cfel_crystfel.py

#    This file is part of cfelpyutils.
#
#    cfelpyutils is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    cfelpyutils is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with cfelpyutils.  If not, see <http://www.gnu.org/licenses/>.
"""
Utilities for interoperability with the CrystFEL software package.

This module contains reimplementation of Crystfel functions and utilities.
"""

from __future__ import (absolute_import, division, print_function,
                        unicode_literals)

import re
from collections import OrderedDict
from copy import deepcopy   
from math import sqrt


def _assplode_algebraic(value):
    items = [item for item in re.split('([+-])', value.strip()) if item != '']

    if items and items[0] not in ('+', '-'):
        items.insert(0, '+')

    return [''.join((items[x], items[x + 1])) for x in range(0, len(items), 2)]


def _dir_conv(direction_x, direction_y, direction_z, value):
    direction = [direction_x, direction_y, direction_z]

    items = _assplode_algebraic(value)

    if items:
        raise RuntimeError('Invalid direction: {}.'.format(value))

    for item in items:
        axis = item[-1]

        if axis != 'x' and axis != 'y' and axis != 'z':
            raise RuntimeError('Invalid Symbol: {} (must be x, y or z).'.format(axis))

        if item[:-1] == '+':
            value = '1.0'
        elif item[:-1] == '-':
            value = '-1.0'
        else:
            value = item[:-1]

        if axis == 'x':
            direction[0] = float(value)
        elif axis == 'y':
            direction[1] = float(value)
        elif axis == 'z':
            direction[2] = float(value)

    return direction


def _set_dim_structure_entry(key, value, panel):
    if panel['dim_structure'] is not None:
        dim = panel['dim_structure']
    else:
        dim = []

    dim_index = int(key[3])

    if dim_index > len(dim) - 1:
        for _ in range(len(dim), dim_index + 1):
            dim.append(None)

    if value == 'ss' or value == 'fs' or value == '%':
        dim[dim_index] = value
    elif value.isdigit():
        dim[dim_index] = int(value)
    else:
        raise RuntimeError('Invalid dim entry: {}.'.format(value))


def _parse_field_for_panel(key, value, panel):
    if key == 'min_fs':
        panel['origin_min_fs'] = int(value)
        panel['min_fs'] = int(value)

    elif key == 'max_fs':
        panel['origin_max_fs'] = int(value)
        panel['max_fs'] = int(value)

    elif key == 'min_ss':
        panel['origin_min_ss'] = int(value)
        panel['min_ss'] = int(value)

    elif key == 'max_ss':
        panel['origin_max_ss'] = int(value)
        panel['max_ss'] = int(value)

    elif key == 'corner_x':
        panel['cnx'] = float(value)

    elif key == 'corner_y':
        panel['cny'] = float(value)

    elif key == 'rail_direction':
        try:
            panel['rail_x'], panel['rail_y'], panel['rail_z'] = _dir_conv(panel['rail_x'],
                                                                          panel['rail_y'],
                                                                          panel['rail_z'],
                                                                          value)
        except RuntimeError as e:
            raise RuntimeError('Invalid rail direction. ', e)

    elif key == 'clen_for_centering':
        panel['clen_for_centering'] = float(value)

    elif key == 'adu_per_eV':
        panel['adu_per_eV'] = float(value)

    elif key == 'adu_per_photon':
        panel['adu_per_photon'] = float(value)

    elif key == 'rigid_group':
        panel['rigid_group'] = value

    elif key == 'clen':
        try:
            panel['clen'] = float(value)
            panel['clen_from'] = None
        except ValueError:
            panel['clen'] = -1
            panel['clen_from'] = value

    elif key == 'data':
        if not value.startswith('/'):
            raise RuntimeError('Invalid data location: {}'.format(value))
        panel['data'] = value

    elif key == 'mask':
        if not value.startswith('/'):
            raise RuntimeError('Invalid data location: {}'.format(value))
        panel['mask'] = value

    elif key == 'mask_file':
        panel['mask_file'] = value

    elif key == 'saturation_map':
        panel['saturation_map'] = value

    elif key == 'saturation_map_file':
        panel['saturation_map_file'] = value

    elif key == 'coffset':
        panel['coffset'] = float(value)

    elif key == 'res':
        panel['res'] = float(value)

    elif key == 'max_adu':
        panel['max_adu'] = value

    elif key == 'badrow_direction':
        if value == 'x':
            panel['badrow'] = 'f'
        elif value == 'y':
            panel['badrow'] = 's'
        elif value == 'f':
            panel['badrow'] = 'f'
        elif value == 's':
            panel['badrow'] = 's'
        elif value == '-':
            panel['badrow'] = '-'
        else:
            print('badrow_direction must be x, t, f, s, or \'-\'')
            print('Assuming \'-\'.')
            panel['badrow'] = '-'

