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Hello community,
here is the log from the commit of package python-lfdfiles for openSUSE:Factory
checked in at 2026-06-28 21:07:21
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-lfdfiles (Old)
and /work/SRC/openSUSE:Factory/.python-lfdfiles.new.11887 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-lfdfiles"
Sun Jun 28 21:07:21 2026 rev:12 rq:1362043 version:2026.6.24
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-lfdfiles/python-lfdfiles.changes
2026-05-18 17:47:15.178408955 +0200
+++
/work/SRC/openSUSE:Factory/.python-lfdfiles.new.11887/python-lfdfiles.changes
2026-06-28 21:08:00.869067006 +0200
@@ -1,0 +2,7 @@
+Sat Jun 27 20:54:28 UTC 2026 - Dirk Müller <[email protected]>
+
+- update to 2026.6.24:
+ * Add VistaTdflim class for reading ISS Vista TDFLIM files.
+ * Support Python 3.15.
+
+-------------------------------------------------------------------
Old:
----
lfdfiles-2026.4.30.tar.gz
New:
----
lfdfiles-2026.6.24.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-lfdfiles.spec ++++++
--- /var/tmp/diff_new_pack.GEMl1Y/_old 2026-06-28 21:08:01.369083854 +0200
+++ /var/tmp/diff_new_pack.GEMl1Y/_new 2026-06-28 21:08:01.369083854 +0200
@@ -25,7 +25,7 @@
%{?sle15_python_module_pythons}
%global skip_python311 1
Name: python-lfdfiles
-Version: 2026.4.30
+Version: 2026.6.24
Release: 0
Summary: Laboratory for Fluorescence Dynamics (LFD) file formats
License: BSD-3-Clause
++++++ lfdfiles-2026.4.30.tar.gz -> lfdfiles-2026.6.24.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/lfdfiles-2026.4.30/CHANGES.rst
new/lfdfiles-2026.6.24/CHANGES.rst
--- old/lfdfiles-2026.4.30/CHANGES.rst 2026-04-29 20:10:59.000000000 +0200
+++ new/lfdfiles-2026.6.24/CHANGES.rst 2026-06-24 20:08:13.000000000 +0200
@@ -1,6 +1,11 @@
Revisions
=========
+2026.6.24
+
+- Add VistaTdflim class for reading ISS Vista TDFLIM files.
+- Support Python 3.15.
+
2026.4.30
- Remove FlimboxFbd, FlimboxFbf, and FlimboxFbs (breaking; use fbdfile).
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/lfdfiles-2026.4.30/README.rst
new/lfdfiles-2026.6.24/README.rst
--- old/lfdfiles-2026.4.30/README.rst 2026-04-29 20:10:59.000000000 +0200
+++ new/lfdfiles-2026.6.24/README.rst 2026-06-24 20:08:13.000000000 +0200
@@ -15,12 +15,12 @@
- CCP4 MAP
- Vaa3D RAW
- Bio-Rad(r) PIC
-- ISS Vista IFLI, IFI
+- ISS Vista IFLI, IFI, TDFLIM
- FlimFast FLIF
:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
:License: BSD-3-Clause
-:Version: 2026.4.30
+:Version: 2026.6.24
:DOI: `10.5281/zenodo.8384166 <https://doi.org/10.5281/zenodo.8384166>`_
Quickstart
@@ -48,17 +48,22 @@
This revision was tested with the following requirements and dependencies
(other versions may work):
-- `CPython <https://www.python.org>`_ 3.12.10, 3.13.13, 3.14.4 64-bit
-- `NumPy <https://pypi.org/project/numpy>`_ 2.4.4
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.4.11
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.9
+- `CPython <https://www.python.org>`_ 3.12.10, 3.13.14, 3.14.6, 3.15.0b3 64-bit
+- `Numpy <https://pypi.org/project/numpy>`_ 2.5.0
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.6.1
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.11.0
(optional, for plotting)
-- `Click <https://pypi.python.org/pypi/click>`_ 8.3.3
+- `Click <https://pypi.python.org/pypi/click>`_ 8.4.1
(optional, for command line apps)
Revisions
---------
+2026.6.24
+
+- Add VistaTdflim class for reading ISS Vista TDFLIM files.
