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ai-content-maker/.venv/Lib/site-packages/imageio/plugins/spe.py

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2024-05-11 23:00:43 +03:00
# -*- coding: utf-8 -*-
# imageio is distributed under the terms of the (new) BSD License.
""" Read SPE files.
This plugin supports reading files saved in the Princeton Instruments
SPE file format.
Parameters
----------
check_filesize : bool
The number of frames in the file is stored in the file header. However,
this number may be wrong for certain software. If this is `True`
(default), derive the number of frames also from the file size and
raise a warning if the two values do not match.
char_encoding : str
Deprecated. Exists for backwards compatibility; use ``char_encoding`` of
``metadata`` instead.
sdt_meta : bool
Deprecated. Exists for backwards compatibility; use ``sdt_control`` of
``metadata`` instead.
Methods
-------
.. note::
Check the respective function for a list of supported kwargs and detailed
documentation.
.. autosummary::
:toctree:
SpePlugin.read
SpePlugin.iter
SpePlugin.properties
SpePlugin.metadata
"""
from datetime import datetime
import logging
import os
from typing import (
Any,
Callable,
Dict,
Iterator,
List,
Mapping,
Optional,
Sequence,
Tuple,
Union,
)
import warnings
import numpy as np
from ..core.request import Request, IOMode, InitializationError
from ..core.v3_plugin_api import PluginV3, ImageProperties
logger = logging.getLogger(__name__)
class Spec:
"""SPE file specification data
Tuples of (offset, datatype, count), where offset is the offset in the SPE
file and datatype is the datatype as used in `numpy.fromfile`()
`data_start` is the offset of actual image data.
`dtypes` translates SPE datatypes (0...4) to numpy ones, e. g. dtypes[0]
is dtype("<f") (which is np.float32).
`controllers` maps the `type` metadata to a human readable name
`readout_modes` maps the `readoutMode` metadata to something human readable
although this may not be accurate since there is next to no documentation
to be found.
"""
basic = {
"datatype": (108, "<h"), # dtypes
"xdim": (42, "<H"),
"ydim": (656, "<H"),
"xml_footer_offset": (678, "<Q"),
"NumFrames": (1446, "<i"),
"file_header_ver": (1992, "<f"),
}
metadata = {
# ROI information
"NumROI": (1510, "<h"),
"ROIs": (
1512,
np.dtype(
[
("startx", "<H"),
("endx", "<H"),
("groupx", "<H"),
("starty", "<H"),
("endy", "<H"),
("groupy", "<H"),
]
),
10,
),
# chip-related sizes
"xDimDet": (6, "<H"),
"yDimDet": (18, "<H"),
"VChipXdim": (14, "<h"),
"VChipYdim": (16, "<h"),
# other stuff
"controller_version": (0, "<h"),
"logic_output": (2, "<h"),
"amp_high_cap_low_noise": (4, "<H"), # enum?
"mode": (8, "<h"), # enum?
"exposure_sec": (10, "<f"),
"date": (20, "<10S"),
"detector_temp": (36, "<f"),
"detector_type": (40, "<h"),
"st_diode": (44, "<h"),
"delay_time": (46, "<f"),
# shutter_control: normal, disabled open, disabled closed
# But which one is which?
"shutter_control": (50, "<H"),
"absorb_live": (52, "<h"),
"absorb_mode": (54, "<H"),
"can_do_virtual_chip": (56, "<h"),
"threshold_min_live": (58, "<h"),
"threshold_min_val": (60, "<f"),
"threshold_max_live": (64, "<h"),
"threshold_max_val": (66, "<f"),
"time_local": (172, "<7S"),
"time_utc": (179, "<7S"),
"adc_offset": (188, "<H"),
"adc_rate": (190, "<H"),
"adc_type": (192, "<H"),
"adc_resolution": (194, "<H"),
"adc_bit_adjust": (196, "<H"),
"gain": (198, "<H"),
"comments": (200, "<80S", 5),
"geometric": (600, "<H"), # flags
"sw_version": (688, "<16S"),
"spare_4": (742, "<436S"),
"XPrePixels": (98, "<h"),
"XPostPixels": (100, "<h"),
"YPrePixels": (102, "<h"),
"YPostPixels": (104, "<h"),
"readout_time": (672, "<f"),
"xml_footer_offset": (678, "<Q"),
"type": (704, "<h"), # controllers
"clockspeed_us": (1428, "<f"),
"readout_mode": (1480, "<H"), # readout_modes
"window_size": (1482, "<H"),
"file_header_ver": (1992, "<f"),
}
data_start = 4100
dtypes = {
0: np.dtype(np.float32),
1: np.dtype(np.int32),
2: np.dtype(np.int16),
3: np.dtype(np.uint16),
8: np.dtype(np.uint32),
}
controllers = [
"new120 (Type II)",
"old120 (Type I)",
"ST130",
"ST121",
"ST138",
"DC131 (PentaMax)",
"ST133 (MicroMax/Roper)",
"ST135 (GPIB)",
"VTCCD",
"ST116 (GPIB)",
"OMA3 (GPIB)",
"OMA4",
]
