1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257
|
import numpy as np
import re
# numpy.exceptions exists from 1.25 onwards, but for Python 3.8 we still support
# numpy 1.24. We can clean this up once we require Python >= 3.9.
try:
from numpy.exceptions import AxisError
except ImportError:
from numpy import AxisError
__all__ = [
'stack_data',
'stack_detector_data',
]
def stack_data(train, data, axis=-3, xcept=()):
"""Stack data from devices in a train.
For detector data, use stack_detector_data instead: it can handle missing
modules, which this function cannot.
The returned array will have an extra dimension. The data will be ordered
according to any groups of digits in the source name, interpreted as
integers. Other characters do not affect sorting. So:
"B_7_0" < "A_12_0" < "A_12_1"
Parameters
----------
train: dict
Train data.
data: str
The path to the device parameter of the data you want to stack.
axis: int, optional
Array axis on which you wish to stack.
xcept: list
List of devices to ignore (useful if you have reccored slow data with
detector data in the same run).
Returns
-------
combined: numpy.array
Stacked data for requested data path.
"""
devices = [dev for dev in train.keys() if dev not in xcept]
if not devices:
raise ValueError("No data after filtering by 'xcept' argument.")
dtypes = set()
ordered_arrays = []
for device in sorted(devices, key=lambda d: list(map(int, re.findall(r'\d+', d)))):
array = train[device][data]
dtypes.add(array.dtype)
ordered_arrays.append(array)
if len(dtypes) > 1:
raise ValueError("Arrays have mismatched dtypes: {}".format(dtypes))
return np.stack(ordered_arrays, axis=axis)
def stack_detector_data(
train, data, axis=-3, modules=16, fillvalue=None, real_array=True, *,
pattern=r'/DET/(\d+)CH', starts_at=0,
):
"""Stack data from detector modules in a train.
Parameters
----------
train: dict
Train data.
data: str
The path to the device parameter of the data you want to stack, e.g. 'image.data'.
axis: int
Array axis on which you wish to stack (default is -3).
modules: int
Number of modules composing a detector (default is 16).
fillvalue: number
Value to use in place of data for missing modules. The default is nan
(not a number) for floating-point data, and 0 for integers.
real_array: bool
If True (default), copy the data together into a real numpy array.
If False, avoid copying the data and return a limited array-like wrapper
around the existing arrays. This is sufficient for assembling images
using detector geometry, and allows better performance.
pattern: str
Regex to find the module number in source names. Should contain a group
which can be converted to an integer. E.g. ``r'/DET/JNGFR(\\d+)'`` for
one JUNGFRAU naming convention.
starts_at: int
By default, uses module numbers starting at 0 (e.g. 0-15 inclusive).
If the numbering is e.g. 1-16 instead, pass starts_at=1. This is not
automatic because the first or last module may be missing from the data.
Returns
-------
combined: numpy.array
Stacked data for requested data path.
"""
if not train:
raise ValueError("No data")
dtypes, shapes, empty_mods = set(), set(), set()
modno_arrays = {}
for src in train:
det_mod_match = re.search(pattern, src)
if not det_mod_match:
raise ValueError(f"Source {src!r} doesn't match pattern {pattern!r}")
modno = int(det_mod_match.group(1)) - starts_at
try:
array = train[src][data]
except KeyError:
continue
dtypes.add(array.dtype)
shapes.add(array.shape)
modno_arrays[modno] = array
if len(dtypes) > 1:
raise ValueError("Arrays have mismatched dtypes: {}".format(dtypes))
if len(shapes) > 1:
s1, s2, *_ = sorted(shapes)
if len(shapes) > 2 or (s1[0] != 0) or (s1[1:] != s2[1:]):
raise ValueError("Arrays have mismatched shapes: {}".format(shapes))
empty_mods = {n for n, a in modno_arrays.items() if a.shape == s1}
for modno in empty_mods:
del modno_arrays[modno]
shapes.remove(s1)
if max(modno_arrays) >= modules:
raise IndexError("Module {} is out of range for a detector with {} modules"
.format(max(modno_arrays), modules))
dtype = dtypes.pop()
shape = shapes.pop()
if fillvalue is None:
fillvalue = np.nan if dtype.kind == 'f' else 0
fillvalue = dtype.type(fillvalue) # check value compatibility with dtype
stack = StackView(
modno_arrays, modules, shape, dtype, fillvalue, stack_axis=axis
)
if real_array:
return stack.asarray()
return stack
class StackView:
"""Limited array-like object holding detector data from several modules.