+- Support Python 3.15.
+
2026.4.30
- Remove FlimboxFbd, FlimboxFbf, and FlimboxFbs (breaking; use fbdfile).
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/lfdfiles-2026.4.30/lfdfiles/lfdfiles.py
new/lfdfiles-2026.6.24/lfdfiles/lfdfiles.py
--- old/lfdfiles-2026.4.30/lfdfiles/lfdfiles.py 2026-04-29 20:10:59.000000000
+0200
+++ new/lfdfiles-2026.6.24/lfdfiles/lfdfiles.py 2026-06-24 20:08:13.000000000
+0200
@@ -42,12 +42,12 @@
- CCP4 MAP
- Vaa3D RAW
- Bio-Rad(r) PIC
-- ISS Vista IFLI, IFI
+- ISS Vista IFLI, IFI, TDFLIM
- FlimFast FLIF
:Author: `Christoph Gohlke <https://www.cgohlke.com>`_
:License: BSD-3-Clause
-:Version: 2026.4.30
+:Version: 2026.6.24
:DOI: `10.5281/zenodo.8384166 <https://doi.org/10.5281/zenodo.8384166>`_
Quickstart
@@ -75,17 +75,22 @@
This revision was tested with the following requirements and dependencies
(other versions may work):
-- `CPython <https://www.python.org>`_ 3.12.10, 3.13.13, 3.14.4 64-bit
-- `NumPy <https://pypi.org/project/numpy>`_ 2.4.4
-- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.4.11
-- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.10.9
+- `CPython <https://www.python.org>`_ 3.12.10, 3.13.14, 3.14.6, 3.15.0b3 64-bit
+- `Numpy <https://pypi.org/project/numpy>`_ 2.5.0
+- `Tifffile <https://pypi.org/project/tifffile/>`_ 2026.6.1
+- `Matplotlib <https://pypi.org/project/matplotlib/>`_ 3.11.0
(optional, for plotting)
-- `Click <https://pypi.python.org/pypi/click>`_ 8.3.3
+- `Click <https://pypi.python.org/pypi/click>`_ 8.4.1
(optional, for command line apps)
Revisions
---------
+2026.6.24
+
+- Add VistaTdflim class for reading ISS Vista TDFLIM files.
+- Support Python 3.15.
+
2026.4.30
- Remove FlimboxFbd, FlimboxFbf, and FlimboxFbs (breaking; use fbdfile).
@@ -233,7 +238,7 @@
from __future__ import annotations
-__version__ = '2026.4.30'
+__version__ = '2026.6.24'
__all__ = [
'FILE_EXTENSIONS',
@@ -270,6 +275,7 @@
'Vaa3dRaw',
'VistaIfi',
'VistaIfli',
+ 'VistaTdflim',
'VoxxMap',
'__version__',
'bioradpic_write',
@@ -1038,7 +1044,7 @@
def imread_func(
filename: str | os.PathLike[Any],
/,
- lfdfile: type[LfdFile] = imread, # type: ignore[assignment]
+ lfdfile: type[LfdFile] = imread,
**kwargs: Any,
) -> NDArray[Any]:
with lfdfile(filename) as lfdf:
@@ -3532,6 +3538,329 @@
)
+class VistaTdflim(LfdFile):
+ """ISS Vista time-domain fluorescence lifetime image.
+
+ VistaTdflim files are ZIP archives containing acquisition metadata in
+ ``dataProps/Core.xml`` and raw photon histogram data in
+ ``data/PrimaryDecayData.bin``.