# This was gathered from random places on the internet and own experiments
# with the camera. May not be accurate.
readout_modes = ["full frame", "frame transfer", "kinetics"]
# Do not decode the following metadata keys into strings, but leave them
# as byte arrays
no_decode = ["spare_4"]
class SDTControlSpec:
"""Extract metadata written by the SDT-control software
Some of it is encoded in the comment strings
(see :py:meth:`parse_comments`). Also, date and time are encoded in a
peculiar way (see :py:meth:`get_datetime`). Use :py:meth:`extract_metadata`
to update the metadata dict.
"""
months = {
# Convert SDT-control month strings to month numbers
"Jän": 1,
"Jan": 1,
"Feb": 2,
"Mär": 3,
"Mar": 3,
"Apr": 4,
"Mai": 5,
"May": 5,
"Jun": 6,
"Jul": 7,
"Aug": 8,
"Sep": 9,
"Okt": 10,
"Oct": 10,
"Nov": 11,
"Dez": 12,
"Dec": 12,
}
sequence_types = {
# TODO: complete
"SEQU": "standard",
"SETO": "TOCCSL",
"KINE": "kinetics",
"SEAR": "arbitrary",
}
class CommentDesc:
"""Describe how to extract a metadata entry from a comment string"""
n: int
"""Which of the 5 SPE comment fields to use."""
slice: slice
"""Which characters from the `n`-th comment to use."""
cvt: Callable[[str], Any]
"""How to convert characters to something useful."""
scale: Union[None, float]
"""Optional scaling factor for numbers"""
def __init__(
self,
n: int,
slice: slice,
cvt: Callable[[str], Any] = str,
scale: Optional[float] = None,
):
self.n = n
self.slice = slice
self.cvt = cvt
self.scale = scale
comment_fields = {
(5, 0): {
"sdt_major_version": CommentDesc(4, slice(66, 68), int),
"sdt_minor_version": CommentDesc(4, slice(68, 70), int),
"sdt_controller_name": CommentDesc(4, slice(0, 6), str),
"exposure_time": CommentDesc(1, slice(64, 73), float, 10**-6),
"color_code": CommentDesc(4, slice(10, 14), str),
"detection_channels": CommentDesc(4, slice(15, 16), int),
"background_subtraction": CommentDesc(4, 14, lambda x: x == "B"),
"em_active": CommentDesc(4, 32, lambda x: x == "E"),
"em_gain": CommentDesc(4, slice(28, 32), int),
"modulation_active": CommentDesc(4, 33, lambda x: x == "A"),
"pixel_size": CommentDesc(4, slice(25, 28), float, 0.1),
"sequence_type": CommentDesc(
4, slice(6, 10), lambda x: __class__.sequence_types[x]
),
"grid": CommentDesc(4, slice(16, 25), float, 10**-6),
"n_macro": CommentDesc(1, slice(0, 4), int),
"delay_macro": CommentDesc(1, slice(10, 19), float, 10**-3),
"n_mini": CommentDesc(1, slice(4, 7), int),
"delay_mini": CommentDesc(1, slice(19, 28), float, 10**-6),
"n_micro": CommentDesc(1, slice(7, 10), int),
"delay_micro": CommentDesc(1, slice(28, 37), float, 10**-6),
"n_subpics": CommentDesc(1, slice(7, 10), int),
"delay_shutter": CommentDesc(1, slice(73, 79), float, 10**-6),
"delay_prebleach": CommentDesc(1, slice(37, 46), float, 10**-6),
"bleach_time": CommentDesc(1, slice(46, 55), float, 10**-6),
"recovery_time": CommentDesc(1, slice(55, 64), float, 10**-6),
},
(5, 1): {
"bleach_piezo_active": CommentDesc(4, slice(34, 35), lambda x: x == "z")
},
}
@staticmethod
def get_comment_version(comments: Sequence[str]) -> Tuple[int, int]:
"""Get the version of SDT-control metadata encoded in the comments
Parameters
----------
comments
List of SPE file comments, typically ``metadata["comments"]``.
