ChessAnalysisPipeline 0.0.14__py3-none-any.whl → 0.0.16__py3-none-any.whl

CHAP/utils/scanparsers.py

@@ -1,1431 +0,0 @@
-#!/usr/bin/env python3
-
-# -*- coding: utf-8 -*-
-
-# System modules
-from csv import reader
-from fnmatch import filter as fnmatch_filter
-from functools import cache
-from json import load
-import os
-import re
-
-# Third party modules
-import numpy as np
-from pyspec.file.spec import FileSpec
-from pyspec.file.tiff import TiffFile
-
-@cache
-def filespec(spec_file_name):
-    return FileSpec(spec_file_name)
-
-class ScanParser:
-    """Partial implementation of a class representing a SPEC scan and
-    some of its metadata.
-
-    :param spec_file_name: path to a SPEC file on the CLASSE DAQ
-    :type spec_file_name: str
-    :param scan_number: the number of a scan in the SPEC file provided
-        with `spec_file_name`
-    :type scan_number: int
-    """
-
-    def __init__(self,
-                 spec_file_name:str,
-                 scan_number:int):
-        """Constructor method"""
-
-        self.spec_file_name = spec_file_name
-        self.scan_number = scan_number
-
-        self._scan_path = None
-        self._scan_name = None
-        self._scan_title = None
-
-        self._spec_scan = None
-        self._spec_command = None
-        self._spec_macro = None
-        self._spec_args = None
-        self._spec_scan_npts = None
-        self._spec_scan_data = None
-        self._spec_positioner_values = None
-
-        self._detector_data_path = None
-
-        if isinstance(self, FMBRotationScanParser) and scan_number > 1:
-            scanparser = FMBRotationScanParser(spec_file_name, scan_number-1)
-            if (scanparser.spec_macro in ('rams4_step_ome', 'rams4_fly_ome')
-                    and len(scanparser.spec_args) == 5):
-                self._rams4_args = scanparser.spec_args
-
-        return (f'{self.__class__.__name__}'
-                f'({self.spec_file_name}, {self.scan_number}) '
-                f'-- {self.spec_command}')
-
-    @property
-    def spec_file(self):
-        # NB This FileSpec instance is not stored as a private
-        # attribute because it cannot be pickled (and therefore could
-        # cause problems for parallel code that uses ScanParsers).
-        return filespec(self.spec_file_name)
-
-    @property
-    def scan_path(self):
-        if self._scan_path is None:
-            self._scan_path = self.get_scan_path()
-        return self._scan_path
-
-    @property
-    def scan_name(self):
-        if self._scan_name is None:
-            self._scan_name = self.get_scan_name()
-        return self._scan_name
-
-    @property
-    def scan_title(self):
-        if self._scan_title is None:
-            self._scan_title = self.get_scan_title()
-        return self._scan_title
-
-    @property
-    def spec_scan(self):
-        if self._spec_scan is None:
-            self._spec_scan = self.get_spec_scan()
-        return self._spec_scan
-
-    @property
-    def spec_command(self):
-        if self._spec_command is None:
-            self._spec_command = self.get_spec_command()
-        return self._spec_command
-
-    @property
-    def spec_macro(self):
-        if self._spec_macro is None:
-            self._spec_macro = self.get_spec_macro()
-        return self._spec_macro
-
-    @property
-    def spec_args(self):
-        if self._spec_args is None:
-            self._spec_args = self.get_spec_args()
-        return self._spec_args
-
-    @property
-    def spec_scan_npts(self):
-        if self._spec_scan_npts is None:
-            self._spec_scan_npts = self.get_spec_scan_npts()
-        return self._spec_scan_npts
-
-    @property
-    def spec_scan_data(self):
-        if self._spec_scan_data is None:
-            self._spec_scan_data = self.get_spec_scan_data()
-        return self._spec_scan_data
-
-    @property
-    def spec_positioner_values(self):
-        if self._spec_positioner_values is None:
-            self._spec_positioner_values = self.get_spec_positioner_values()
-        return self._spec_positioner_values
-
-    @property
-    def detector_data_path(self):
-        if self._detector_data_path is None:
-            self._detector_data_path = self.get_detector_data_path()
-        return self._detector_data_path
-
-    def get_scan_path(self):
-        """Return the name of the directory containining the SPEC file
-        for this scan.
-
-        :rtype: str
-        """
-        return os.path.dirname(self.spec_file_name)
-
-    def get_scan_name(self):
-        """Return the name of this SPEC scan (not unique to scans
-        within a single spec file).
-
-        :rtype: str
-        """
-        raise NotImplementedError
-
-    def get_scan_title(self):
-        """Return the title of this spec scan (unique to each scan
-        within a spec file).
-
-        :rtype: str
-        """
-        raise NotImplementedError
-
-    def get_spec_scan(self):
-        """Return the `pyspec.file.spec.Scan` object parsed from the
-        spec file and scan number provided to the constructor.
-
-        :rtype: pyspec.file.spec.Scan
-        """
-        return self.spec_file.getScanByNumber(self.scan_number)
-
-    def get_spec_command(self):
-        """Return the string command of this SPEC scan.
-
-        :rtype: str
-        """
-        return self.spec_scan.command
-
-    def get_spec_macro(self):
-        """Return the macro used in this scan's SPEC command.
-
-        :rtype: str
-        """
-        return self.spec_command.split()[0]
-
-    def get_spec_args(self):
-        """Return a list of the arguments provided to the macro for
-        this SPEC scan.
-
-        :rtype: list[str]
-        """
-        return self.spec_command.split()[1:]
-
-    def get_spec_scan_npts(self):
-        """Return the number of points collected in this SPEC scan
-
-        :rtype: int
-        """
-        raise NotImplementedError
-
-    def get_spec_scan_data(self):
-        """Return a dictionary of all the counter data collected by
-        this SPEC scan.
-
-        :rtype: dict[str, numpy.ndarray]
-        """
-        return dict(zip(self.spec_scan.labels, self.spec_scan.data.T))
-
-    def get_spec_positioner_values(self):
-        """Return a dictionary of all the SPEC positioner values
-        recorded by SPEC just before the scan began.