+
+ Two binary format variants exist, identified by the ``<FileVersion>``
+ element in the XML:
+
+ - Version 1 (``<FileVersion>`` absent):
+ ``uint16``, dimension order ``TCYXH``.
+ - Version 2 (``<iVersionNumber>2</iVersionNumber>``):
+ ``uint32``, dimension order ``TCYX(H+2)``.
+ The last dimension contains two trailing uint32 words per pixel
+ (reserved zero word and a pre-computed float32 lifetime preview).
+
+ The returned array has shape ``(T, C, Y, X, H)``, where T is the number
+ of time series points, C is the channel count, Y and X are spatial
+ dimensions, and H is the photon histogram bin count.
+
+ Parameters:
+ filename: Name of file to open.
+
+ Examples:
+ >>> with VistaTdflim(DATA / 'version1.iss-tdflim') as f:
+ ... data = f.asarray()
+ ... f.axes
+ ...
+ 'TCYXH'
+ >>> data.shape
+ (1, 2, 128, 128, 1024)
+ >>> with VistaTdflim(DATA / 'version2.iss-tdflim') as f:
+ ... data = f.asarray()
+ ... data.shape
+ ...
+ (1, 1, 128, 128, 4096)
+
+ """
+
+ _filepattern = r'.*\.(iss-tdflim|tdflim)$'
+
+ attrs: dict[str, Any]
+ """Metadata from Core.xml."""
+
+ coords: dict[str, NDArray[Any]]
+ """Coordinate arrays keyed by one-letter axis codes."""
+
+ @override
+ def _init(self, **kwargs: Any) -> None:
+ """Read and parse metadata from Core.xml inside ZIP archive."""
+ from xml.etree import ElementTree
+
+ assert self._fh is not None
+ try:
+ with zipfile.ZipFile(self._fh) as zf:
+ xml_files = [
+ n for n in zf.namelist() if n.endswith('Core.xml')
+ ]
+ if not xml_files:
+ raise LfdFileError(self, 'Core.xml not found')
+ with zf.open(xml_files[0]) as fh:
+ root = ElementTree.parse(fh).getroot() # noqa: S314
+ bin_files = [
+ n
+ for n in zf.namelist()
+ if n.endswith('PrimaryDecayData.bin')
+ ]
+ if not bin_files:
+ raise LfdFileError(self, 'PrimaryDecayData.bin not found')
+ bin_size = zf.getinfo(bin_files[0]).file_size
+ except zipfile.BadZipFile as exc:
+ raise LfdFileError(self) from exc
+
+ data_type = root.findtext('DataType')
+ if data_type != 'TDFlimData':
+ raise LfdFileError(
+ self,
+ f'unsupported DataType {data_type!r}, expected TDFlimData',
+ )
+
+ # parse dimensions
+ dims = root.find('Dimensions')
+ pcs = root.find('PhotonCountingSettings')
+ if dims is None or pcs is None:
+ raise LfdFileError(self, 'missing required XML elements')
+
+ def _int(node: ElementTree.Element, tag: str) -> int:
+ el = node.find(tag)
+ if el is None or not el.text:
+ raise LfdFileError(self, f'<{tag}> not found')
+ return int(el.text.strip())
+
+ def _float(node: ElementTree.Element, tag: str) -> float:
+ el = node.find(tag)
+ if el is None or not el.text:
+ raise LfdFileError(self, f'<{tag}> not found')
+ return float(el.text.strip())
+
+ sizet = _int(dims, 'TimeSeriesCount')
+ sizec = _int(dims, 'ChannelCount')
+ sizey = _int(dims, 'FrameHeight')
+ sizex = _int(dims, 'FrameWidth')
+ sizeh = _int(pcs, 'AdcResolution')
+
+ fv_node = root.find('FileVersion')
+ if fv_node is not None:
+ iv = fv_node.find('iVersionNumber')
+ file_version = (
+ int(iv.text.strip()) if iv is not None and iv.text else 1
+ )
+ else:
+ file_version = 1
+
+ size = sizet * sizec * sizey * sizex
+ if file_version == 1:
+ expected = size * sizeh * 2
+ if bin_size != expected:
+ raise LfdFileError(
+ self,