Returns
-------
Major and minor version. ``-1, -1`` if detection failed.
"""
if comments[4][70:76] != "COMVER":
return -1, -1
try:
return int(comments[4][76:78]), int(comments[4][78:80])
except ValueError:
return -1, -1
@staticmethod
def parse_comments(
comments: Sequence[str], version: Tuple[int, int]
) -> Dict[str, Any]:
"""Extract SDT-control metadata from comments
Parameters
----------
comments
List of SPE file comments, typically ``metadata["comments"]``.
version
Major and minor version of SDT-control metadata format
Returns
-------
Dict of metadata
"""
sdt_md = {}
for minor in range(version[1] + 1):
# Metadata with same major version is backwards compatible.
# Fields are specified incrementally in `comment_fields`.
# E.g. if the file has version 5.01, `comment_fields[5, 0]` and
# `comment_fields[5, 1]` need to be decoded.
try:
cmt = __class__.comment_fields[version[0], minor]
except KeyError:
continue
for name, spec in cmt.items():
try:
v = spec.cvt(comments[spec.n][spec.slice])
if spec.scale is not None:
v *= spec.scale
sdt_md[name] = v
except Exception as e:
warnings.warn(
f"Failed to decode SDT-control metadata field `{name}`: {e}"
)
sdt_md[name] = None
if version not in __class__.comment_fields:
supported_ver = ", ".join(
map(lambda x: f"{x[0]}.{x[1]:02}", __class__.comment_fields)
)
warnings.warn(
f"Unsupported SDT-control metadata version {version[0]}.{version[1]:02}. "
f"Only versions {supported_ver} are supported. "
"Some or all SDT-control metadata may be missing."
)
comment = comments[0] + comments[2]
sdt_md["comment"] = comment.strip()
return sdt_md
@staticmethod
def get_datetime(date: str, time: str) -> Union[datetime, None]:
"""Turn date and time saved by SDT-control into proper datetime object
Parameters
----------
date
SPE file date, typically ``metadata["date"]``.
time
SPE file date, typically ``metadata["time_local"]``.
Returns
-------
File's datetime if parsing was succsessful, else None.
"""
try:
month = __class__.months[date[2:5]]
return datetime(
int(date[5:9]),
month,
int(date[0:2]),
int(time[0:2]),
int(time[2:4]),
int(time[4:6]),
)
except Exception as e:
logger.info(f"Failed to decode date from SDT-control metadata: {e}.")
@staticmethod
def extract_metadata(meta: Mapping, char_encoding: str = "latin1"):
"""Extract SDT-control metadata from SPE metadata
SDT-control stores some metadata in comments and other fields.
Extract them and remove unused entries.
Parameters
----------
meta
SPE file metadata. Modified in place.
char_encoding
Character encoding used to decode strings in the metadata.
"""
comver = __class__.get_comment_version(meta["comments"])
if any(c < 0 for c in comver):
# This file most likely was not created by SDT-control
logger.debug("SDT-control comments not found.")
return
sdt_meta = __class__.parse_comments(meta["comments"], comver)
meta.pop("comments")
meta.update(sdt_meta)
# Get date and time in a usable format
dt = __class__.get_datetime(meta["date"], meta["time_local"])
if dt:
meta["datetime"] = dt
meta.pop("date")
meta.pop("time_local")
sp4 = meta["spare_4"]
try:
meta["modulation_script"] = sp4.decode(char_encoding)
meta.pop("spare_4")
except UnicodeDecodeError:
warnings.warn(
"Failed to decode SDT-control laser "
"modulation script. Bad char_encoding?"
)
# Get rid of unused data
meta.pop("time_utc")
meta.pop("exposure_sec")
class SpePlugin(PluginV3):
def __init__(
self,
request: Request,
check_filesize: bool = True,
char_encoding: Optional[str] = None,
sdt_meta: Optional[bool] = None,
) -> None:
"""Instantiate a new SPE file plugin object
Parameters
----------
request : Request
A request object representing the resource to be operated on.
check_filesize : bool
If True, compute the number of frames from the filesize, compare it
to the frame count in the file header, and raise a warning if the
counts don't match. (Certain software may create files with
char_encoding : str
Deprecated. Exists for backwards compatibility; use ``char_encoding`` of
``metadata`` instead.
sdt_meta : bool
Deprecated. Exists for backwards compatibility; use ``sdt_control`` of
``metadata`` instead.