-
-        :rtype: dict[str,str]
-        """
-        positioner_values = dict(self.spec_scan.motor_positions)
-        names = list(positioner_values.keys())
-        mnemonics = self.spec_scan.motors
-        if mnemonics is not None:
-            for name,mnemonic in zip(names,mnemonics):
-                if name != mnemonic:
-                    positioner_values[mnemonic] = positioner_values[name]
-        return positioner_values
-
-    def get_detector_data_path(self):
-        """Return the name of the directory containing detector data
-        collected by this scan.
-
-        :rtype: str
-        """
-        raise NotImplementedError
-
-    def get_detector_data_file(self, detector_prefix, scan_step_index:int):
-        """Return the name of the file containing detector data
-        collected at a certain step of this scan.
-
-        :param detector_prefix: the prefix used in filenames for the
-            detector
-        :type detector_prefix: str
-        :param scan_step_index: the index of the point in this scan
-            whose detector file name should be returned.
-        :type scan_step_index: int
-        :rtype: str
-        """
-        raise NotImplementedError
-
-    def get_detector_data(self, detector_prefix, scan_step_index:int):
-        """Return the detector data collected at a certain step of
-        this scan.
-
-        :param detector_prefix: the prefix used in filenames for the
-            detector
-        :type detector_prefix: str
-        :param scan_step_index: the index of the point in this scan
-            whose detector data should be returned.
-        :type scan_step_index: int
-        :rtype: numpy.ndarray
-        """
-        raise NotImplementedError
-
-    def get_spec_positioner_value(self, positioner_name):
-        """Return the value of a spec positioner recorded before this
-        scan began.
-
-        :param positioner_name: the name or mnemonic of a SPEC motor
-            whose position should be returned.
-        :raises KeyError: if `positioner_name` is not the name or
-            mnemonic of a SPEC motor recorded for this scan.
-        :raises ValueError: if the recorded string value of the
-            positioner in the SPEC file cannot be converted to a
-            float.
-        :rtype: float
-        """
-        try:
-            positioner_value = self.spec_positioner_values[positioner_name]
-            positioner_value = float(positioner_value)
-        except KeyError:
-            raise KeyError(f'{self.scan_title}: motor {positioner_name} '
-                           'not found for this scan')
-        except ValueError:
-            raise ValueError(f'{self.scan_title}: could not convert value of'
-                             f' {positioner_name} to float: '
-                             f'{positioner_value}')
-        return positioner_value
-
-
-class FMBScanParser(ScanParser):
-    """Partial implementation of a class representing a SPEC scan
-    collected at FMB.
-    """
-
-    def get_scan_name(self):
-        return os.path.basename(self.spec_file.abspath)
-
-    def get_scan_title(self):
-        return f'{self.scan_name}_{self.scan_number:03d}'
-
-
-class SMBScanParser(ScanParser):
-    """Partial implementation of a class representing a SPEC scan
-    collected at SMB or FAST.
-    """
-
-    def __init__(self, spec_file_name, scan_number):
-        super().__init__(spec_file_name, scan_number)
-
-        self._pars = None
-        self._par_file_pattern = f'*-*-{self.scan_name}'
-
-    def get_scan_name(self):
-        return os.path.basename(self.scan_path)
-
-    def get_scan_title(self):
-        return f'{self.scan_name}_{self.scan_number}'
-
-    @property
-    def pars(self):
-        if self._pars is None:
-            self._pars = self.get_pars()
-        return self._pars
-
-    def get_pars(self):
-        """Return a dictionary of values recorded in the .par file
-        associated with this SPEC scan.
-
-        :rtype: dict[str,object]
-        """
-        # JSON file holds titles for columns in the par file
-        json_files = fnmatch_filter(
-            os.listdir(self.scan_path),
-            f'{self._par_file_pattern}.json')
-        if not json_files:
-            json_files = fnmatch_filter(
-                os.listdir(self.scan_path),
-                f'*.json')
-        if len(json_files) != 1:
-            raise RuntimeError(f'{self.scan_title}: cannot find the '
-                               '.json file to decode the .par file')
-        with open(os.path.join(self.scan_path, json_files[0])) as json_file:
-            par_file_cols = load(json_file)
-        try:
-            par_col_names = list(par_file_cols.values())
-            scann_val_idx = par_col_names.index('SCAN_N')
-            scann_col_idx = int(list(par_file_cols.keys())[scann_val_idx])
-        except:
-            raise RuntimeError(f'{self.scan_title}: cannot find scan pars '
-                               'without a "SCAN_N" column in the par file')
-
-        if hasattr(self, '_par_file'):
-            par_file = self._par_file
-        else:
-            par_files = fnmatch_filter(
-                os.listdir(self.scan_path),
-                f'{self._par_file_pattern}.par')
-            if len(par_files) != 1:
-                raise RuntimeError(f'{self.scan_title}: cannot find the .par '
-                                   'file for this scan directory')
-            par_file = os.path.join(self.scan_path, par_files[0])
-        par_dict = None
-        with open(par_file) as f:
-            par_reader = reader(f, delimiter=' ')
-            for row in par_reader:
-                if len(row) == len(par_col_names):
-                    row_scann = int(row[scann_col_idx])
-                    if row_scann == self.scan_number:
-                        par_dict = {}
-                        for par_col_idx,par_col_name in par_file_cols.items():
-                            # Convert the string par value from the
-                            # file to an int or float, if possible.
-                            par_value = row[int(par_col_idx)]
-                            try:
-                                par_value = int(par_value)
-                            except ValueError:
-                                try:
-                                    par_value = float(par_value)
-                                except:
-                                    pass
-                            par_dict[par_col_name] = par_value
-
-        if par_dict is None:
-            raise RuntimeError(f'{self.scan_title}: could not find scan pars '
-                               f'for scan number {self.scan_number}')
-        return par_dict
-
-    def get_counter_gain(self, counter_name):
-        """Return the gain of a counter as recorded in the comments of
-        a scan in a SPEC file converted to nA/V.
