diff --git a/crystfel_utils.py b/crystfel_utils.py
index 18de74221109bad11a896fb34fd966d190a742af..5825fc176d987fbc9efcb1b7944aaed90bf23266 100644
--- a/crystfel_utils.py
+++ b/crystfel_utils.py
@@ -32,42 +32,39 @@ import re
def _assplode_algebraic(value):
# Reimplementation of assplode_algegraic from
# libcrystfel/src/detector.c.
-
items = [
- item for item in re.split(
- pattern='([+-])', string=value.strip()
- ) if item != ''
+ item
+ for item in re.split(pattern='([+-])', string=value.strip())
+ if item != ''
]
if items and items[0] not in ('+', '-'):
items.insert(index=0, object='+')
return [
- ''.join(
- iterable=(items[x], items[x + 1])
- ) for x in range(start=0, stop=len(items), step=2)
+ ''.join((items[x], items[x + 1]))
+ for x in range(0, len(items), 2)
]
def _dir_conv(direction_x, direction_y, direction_z, value):
# Reimplementation of dir_conv from
# libcrystfel/src/detector.c.
-
direction = [
- direction_x, direction_y, direction_z
+ direction_x,
+ direction_y,
+ direction_z
]
items = _assplode_algebraic(value)
-
- if items:
- raise RuntimeError('Invalid direction: {}.'.format(value))
+ if not 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)
+ "Invalid Symbol: {} (must be x, y or z).".format(axis)
)
if item[:-1] == '+':
@@ -90,16 +87,14 @@ def _dir_conv(direction_x, direction_y, direction_z, value):
def _set_dim_structure_entry(key, value, panel):
# Reimplementation of set_dim_structure_entry from
# libcrystfel/src/events.c.
-
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(start=len(dim), stop=dim_index + 1):
+ for _ in range(len(dim), dim_index + 1):
dim.append(None)
if value == 'ss' or value == 'fs' or value == '%':
@@ -107,35 +102,28 @@ def _set_dim_structure_entry(key, value, panel):
elif value.isdigit():
dim[dim_index] = int(value)
else:
- raise RuntimeError('Invalid dim entry: {}.'.format(value))
+ raise RuntimeError("Invalid dim entry: {}.".format(value))
def _parse_field_for_panel(key, value, panel):
# Reimplementation of parse_field_for_panel from
# libcrystfel/src/detector.c.
-
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(
@@ -145,20 +133,16 @@ def _parse_field_for_panel(key, value, panel):
value=value
)
except RuntimeError as exc:
- raise RuntimeError('Invalid rail direction. ', exc)
+ raise RuntimeError("Invalid rail direction. ", exc)
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)
@@ -168,33 +152,27 @@ def _parse_field_for_panel(key, value, panel):
panel['clen_from'] = value
elif key == 'data':
- if not value.startswith('/'):
- raise RuntimeError('Invalid data location: {}'.format(value))
+ 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))
+ 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'
@@ -207,13 +185,12 @@ def _parse_field_for_panel(key, value, panel):
elif value == '-':
panel['badrow'] = '-'
else:
- print('badrow_direction must be x, t, f, s, or \'-\'')
- print('Assuming \'-\'.')
+ 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(
@@ -222,9 +199,8 @@ def _parse_field_for_panel(key, value, panel):
direction_z=panel['fsz'],
value=value
)
-
except RuntimeError as exc:
- raise RuntimeError('Invalid fast scan direction. ', exc)
+ raise RuntimeError("Invalid fast scan direction.", exc)
elif key == 'ss':
try:
@@ -234,25 +210,22 @@ def _parse_field_for_panel(key, value, panel):
direction_z=panel['ssz'],
value=value
)
-
except RuntimeError as exc:
- raise RuntimeError('Invalid slow scan direction. ', exc)
+ raise RuntimeError("Invalid slow scan direction.", exc)
- elif key.startswith('dim'):
+ elif key.startswith("dim"):
_set_dim_structure_entry(
key=key,
value=value,
panel=panel
)
-
else:
- raise RuntimeError('Unrecognised field: {}'.format(key))
+ raise RuntimeError("Unrecognised field: {}".format(key))
def _parse_toplevel(key, value, detector, beam, panel):