+ f'binary size mismatch (version 1): '
+ f'expected {expected}, got {bin_size}',
+ )
+ self.dtype = numpy.dtype(numpy.uint16)
+ elif file_version == 2:
+ expected = size * (sizeh + 2) * 4
+ if bin_size != expected:
+ raise LfdFileError(
+ self,
+ f'binary size mismatch (version 2): '
+ f'expected {expected}, got {bin_size}',
+ )
+ self.dtype = numpy.dtype(numpy.uint32)
+ else:
+ raise LfdFileError(
+ self, f'unsupported file version {file_version!r}'
+ )
+
+ # parse metadata attributes
+ channel_ids_node = root.find('ChannelIds')
+ if channel_ids_node is not None:
+ channel_ids = [
+ int(el.text.strip())
+ for el in channel_ids_node.findall('ChannelId')
+ if el.text
+ ]
+ else:
+ channel_ids = list(range(sizec))
+ if len(channel_ids) != sizec:
+ channel_ids = list(range(sizec))
+
+ units = {
+ 'micrometer': 'um',
+ 'nanometer': 'nm',
+ 'millimeter': 'mm',
+ 'pixel': 'px',
+ }
+ coord_unit_type = root.findtext('CoordUnitType') or ''
+ spatial_unit = units.get(coord_unit_type.lower(), coord_unit_type)
+
+ tac_time_range = _float(pcs, 'TacTimeRange')
+
+ ef_node = root.find('.//ExcitationFrequency')
+ if ef_node is not None and ef_node.text:
+ frequency = float(ef_node.text.strip()) / 1e6
+ else:
+ frequency = 1e3 / tac_time_range
+
+ self.attrs = {
+ 'file_version': file_version,
+ 'datetime_stamp': root.findtext('DateTimeStamp') or '',
+ 'channel_ids': channel_ids,
+ 'frequency': frequency,
+ 'tac_time_range': tac_time_range,
+ 'macro_time_clock_frequency': _float(
+ pcs, 'MacroTimeClockFrequency'
+ ),
+ 'pixel_dwell_time': _float(root, 'PixelDwellTime'),
+ 'coord_unit_type': coord_unit_type,
+ 'spatial_unit': spatial_unit,
+ }
+
+ # parse axes coordinates
+ self.coords = {}
+ time_series = root.find('TimeSeries')
+ if time_series is not None:
+ tags_node = time_series.find('TimeSeriesTags')
+ if tags_node is not None:
+ tags = [
+ float(el.text.strip())
+ for el in tags_node.findall('TimeTag')
+ if el.text
+ ]
+ if len(tags) == sizet:
+ self.coords['T'] = numpy.asarray(tags, dtype=numpy.float64)
+
+ self.coords['C'] = numpy.asarray(channel_ids, dtype=numpy.uint16)
+
+ boundary = root.find('Boundary')
+ if boundary is not None:
+ frame_top = boundary.findtext('FrameTop')
+ frame_bottom = boundary.findtext('FrameBottom')
+ frame_left = boundary.findtext('FrameLeft')
+ frame_right = boundary.findtext('FrameRight')
+
+ if frame_top is not None and frame_bottom is not None:
+ self.coords['Y'] = numpy.linspace(
+ float(frame_top),
+ float(frame_bottom),
+ sizey,
+ endpoint=False,
+ )
+ if frame_left is not None and frame_right is not None:
+ self.coords['X'] = numpy.linspace(
+ float(frame_left),
+ float(frame_right),
+ sizex,
+ endpoint=False,
+ )
+
+ bnd_width = boundary.findtext('FrameWidth')
+ bnd_height = boundary.findtext('FrameHeight')
+ if bnd_width is not None:
+ self.attrs['frame_width'] = float(bnd_width)
+ if bnd_height is not None:
+ self.attrs['frame_height'] = float(bnd_height)
+
+ self.coords['H'] = numpy.linspace(
+ 0, tac_time_range, sizeh, endpoint=False
+ )
+
+ self.shape = (sizet, sizec, sizey, sizex, sizeh)
+ self.axes = 'TCYXH'
+
+ @override
+ def _asarray(self, **kwargs: Any) -> NDArray[Any]:
+ """Return photon histogram array of shape (T, C, Y, X, H)."""