-
-        :param counter_name: the name of the counter
-        :type counter_name: str
-        :rtype: str
-        """
-        counter_gain = None
-        for comment in self.spec_scan.comments:
-            match = re.search(
-                f'{counter_name} gain: '  # start of counter gain comments
-                '(?P<gain_value>\d+) '  # gain numerical value
-                '(?P<unit_prefix>[m|u|n])A/V',  # gain units
-                comment)
-            if match:
-                unit_prefix = match['unit_prefix']
-                gain_scalar = 1 if unit_prefix == 'n' \
-                    else 1e3 if unit_prefix == 'u' else 1e6
-                counter_gain = f'{float(match["gain_value"])*gain_scalar} nA/V'
-
-        if counter_gain is None:
-            raise RuntimeError(f'{self.scan_title}: could not get gain for '
-                               f'counter {counter_name}')
-        return counter_gain
-
-
-class LinearScanParser(ScanParser):
-    """Partial implementation of a class representing a typical line
-    or mesh scan in SPEC.
-    """
-    def __init__(self, spec_file_name, scan_number):
-        super().__init__(spec_file_name, scan_number)
-
-        self._spec_scan_motor_mnes = None
-        self._spec_scan_motor_vals = None
-        self._spec_scan_shape = None
-        self._spec_scan_dwell = None
-
-    @property
-    def spec_scan_motor_mnes(self):
-        if self._spec_scan_motor_mnes is None:
-            self._spec_scan_motor_mnes = self.get_spec_scan_motor_mnes()
-        return self._spec_scan_motor_mnes
-
-    @property
-    def spec_scan_motor_vals(self):
-        if self._spec_scan_motor_vals is None:
-            self._spec_scan_motor_vals = self.get_spec_scan_motor_vals()
-        return self._spec_scan_motor_vals
-
-    @property
-    def spec_scan_shape(self):
-        if self._spec_scan_shape is None:
-            self._spec_scan_shape = self.get_spec_scan_shape()
-        return self._spec_scan_shape
-
-    @property
-    def spec_scan_dwell(self):
-        if self._spec_scan_dwell is None:
-            self._spec_scan_dwell = self.get_spec_scan_dwell()
-        return self._spec_scan_dwell
-
-    def get_spec_scan_motor_mnes(self):
-        """Return the mnemonics of the SPEC motor(s) provided to the
-        macro for this scan. If there is more than one motor scanned
-        (in a "flymesh" scan, for example), the order of motors in the
-        returned tuple will go from the fastest moving motor first to
-        the slowest moving motor last.
-
-        :rtype: tuple
-        """
-        raise NotImplementedError
-
-    def get_spec_scan_motor_vals(self):
-        """Return the values visited by each of the scanned motors. If
-        there is more than one motor scanned (in a "flymesh" scan, for
-        example), the order of motor values in the returned tuple will
-        go from the fastest moving motor's values first to the slowest
-        moving motor's values last.
-
-        :rtype: tuple
-        """
-        raise NotImplementedError
-
-    def get_spec_scan_shape(self):
-        """Return the number of points visited by each of the scanned
-        motors. If there is more than one motor scanned (in a
-        "flymesh" scan, for example), the order of number of motor
-        values in the returned tuple will go from the number of points
-        visited by the fastest moving motor first to the the number of
-        points visited by the slowest moving motor last.
-
-        :rtype: tuple
-        """
-        raise NotImplementedError
-
-    def get_spec_scan_dwell(self):
-        """Return the dwell time for each point in the scan as it
-        appears in the command string.
-
-        :rtype: float
-        """
-        raise NotImplementedError
-
-    def get_spec_scan_npts(self):
-        """Return the number of points collected in this SPEC scan.
-
-        :rtype: int
-        """
-        return np.prod(self.spec_scan_shape)
-
-    def get_scan_step(self, scan_step_index:int):
-        """Return the index of each motor coordinate corresponding to
-        the index of a single point in the scan. If there is more than
-        one motor scanned (in a "flymesh" scan, for example), the
-        order of indices in the returned tuple will go from the index
-        of the value of the fastest moving motor first to the index of
-        the value of the slowest moving motor last.
-
-        :param scan_step_index: the index of a single point in the
-            scan.
-        :type scan_step_index: int
-        :rtype: tuple
-        """
-        scan_steps = np.ndindex(self.spec_scan_shape[::-1])
-        i = 0
-        while i <= scan_step_index:
-            scan_step = next(scan_steps)
-            i += 1
-        return scan_step
-
-    def get_scan_step_index(self, scan_step:tuple):
-        """Return the index of a single scan point corresponding to a
-        tuple of indices for each scanned motor coordinate.
-
-        :param scan_step: a tuple of the indices of each scanned motor
-            coordinate. If there is more than one motor scanned (in a
-            "flymesh" scan, for example), the order of indices should
-            go from the index of the value of the fastest moving motor
-            first to the index of the value of the slowest moving
-            motor last.
-        :type scan_step: tuple
-        :trype: int
-        """
-        scan_steps = np.ndindex(self.spec_scan_shape[::-1])
-        scan_step_found = False
-        scan_step_index = -1
-        while not scan_step_found:
-            next_scan_step = next(scan_steps)
-            scan_step_index += 1
-            if next_scan_step == scan_step:
-                scan_step_found = True
-                break
-        return scan_step_index
-
-
-class FMBLinearScanParser(LinearScanParser, FMBScanParser):
-    """Partial implementation of a class representing a typical line
-    or mesh scan in SPEC collected at FMB.