# Reimplementation of parse_toplevel from
# libcrystfel/src/detector.c.
-
if key == 'mask_bad':
try:
detector['mask_bad'] = int(value)
@@ -267,7 +240,6 @@ def _parse_toplevel(key, value, detector, beam, panel):
elif key == 'coffset':
panel['coffset'] = float(value)
-
elif key == 'photon_energy':
if value.startswith('/'):
beam['photon_energy'] = 0.0
@@ -278,19 +250,15 @@ def _parse_toplevel(key, value, detector, beam, panel):
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')
+ key.startswith("rigid_group") and not
+ key.startswith("rigid_group_collection")
):
detector['rigid_groups'][key[12:]] = value.split(',')
-
- elif key.startswith('rigid_group_collection'):
+ elif key.startswith("rigid_group_collection"):
detector['rigid_group_collections'][key[23:]] = value.split(',')
-
else:
_parse_field_for_panel(
key=key,
@@ -316,58 +284,54 @@ def _parse_field_bad(key, value, bad):
# Reimplementation of parse_field_bad from
# libcrystfel/src/detector.c.
if key == 'min_x':
- bad['min_x'] = float(x=value)
+ bad['min_x'] = float(value)
_check_bad_fsss(bad_region=bad, is_fsss=False)
elif key == 'max_x':
- bad['max_x'] = float(x=value)
+ bad['max_x'] = float(value)
_check_bad_fsss(bad_region=bad, is_fsss=False)
elif key == 'min_y':
- bad['min_y'] = float(x=value)
+ bad['min_y'] = float(value)
_check_bad_fsss(bad_region=bad, is_fsss=False)
elif key == 'max_y':
- bad['max_y'] = float(x=value)
+ bad['max_y'] = float(value)
_check_bad_fsss(bad_region=bad, is_fsss=False)
elif key == 'min_fs':
- bad['min_fs'] = int(x=value)
+ bad['min_fs'] = int(value)
_check_bad_fsss(bad_region=bad, is_fsss=True)
elif key == 'max_fs':
- bad['max_fs'] = int(x=value)
+ bad['max_fs'] = int(value)
_check_bad_fsss(bad_region=bad, is_fsss=True)
elif key == 'min_ss':
- bad['min_ss'] = int(x=value)
+ bad['min_ss'] = int(value)
_check_bad_fsss(bad_region=bad, is_fsss=True)
elif key == 'max_ss':
- bad['max_ss'] = int(x=value)
+ bad['max_ss'] = int(value)
_check_bad_fsss(bad_region=bad, is_fsss=True)
elif key == 'panel':
bad['panel'] = value
else:
- raise RuntimeError('Unrecognised field: {}'.format(key))
+ raise RuntimeError("Unrecognised field: {}".format(key))
return
-def _check_point(name, panel, fs_, ss_, min_d, max_d, detector):
+def _check_point(name, panel, fs, ss, min_d, max_d, detector):
# Reimplementation of check_point from
# libcrystfel/src/detector.c.
-
- 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 = math.sqrt(x=rx_ * rx_ + ry_ * ry_)
-
+ 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 = math.sqrt(rx * rx + ry * ry)
if dist > max_d:
detector['furthest_out_panel'] = name
- detector['furthest_out_fs'] = fs_
- detector['furthest_out_ss'] = ss_
+ 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_
+ detector['furthest_in_fs'] = fs
+ detector['furthest_in_ss'] = ss
min_d = dist
return min_d, max_d
@@ -376,17 +340,14 @@ def _check_point(name, panel, fs_, ss_, min_d, max_d, detector):
def _find_min_max_d(detector):
# Reimplementation of find_min_max_d from
# libcrystfel/src/detector.c.
-
min_d = float('inf')
max_d = 0.0
-
for name, panel in detector['panels'].items():
-
min_d, max_d = _check_point(
name=name,
panel=panel,
- fs_=0,
- ss_=0,
+ fs=0,
+ ss=0,
min_d=min_d,
max_d=max_d,
detector=detector
@@ -395,18 +356,18 @@ def _find_min_max_d(detector):
min_d, max_d = _check_point(
name=name,
panel=panel,
- fs_=panel['w'],
- ss_=0,
+ fs=panel['w'],
+ ss=0,
min_d=min_d,
max_d=max_d,
detector=detector
-
)
+
min_d, max_d = _check_point(
name=name,
panel=panel,
- fs_=0,
- ss_=panel['h'],
+ fs=0,
+ ss=panel['h'],
min_d=min_d,
max_d=max_d,
detector=detector
@@ -415,8 +376,8 @@ def _find_min_max_d(detector):
min_d, max_d = _check_point(
name=name,
panel=panel,
- fs_=panel['w'],
- ss_=panel['h'],
+ fs=panel['w'],
+ ss=panel['h'],
min_d=min_d,
max_d=max_d,
detector=detector
@@ -424,13 +385,14 @@ def _find_min_max_d(detector):
def load_crystfel_geometry(filename):
- """Load a CrystFEL geometry file into a dictionary.
