
[
PackageLoader("dials", "templates"),
PackageLoader("dials", "static", encoding="utf-8"),
]
)
env = Environment(loader=loader)
template = env.get_template("simple_report.html")
html = template.render(
page_title="DIALS error model refinement report",
panel_title="Error distribution plots",
panel_id="error_model_plots",
graphs=d["error_model_plots"],
)
with open(params.output.html, "wb") as f:
f.write(html.encode("utf-8", "xmlcharrefreplace"))
if params.output.json:
logger.info("Writing html report data to: %s", params.output.json)
with open(params.output.json, "w") as outfile:
json.dump(d, outfile)
def make_plots(self):
"""Generate normal probability plot data."""
d = {"error_model_plots": {}, "error_model_summary": "No error model applied"}
if "delta_hl" in self.data:
d["error_model_plots"].update(normal_probability_plot(self.data))
d["error_model_plots"].update(
i_over_sig_i_vs_i_plot(self.data["intensity"], self.data["sigma"])
)
d["error_model_plots"].update(error_model_variance_plot(self.data))
if "regression_x" in self.data:
d["error_model_plots"].update(error_regression_plot(self.data))
if "summary" in self.data:
d["error_model_summary"] = self.data["summary"]
return d
def test_normal_probability_plot():
data = {"delta_hl": list(range(20))}
d = normal_probability_plot(data)
assert "normal_distribution_plot" in d
def test_normal_probability_plot():
data = {"delta_hl": np.arange(20, dtype=float)}
d = normal_probability_plot(data)
assert "normal_distribution_plot" in d