-    """
-
-    def get_spec_scan_motor_mnes(self):
-        if self.spec_macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
-            m1_mne = self.spec_args[0]
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                m2_mne_i = 4
-            else:
-                m2_mne_i = 5
-            m2_mne = self.spec_args[m2_mne_i]
-            return (m1_mne, m2_mne)
-        if self.spec_macro in ('flyscan', 'ascan'):
-            return (self.spec_args[0],)
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return ('Time',)
-        raise RuntimeError(f'{self.scan_title}: cannot determine scan motors '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_spec_scan_motor_vals(self):
-        if self.spec_macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
-            m1_start = float(self.spec_args[1])
-            m1_end = float(self.spec_args[2])
-            m1_npt = int(self.spec_args[3]) + 1
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                m2_start_i = 5
-                m2_end_i = 6
-                m2_nint_i = 7
-            else:
-                m2_start_i = 6
-                m2_end_i = 7
-                m2_nint_i = 8
-            m2_start = float(self.spec_args[m2_start_i])
-            m2_end = float(self.spec_args[m2_end_i])
-            m2_npt = int(self.spec_args[m2_nint_i]) + 1
-            fast_mot_vals = np.linspace(m1_start, m1_end, m1_npt)
-            slow_mot_vals = np.linspace(m2_start, m2_end, m2_npt)
-            return (fast_mot_vals, slow_mot_vals)
-        if self.spec_macro in ('flyscan', 'ascan'):
-            mot_vals = np.linspace(float(self.spec_args[1]),
-                                   float(self.spec_args[2]),
-                                   int(self.spec_args[3])+1)
-            return (mot_vals,)
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return self.spec_scan.data[:,0]
-        raise RuntimeError(f'{self.scan_title}: cannot determine scan motors '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_spec_scan_shape(self):
-        if self.spec_macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
-            fast_mot_npts = int(self.spec_args[3]) + 1
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                m2_nint_i = 7
-            else:
-                m2_nint_i = 8
-            slow_mot_npts = int(self.spec_args[m2_nint_i]) + 1
-            return (fast_mot_npts, slow_mot_npts)
-        if self.spec_macro in ('flyscan', 'ascan'):
-            mot_npts = int(self.spec_args[3])+1
-            return (mot_npts,)
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return len(np.array(self.spec_scan.data[:,0]))
-        raise RuntimeError(f'{self.scan_title}: cannot determine scan shape '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_spec_scan_dwell(self):
-        if self.macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                dwell = float(self.spec_args[8])
-            return dwell
-        if self.spec_macro in ('flyscan', 'ascan'):
-            return float(self.spec_args[4])
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return float(self.spec_args[1])
-        raise RuntimeError(f'{self.scan_title}: cannot determine dwell for '
-                           f'scans of type {self.spec_macro}')
-
-    def get_detector_data_path(self):
-        return os.path.join(self.scan_path, self.scan_title)
-
-
-
-@cache
-def list_fmb_saxswaxs_detector_files(detector_data_path, detector_prefix):
-    """Return a sorted list of all data files for the given detector
-    in the given directory. This function is cached to improve
-    performace for carrying our full FAMB SAXS/WAXS data-processing
-    workflows.
-
-    :param detector_data_path: directory in which to look for detector
-        data files
-    :type detector_data_path: str
-    :param detector_prefix: detector name to list files for
-    :type detector_prefix: str
-    :return: list of detector filenames
-    :rtype: list[str]
-    """
-    return sorted(
-        [f for f in os.listdir(detector_data_path)
-        if detector_prefix in f
-        and not f.endswith('.log')])
-
-class FMBSAXSWAXSScanParser(FMBLinearScanParser):
-    """Concrete implementation of a class representing a scan taken
-    with the typical SAXS/WAXS setup at FMB.
-    """
-
-    def get_scan_title(self):
-        return f'{self.scan_name}_{self.scan_number:03d}'
-
-    def get_detector_data_file(self, detector_prefix, scan_step_index:int):
-        detector_files = list_fmb_saxswaxs_detector_files(
-            self.detector_data_path, detector_prefix)
-        return os.path.join(
-            self.detector_data_path, detector_files[scan_step_index])
-
-    def get_detector_data(self, detector_prefix, scan_step_index:int):
-        image_file = self.get_detector_data_file(detector_prefix,
-                                                 scan_step_index)
-        with TiffFile(image_file) as tiff_file:
-            image_data = tiff_file.asarray()
-        return image_data
-
-
-class FMBXRFScanParser(FMBLinearScanParser):
-    """Concrete implementation of a class representing a scan taken
-    with the typical XRF setup at FMB.
-    """
-
-    def get_scan_title(self):
-        return f'{self.scan_name}_scan{self.scan_number}'
-
-    def get_detector_data_file(self, detector_prefix, scan_step_index:int):
-        scan_step = self.get_scan_step(scan_step_index)
-        file_name = f'scan{self.scan_number}_{scan_step[0]:03d}.hdf5'
-        file_name_full = os.path.join(self.detector_data_path, file_name)
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        raise RuntimeError(f'{self.scan_title}: could not find detector image '
-                           f'file for detector {detector_prefix} scan step '
-                           f'({scan_step_index})')
-
-    def get_detector_data(self, detector_prefix, scan_step_index:int):
-        # Third party modules
-        from h5py import File
-
-        detector_file = self.get_detector_data_file(
-            detector_prefix, scan_step_index)
-        scan_step = self.get_scan_step(scan_step_index)
-        with File(detector_file) as h5_file:
-            detector_data = \
-                h5_file['/entry/instrument/detector/data'][scan_step[0]]
-        return detector_data
-
-
-class SMBLinearScanParser(LinearScanParser, SMBScanParser):
-    """Concrete implementation of a class representing a scan taken
-    with the typical powder diffraction setup at SMB.