+ """
+ Load a CrystFEL geometry file into a dictionary.
- Reimplementation of the get_detector_geometry_2 function from CrystFEL
- in python. Return a dictionary with the geometry information read from
- the file. Convert entries in the geometry file to keys in the
- returned dictionary. For a full documentation on the CrystFEL geometry
- format, see:
+ Reimplementation of the get_detector_geometry_2 function from
+ CrystFEL in python. Return a dictionary with the geometry
+ information read from the file. Convert entries in the geometry
+ file to keys in the returned dictionary. For a full documentation
+ on the CrystFEL geometry format, see:
http://www.desy.de/~twhite/crystfel/manual-crystfel_geometry.html
@@ -444,11 +406,9 @@ def load_crystfel_geometry(filename):
Returns:
- dict: dictionary with the geometry information loaded from the file.
+ dict: dictionary with the geometry information loaded from the
+ file.
"""
-
- fhandle = open(file=filename, mode='r')
-
beam = {
'photon_energy': 0.0,
'photon_energy_from': None,
@@ -507,33 +467,34 @@ def load_crystfel_geometry(filename):
'name': ''
}
- default_dim = ['ss', 'fs']
+ default_dim = [
+ 'ss', 'fs'
+ ]
+ fhandle = open(file=filename, mode='r')
fhlines = fhandle.readlines()
-
for line in fhlines:
-
- if line.startswith(';'):
+ if line.startswith(";"):
continue
line_without_comments = line.strip().split(sep=';')[0]
line_items = re.split(pattern='([ \t])', string=line_without_comments)
line_items = [
- item for item in line_items if item not in ('', ' ', '\t')
+ item
+ for item in line_items
+ if item not in ('', ' ', '\t')
]
- if len(s=line_items) < 3:
+ 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(s=path) < 2:
+ if len(path) < 2:
_parse_toplevel(
key=line_items[0],
value=value,
@@ -545,9 +506,7 @@ def load_crystfel_geometry(filename):
curr_bad = None
curr_panel = None
-
- if path[0].startswith('bad'):
-
+ if path[0].startswith("bad"):
if path[0] in detector['bad']:
curr_bad = detector['bad'][path[0]]
else:
@@ -555,7 +514,6 @@ def load_crystfel_geometry(filename):
detector['bad'][path[0]] = curr_bad
else:
-
if path[0] in detector['panels']:
curr_panel = detector['panels'][path[0]]
else:
@@ -579,9 +537,7 @@ def load_crystfel_geometry(filename):
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:
@@ -592,14 +548,12 @@ def load_crystfel_geometry(filename):
else:
if curr_num_placeholders != num_placeholders_in_panels:
raise RuntimeError(
- 'All panels\' data and mask entries must have the same '
- 'number of placeholders.'
+ "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:
@@ -610,50 +564,50 @@ def load_crystfel_geometry(filename):
else:
if curr_num_placeholders != num_placeholders_in_masks:
raise RuntimeError(
- 'All panels\' data and mask entries must have the same '
- 'number of placeholders.'
+ "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 larger the number '
- 'than for data.'
+ "Number of placeholders in mask cannot be larger the number "
+ "than for data."
)
dim_length = None
-
for panel in detector['panels'].values():
-
if panel['dim_structure'] is None:
panel['dim_structure'] = copy.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.'
+ "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.'
+ "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.'
+ "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.'
+ "Only one placeholder dim coordinate is allowed."
)
else:
found_placeholder = True
@@ -662,68 +616,67 @@ def load_crystfel_geometry(filename):
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.'
+ "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.'
+ "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'])
+ "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'])
+ "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'])
+ "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'])
+ "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'])
+ "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'])
+ "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'])
+ "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'])
+ "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'])
+ "You must specify clen_for_centering if you specify the "
+ "rail direction (panel {})".format(panel['name'])
)
if panel['rail_x'] is None:
@@ -740,37 +693,34 @@ def load_crystfel_geometry(filename):
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'])
+ "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)
+ "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)
+ "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__
+ 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)
fhandle.close()
diff --git a/geometry_utils.py b/geometry_utils.py
index 58533e45b5538cb77c4e5a1cb8a31bff199e0570..699d8223cd535cea34d711f17ad5bb2b200c7038 100644
--- a/geometry_utils.py
+++ b/geometry_utils.py
@@ -15,8 +15,8 @@
"""
Geometry utilities.
