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Handle None in axes_to_array

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None values should be treated the same as missing ones -
previously it would just crash.
This commit is contained in:
Richard Bowman 2021-04-27 10:52:52 +01:00
parent e86e4d983a
commit 2eade9ed30
1 changed files with 30 additions and 7 deletions
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37
openflexure_microscope/utilities.py
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@ -4,7 +4,7 @@ import logging
import sys import sys
import time import time
from contextlib import contextmanager from contextlib import contextmanager
from typing import Dict, List, Optional, Tuple, Type, Union from typing import Dict, List, Optional, Tuple, Type, Union, Sequence
import numpy as np import numpy as np
@ -102,12 +102,29 @@ def set_properties(obj, **kwargs):
def axes_to_array( def axes_to_array(
coordinate_dictionary: Dict[str, int], coordinate_dictionary: Dict[str, Optional[int]],
axis_keys=("x", "y", "z"), axis_keys: Sequence[str] = ("x", "y", "z"),
base_array: Optional[List[int]] = None, base_array: Optional[List[int]] = None,
asint: bool = True, asint: bool = True,
) -> List[int]: ) -> List[int]:
"""Takes key-value pairs of a JSON value, and maps onto an array""" """Takes key-value pairs of a JSON value, and maps onto an array
This is designed to take a dictionary like `{"x": 1, "y":2, "z":3}`
and return a list like `[1, 2, 3]` to convert between the argument
format expected by most of our stages, and the usual argument
format in JSON.
`axis_keys` is an ordered sequence of key names to extract from
the input dictionary.
`base_array` specifies a default value for each axis. It must
have the same length as `axis_keys`.
`asint` casts values to integers if it is `True` (default).
Missing keys, or keys that have a `None` value will be left
at the specified default value, or zero if none is specified.
"""
# If no base array is given # If no base array is given
if not base_array: if not base_array:
# Create an array of zeros # Create an array of zeros
@ -119,8 +136,14 @@ def axes_to_array(
# Do the mapping # Do the mapping
for axis, key in enumerate(axis_keys): for axis, key in enumerate(axis_keys):
if key in coordinate_dictionary: if key in coordinate_dictionary:
base_array[axis] = ( value = coordinate_dictionary[key]
int(coordinate_dictionary[key]) if asint else coordinate_dictionary[key] if value is None:
) # Values set to None should be treated as if they
# are missing
# i.e. we leave the default value in place.
break
if asint:
value = int(value)
base_array[axis] = value
return base_array return base_array