load_utils.py

# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
#     NScD Oak Ridge National Laboratory, European Spallation Source
#     & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, division, print_function)

import os
import mantid.simpleapi as mantid
from mantid.api import WorkspaceGroup
from mantid.api import ITableWorkspace
from mantid.simpleapi import mtd
from mantid import api
from mantid.kernel import ConfigServiceImpl
import Muon.GUI.Common.utilities.muon_file_utils as file_utils
from Muon.GUI.Common.ADSHandler.muon_workspace_wrapper import MuonWorkspaceWrapper
import Muon.GUI.Common.utilities.algorithm_utils as algorithm_utils


class LoadUtils(object):
    """
    A simple class for identifing the current run
    and it can return the name, run and instrument.
    The current run is the same as the one in MonAnalysis
    """

    def __init__(self, parent=None):
        exists, tmpWS = self.MuonAnalysisExists()
        if exists:
            self.setUp(tmpWS)
        else:
            raise RuntimeError("No data loaded. \n Please load data using Muon Analysis")

    def setUp(self, tmpWS):
        # get everything from the ADS
        self.options = mantid.AnalysisDataService.getObjectNames()
        self.options = [item.replace(" ", "") for item in self.options]
        self.N_points = len(tmpWS.readX(0))
        self.instrument = tmpWS.getInstrument().getName()

        self.runName = self.instrument + str(tmpWS.getRunNumber()).zfill(8)

    # get methods
    def getNPoints(self):
        return self.N_points

    def getCurrentWS(self):
        return self.runName, self.options

    def getRunName(self):
        return self.runName

    def getInstrument(self):
        return self.instrument

    # check if data matches current
    def digit(self, x):
        return int(filter(str.isdigit, x) or 0)

    def hasDataChanged(self):
        exists, ws = self.MuonAnalysisExists()
        if exists:
            current = ws.getInstrument().getName() + str(ws.getRunNumber()).zfill(8)
            if self.runName != current:
                mantid.logger.error("Active workspace has changed. Reloading the data")
                self.setUp(ws)
                return True
        return False

    # check if muon analysis exists
    def MuonAnalysisExists(self):
        # if period data look for the first period
        if mantid.AnalysisDataService.doesExist("MuonAnalysis_1"):
            tmpWS = mantid.AnalysisDataService.retrieve("MuonAnalysis_1")
            return True, tmpWS
            # if its not period data
        elif mantid.AnalysisDataService.doesExist("MuonAnalysis"):
            tmpWS = mantid.AnalysisDataService.retrieve("MuonAnalysis")
            return True, tmpWS
        else:
            return False, None

    # Get the groups/pairs for active WS
    # ignore raw files
    def getWorkspaceNames(self):
        # gets all WS in the ADS
        runName, options = self.getCurrentWS()
        final_options = []
        # only keep the relevant WS (same run as Muon Analysis)
        for pick in options:
            if ";" in pick and "Raw" not in pick and runName in pick:
                final_options.append(pick)
        return final_options

    # Get the groups/pairs for active WS
    def getGroupedWorkspaceNames(self):
        # gets all WS in the ADS
        runName, options = self.getCurrentWS()
        final_options = []
        # only keep the relevant WS (same run as Muon Analysis)
        for pick in options:
            if "MuonAnalysisGrouped_" in pick and ";" not in pick:
                final_options.append(pick)
        return final_options


def get_default_instrument():
    default_instrument = ConfigServiceImpl.Instance().getInstrument().name()
    if default_instrument not in file_utils.allowed_instruments:
        default_instrument = 'MUSR'
    return default_instrument


def run_LoadInstrument(parameter_dict):
    """
    Apply the LoadInstrument algorithm with the properties supplied through
    the input dictionary of {proeprty_name:property_value} pairs.
    Returns the calculated value of alpha.
    """
    alg = mantid.AlgorithmManager.create("LoadInstrument")
    alg.initialize()
    alg.setAlwaysStoreInADS(False)
    alg.setProperties(parameter_dict)
    alg.execute()
    return alg.getProperty("Workspace").value


def __default_workspace():
    default_instrument = get_default_instrument()
    workspace = api.WorkspaceFactoryImpl.Instance().create("Workspace2D", 2, 10, 10)
    workspace = run_LoadInstrument(
        {"Workspace": workspace,
         "RewriteSpectraMap": True,
         "InstrumentName": default_instrument})
    return MuonWorkspaceWrapper(workspace)