-Functions that load, manipulate and apply geometry information to detector
-pixel data.
+Functions that load, manipulate and apply geometry information to
+detector pixel data.
"""
from __future__ import (absolute_import, division, print_function,
@@ -27,63 +27,58 @@ import collections
import numpy
-PixelMaps = collections.namedtuple('PixelMaps', ['x', 'y', 'r'])
-'''A namedtuple used for pixel maps objects.
-
-Pixel maps are arrays of the same shape of the data whose geometry they
-describe. Each cell in the array holds the coordinate, in the reference system
-of the physical detector, of the corresponding pixel in the data array.
-
-The first two fields store the pixel maps for the x coordinate
-and the y coordinate respectively. The third field is instead a pixel map
-storing the distance of each pixel in the data array from the center of the
-reference system.
-'''
-
-
def compute_pixel_maps(geometry):
- """Compute pixel maps from a CrystFEL geometry object.
+ """
+ Compute pixel maps from a CrystFEL geometry object.
Take as input a CrystFEL-style geometry object (A dictionary
returned by the function load_crystfel_geometry function in the
- crystfel_utils module) and return a PixelMap tuple . The origin
- the reference system used by the pixel maps is set at the beam interaction
- point.
+ crystfel_utils module) and return a PixelMap tuple . The origin the
+ reference system used by the pixel maps is set at the beam
+ interaction point.
Args:
- geometry (dict): A CrystFEL geometry object (A dictionary returned by
- the :obj:`cfelpyutils.crystfel_utils.load_crystfel_geometry`
+ geometry (dict): A CrystFEL geometry object (A dictionary
+ returned by the
+ :obj:`cfelpyutils.crystfel_utils.load_crystfel_geometry`
function).
Returns:
- PixelMaps: a PixelMaps tuple.
+ Tuple[ndarray, ndarray, ndarray] A tuple containing the pixel
+ maps. The first two fields, named "x" and "y" respectively,
+ store the pixel maps for the x coordinate and the y coordinate.
+ The third field, named "r", is instead a pixel map storing the
+ distance of each pixel in the data array from the center of the
+ reference system.
"""
-
# Determine the max fs and ss in the geometry object.
- max_slab_fs = numpy.array(
- [geometry['panels'][k]['max_fs'] for k in geometry['panels']]
- ).max()
-
- max_slab_ss = numpy.array(
- [geometry['panels'][k]['max_ss'] for k in geometry['panels']]
- ).max()
-
- # Create the empty arrays that will store the pixel maps.
+ max_slab_fs = numpy.array([
+ geometry['panels'][k]['max_fs']
+ for k in geometry['panels']
+ ]).max()
+
+ max_slab_ss = numpy.array([
+ geometry['panels'][k]['max_ss']
+ for k in geometry['panels']
+ ]).max()
+
+ # Create empty arrays, of the same size of the input data, that
+ # will store the x and y pixel maps.
x_map = numpy.zeros(
shape=(max_slab_ss + 1, max_slab_fs + 1),
dtype=numpy.float32
)
+
y_map = numpy.zeros(
shape=(max_slab_ss + 1, max_slab_fs + 1),
dtype=numpy.float32
)
- # Iterate over the panels.
+ # Iterate over the panels. For each panel, determine the pixel
+ # indeces, then compute the x,y vectors using a comples notation.
for pan in geometry['panels']:
-
- # Determine the pixel indexes for the current panel.
i, j = numpy.meshgrid(
numpy.arange(
geometry['panels'][pan]['max_ss'] -
@@ -98,46 +93,43 @@ def compute_pixel_maps(geometry):
indexing='ij'
)
- # Compute the x,y vectors, using the complex notation.
