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from datetime import datetime
import os
import shutil
import struct
import numpy as np
import pytest
import imageio.v3 as iio
from imageio.plugins import spe
frame0 = np.zeros((32, 32), np.uint16)
frame1 = np.ones_like(frame0)
def test_imopen(test_images, tmp_path):
with iio.imopen(test_images / "test_000_.SPE", "r") as img:
assert isinstance(img, spe.SpePlugin)
with pytest.raises(OSError):
iio.imopen(tmp_path / "test.spe", "w", plugin="SPE")
with open(tmp_path / "stub.spe", "wb") as f:
f.write(b"\x00\x01\x02\x03")
with pytest.raises(OSError):
iio.imopen(tmp_path / "stub.spe", "r", plugin="SPE")
def test_read(test_images):
fname = test_images / "test_000_.SPE"
im = iio.imread(fname, index=0)
np.testing.assert_equal(im, frame0)
ims = iio.imread(fname, index=...)
np.testing.assert_equal(ims, [frame0, frame1])
with pytest.raises(IndexError):
iio.imread(fname, index=-1)
with pytest.raises(IndexError):
iio.imread(fname, index=2)
def test_iter(test_images):
for actual, desired in zip(
iio.imiter(test_images / "test_000_.SPE"), (frame0, frame1)
):
np.testing.assert_equal(actual, desired)
def test_metadata(test_images, tmp_path):
fname = test_images / "test_000_.SPE"
meta = iio.immeta(fname, sdt_control=False)
with pytest.deprecated_call():
meta2 = iio.imopen(fname, "r", sdt_meta=False).metadata()
for md in (meta, meta2):
assert md.get("ROIs") == [
{"top_left": [238, 187], "bottom_right": [269, 218], "bin": [1, 1]}
]
cmt = [
"OD 1.0 in r, g "
" ",
"000200000000000004800000000000000000000000000000000000000000000000"
"0002000001000X",
" "
" ",
" "
" ",
"ACCI2xSEQU-1---10000010001600300EA SW"
"0218COMVER0500",
]
assert md.get("comments") == cmt
assert md.get("geometric") == []
assert md.get("type", "") is None
assert md.get("readout_mode", "") is None
sdt_meta = iio.immeta(fname, sdt_control=True)
with pytest.deprecated_call():
sdt_meta2 = iio.imopen(fname, "r", sdt_meta=True).metadata()
for md in (sdt_meta, sdt_meta2):
assert md.get("delay_shutter") == pytest.approx(0.001)
assert md.get("delay_macro") == pytest.approx(0.048)
assert md.get("exposure_time") == pytest.approx(0.002)
assert md.get("comment") == "OD 1.0 in r, g"
assert md.get("datetime") == datetime(2018, 7, 2, 9, 46, 15)
assert md.get("sdt_major_version") == 2
assert md.get("sdt_minor_version") == 18
assert isinstance(md.get("modulation_script"), str)
assert md.get("sequence_type") == "standard"
assert "bleach_piezo_active" not in md
patched = tmp_path / fname.name
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Scramble "COMVER" in the comments. In this case, SDT-control metadata
# should not be extracted.
f.seek(595)
f.write(b"x")
# Add something to `geometric`
f.seek(600)
f.write(struct.pack("<H", 7))
# Set `type`
f.seek(704)
f.write(struct.pack("<h", 1))
# Set `readout_mode`
f.seek(1480)
f.write(struct.pack("<H", 2))
patched_cmt = cmt.copy()
patched_cmt[4] = patched_cmt[4].replace("COMVER0500", "COMVEx0500")
patched_meta = iio.immeta(patched, sdt_control=True)
# Parsing any SDT-control metadata should fail
assert patched_meta.get("comments") == patched_cmt
assert "delay_shutter" not in patched_meta
assert patched_meta.get("geometric") == ["rotate", "reverse", "flip"]
assert patched_meta.get("type", "") == "new120 (Type II)"
assert patched_meta.get("readout_mode", "") == "frame transfer"
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Set SDT-control sequence type to something invalid.