+ assert self._fh is not None
+ assert self.shape is not None
+ assert self.dtype is not None
+ sizet, sizec, sizey, sizex, sizeh = self.shape
+ file_version = self.attrs['file_version']
+
+ with zipfile.ZipFile(self._fh) as zf:
+ bin_files = [
+ n for n in zf.namelist() if n.endswith('PrimaryDecayData.bin')
+ ]
+ with zf.open(bin_files[0]) as fh:
+ raw = fh.read()
+
+ if file_version == 1:
+ data = numpy.frombuffer(raw, dtype=numpy.uint16)
+ return data.reshape(self.shape).copy()
+ # version 2: each pixel has H uint32 counts + 2 uint32 footer words
+ data32 = numpy.frombuffer(raw, dtype=numpy.uint32)
+ counts = data32.reshape(sizet * sizec * sizey * sizex, sizeh + 2)[
+ :, :sizeh
+ ]
+ return counts.reshape(self.shape).copy()
+
+ def lifetime(self) -> NDArray[numpy.float32]:
+ """Return lifetime image from version 2 file as NumPy array.
+
+ The returned array has shape ``(T, C, Y, X)`` and type float32.
+ The lifetime values are pre-computed by the ISS Vista acquisition
+ software.
+
+ """
+ assert self._fh is not None
+ assert self.shape is not None
+ if self.attrs['file_version'] != 2:
+ msg = 'lifetime is only available for version 2 files'
+ raise ValueError(self, msg)
+ sizet, sizec, sizey, sizex, sizeh = self.shape
+ with zipfile.ZipFile(self._fh) as zf:
+ bin_file = next(
+ n for n in zf.namelist() if n.endswith('PrimaryDecayData.bin')
+ )
+ with zf.open(bin_file) as fh:
+ buffer = fh.read()
+ # layout: (pixels, H + 2); last column is float32 lifetime
+ lifetime = numpy.frombuffer(buffer, dtype=numpy.float32)
+ lifetime = lifetime.reshape((sizet, sizec, sizey, sizex, sizeh + 2))
+ return lifetime[..., -1].copy()
+
+ @override
+ def _plot(self, figure: Figure, /, **kwargs: Any) -> None:
+ """Display data in matplotlib figure."""
+ assert pyplot is not None
+ update_kwargs(kwargs, cmap='viridis')
+ pyplot.subplots_adjust(bottom=0.07, top=0.93)
+
+ channel = kwargs.pop('channel', 0)
+
+ data = self.asarray()
+ image = numpy.mean(data[:, channel], axis=(0, -1))
+ hist = numpy.mean(data, axis=(0, 2, 3))
+
+ ax = pyplot.subplot2grid((3, 1), (0, 0), colspan=2, rowspan=2)
+ ax.set_title(self._filename + f' (Ch{channel})')
+ ax.imshow(image, **kwargs)
+ ax = pyplot.subplot2grid((3, 1), (2, 0))
+ ax.set_title('Mean')
+ ax.set_xlim([0, hist.shape[-1] - 1])
+ ax.set_xlabel('Histogram bin')
+ for h in hist:
+ ax.plot(h)
+
+ @override
+ def _totiff(self, tif: TiffWriter, /, **kwargs: Any) -> None:
+ """Write image data to TIFF file."""