- d_x = (
- geometry['panels'][pan]['fsy'] +
- 1J * geometry['panels'][pan]['fsx']
- )
- d_y = (
- geometry['panels'][pan]['ssy'] +
- 1J * geometry['panels'][pan]['ssx']
- )
- r_0 = (
- geometry['panels'][pan]['cny'] +
- 1J * geometry['panels'][pan]['cnx']
- )
+ d_x = (geometry['panels'][pan]['fsy'] +
+ 1J * geometry['panels'][pan]['fsx'])
+ d_y = (geometry['panels'][pan]['ssy'] +
+ 1J * geometry['panels'][pan]['ssx'])
+
+ r_0 = (geometry['panels'][pan]['cny'] +
+ 1J * geometry['panels'][pan]['cnx'])
cmplx = i * d_y + j * d_x + r_0
- # Compute values for the x and y maps.
- y_map[
+ x_map[
geometry['panels'][pan]['min_ss']:
geometry['panels'][pan]['max_ss'] + 1,
geometry['panels'][pan]['min_fs']:
geometry['panels'][pan]['max_fs'] + 1
- ] = cmplx.real
+ ] = cmplx.imag
- x_map[
+ y_map[
geometry['panels'][pan]['min_ss']:
geometry['panels'][pan]['max_ss'] + 1,
geometry['panels'][pan]['min_fs']:
geometry['panels'][pan]['max_fs'] + 1
- ] = cmplx.imag
+ ] = cmplx.real
- # Compute the values for the radius pixel map.
+ # Finally, compute the values for the radius pixel map.
r_map = numpy.sqrt(numpy.square(x_map) + numpy.square(y_map))
- # Return the pixel maps as a tuple.
+ PixelMaps = collections.namedtuple(
+ typename='PixelMaps',
+ field_names=['x', 'y', 'r']
+ )
return PixelMaps(x_map, y_map, r_map)
def apply_pixel_maps(data, pixel_maps, output_array=None):
- """Apply geometry in pixel map format to the input data.
+ """
+ Apply geometry in pixel map format to the input data.
Turn an array of detector pixel values into an array
containing a representation of the physical layout of the detector.
@@ -150,20 +142,19 @@ def apply_pixel_maps(data, pixel_maps, output_array=None):
pixel_maps (PixelMaps): a pixelmap tuple, as returned by the
:obj:`compute_pixel_maps` function in this module.
- output_array (Optional[ndarray]): a preallocated array (of dtype
- numpy.float32) to store the function output. If provided, this
- array will be filled by the function and returned to the user.
- If not provided, the function will create a new array
- automatically and return it to the user. Defaults to None
- (No array provided).
+ output_array (Optional[ndarray]): a preallocated array (of
+ dtype numpy.float32) to store the function output. If
+ provided, this array will be filled by the function and
+ and returned to the user. If not provided, the function
+ will create a new array automatically and return it to the
+ user. Defaults to None (No array provided).
Returns:
- ndarray: a numpy.float32 array containing the geometry information
- applied to the input data (i.e.: a physical representation of the
- layout of the detector).
+ ndarray: a numpy.float32 array containing the geometry
+ information applied to the input data (i.e.: a representation
+ of the physical layout of the detector).
"""
-
# If no output array was provided, create one.
if output_array is None:
output_array = numpy.zeros(
@@ -171,70 +162,83 @@ def apply_pixel_maps(data, pixel_maps, output_array=None):
dtype=numpy.float32
)
- # Apply the pixel map geometry information the data.
+ # Apply the pixel map geometry information the data, then return
+ # the resulting array.
output_array[pixel_maps.y, pixel_maps.x] = data.ravel()
-
- # Return the output array.
return output_array
def compute_minimum_array_size(pixel_maps):
"""
- Compute the minimum size of an array that can store the applied geometry.
+ Compute the minimum size of an array that can store the applied
+ geometry.
- Return the minimum size of an array that can store data on which the
- geometry information described by the pixel maps has been applied.
+ Return the minimum size of an array that can store data on which
+ the geometry information described by the pixel maps has been
+ applied.
- The returned array shape is big enough to display all the input pixel
- values in the reference system of the physical detector. The array is
- supposed to be centered at the center of the reference system of the
- detector (i.e: the beam interaction point).
+ The returned array shape is big enough to display all the input
+ pixel values in the reference system of the physical detector. The
+ array is supposed to be centered at the center of the reference
+ system of the detector (i.e: the beam interaction point).
Args:
- pixel_maps (PixelMaps): a PixelMaps tuple, as returned by the
- :obj:`compute_pixel_maps` function in this module.
+ Tuple[ndarray, ndarray, ndarray]: a named tuple containing the
+ pixel maps. The first two fields, "x" and "y", should store
+ the pixel maps for the x coordinateand the y coordinate.
