Source code for ewoksfluo.tasks.normalization.norm_results_stack

import logging
from typing import List
from typing import Optional

from ewokscore import Task
from ewokscore.model import BaseOutputModel
from pydantic import Field

from ..models import FluoInputs
from .norm_utils import normalization_coefficient_stack
from .norm_utils import normalization_template
from .norm_utils import save_normalized_xrf_results

_logger = logging.getLogger(__name__)




class Inputs(FluoInputs):
    bliss_scan_uris: List[str] = Field(
        description="Bliss scan URI's.",
        examples=[["/data/dataset.h5::/1.1", "/data/dataset.h5::/2.1"]],
    )

    output_root_uri: str = Field(
        description="Output root URI.",
        examples=[
            "/results/dataset.h5",
            "/results/dataset.h5::/1.1",
            "/results/dataset.h5::/1.1/norm",
        ],
    )

    xrf_results_uri: Optional[str] = Field(
        description="Previous XRF NXprocess URI to normalize.",
        examples=["/results/dataset.h5::/1.1/sum/results"],
    )

    normalization_expression: Optional[str] = Field(
        default=None, description="Arithmetic expression to be used for normalization."
    )
    counter_normalization_template: str = Field(
        default="np.nanmean(<instrument/{}/data>)/<instrument/{}/data>",
        description="Arithmetic expression to be used for normalization.",
    )
    counter_name: Optional[str] = Field(
        default=None,
        description="To be used in :math:`counter_normalization_template`.",
    )
    detector_normalization_template: str = Field(
        default="1./<instrument/{}/live_time>",
        description="Arithmetic expression to be used for normalization.",
    )
    detector_name: Optional[str] = Field(
        default=None,
        description="To be used in :math:`detector_normalization_template`.",
    )





class Outputs(BaseOutputModel):
    bliss_scan_uris: List[str] = Field(
        description="Bliss scan URI's.",
        examples=[["/data/dataset.h5::/1.1", "/data/dataset.h5::/2.1"]],
    )
    output_root_uri: str = Field(
        description="Output NXentry URI.", examples=["/results/dataset.h5::/1.1"]
    )
    xrf_results_uri: str = Field(
        description="Output NXprocess results URI.",
        examples=["/results/dataset.h5::/1.1/norm/results"],
    )





class NormalizeXrfResultsStack(Task, input_model=Inputs, output_model=Outputs):
    """Normalize XRF stack results with raw scan counters.

    Typical normalizers are beam monitors and measurement (live) time.
    """



    def run(self):
        expression = self.inputs.normalization_expression
        detector_name = self.inputs.detector_name
        counter_name = self.inputs.counter_name
        if not (expression or detector_name or counter_name):
            _logger.warning(
                "Neither 'normalization_expression', 'counter_name', nor 'detector_name' was specified. Normalization is skipped."
            )
            self.outputs.xrf_results_uri = self.inputs.xrf_results_uri
            self.outputs.bliss_scan_uris = self.inputs.bliss_scan_uris
            self.outputs.output_root_uri = self.inputs.output_root_uri
            return

        counter_normalization_template = self.inputs.counter_normalization_template
        detector_normalization_template = self.inputs.detector_normalization_template

        normalization_expression = normalization_template(
            expression,
            counter_normalization_template,
            counter_name,
            detector_normalization_template,
            detector_name,
        )
        _logger.info("Multiply XRF results with: %s", normalization_expression)
        coefficient = normalization_coefficient_stack(
            self.inputs.bliss_scan_uris, normalization_expression
        )

        process_config = {"normalization_expression": normalization_expression}
        self.outputs.xrf_results_uri = save_normalized_xrf_results(
            self.inputs.xrf_results_uri,
            coefficient,
            self.inputs.output_root_uri,
            process_config,
        )
        self.outputs.bliss_scan_uris = self.inputs.bliss_scan_uris
        self.outputs.output_root_uri = self.inputs.output_root_uri