+ update_kwargs(kwargs, metadata={'axes': self.axes})
+ tif.write(self.asarray(), **kwargs)
+
+ @override
+ def _str(self) -> str | None:
+ """Return additional information about file."""
+ return indent(
+ 'attrs:',
+ *(f'{k}: {v}' for k, v in self.attrs.items()),
+ )
+
+
class FlimfastFlif(LfdFile):
"""FlimFast fluorescence lifetime image.
@@ -5156,6 +5485,8 @@
'.z64': SimfcsZ64,
'.cyl': SimfcsCyl,
'.ifli': VistaIfli,
+ '.iss-tdflim': VistaTdflim,
+ '.tdflim': VistaTdflim,
'.vpl': SimfcsVpl,
'.vpp': SimfcsVpp,
'.ifi': VistaIfi,
@@ -5163,6 +5494,7 @@
'.flif': FlimfastFlif,
'.v3draw': Vaa3dRaw,
}
+"""Supported LFD file extensions."""
if __name__ == '__main__':
main()
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/lfdfiles-2026.4.30/setup.py
new/lfdfiles-2026.6.24/setup.py
--- old/lfdfiles-2026.4.30/setup.py 2026-04-29 20:10:59.000000000 +0200
+++ new/lfdfiles-2026.6.24/setup.py 2026-06-24 20:08:13.000000000 +0200
@@ -96,7 +96,7 @@
project_urls={
'Bug Tracker': 'https://github.com/cgohlke/lfdfiles/issues',
'Source Code': 'https://github.com/cgohlke/lfdfiles',
- # 'Documentation': 'https://',
+ 'Documentation': 'https://www.cgohlke.com/docs/lfdfiles',
},
packages=['lfdfiles'],
package_data={'lfdfiles': ['py.typed']},
@@ -116,5 +116,6 @@
'Programming Language :: Python :: 3.12',
'Programming Language :: Python :: 3.13',
'Programming Language :: Python :: 3.14',
+ 'Programming Language :: Python :: 3.15',
],
)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/lfdfiles-2026.4.30/tests/test_lfdfiles.py
new/lfdfiles-2026.6.24/tests/test_lfdfiles.py
--- old/lfdfiles-2026.4.30/tests/test_lfdfiles.py 2026-04-29
20:10:59.000000000 +0200
+++ new/lfdfiles-2026.6.24/tests/test_lfdfiles.py 2026-06-24
20:08:13.000000000 +0200
@@ -29,7 +29,7 @@
"""Unittests for the lfdfiles package.
-:Version: 2026.4.30
+:Version: 2026.6.24
"""
@@ -59,6 +59,7 @@
GlobalsAscii,
GlobalsLif,
LfdFile,
+ LfdFileError,
LfdFileSequence,
RawPal,
SimfcsB64,
@@ -80,6 +81,7 @@
Vaa3dRaw,
VistaIfi,
VistaIfli,
+ VistaTdflim,
VoxxMap,
bioradpic_write,
ccp4map_write,
@@ -124,13 +126,13 @@
) as f:
assert type(f) is SimfcsBin
- with pytest.raises(lfdfiles.LfdFileError):
+ with pytest.raises(LfdFileError):
LfdFile.open(DATA / 'flimfast.flif', registry=[])
def test_lfdfileerror():
"""Test LfdFileError is a ValueError subclass."""
- assert issubclass(lfdfiles.LfdFileError, ValueError)
+ assert issubclass(LfdFileError, ValueError)
def test_module_docstring_example():
@@ -203,7 +205,7 @@
def test_lfdfile_validate():
"""Test LfdFile raises LfdFileError on filename pattern mismatch."""