    elif key == 'no_index':
        panel['no_index'] = bool(value)

    elif key == 'fs':
        try:
            panel['fsx'], panel['fsy'], panel['fsz'] = _dir_conv(panel['fsx'], panel['fsy'],
                                                                 panel['fsz'], value)

        except RuntimeError as e:
            raise RuntimeError('Invalid fast scan direction. ', e)

    elif key == 'ss':
        try:
            panel['ssx'], panel['ssy'], panel['ssz'] = _dir_conv(panel['ssx'], panel['ssy'],
                                                                 panel['ssz'], value)

        except RuntimeError as e:
            raise RuntimeError('Invalid slow scan direction. ', e)

    elif key.startswith('dim'):
        _set_dim_structure_entry(key, value, panel)

    else:
        raise RuntimeError('Unrecognised field: {}'.format(key))


def _parse_top_level(key, value, detector, beam, panel):
    if key == 'mask_bad':
        try:
            detector['mask_bad'] = int(value)
        except ValueError:
            detector['mask_bad'] = int(value, 16)

    elif key == 'mask_good':
        try:
            detector['mask_good'] = int(value)
        except ValueError:
            detector['mask_good'] = int(value, 16)

    elif key == 'coffset':
        panel['coffset'] = float(value)

    elif key == 'photon_energy':
        if value.startswith('/'):
            beam['photon_energy'] = 0.0
            beam['photon_energy_from'] = value
        else:
            beam['photon_energy'] = float(value)
            beam['photon_energy_from'] = None

    elif key == 'photon_energy_scale':
        beam['photon_energy_scale'] = float(value)

    elif key == 'peak_info_location':
        detector['peak_info_location'] = value

    elif key.startswith('rigid_group') and not key.startswith('rigid_group_collection'):
        detector['rigid_groups'][key[12:]] = value.split(',')

    elif key.startswith('rigid_group_collection'):
        detector['rigid_group_collections'][key[23:]] = value.split(',')

    else:
        _parse_field_for_panel(key, value, panel)


def _check_bad_fsss(bad_region, is_fsss):
    if bad_region['is_fsss'] == 99:
        bad_region['is_fsss'] = is_fsss
        return

    if is_fsss != bad_region['is_fsss']:
        raise RuntimeError("You can't mix x/y and fs/ss in a bad region")

    return


def _parse_field_bad(key, value, bad):
    if key == 'min_x':
        bad['min_x'] = float(value)
        _check_bad_fsss(bad, False)
    elif key == 'max_x':
        bad['max_x'] = float(value)
        _check_bad_fsss(bad, False)
    elif key == 'min_y':
        bad['min_y'] = float(value)
        _check_bad_fsss(bad, False)
    elif key == 'max_y':
        bad['max_y'] = float(value)
        _check_bad_fsss(bad, False)
    elif key == 'min_fs':
        bad['min_fs'] = int(value)
        _check_bad_fsss(bad, True)
    elif key == 'max_fs':
        bad['max_fs'] = int(value)
        _check_bad_fsss(bad, True)
    elif key == 'min_ss':
        bad['min_ss'] = int(value)
        _check_bad_fsss(bad, True)
    elif key == 'max_ss':
        bad['max_ss'] = int(value)
        _check_bad_fsss(bad, True)
    elif key == 'panel':
        bad['panel'] = value
    else:
        raise RuntimeError('Unrecognised field: {}'.format(key))

    return


def _check_point(name, panel, fs, ss, min_d, max_d, detector):
    xs = fs * panel['fsx'] + ss * panel['ssx']
    ys = fs * panel['fsy'] + ss * panel['ssy']

    rx = (xs + panel['cnx']) / panel['res']
    ry = (ys + panel['cny']) / panel['res']

    dist = sqrt(rx * rx + ry * ry)

    if dist > max_d:
        detector['furthest_out_panel'] = name
        detector['furthest_out_fs'] = fs
        detector['furthest_out_ss'] = ss
        max_d = dist
    elif dist < min_d:
        detector['furthest_in_panel'] = name
        detector['furthest_in_fs'] = fs
        detector['furthest_in_ss'] = ss
        min_d = dist

    return min_d, max_d


def _find_min_max_d(detector):
    min_d = float('inf')
    max_d = 0.0

    for name, panel in detector['panels'].items():
        min_d, max_d = _check_point(name, panel, 0, 0, min_d, max_d, detector)
        min_d, max_d = _check_point(name, panel, panel['w'], 0, min_d, max_d, detector)
        min_d, max_d = _check_point(name, panel, 0, panel['h'], min_d, max_d, detector)
        min_d, max_d = _check_point(name, panel, panel['w'], panel['h'], min_d, max_d, detector)


def load_crystfel_geometry(filename):
    """Loads a CrystFEL geometry file into a dictionary.