+ The third, "r", should instead store the distance of each
+ pixel in the data array from the center of the reference
+ system.
Returns:
- tuple: numpy shape-like tuple storing the minimum array size.
+ Tuple[int, int]: a numpy-style shape tuple storing the minimum
+ array size.
"""
-
- # Recover the x and y pixel maps.
+ # Find the largest absolute values of x and y in the maps. Since
+ # the returned array is centered on the origin, the minimum array
+ # size along a certain axis must be at least twice the maximum
+ # value for that axis. 2 pixels are added for good measure.
x_map, y_map = pixel_maps.x, pixel_maps.x.y
+ y_minimum = 2 * int(max(abs(y_map.max()), abs(y_map.min()))) + 2
+ x_minimum = 2 * int(max(abs(x_map.max()), abs(x_map.min()))) + 2
- # Find the largest absolute values of x and y in the maps.
- y_largest = 2 * int(max(abs(y_map.max()), abs(y_map.min()))) + 2
- x_largest = 2 * int(max(abs(x_map.max()), abs(x_map.min()))) + 2
-
- # Return a tuple with the computed shape.
- return (y_largest, x_largest)
+ # Return a numpy-style tuple with the computed shape.
+ return (y_minimum, x_minimum)
def adjust_pixel_maps_for_pyqtgraph(pixel_maps):
"""
- Adjust pixel maps for visualization of the data in a pyqtgraph widget.
+ Adjust pixel maps for visualization of the data in a pyqtgraph
+ widget.
The adjusted maps can be used for a Pyqtgraph ImageView widget.
- Essentially, the origin of the reference system is moved to the
- top-left of the image.
Args:
- pixel_maps (PixelMaps): pixel maps, as returned by the
- :obj:`compute_pixel_maps` function in this module.
+ Tuple[ndarray, ndarray, ndarray]: a named tuple containing the
+ pixel maps. The first two fields, "x" and "y", should store the
+ pixel maps for the x coordinateand the y coordinate. The third,
+ "r", should instead store the distance of each pixel in the
+ data array from the center of the reference system.
Returns:
- PixelMaps: a PixelMaps tuple containing the ajusted pixel maps for
- the x and y coordinates in the first two fields, and the
- value None in the third.
+ Tuple[ndarray, ndarray] A tuple containing the pixel
+ maps. The first two fields, named "x" and "y" respectively,
+ store the pixel maps for the x coordinate and the y
+ coordinate. The third field, named "r", is instead a pixel
+ map storing the distance of each pixel in the data array
+ from the center of the reference system.
"""
-
- # Compute the minimum image shape needed to represent the coordinates.
+ # Essentially, the origin of the reference system needs to be
+ # moved from the beam position to the top-left of the image that
+ # will be displayed. First, compute the size of the array used to
+ # display the data, then use this information to estimate the
+ # magnitude of the shift that needs to be applied to the origin of
+ # the system.
min_shape = compute_minimum_array_size(pixel_maps)
-
- # Convert the old pixemap values to the new pixelmap values.
new_x_map = numpy.array(
object=pixel_maps.x,
dtype=numpy.int
@@ -245,4 +249,8 @@ def adjust_pixel_maps_for_pyqtgraph(pixel_maps):
dtype=numpy.int
) + min_shape[0] // 2 - 1
- return PixelMaps(new_x_map, new_y_map, None)
+ PixelMapsForIV = collections.namedtuple(
+ typename='PixelMapsForIV',
+ field_names=['x', 'y']
+ )
+ return PixelMapsForIV(new_x_map, new_y_map)
diff --git a/parameter_utils.py b/parameter_utils.py
index 6e3f977d61c6d9ba94d9edc87a226cc1b0f15f4d..4a3fde67e974e14c1bdeeb734331021a91b40722 100644
--- a/parameter_utils.py
+++ b/parameter_utils.py
@@ -24,36 +24,35 @@ import ast
def _parsing_error(section, option):
# Raise an exception after a parsing error.
-
raise RuntimeError(
- 'Error parsing parameter {0} in section [{1}]. Make sure that the '
- 'syntax is correct: list elements must be separated by commas and '
- 'dict entries must contain the colon symbol. Strings must be quoted, '
- 'even in lists and dicts.'.format(
- option,
- section
- )
+ "Error parsing parameter {0} in section [{1}]. Make sure that the "
+ "syntax is correct: list elements must be separated by commas and "
+ "dict entries must contain the colon symbol. Strings must be quoted, "
+ "even in lists and dicts.".format(option, section)
)
def convert_parameters(config_dict):
"""Convert strings in parameter dictionaries to the corrent data type.