- with pytest.raises(lfdfiles.LfdFileError):
+ with pytest.raises(LfdFileError):
SimfcsRef('wrong_extension.xyz')
@@ -569,6 +571,65 @@
assert_array_equal(tif.asarray()[0, 0], data[..., 0, 0])
+def test_vistatdflim_v1():
+ """Test VistaTdflim with version 1 file (uint16)."""
+ with VistaTdflim(DATA / 'version1.iss-tdflim') as f:
+ data = f.asarray()
+ f.totiff(TEMP / '_vista_tdflim_v1.tif')
+ assert f.axes == 'TCYXH'
+ assert f.shape == (1, 2, 128, 128, 1024)
+ assert f.dtype == numpy.uint16
+ assert f.attrs['file_version'] == 1
+ assert f.attrs['datetime_stamp'] == '2022-11-18T16:40:35.9871206+01:00'
+ assert f.attrs['channel_ids'] == [0, 2]
+ assert pytest.approx(f.attrs['frequency'], 0.001) == 79.9463
+ assert pytest.approx(f.attrs['tac_time_range'], 1e-6) == 12.5083933
+ assert sorted(f.coords.keys()) == ['C', 'H', 'T', 'X', 'Y']
+ assert f.coords['T'].shape == (1,)
+ assert f.coords['C'].tolist() == [0, 2]
+ assert f.coords['Y'].shape == (128,)
+ assert f.coords['X'].shape == (128,)
+ assert f.coords['H'].shape == (1024,)
+ assert data.shape == f.shape
+ assert int(data[0, 0, 3, 0, 97]) == 1980
+
+ with pytest.raises(ValueError):
+ f.lifetime()
+
+ with TiffFile(TEMP / '_vista_tdflim_v1.tif') as tif:
+ assert_array_equal(tif.asarray(), data)
+
+
+def test_vistatdflim_v2():
+ """Test VistaTdflim with version 2 file (uint32, with per-pixel footer)."""
+ with VistaTdflim(DATA / 'version2.iss-tdflim') as f:
+ data = f.asarray()
+ f.totiff(TEMP / '_vista_tdflim_v2.tif')
+ assert f.axes == 'TCYXH'
+ assert f.shape == (1, 1, 128, 128, 4096)
+ assert f.dtype == numpy.uint32
+ assert f.attrs['file_version'] == 2
+ assert f.attrs['datetime_stamp'] == '2026-04-22T13:00:42.4049325+02:00'
+ assert f.attrs['channel_ids'] == [2]
+ assert f.attrs['frequency'] == 20.0
+ assert sorted(f.coords.keys()) == ['C', 'H', 'T', 'X', 'Y']
+ assert f.coords['T'].shape == (1,)
+ assert f.coords['C'].tolist() == [2]
+ assert f.coords['Y'].shape == (128,)
+ assert f.coords['X'].shape == (128,)
+ assert f.coords['H'].shape == (4096,)
+ assert data.shape == f.shape
+ assert int(data[0, 0, 114, 34, 325]) == 11
+
+ lifetime = f.lifetime()
+ assert lifetime.shape == (1, 1, 128, 128)
+ assert lifetime.dtype == numpy.float32
+ assert lifetime.mean() == pytest.approx(3.007484)
+
+ with TiffFile(TEMP / '_vista_tdflim_v2.tif') as tif:
+ assert_array_equal(tif.asarray(), data)
+
+
def test_flimfastflif():
"""Test FlimfastFlif."""
f = FlimfastFlif(DATA / 'flimfast.flif')
@@ -830,9 +891,11 @@
@pytest.mark.parametrize(
'filename',
- itertools.chain.from_iterable(
- glob.glob(f'**/*{ext}', root_dir=DATA, recursive=True)
- for ext in FILE_EXTENSIONS
+ tuple(
+ itertools.chain.from_iterable(
+ glob.glob(f'**/*{ext}', root_dir=DATA, recursive=True)
+ for ext in FILE_EXTENSIONS
+ )
),
)
def test_glob(filename):