# Dictionary of (property name):(property value) pairs to put into Load algorithm
# NOT including "OutputWorkspace" and "Filename"
DEFAULT_INPUTS = {
    "DeadTimeTable": "__notUsed",
    "DetectorGroupingTable": "__notUsed"}
# List of property names to be extracted from the result of the Load algorithm
DEFAULT_OUTPUTS = ["OutputWorkspace",
                   "DeadTimeTable",
                   "DetectorGroupingTable",
                   "TimeZero",
                   "FirstGoodData",
                   "MainFieldDirection"]
# List of default values for the DEFAULT_OUTPUTS list
DEFAULT_OUTPUT_VALUES = [__default_workspace(),
                         None,  # api.WorkspaceFactoryImpl.Instance().createTable("TableWorkspace"),
                         api.WorkspaceFactoryImpl.Instance().createTable("TableWorkspace"),
                         0.0,
                         0.0, "Unknown direction"]


def is_workspace_group(workspace):
    return isinstance(workspace, WorkspaceGroup)


def get_run_from_multi_period_data(workspace_list):
    """Checks if multi-period data has a single consistent
    run number and returns it, otherwise raises ValueError."""
    runs = [ws.getRunNumber() for ws in workspace_list]
    unique_runs = list(set(runs))
    if len(unique_runs) != 1:
        raise ValueError("Multi-period data contains >1 unique run number.")
    else:
        return unique_runs[0]


def load_dead_time_from_filename(filename):
    """
    From a neXus file, load the dead time ITableWorkspace from it and add to the ADS
    with a name <Instrument><Run>_deadTimes , e.g. EMU0001234_deadTimes.

    :param filename: The full path to the .nxs file.
    :return: The name of the workspace in the ADS.
    """
    loaded_data, run, _ = load_workspace_from_filename(filename)

    if is_workspace_group(loaded_data["OutputWorkspace"]):
        dead_times = loaded_data["DataDeadTimeTable"][0]
    else:
        dead_times = loaded_data["DataDeadTimeTable"]

    if dead_times is None:
        return ""
    assert isinstance(dead_times, ITableWorkspace)

    instrument = loaded_data["OutputWorkspace"].workspace.getInstrument().getName()
    name = str(instrument) + file_utils.format_run_for_file(run) + "_deadTimes"
    api.AnalysisDataService.Instance().addOrReplace(name, dead_times)

    return name


def load_workspace_from_filename(filename,
                                 input_properties=DEFAULT_INPUTS,
                                 output_properties=DEFAULT_OUTPUTS):
    try:
        alg = create_load_algorithm(filename, input_properties)
        alg.execute()
    except:
        alg = create_load_algorithm(filename.split(os.sep)[-1], input_properties)
        alg.execute()

    workspace = alg.getProperty("OutputWorkspace").value
    if is_workspace_group(workspace):
        # handle multi-period data
        load_result = _get_algorithm_properties(alg, output_properties)
        load_result["OutputWorkspace"] = [MuonWorkspaceWrapper(ws) for ws in load_result["OutputWorkspace"]]
        run = get_run_from_multi_period_data(workspace)

    else:
        # single period data
        load_result = _get_algorithm_properties(alg, output_properties)
        load_result["OutputWorkspace"] = MuonWorkspaceWrapper(load_result["OutputWorkspace"])
        run = int(workspace.getRunNumber())

    load_result["DataDeadTimeTable"] = load_result["DeadTimeTable"]
    load_result["DeadTimeTable"] = None

    filename = alg.getProperty("Filename").value

    return load_result, run, filename


def empty_loaded_data():
    return dict(zip(DEFAULT_OUTPUTS + ["DataDeadTimeTable"], DEFAULT_OUTPUT_VALUES + [None]))


def create_load_algorithm(filename, property_dictionary):
    alg = mantid.AlgorithmManager.create("LoadMuonNexus")
    alg.initialize()
    alg.setAlwaysStoreInADS(False)
    alg.setProperty("OutputWorkspace", "__notUsed")
    alg.setProperty("Filename", filename)
    alg.setProperties(property_dictionary)
    return alg


def _get_algorithm_properties(alg, property_dict):
    return {key: alg.getProperty(key).value for key in alg.keys() if key in property_dict}


def get_table_workspace_names_from_ADS():
    """
    Return a list of names of TableWorkspace objects which are in the ADS.
    """
    names = api.AnalysisDataService.Instance().getObjectNames()
    table_names = [name for name in names if isinstance(mtd[name], ITableWorkspace)]
    return table_names


def combine_loaded_runs(model, run_list):
    return_ws = model._loaded_data_store.get_data(run=run_list[0])["workspace"]
    running_total = return_ws["OutputWorkspace"].workspace

    for run in run_list[1:]:
        ws = model._loaded_data_store.get_data(run=run)["workspace"]["OutputWorkspace"].workspace
        running_total = algorithm_utils.run_Plus({
            "LHSWorkspace": running_total,
            "RHSWorkspace": ws,
            "AllowDifferentNumberSpectra": False}
        )
        # remove the single loaded filename
        model._loaded_data_store.remove_data(run=run)
    model._loaded_data_store.remove_data(run=run_list[0])
    return_ws["OutputWorkspace"] = MuonWorkspaceWrapper(running_total)
    model._loaded_data_store.add_data(run=flatten_run_list(run_list), workspace=return_ws,
                                      filename="Co-added")


def flatten_run_list(run_list):
    """
    run list might be [1,2,[3,4]] where the [3,4] are co-added
    """
    new_list = []
    for run_item in run_list:
        if isinstance(run_item, int):
            new_list += [run_item]
        elif isinstance(run_item, list):
            for run in run_item:
                new_list += [run]
    return new_list


def exception_message_for_failed_files(failed_file_list):
    return "Could not load the following files : \n - " + "\n - ".join(failed_file_list)