    Reimplements the get_detector_geometry_2 function from CrystFEL amost verbatim. Returns a dictionary with the
    geometry information. Entries in the geometry file appears as keys in the returned dictionary. For a full
    documentation on the CrystFEL geometry format, see:

    tfel/manual-crystfel_geometry.html

    Args:

        filename (str): filename of the geometry file

    Returns:

        detector (dict): dictionary with the geometry loaded from the file
    """

    fh = open(filename, 'r')

    beam = {
        'photon_energy': 0.0,
        'photon_energy_from': None,
        'photon_energy_scale': 1
    }

    detector = {
        'panels': OrderedDict(),
        'bad': OrderedDict(),
        'mask_good': 0,
        'mask_bad': 0,
        'rigid_groups': {},
        'rigid_group_collections': {}
    }

    default_panel = {
        'cnx': None,
        'cny': None,
        'clen': None,
        'coffset': 0.0,
        'res': -1.0,
        'badrow': '-',
        'no_index': False,
        'fsx': 1.0,
        'fsy': 0.0,
        'fsz': 0.0,
        'ssx': 0.0,
        'ssy': 1.0,
        'ssz': 0.0,
        'rail_x': None,
        'rail_y': None,
        'rail_z': None,
        'clen_for_centering': None,
        'adu_per_eV': None,
        'adu_per_photon': None,
        'max_adu': float('inf'),
        'mask': None,
        'mask_file': None,
        'satmap': None,
        'satmap_file': None,
        'data': None,
        'dim_structure': None,
        'name': ''
    }

    default_bad_region = {
        'min_x': None,
        'max_x': None,
        'min_y': None,
        'max_y': None,
        'min_fs': 0,
        'max_fs': 0,
        'min_ss': 0,
        'max_ss': 0,
        'is_fsss': 99,
        'name': ''
    }

    default_dim = ['ss', 'fs']

    fhlines = fh.readlines()

    for line in fhlines:

        if line.startswith(';'):
            continue

        line_without_comments = line.strip().split(';')[0]
        line_items = re.split('([ \t])', line_without_comments)
        line_items = [item for item in line_items if item not in ('', ' ', '\t')]

        if len(line_items) < 3:
            continue

        value = ''.join(line_items[2:])

        if line_items[1] != '=':
            continue

        path = re.split('(/)', line_items[0])
        path = [item for item in path if item not in '/']

        if len(path) < 2:
            _parse_top_level(line_items[0], value, detector, beam, default_panel)
            continue

        curr_bad = None
        curr_panel = None

        if path[0].startswith('bad'):

            if path[0] in detector['bad']:
                curr_bad = detector['bad'][path[0]]
            else:
                curr_bad = deepcopy(default_bad_region)
                detector['bad'][path[0]] = curr_bad

        else:

            if path[0] in detector['panels']:
                curr_panel = detector['panels'][path[0]]
            else:
                curr_panel = deepcopy(default_panel)
                detector['panels'][path[0]] = curr_panel

        if curr_panel is not None:
            _parse_field_for_panel(path[1], value, curr_panel)
        else:
            _parse_field_bad(path[1], value, curr_bad)

    if not detector['panels']:
        raise RuntimeError("No panel descriptions in geometry file.")

    num_placeholders_in_panels = None

    for panel in detector['panels'].values():

        if panel['dim_structure'] is not None:
            curr_num_placeholders = panel['dim_structure'].values().count('%')
        else:
            curr_num_placeholders = 0

        if num_placeholders_in_panels is None:
            num_placeholders_in_panels = curr_num_placeholders
        else:
            if curr_num_placeholders != num_placeholders_in_panels:
                raise RuntimeError('All panels\' data and mask entries must have the same number of placeholders.')

    num_placeholders_in_masks = None

    for panel in detector['panels'].values():

        if panel['mask'] is not None:
            curr_num_placeholders = panel['mask'].count('%')
        else:
            curr_num_placeholders = 0

        if num_placeholders_in_masks is None:
            num_placeholders_in_masks = curr_num_placeholders
        else:
            if curr_num_placeholders != num_placeholders_in_masks:
                raise RuntimeError('All panels\' data and mask entries must have the same number of placeholders.')