"""
super().__init__(request)
if request.mode.io_mode == IOMode.write:
raise InitializationError("cannot write SPE files")
if char_encoding is not None:
warnings.warn(
"Passing `char_encoding` to the constructor is deprecated. "
"Use `char_encoding` parameter of the `metadata()` method "
"instead.",
DeprecationWarning,
)
self._char_encoding = char_encoding
if sdt_meta is not None:
warnings.warn(
"Passing `sdt_meta` to the constructor is deprecated. "
"Use `sdt_control` parameter of the `metadata()` method "
"instead.",
DeprecationWarning,
)
self._sdt_meta = sdt_meta
self._file = self.request.get_file()
try:
# Spec.basic contains no string, no need to worry about character
# encoding.
info = self._parse_header(Spec.basic, "latin1")
self._file_header_ver = info["file_header_ver"]
self._dtype = Spec.dtypes[info["datatype"]]
self._shape = (info["ydim"], info["xdim"])
self._len = info["NumFrames"]
if check_filesize:
# Some software writes incorrect `NumFrames` metadata.
# To determine the number of frames, check the size of the data
# segment -- until the end of the file for SPE<3, until the
# xml footer for SPE>=3.
if info["file_header_ver"] >= 3:
data_end = info["xml_footer_offset"]
else:
self._file.seek(0, os.SEEK_END)
data_end = self._file.tell()
line = data_end - Spec.data_start
line //= self._shape[0] * self._shape[1] * self._dtype.itemsize
if line != self._len:
warnings.warn(
f"The file header of {self.request.filename} claims there are "
f"{self._len} frames, but there are actually {line} frames."
)
self._len = min(line, self._len)
self._file.seek(Spec.data_start)
except Exception:
raise InitializationError("SPE plugin cannot read the provided file.")
def read(self, *, index: int = ...) -> np.ndarray:
"""Read a frame or all frames from the file
Parameters
----------
index : int
Select the index-th frame from the file. If index is `...`,
select all frames and stack them along a new axis.
Returns
-------
A Numpy array of pixel values.
"""
if index is Ellipsis:
read_offset = Spec.data_start
count = self._shape[0] * self._shape[1] * self._len
out_shape = (self._len, *self._shape)
elif index < 0:
raise IndexError(f"Index `{index}` is smaller than 0.")
elif index >= self._len:
raise IndexError(
f"Index `{index}` exceeds the number of frames stored in this file (`{self._len}`)."
)
else:
read_offset = (
Spec.data_start
+ index * self._shape[0] * self._shape[1] * self._dtype.itemsize
)
count = self._shape[0] * self._shape[1]
out_shape = self._shape
self._file.seek(read_offset)
data = np.fromfile(self._file, dtype=self._dtype, count=count)
return data.reshape(out_shape)
def iter(self) -> Iterator[np.ndarray]:
"""Iterate over the frames in the file
Yields
------
A Numpy array of pixel values.
"""
return (self.read(index=i) for i in range(self._len))
def metadata(
self,
index: int = ...,
exclude_applied: bool = True,
char_encoding: str = "latin1",
sdt_control: bool = True,
) -> Dict[str, Any]:
"""SPE specific metadata.
Parameters
----------
index : int
Ignored as SPE files only store global metadata.
exclude_applied : bool
Ignored. Exists for API compatibility.
char_encoding : str
The encoding to use when parsing strings.
sdt_control : bool
If `True`, decode special metadata written by the
SDT-control software if present.
Returns
-------
metadata : dict
Key-value pairs of metadata.
Notes
-----
SPE v3 stores metadata as XML, whereas SPE v2 uses a binary format.
.. rubric:: Supported SPE v2 Metadata fields
ROIs : list of dict
Regions of interest used for recording images. Each dict has the
"top_left" key containing x and y coordinates of the top left corner,
the "bottom_right" key with x and y coordinates of the bottom right
corner, and the "bin" key with number of binned pixels in x and y
directions.
comments : list of str
The SPE format allows for 5 comment strings of 80 characters each.