f.seek(526)
f.write(b"INVA")
# Change date to something invalid.
f.seek(20)
f.write(b"02Inv2018")
# Add non-ASCII character to laser modulation script
f.seek(745)
f.write(b"\xff")
# Add non-ASCII character to `sw_version`
f.seek(690)
f.write(b"\xff")
with pytest.warns(UserWarning):
patched_meta = iio.immeta(patched, sdt_control=True, char_encoding="ascii")
# Decoding `sequence_type` should fail
assert patched_meta.get("sequence_type", "") is None
# Decoding `date` and `time_local` into `datetime` should fail
assert patched_meta.get("date") == "02Inv2018"
assert "datetime" not in patched_meta
# Decoding `spare_4` into `modulation_script` should fail
assert "modulation_script" not in patched_meta
assert isinstance(patched_meta.get("spare_4"), bytes)
# Decoding `sw_version` should fail
assert isinstance(patched_meta.get("sw_version"), bytes)
with pytest.deprecated_call():
patched_meta2 = iio.imopen(
patched, "r", sdt_meta=True, char_encoding="ascii"
).metadata()
assert patched_meta2.get("sequence_type", "") is None
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Scramble version numbers following "COMVER" in the comments. In this
# case, SDT-control metadata should not be extracted.
f.seek(597)
f.write(b"x")
patched_cmt = cmt.copy()
patched_cmt[4] = patched_cmt[4].replace("COMVER0500", "COMVER0x00")
patched_meta = iio.immeta(patched, sdt_control=True)
# Parsing any SDT-control metadata should fail
assert patched_meta.get("comments") == patched_cmt
assert "delay_shutter" not in patched_meta
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Set SDT-control metadata version to 6.00. No metadata should be
# extracted and there should be a warning.
f.seek(597)
f.write(b"6")
with pytest.warns(UserWarning):
patched_meta = iio.immeta(patched, sdt_control=True)
# Parsing any SDT-control metadata should fail, only comment should be there
assert patched_meta.get("comment") == "OD 1.0 in r, g"
assert "delay_shutter" not in patched_meta
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Set SDT-control metadata version to 5.99. Metadata should still be
# extracted, but there should be a warning
f.seek(599)
f.write(b"99")
with pytest.warns(UserWarning):
patched_meta = iio.immeta(patched, sdt_control=True)
assert patched_meta.get("delay_shutter") == pytest.approx(0.001)
assert patched_meta.get("delay_macro") == pytest.approx(0.048)
assert patched_meta.get("exposure_time") == pytest.approx(0.002)
assert patched_meta.get("comment") == "OD 1.0 in r, g"
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Create a fake SPE v3 file
f.seek(1992)
f.write(struct.pack("<f", 3.0))
f.seek(0, os.SEEK_END)
sz = f.tell()
f.write(b"Here could be your XML.")
f.seek(678)
f.write(struct.pack("<Q", sz))
patched_meta = iio.immeta(patched)
assert patched_meta == {"__xml": b"Here could be your XML."}
def test_sdtcontrol_v0501(test_images):
fname = test_images / "test_v0501_000_.SPE"
md = iio.immeta(fname)
assert md.get("bleach_piezo_active") is False
assert md.get("sdt_major_version") == 3
assert md.get("sdt_minor_version") == 4
assert md.get("datetime") == datetime(2023, 5, 3, 15, 13, 16)
def test_properties(test_images, tmp_path):
fname = test_images / "test_000_.SPE"
props0 = iio.improps(fname, index=0)
assert props0.shape == (32, 32)
assert props0.dtype == np.uint16
assert props0.n_images is None
assert not props0.is_batch
props = iio.improps(fname, index=...)
assert props.shape == (2, 32, 32)
assert props.dtype == np.uint16
assert props.n_images == 2
assert props.is_batch
patched = tmp_path / fname.name
shutil.copy(fname, patched)
with patched.open("r+b") as f:
# Set incorrect number of images
f.seek(1446)
f.write(struct.pack("<i", 3))
# Test `check_filesize`
with iio.imopen(patched, "r", check_filesize=False) as img:
assert (
img.properties(
index=...,
).n_images
== 3
)
with pytest.warns():
with iio.imopen(patched, "r", check_filesize=True) as img:
assert (
img.properties(
index=...,
).n_images
== 2
)
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