    if num_placeholders_in_masks > num_placeholders_in_panels:
        raise RuntimeError('Number of placeholders in mask cannot be larget than for data.')

    dim_length = None

    for panel in detector['panels'].values():

        if panel['dim_structure'] is None:
            panel['dim_structure'] = deepcopy(default_dim)

        found_ss = False
        found_fs = False
        found_placeholder = False

        for entry in panel['dim_structure']:
            if entry is None:
                raise RuntimeError('Not all dim entries are defined for all panels.')
            elif entry == 'ss':
                if found_ss is True:
                    raise RuntimeError('Only one slow scan dim coordinate is allowed.')
                else:
                    found_ss = True
            elif entry == 'fs':
                if found_fs is True:
                    raise RuntimeError('Only one fast scan dim coordinate is allowed.')
                else:
                    found_fs = True
            elif entry == '%':
                if found_placeholder is True:
                    raise RuntimeError('Only one placeholder dim coordinate is allowed.')
                else:
                    found_placeholder = True

        if dim_length is None:
            dim_length = len(panel['dim_structure'])
        elif dim_length != len(panel['dim_structure']):
            raise RuntimeError('Number of dim coordinates must be the same for all panels.')

        if dim_length == 1:
            raise RuntimeError('Number of dim coordinates must be at least two.')

    for panel in detector['panels'].values():

        if panel['origin_min_fs'] < 0:
            raise RuntimeError('Please specify the minimum fs coordinate for panel {}.'.format(panel['name']))

        if panel['origin_max_fs'] < 0:
            raise RuntimeError('Please specify the maximum fs coordinate for panel {}.'.format(panel['name']))

        if panel['origin_min_ss'] < 0:
            raise RuntimeError('Please specify the minimum ss coordinate for panel {}.'.format(panel['name']))

        if panel['origin_max_ss'] < 0:
            raise RuntimeError('Please specify the maximum ss coordinate for panel {}.'.format(panel['name']))

        if panel['cnx'] is None:
            raise RuntimeError('Please specify the corner X coordinate for panel {}.'.format(panel['name']))

        if panel['clen'] is None and panel['clen_from'] is None:
            raise RuntimeError('Please specify the camera length for panel {}.'.format(panel['name']))

        if panel['res'] < 0:
            raise RuntimeError('Please specify the resolution or panel {}.'.format(panel['name']))

        if panel['adu_per_eV'] is None and panel['adu_per_photon'] is None:
            raise RuntimeError('Please specify either adu_per_eV or adu_per_photon for '
                               'panel {}.'.format(panel['name']))

        if panel['clen_for_centering'] is None and panel['rail_x'] is not None:
            raise RuntimeError('You must specify clen_for_centering if you specify the rail direction '
                               '(panel {})'.format(panel['name']))

        if panel['rail_x'] is None:
            panel['rail_x'] = 0.0
            panel['rail_y'] = 0.0
            panel['rail_z'] = 1.0

        if panel['clen_for_centering'] is None:
            panel['clen_for_centering'] = 0.0

        panel['w'] = panel['origin_max_fs'] - panel['origin_min_fs'] + 1
        panel['h'] = panel['origin_max_ss'] - panel['origin_min_ss'] + 1

    for bad_region in detector['bad'].values():
        if bad_region['is_fsss'] == 99:
            raise RuntimeError('Please specify the coordinate ranges for bad region {}.'.format(bad_region['name']))

    for group in detector['rigid_groups']:
        for name in detector['rigid_groups'][group]:
            if name not in detector['panels']:
                raise RuntimeError('Cannot add panel to rigid_group. Panel not found: {}'.format(name))

    for group_collection in detector['rigid_group_collections']:
        for name in detector['rigid_group_collections'][group_collection]:
            if name not in detector['rigid_groups']:
                raise RuntimeError('Cannot add rigid_group to collection. Rigid group not found: {}'.format(name))

    for panel in detector['panels'].values():

        d = panel['fsx'] * panel['ssy'] - panel['ssx'] * panel['fsy']

        if d == 0.0:
            raise RuntimeError('Panel {} transformation is singluar.')

        panel['xfs'] = panel['ssy'] / d
        panel['yfs'] = panel['ssx'] / d
        panel['xss'] = panel['fsy'] / d
        panel['yss'] = panel['fsx'] / d

    _find_min_max_d(detector)
    fh.close()

    # The code of this function is synced with the code of the function
    # 'get_detector_geometry_2' in CrystFEL at commit 41a8fa9819010fe8ddeb66676fee717f5226c7b8

    return detector