-    """
-
-    def get_spec_scan_dwell(self):
-        if self.spec_macro in ('flymesh', 'mesh'):
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                dwell = float(self.spec_args[8])
-            return dwell
-        if self.spec_macro in ('flyscan', 'ascan'):
-            return float(self.spec_args[4])
-        if self.spec_macro == 'tseries':
-            return float(self.spec_args[1])
-        if self.spec_macro == 'wbslew_scan':
-            return float(self.spec_args[3])
-        raise RuntimeError(f'{self.scan_title}: cannot determine dwell time '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_spec_scan_motor_mnes(self):
-        if self.spec_macro in ('flymesh', 'mesh'):
-            m1_mne = self.spec_args[0]
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                m2_mne_i = 4
-            else:
-                m2_mne_i = 5
-            m2_mne = self.spec_args[m2_mne_i]
-            return (m1_mne, m2_mne)
-        if self.spec_macro in ('flyscan', 'ascan'):
-            return (self.spec_args[0],)
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return ('Time',)
-        raise RuntimeError(f'{self.scan_title}: cannot determine scan motors '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_spec_scan_motor_vals(self):
-        if self.spec_macro in ('flymesh', 'mesh'):
-            m1_start = float(self.spec_args[1])
-            m1_end = float(self.spec_args[2])
-            m1_npt = int(self.spec_args[3]) + 1
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                m2_start_i = 5
-                m2_end_i = 6
-                m2_nint_i = 7
-            else:
-                m2_start_i = 6
-                m2_end_i = 7
-                m2_nint_i = 8
-            m2_start = float(self.spec_args[m2_start_i])
-            m2_end = float(self.spec_args[m2_end_i])
-            m2_npt = int(self.spec_args[m2_nint_i]) + 1
-            fast_mot_vals = np.linspace(m1_start, m1_end, m1_npt)
-            slow_mot_vals = np.linspace(m2_start, m2_end, m2_npt)
-            return (fast_mot_vals, slow_mot_vals)
-        if self.spec_macro in ('flyscan', 'ascan'):
-            mot_vals = np.linspace(float(self.spec_args[1]),
-                                   float(self.spec_args[2]),
-                                   int(self.spec_args[3])+1)
-            return (mot_vals,)
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return (self.spec_scan.data[:,0],)
-        raise RuntimeError(f'{self.scan_title}: cannot determine scan motors '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_spec_scan_shape(self):
-        if self.spec_macro in ('flymesh', 'mesh'):
-            fast_mot_npts = int(self.spec_args[3]) + 1
-            try:
-                # Try post-summer-2022 format
-                dwell = float(self.spec_args[4])
-            except:
-                # Accommodate pre-summer-2022 format
-                m2_nint_i = 7
-            else:
-                m2_nint_i = 8
-            slow_mot_npts = int(self.spec_args[m2_nint_i]) + 1
-            return (fast_mot_npts, slow_mot_npts)
-        if self.spec_macro in ('flyscan', 'ascan'):
-            mot_npts = int(self.spec_args[3])+1
-            return (mot_npts,)
-        if self.spec_macro in ('tseries', 'loopscan'):
-            return (len(np.array(self.spec_scan.data[:,0])),)
-        raise RuntimeError(f'{self.scan_title}: cannot determine scan shape '
-                           f'for scans of type {self.spec_macro}')
-
-    def get_detector_data_path(self):
-        return os.path.join(self.scan_path, str(self.scan_number))
-
-    def get_detector_data_file(self, detector_prefix, scan_step_index:int):
-        scan_step = self.get_scan_step(scan_step_index)
-        if len(scan_step) == 1:
-            scan_step = (0, *scan_step)
-        file_name_pattern = (f'{detector_prefix}_'
-                             f'{self.scan_name}_*_'
-                             f'{scan_step[0]}_data_'
-                             f'{(scan_step[1]+1):06d}.h5')
-        file_name_matches = fnmatch_filter(
-            os.listdir(self.detector_data_path),
-            file_name_pattern)
-        if len(file_name_matches) == 1:
-            return os.path.join(self.detector_data_path, file_name_matches[0])
-        raise RuntimeError(f'{self.scan_title}: could not find detector image '
-                           f'file for detector {detector_prefix} scan step '
-                           f'({scan_step_index})')
-
-    def get_detector_data(self, detector_prefix, scan_step_index:int):
-        # Third party modules
-        from h5py import File
-
-        image_file = self.get_detector_data_file(
-            detector_prefix, scan_step_index)
-        with File(image_file) as h5_file:
-            image_data = h5_file['/entry/data/data'][0]
-        return image_data
-
-
-class RotationScanParser(ScanParser):
-    """Partial implementation of a class representing a rotation
-    scan.
-    """
-
-    def __init__(self, spec_file_name, scan_number):
-        super().__init__(spec_file_name, scan_number)
-        self._starting_image_index = None
-        self._starting_image_offset = None
-
-    @property
-    def starting_image_index(self):
-        if self._starting_image_index is None:
-            self._starting_image_index = self.get_starting_image_index()
-        return self._starting_image_index
-
-    @property
-    def starting_image_offset(self):
-        if self._starting_image_offset is None:
-            self._starting_image_offset = self.get_starting_image_offset()
-        return self._starting_image_offset
-
-    def get_starting_image_index(self):
-        """Return the first frame of the detector data collected by
-        this scan from the index of the first frame of detector data
-        collected by this scan.
-
-        :rtype: int
-        """
-        raise NotImplementedError
-
-    def get_starting_image_offset(self):
-        """Return the offset of the index of the first "good" frame of
-        detector data collected by this scan from the index of the
-        first frame of detector data collected by this scan.
-
-        :rtype: int
-        """
-        raise NotImplementedError
-
-
-class FMBRotationScanParser(RotationScanParser, FMBScanParser):
-    """Concrete implementation of a class representing a scan taken
-    with the typical tomography setup at FMB.
-    """
-
-    def get_spec_scan_data(self):
-        spec_scan_data = super().get_spec_scan_data()
-        if hasattr(self, '_rams4_args'):
-            spec_scan_data['theta'] = np.linspace(
-                float(self._rams4_args[0]), float(self._rams4_args[1]),
-                1+int(self._rams4_args[2]))
-        return spec_scan_data
-
-    def get_spec_scan_npts(self):
-        if hasattr(self, '_rams4_args'):
-            return 1+int(self._rams4_args[2])
-        if self.spec_macro == 'flyscan':
-            if len(self.spec_args) == 2:
-                return 1+int(self.spec_args[0])
-            if len(self.spec_args) == 5:
-                return 1+int(self.spec_args[3])
-            raise RuntimeError(f'{self.scan_title}: cannot obtain number of '
-                               f'points from {self.spec_macro} with arguments '
-                               f'{self.spec_args}')
-#        if self.spec_macro == 'ascan':
-#            if len(self.spec_args) == 5:
-#                return int(self.spec_args[3])
-#            raise RuntimeError(f'{self.scan_title}: cannot obtain number of '
-#                               f'points from {self.spec_macro} with arguments '
-#                               f'{self.spec_args}')
-        raise RuntimeError(f'{self.scan_title}: cannot determine rotation '
-                           f' angles for scans of type {self.spec_macro}')
-
-    def get_starting_image_index(self):
-        return 0
-
-    def get_starting_image_offset(self):
-        if hasattr(self, '_rams4_args'):
-            return int(self.spec_args[0]) - self.spec_scan_npts
-        if self.spec_macro == 'flyscan':
-            return 1
-        raise RuntimeError(f'{self.scan_title}: cannot determine starting '
-                           f'image offset for scans of type {self.spec_macro}')
-
-    def get_detector_data_path(self):
-        return self.scan_path
-
-    def get_detector_data_file(self, detector_prefix):
-        prefix = detector_prefix.upper()