controller_version : int
Hardware version
logic_output : int
Definition of output BNC
amp_hi_cap_low_noise : int
Amp switching mode
mode : int
Timing mode
exp_sec : float
Alternative exposure in seconds
date : str
Date string
detector_temp : float
Detector temperature
detector_type : int
CCD / diode array type
st_diode : int
Trigger diode
delay_time : float
Used with async mode
shutter_control : int
Normal, disabled open, or disabled closed
absorb_live : bool
on / off
absorb_mode : int
Reference strip or file
can_do_virtual_chip : bool
True or False whether chip can do virtual chip
threshold_min_live : bool
on / off
threshold_min_val : float
Threshold minimum value
threshold_max_live : bool
on / off
threshold_max_val : float
Threshold maximum value
time_local : str
Experiment local time
time_utc : str
Experiment UTC time
adc_offset : int
ADC offset
adc_rate : int
ADC rate
adc_type : int
ADC type
adc_resolution : int
ADC resolution
adc_bit_adjust : int
ADC bit adjust
gain : int
gain
sw_version : str
Version of software which created this file
spare_4 : bytes
Reserved space
readout_time : float
Experiment readout time
type : str
Controller type
clockspeed_us : float
Vertical clock speed in microseconds
readout_mode : ["full frame", "frame transfer", "kinetics", ""]
Readout mode. Empty string means that this was not set by the
Software.
window_size : int
Window size for Kinetics mode
file_header_ver : float
File header version
chip_size : [int, int]
x and y dimensions of the camera chip
virt_chip_size : [int, int]
Virtual chip x and y dimensions
pre_pixels : [int, int]
Pre pixels in x and y dimensions
post_pixels : [int, int],
Post pixels in x and y dimensions
geometric : list of {"rotate", "reverse", "flip"}
Geometric operations
sdt_major_version : int
(only for files created by SDT-control)
Major version of SDT-control software
sdt_minor_version : int
(only for files created by SDT-control)
Minor version of SDT-control software
sdt_controller_name : str
(only for files created by SDT-control)
Controller name
exposure_time : float
(only for files created by SDT-control)
Exposure time in seconds
color_code : str
(only for files created by SDT-control)
Color channels used
detection_channels : int
(only for files created by SDT-control)
Number of channels
background_subtraction : bool
(only for files created by SDT-control)
Whether background subtraction war turned on
em_active : bool
(only for files created by SDT-control)
Whether EM was turned on
em_gain : int
(only for files created by SDT-control)
EM gain
modulation_active : bool
(only for files created by SDT-control)
Whether laser modulation (“attenuate”) was turned on
pixel_size : float
(only for files created by SDT-control)
Camera pixel size
sequence_type : str
(only for files created by SDT-control)
Type of sequnce (standard, TOCCSL, arbitrary, …)
grid : float
(only for files created by SDT-control)
Sequence time unit (“grid size”) in seconds
n_macro : int
(only for files created by SDT-control)
Number of macro loops
delay_macro : float
(only for files created by SDT-control)
Time between macro loops in seconds
n_mini : int
(only for files created by SDT-control)
Number of mini loops
delay_mini : float
(only for files created by SDT-control)
Time between mini loops in seconds
n_micro : int (only for files created by SDT-control)
Number of micro loops
delay_micro : float (only for files created by SDT-control)
Time between micro loops in seconds
n_subpics : int
(only for files created by SDT-control)
Number of sub-pictures
delay_shutter : float
(only for files created by SDT-control)
Camera shutter delay in seconds
delay_prebleach : float
(only for files created by SDT-control)
Pre-bleach delay in seconds
bleach_time : float
(only for files created by SDT-control)
Bleaching time in seconds
recovery_time : float
(only for files created by SDT-control)
Recovery time in seconds
comment : str
(only for files created by SDT-control)
User-entered comment. This replaces the "comments" field.
datetime : datetime.datetime
(only for files created by SDT-control)
Combines the "date" and "time_local" keys. The latter two plus
"time_utc" are removed.
modulation_script : str
(only for files created by SDT-control)
Laser modulation script. Replaces the "spare_4" key.
bleach_piezo_active : bool
(only for files created by SDT-control)
Whether piezo for bleaching was enabled
"""
if self._file_header_ver < 3:
if self._char_encoding is not None:
char_encoding = self._char_encoding
if self._sdt_meta is not None:
sdt_control = self._sdt_meta
return self._metadata_pre_v3(char_encoding, sdt_control)
return self._metadata_post_v3()
def _metadata_pre_v3(self, char_encoding: str, sdt_control: bool) -> Dict[str, Any]:
"""Extract metadata from SPE v2 files
Parameters
----------
char_encoding
String character encoding
sdt_control
If `True`, try to decode special metadata written by the
SDT-control software.
Returns
-------
dict mapping metadata names to values.