Access is limited to either a single module at a time or all modules
together, but this is enough to assemble detector images.
"""
def __init__(self, data, nmodules, mod_shape, dtype, fillvalue,
stack_axis=-3):
self._nmodules = nmodules
self._data = data # {modno: array}
self.dtype = dtype
self._fillvalue = fillvalue
self._mod_shape = mod_shape
self.ndim = len(mod_shape) + 1
self._stack_axis = stack_axis
if self._stack_axis < 0:
self._stack_axis += self.ndim
sax = self._stack_axis
self.shape = mod_shape[:sax] + (nmodules,) + mod_shape[sax:]
def __repr__(self):
return "<VirtualStack (shape={}, {}/{} modules, dtype={})>".format(
self.shape, len(self._data), self._nmodules, self.dtype,
)
# Multidimensional slicing
def __getitem__(self, slices):
if not isinstance(slices, tuple):
slices = (slices,)
missing_dims = self.ndim - len(slices)
if Ellipsis in slices:
ix = slices.index(Ellipsis)
missing_dims += 1
slices = slices[:ix] + (slice(None, None),) * missing_dims + slices[ix + 1:]
else:
slices = slices + (slice(None, None),) * missing_dims
modno = slices[self._stack_axis]
mod_slices = slices[:self._stack_axis] + slices[self._stack_axis + 1:]
if isinstance(modno, int):
if modno < 0:
modno += self._nmodules
return self._get_single_mod(modno, mod_slices)
elif modno == slice(None, None):
return self._get_all_mods(mod_slices)
else:
raise Exception(
"VirtualStack can only slice a single module or all modules"
)
def _get_single_mod(self, modno, mod_slices):
try:
mod_data = self._data[modno]
except KeyError:
if modno >= self._nmodules:
raise IndexError(modno)
mod_data = np.full(self._mod_shape, self._fillvalue, self.dtype)
self._data[modno] = mod_data
# Now slice the module data as requested
return mod_data[mod_slices]
def _get_all_mods(self, mod_slices):
new_data = {modno: self._get_single_mod(modno, mod_slices)
for modno in self._data}
new_mod_shape = list(new_data.values())[0].shape
return StackView(new_data, self._nmodules, new_mod_shape, self.dtype,
self._fillvalue)
def asarray(self):
"""Copy this data into a real numpy array
Don't do this until necessary - the point of using VirtualStack is to
avoid copying the data unnecessarily.
"""
start_shape = (self._nmodules,) + self._mod_shape
arr = np.full(start_shape, self._fillvalue, dtype=self.dtype)
for modno, data in self._data.items():
arr[modno] = data
return np.moveaxis(arr, 0, self._stack_axis)
def squeeze(self, axis=None):
"""Drop axes of length 1 - see numpy.squeeze()"""
if axis is None:
slices = [0 if d == 1 else slice(None, None) for d in self.shape]
elif isinstance(axis, (int, tuple)):
if isinstance(axis, int):
axis = (axis,)
slices = [slice(None, None)] * self.ndim
for ax in axis:
try:
slices[ax] = 0
except IndexError:
raise AxisError(
"axis {} is out of bounds for array of dimension {}"
.format(ax, self.ndim)
)
if self.shape[ax] != 1:
raise ValueError("cannot squeeze out an axis with size != 1")
else:
raise TypeError("axis={!r} not supported".format(axis))
return self[tuple(slices)]
|