-        file_name = f'{self.scan_name}_{prefix}_{self.scan_number:03d}.h5'
-        file_name_full = os.path.join(self.detector_data_path, file_name)
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        raise RuntimeError(f'{self.scan_title}: could not find detector image '
-                           f'file for detector {detector_prefix}')
-
-    def get_all_detector_data_in_file(
-            self, detector_prefix, scan_step_index=None):
-        # Third party modules
-        from h5py import File
-
-        detector_file = self.get_detector_data_file(detector_prefix)
-        with File(detector_file) as h5_file:
-            if scan_step_index is None:
-                detector_data = h5_file['/entry/instrument/detector/data'][
-                    self.starting_image_offset:]
-            elif isinstance(scan_step_index, int):
-                detector_data = h5_file['/entry/instrument/detector/data'][
-                    self.starting_image_offset+scan_step_index]
-            elif (isinstance(scan_step_index, (list, tuple))
-                    and len(scan_step_index) == 2):
-                detector_data = h5_file['/entry/instrument/detector/data'][
-                    self.starting_image_offset+scan_step_index[0]:
-                    self.starting_image_offset+scan_step_index[1]]
-            else:
-                raise ValueError('Invalid parameter scan_step_index '
-                                 f'({scan_step_index})')
-        return detector_data
-
-    def get_detector_data(self, detector_prefix, scan_step_index=None):
-        try:
-            # Detector files in h5 format
-            detector_data = self.get_all_detector_data_in_file(
-                detector_prefix, scan_step_index)
-        except:
-            # Detector files in tiff format
-            if scan_step_index is None:
-                detector_data = []
-                for index in range(self.spec_scan_npts):
-                    detector_data.append(
-                        self.get_detector_data(detector_prefix, index))
-                detector_data = np.asarray(detector_data)
-            elif isinstance(scan_step_index, int):
-                image_file = self._get_detector_tiff_file(
-                    detector_prefix, scan_step_index)
-                if image_file is None:
-                    detector_data = None
-                else:
-                    with TiffFile(image_file) as tiff_file:
-                        detector_data = tiff_file.asarray()
-            elif (isinstance(scan_step_index, (list, tuple))
-                    and len(scan_step_index) == 2):
-                detector_data = []
-                for index in range(scan_step_index[0], scan_step_index[1]):
-                    detector_data.append(
-                        self.get_detector_data(detector_prefix, index))
-                detector_data = np.asarray(detector_data)
-            else:
-                raise ValueError('Invalid parameter scan_step_index '
-                                 f'({scan_step_index})')
-        return detector_data
-
-    def _get_detector_tiff_file(self, detector_prefix, scan_step_index):
-        file_name_full = f'{self.spec_file_name}_{detector_prefix.upper()}_' \
-            f'{self.scan_number:03d}_' \
-            f'{self.starting_image_offset+scan_step_index:03d}.tiff'
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        return None
-#        raise RuntimeError(f'{self.scan_title}: could not find detector image '
-#                           f'file for scan step ({scan_step_index})')
-
-
-class SMBRotationScanParser(RotationScanParser, SMBScanParser):
-    """Concrete implementation of a class representing a scan taken
-    with the typical tomography setup at SMB.
-    """
-
-    def __init__(self, spec_file_name, scan_number, par_file=None):
-        self._scan_type = None
-        super().__init__(spec_file_name, scan_number)
-
-        self._katefix = 0  # RV remove when no longer needed
-        self._par_file_pattern = f'id*-*tomo*-{self.scan_name}'
-        if par_file is not None:
-            self._par_file = par_file
-
-    @property
-    def scan_type(self):
-        if self._scan_type is None:
-            self._scan_type = self.get_scan_type()
-        return self._scan_type
-
-    def get_spec_scan_data(self):
-        spec_scan_data = super().get_spec_scan_data()
-        spec_scan_data['theta'] = np.linspace(
-            float(self.pars['ome_start_real']),
-            float(self.pars['ome_end_real']), int(self.pars['nframes_real']))
-        return spec_scan_data
-
-    def get_spec_scan_npts(self):
-        return int(self.pars['nframes_real'])
-
-    def get_scan_type(self):
-        scan_type = self.pars.get(
-            'tomo_type', self.pars.get(
-            'tomotype', self.pars.get('scan_type', None)))
-        if scan_type is None:
-            raise RuntimeError(
-                f'{self.scan_title}: cannot determine the scan_type')
-        return scan_type
-
-    def get_starting_image_index(self):
-        try:
-            junkstart = int(self.pars['junkstart'])
-            #RV temp fix for error in par files at Kate's beamline
-            #Remove this and self._katefix when no longer needed
-            file_name = f'nf_{junkstart:06d}.tif'
-            file_name_full = os.path.join(self.detector_data_path, file_name)
-            if not os.path.isfile(file_name_full):
-                self._katefix = min([
-                    int(re.findall(r'\d+', f)[0])
-                        for f in os.listdir(self.detector_data_path)
-                        if re.match(r'nf_\d+\.tif', f)])
-            return junkstart
-            #return int(self.pars['junkstart'])
-        except:
-            raise RuntimeError(f'{self.scan_title}: cannot determine first '
-                               'detector image index')
-
-    def get_starting_image_offset(self):
-        try:
-            return (int(self.pars['goodstart'])-self.starting_image_index)
-        except:
-            raise RuntimeError(f'{self.scan_title}: cannot determine index '
-                               'offset of first good detector image')
-
-    def get_detector_data_path(self):
-        return os.path.join(self.scan_path, str(self.scan_number), 'nf')
-
-    def get_detector_data_file(self, scan_step_index:int):
-        index = self.starting_image_index + self.starting_image_offset \
-            + scan_step_index
-        file_name = f'nf_{index:06d}.tif'
-        file_name_full = os.path.join(self.detector_data_path, file_name)
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        #RV temp fix for error in par files at Kate's beamline
-        #Remove this and self._katefix when no longer needed
-        index += self._katefix
-        file_name = f'nf_{index:06d}.tif'
-        file_name_full = os.path.join(self.detector_data_path, file_name)
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        raise RuntimeError(f'{self.scan_title}: could not find detector image '
-                           f'file ({file_name_full}) for scan step '
-                           f'({scan_step_index})')
-
-    def get_detector_data(self, detector_prefix, scan_step_index=None):
-        if scan_step_index is None:
-            detector_data = []
-            for index in range(self.spec_scan_npts):
-                detector_data.append(
-                    self.get_detector_data(detector_prefix, index))
-            detector_data = np.asarray(detector_data)
-        elif isinstance(scan_step_index, int):
-            image_file = self.get_detector_data_file(scan_step_index)
-            with TiffFile(image_file) as tiff_file:
-                detector_data = tiff_file.asarray()
-        elif (isinstance(scan_step_index, (list, tuple))
-                and len(scan_step_index) == 2):
-            detector_data = []
-            for index in range(scan_step_index[0], scan_step_index[1]):
-                detector_data.append(
-                    self.get_detector_data(detector_prefix, index))
-            detector_data = np.asarray(detector_data)
-        else:
-            raise ValueError('Invalid parameter scan_step_index '
-                             f'({scan_step_index})')
-        return detector_data
-
-
-class MCAScanParser(ScanParser):
-    """Partial implementation of a class representing a scan taken
-    while collecting SPEC MCA data.