"""
m = self._parse_header(Spec.metadata, char_encoding)
nr = m.pop("NumROI", None)
nr = 1 if nr < 1 else nr
m["ROIs"] = roi_array_to_dict(m["ROIs"][:nr])
# chip sizes
m["chip_size"] = [m.pop(k, None) for k in ("xDimDet", "yDimDet")]
m["virt_chip_size"] = [m.pop(k, None) for k in ("VChipXdim", "VChipYdim")]
m["pre_pixels"] = [m.pop(k, None) for k in ("XPrePixels", "YPrePixels")]
m["post_pixels"] = [m.pop(k, None) for k in ("XPostPixels", "YPostPixels")]
# convert comments from numpy.str_ to str
m["comments"] = [str(c) for c in m["comments"]]
# geometric operations
g = []
f = m.pop("geometric", 0)
if f & 1:
g.append("rotate")
if f & 2:
g.append("reverse")
if f & 4:
g.append("flip")
m["geometric"] = g
# Make some additional information more human-readable
t = m["type"]
if 1 <= t <= len(Spec.controllers):
m["type"] = Spec.controllers[t - 1]
else:
m["type"] = None
r = m["readout_mode"]
if 1 <= r <= len(Spec.readout_modes):
m["readout_mode"] = Spec.readout_modes[r - 1]
else:
m["readout_mode"] = None
# bools
for k in (
"absorb_live",
"can_do_virtual_chip",
"threshold_min_live",
"threshold_max_live",
):
m[k] = bool(m[k])
# Extract SDT-control metadata if desired
if sdt_control:
SDTControlSpec.extract_metadata(m, char_encoding)
return m
def _metadata_post_v3(self) -> Dict[str, Any]:
"""Extract XML metadata from SPE v3 files
Returns
-------
dict with key `"__xml"`, whose value is the XML metadata
"""
info = self._parse_header(Spec.basic, "latin1")
self._file.seek(info["xml_footer_offset"])
xml = self._file.read()
return {"__xml": xml}
def properties(self, index: int = ...) -> ImageProperties:
"""Standardized ndimage metadata.
Parameters
----------
index : int
If the index is an integer, select the index-th frame and return
its properties. If index is an Ellipsis (...), return the
properties of all frames in the file stacked along a new batch
dimension.
Returns
-------
properties : ImageProperties
A dataclass filled with standardized image metadata.
"""
if index is Ellipsis:
return ImageProperties(
shape=(self._len, *self._shape),
dtype=self._dtype,
n_images=self._len,
is_batch=True,
)
return ImageProperties(shape=self._shape, dtype=self._dtype, is_batch=False)
def _parse_header(
self, spec: Mapping[str, Tuple], char_encoding: str
) -> Dict[str, Any]:
"""Get information from SPE file header
Parameters
----------
spec
Maps header entry name to its location, data type description and
optionally number of entries. See :py:attr:`Spec.basic` and
:py:attr:`Spec.metadata`.
char_encoding
String character encoding
Returns
-------
Dict mapping header entry name to its value
"""
ret = {}
# Decode each string from the numpy array read by np.fromfile
decode = np.vectorize(lambda x: x.decode(char_encoding))
for name, sp in spec.items():
self._file.seek(sp[0])
cnt = 1 if len(sp) < 3 else sp[2]
v = np.fromfile(self._file, dtype=sp[1], count=cnt)
if v.dtype.kind == "S" and name not in Spec.no_decode:
# Silently ignore string decoding failures
try:
v = decode(v)
except Exception:
warnings.warn(
f'Failed to decode "{name}" metadata '
"string. Check `char_encoding` parameter."
)
try:
# For convenience, if the array contains only one single
# entry, return this entry itself.
v = v.item()
except ValueError:
v = np.squeeze(v)
ret[name] = v
return ret
def roi_array_to_dict(a: np.ndarray) -> List[Dict[str, List[int]]]:
"""Convert the `ROIs` structured arrays to :py:class:`dict`
Parameters
----------
a
Structured array containing ROI data
Returns
-------
One dict per ROI. Keys are "top_left", "bottom_right", and "bin",
values are tuples whose first element is the x axis value and the
second element is the y axis value.
"""
dict_list = []
a = a[["startx", "starty", "endx", "endy", "groupx", "groupy"]]
for sx, sy, ex, ey, gx, gy in a:
roi_dict = {
"top_left": [int(sx), int(sy)],
"bottom_right": [int(ex), int(ey)],
"bin": [int(gx), int(gy)],
}
dict_list.append(roi_dict)
return dict_list