- Read a parameter dictionary returned by the ConfigParser python module,
- and convert each entry in an object of the corresponding type,
- without changing the structure of the dictionary.
+ Read a parameter dictionary returned by the ConfigParser python
+ module, and convert each entry in an object of the corresponding
+ type, without changing the structure of the dictionary.
- Try to convert each entry in the dictionary according to the following
- rules. The first rule that applies to the entry determines the type.
+ Try to convert each entry in the dictionary according to the
+ following rules. The first rule that applies to the entry
+ determines the type.
- If the entry starts and ends with a single quote or double quote,
leave it as a string.
- - If the entry starts and ends with a square bracket, convert it to a list.
+ - If the entry starts and ends with a square bracket, convert it to
+ a list.
- If the entry starts and ends with a curly braces, convert it to a
dictionary or a set.
- - If the entry is the word None, without quotes, convert it to NoneType.
- - If the entry is the word False, without quotes, convert it to a boolean
- False.
+ - If the entry is the word None, without quotes, convert it to
+ NoneType.
+ - If the entry is the word False, without quotes, convert it to a
+ boolean False.
- If the entry is the word True, without quotes, convert it to a
boolean True.
- If none of the previous options match the content of the entry,
@@ -77,26 +76,24 @@ def convert_parameters(config_dict):
Raises:
- RuntimeError: if an entry cannot be converted to any supported type.
+ RuntimeError: if an entry cannot be converted to any supported
+ type.
"""
- # Create the dictionary that will be returned.
monitor_params = {}
- # Iterate over the sections in the dictionary (first level).
+ # Iterate over the sections in the dictionary (first level in the
+ # configuration file). Add the section to the dictionary that will
+ # be returned.
for section in config_dict.keys():
-
- # Add the section to the dictionary that will be returned.
monitor_params[section] = {}
- # Iterate over the content of the section (second level in the
- # configuratio).
+ # Iterate then over the content of the section (second level in
+ # the configuration file). Get each option in turn and perform
+ # all the checks. If all checks fail, call the parsing_error
+ # function.
for option in config_dict['section'].keys():
-
- # Get the option from the dictionary.
recovered_option = config_dict['section']
-
- # Check if the option is a string delimited by single quotes.
if (
recovered_option.startswith("'") and
recovered_option.endswith("'")
@@ -104,7 +101,6 @@ def convert_parameters(config_dict):
monitor_params[section][option] = recovered_option[1:-1]
continue
- # Check if the option is a string delimited by double quotes.
if (
recovered_option.startswith('"') and
recovered_option.endswith('"')
@@ -112,8 +108,6 @@ def convert_parameters(config_dict):
monitor_params[section][option] = recovered_option[1:-1]
continue
- # Check if the option is a list. If it is, interpret it using the
- # literal_eval function.
if (
recovered_option.startswith("[") and
recovered_option.endswith("]")
@@ -126,8 +120,6 @@ def convert_parameters(config_dict):
except (SyntaxError, ValueError):
_parsing_error(section, option)
- # Check if the option is a dictionary or a set. If it is,
- # interpret it using the literal_eval function.
if (
recovered_option.startswith("{") and
recovered_option.endswith("}")
@@ -140,40 +132,28 @@ def convert_parameters(config_dict):
except (SyntaxError, ValueError):
_parsing_error(section, option)
- # Check if the option is the special string 'None' (without
- # quotes).
if recovered_option == 'None':
monitor_params[section][option] = None
continue
- # Check if the option is the special string 'False' (without
- # quotes).
if recovered_option == 'False':
monitor_params[section][option] = False
continue
- # Check if the option is the special string 'True' (without
- # quotes).
if recovered_option == 'True':
monitor_params[section][option] = True
continue
- # Check if the option is an int by trying to convert it to an int.
try:
monitor_params[section][option] = int(recovered_option)
continue
except ValueError:
- # If the conversion to int failed, try to convert it to a
- # float.
try:
monitor_params[section][option] = float(
recovered_option
)
continue
except ValueError:
- # If the conversion to float also failed, return a parsing
- # error.
_parsing_error(section, option)
- # Returned the converted dictionary.
return monitor_params