-    """
-
-    def __init__(self, spec_file_name, scan_number):
-        super().__init__(spec_file_name, scan_number)
-
-        self._detector_num_bins = None
-
-    def get_detector_num_bins(self, detector_prefix):
-        """Return the number of bins for the detector with the given
-        prefix.
-
-        :param detector_prefix: the detector prefix as used in SPEC
-            MCA data files
-        :type detector_prefix: str
-        :rtype: int
-        """
-        raise NotImplementedError
-
-
-class SMBMCAScanParser(MCAScanParser, SMBLinearScanParser):
-    """Concrete implementation of a class representing a scan taken
-    with the typical EDD setup at SMB or FAST.
-    """
-    detector_data_formats = ('spec', 'h5')
-    def __init__(self, spec_file_name, scan_number, detector_data_format=None):
-        """Constructor for SMBMCAScnaParser.
-
-        :param spec_file: Path to scan's SPEC file
-        :type spec_file: str
-        :param scan_number: Number of the SPEC scan
-        :type scan_number: int
-        :param detector_data_format: Format of the MCA data collected,
-            defaults to None
-        :type detector_data_format: Optional[Literal["spec", "h5"]]
-        """
-        super().__init__(spec_file_name, scan_number)
-
-        self.detector_data_format = None
-        if detector_data_format is None:
-            self.init_detector_data_format()
-        else:
-            if detector_data_format.lower() in self.detector_data_formats:
-                self.detector_data_format = detector_data_format.lower()
-            else:
-                raise ValueError(
-                    'Unrecognized value for detector_data_format: '
-                    + f'{detector_data_format}. Allowed values are: '
-                    + ', '.join(self.detector_data_formats))
-
-    def init_detector_data_format(self):
-        """Determine and set a value for the instance variable
-        `detector_data_format` based on the presence / absence of
-        detector data files of different formats conventionally
-        associated with this scan. Also set the corresponding
-        appropriate value for `_detector_data_path`.
-        """
-        try:
-            self._detector_data_path = self.scan_path
-            detector_file = self.get_detector_data_file_spec()
-        except OSError:
-            try:
-                self._detector_data_path = os.path.join(
-                    self.scan_path, str(self.scan_number), 'edd')
-                detector_file = self.get_detector_data_file_h5()
-            except OSError:
-                raise RuntimeError(
-                    f"{self.scan_title}: Can't determine detector data format")
-            else:
-                self.detector_data_format = 'h5'
-        else:
-            self.detector_data_format = 'spec'
-
-    def get_detector_data_path(self):
-        raise NotImplementedError
-
-    def get_detector_num_bins(self, element_index=0):
-        if self.detector_data_format == 'spec':
-            return self.get_detector_num_bins_spec()
-        elif self.detector_data_format == 'h5':
-            return self.get_detector_num_bins_h5(element_index)
-
-    def get_detector_num_bins_spec(self):
-        with open(self.get_detector_data_file_spec()) as detector_file:
-            lines = detector_file.readlines()
-        for line in lines:
-            if line.startswith('#@CHANN'):
-                try:
-                    line_prefix, number_saved, first_saved, last_saved, \
-                        reduction_coef = line.split()
-                    return int(number_saved)
-                except:
-                    continue
-        raise RuntimeError(f'{self.scan_title}: could not find num_bins')
-
-    def get_detector_num_bins_h5(self, element_index):
-        from h5py import File
-        detector_file = self.get_detector_data_file_h5()
-        with File(detector_file) as h5_file:
-            dset_shape = h5_file['/entry/data/data'].shape
-        return dset_shape[-1]
-
-    def get_detector_data_file(self, scan_step_index=0):
-        if self.detector_data_format == 'spec':
-            return self.get_detector_data_file_spec()
-        elif self.detector_data_format == 'h5':
-            return self.get_detector_data_file_h5(
-                scan_step_index=scan_step_index)
-
-    def get_detector_data_file_spec(self):
-        """Return the filename (full absolute path) to the file
-        containing spec-formatted MCA data for this scan.
-        """
-        file_name = f'spec.log.scan{self.scan_number}.mca1.mca'
-        file_name_full = os.path.join(self.detector_data_path, file_name)
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        raise OSError(
-            '{self.scan_title}: could not find detector image file'
-        )
-
-    def get_detector_data_file_h5(self, scan_step_index=0):
-        """Return the filename (full absolute path) to the file
-        containing h5-formatted MCA data for this scan.
-
-        :param scan_step_index:
-        """
-        scan_step = self.get_scan_step(scan_step_index)
-        if len(self.spec_scan_shape) == 1:
-            filename_index = 0
-        elif len(self.spec_scan_shape) == 2:
-            scan_step = self.get_scan_step(scan_step_index)
-            filename_index = scan_step[0]
-        else:
-            raise NotImplementedError(
-                'Cannot find detector file for scans with dimension > 2')
-        file_name = list_smb_mca_detector_files_h5(
-            self.detector_data_path)[filename_index]
-        file_name_full = os.path.join(self.detector_data_path, file_name)
-        if os.path.isfile(file_name_full):
-            return file_name_full
-        raise OSError(
-            '{self.scan_title}: could not find detector image file'
-        )
-
-
-    def get_all_detector_data(self, detector):
-        """Return a 2D array of all MCA spectra collected in this scan
-        by the detector element indicated with `detector`.
-
-        :param detector: For detector data collected in SPEC format,
-            this is the detector prefix as it appears in the spec MCA
-            data file. For detector data collected in H5 format, this
-            is the index of a particular detector element.
-        :type detector: Union[str, int]
-        :rtype: numpy.ndarray
-        """
-        if self.detector_data_format == 'spec':
-            return self.get_all_detector_data_spec(detector)
-        elif self.detector_data_format == 'h5':
-            try:
-                element_index = int(detector)
-            except:
-                raise TypeError(f'{detector} is not an integer element index')
-            return self.get_all_detector_data_h5(element_index)
-
-    def get_all_detector_data_spec(self, detector_prefix):
-        """Return a 2D array of all MCA spectra collected by a
-        detector in the spec MCA file format during the scan.
-
-        :param detector_prefix: Detector name at is appears in the
-            spec MCA file.
-        :type detector_prefix: str
-        :returns: 2D array of MCA spectra
-        :rtype: numpy.ndarray
-        """
-        # This should be easy with pyspec, but there are bugs in
-        # pyspec for MCA data.....  or is the 'bug' from a nonstandard
-        # implementation of some macro on our end?  According to spec
-        # manual and pyspec code, mca data should always begin w/ '@A'
-        # In example scans, it begins with '@{detector_prefix}'
-        # instead
-        data = []
-
-        with open(self.get_detector_data_file_spec()) as detector_file:
-            lines = [line.strip("\\\n") for line in detector_file.readlines()]
-
-        num_bins = self.get_detector_num_bins()
-
-        counter = 0
-        for line in lines:
-            a = line.split()
-
-            if len(a) > 0:
-                if a[0] == ("@"+detector_prefix):
-                    counter = 1
-                    spectrum = np.zeros(num_bins)
-            if counter == 1:
-                b = np.array(a[1:]).astype('uint16')
-                spectrum[(counter-1) * 25:((counter-1) * 25 + 25)] = b
-                counter = counter + 1
-            elif counter > 1 and counter <= (np.floor(num_bins / 25.)):
-                b = np.array(a).astype('uint16')
-                spectrum[(counter-1) * 25:((counter-1) * 25 + 25)] = b
-                counter = counter + 1
-            elif counter == (np.ceil(num_bins/25.)):
-                b = np.array(a).astype('uint16')
-                spectrum[(counter-1) * 25:
-                         ((counter-1) * 25 + (np.mod(num_bins, 25)))] = b
-                data.append(spectrum)
-                counter = 0
-
-        return np.array(data)
-
-    def get_all_detector_data_h5(self, element_index):
-        """Return a 2D array of all MCA spectra collected by a
-        detector in the h5 file format during the scan.
-
-        :param element_index: The index of a particualr MCA element to
-            return data for.
-        :type element_index: int
-        :returns: 2D array of MCA spectra
-        :rtype: numpy.ndarray
-        """
-        detector_data = np.empty(
-            (self.spec_scan_npts,
-             self.get_detector_num_bins_h5(element_index)))
-        detector_files = list_smb_mca_detector_files_h5(
-            self.detector_data_path)
-        for i, detector_file in enumerate(detector_files):
-            full_filename = os.path.join(
-                self.detector_data_path, detector_file)
-            element_data = get_all_mca_data_h5(
-                full_filename)[:,element_index,:]
-            i_0 = i * self.spec_scan_shape[0]
-            if len(self.spec_scan_shape) == 2:
-                i_f = i_0 + self.spec_scan_shape[1]
-            else:
-                i_f = self.spec_scan_npts
-            detector_data[i_0:i_f] = element_data
-        return detector_data
-
-    def get_detector_data(self, detector, scan_step_index:int):
-        """Return a single MCA spectrum for the detector indicated.
-
-        :param detector: If this scan collected MCA data in "spec"
-            format, this is the detector prefix as it appears in the
-            spec MCA data file. If this scan collected data in .h5
-            format, this is the index of the detector element of
-            interest.:type detector: typing.Union[str, int]
-        :param scan_step_index: Index of the scan step to return the
-            spectrum from.
-        :type scan_step_index: int
-        :returns: A single MCA spectrum
-        :rtype: numpy.ndarray
-        """
-        detector_data = self.get_all_detector_data(detector)
-        return detector_data[scan_step_index]
-
-@cache
-def list_smb_mca_detector_files_h5(detector_data_path):
-    """Return a sorted list of all *.hdf5 files in a directory
-
-    :param detector_data_path: Directory to return *.hdf5 files from
-    :type detector_data_path: str
-    :returns: Sorted list of detector data filenames
-    :rtype: list[str]
-    """
-    return sorted(
-        [f for f in os.listdir(detector_data_path) if f.endswith('.hdf5')])
-
-@cache
-def get_all_mca_data_h5(filename):
-    """Return all data from all elements from an MCA data file
-
-    :param filename: Name of the MCA h5 data file
-    :type filename: str
-    :returns: 3D array of MCA spectra where the first axis is scan
-        step, second index is detector element, third index is channel
-        energy.
-    :rtype: numpy.ndarray
-    """
-    import os
-
-    from h5py import File
-    import numpy as np
-
-    with File(filename) as h5_file:
-        data = h5_file['/entry/data/data'][:]
-
-    # Prior to 2023-12-12, there was an issue where the XPS23 detector
-    # was capturing one or two frames of all 0s at the start of the
-    # dataset in every hdf5 file. In both cases, there is only ONE
-    # extra frame of data relative to the number of frames that should
-    # be there (based on the number of points in the spec scan). If
-    # one frame of all 0s is present: skip it and deliver only the
-    # real data. If two frames of all 0s are present: detector data
-    # will be missing for the LAST step in the scan. Skip the first
-    # two frames of all 0s in the hdf5 dataset, then add a frame of
-    # fake data (all 0-s) to the end of that real data so that the
-    # number of detector data frames matches the number of points in
-    # the spec scan.
-    check_zeros_before = 1702357200
-    file_mtime = os.path.getmtime(filename)
-    if file_mtime <= check_zeros_before:
-        if not np.any(data[0]):
-            # If present, remove first frame of blank data
-            print('Warning: removing blank first frame of detector data')
-            data = data[1:]
-            if not np.any(data[0]):
-                # If present, shift second frame of blank data to the
-                # end
-                print('Warning: shifting second frame of blank detector data '
-                      + 'to the end of the scan')
-                data = np.concatenate((data[1:], np.asarray([data[0]])))
-
-    return data