1. Reading Microscopy Data in Python#
Choosing the right Python library for microscopy data analysis is crucial for optimizing workflow efficiency and gaining valuable insights. This guide offers a comprehensive overview of available libraries, helping you make informed decisions based on your priorities, whether it’s speed, versatility, or integration with other tools. Empower your microscopy data analysis by exploring the options tailored to meet your specific requirements.
For opening microscopy data files in Python, you have several options, each with its own advantages. Here’s a breakdown of the options and some considerations:
scikit-image (skimage.io.imread and skimage.io.imread_collection):
Used for reading standard image formats.
Provides simple and efficient functions for reading individual images or collections of images.
tifffile (tifffile.TiffFile and tifffile.TiffSequence):
Specialized for working with TIFF files, including multi-dimensional arrays.
TiffSequence is useful for handling sequences of TIFF files.
bioformats (bioformats.ImageReader):
Supports a variety of microscopy formats, especially those using the OME data model.
Handles multi-dimensional data and can read metadata.
Regarding ImageJ hyperstack organization (TZCYXS):
T: Time
Z: Z-stack (slices)
C: Channels
Y: Height
X: Width
S: Series (used for distinguishing multiple acquisitions)
For Holoviews:
It’s used for interactive visualization but doesn’t directly handle file reading. Check for memmap support and disk reading capabilities.
Regarding Bioformats standard:
Bioformats follows the OME (Open Microscopy Environment) standard, where each channel and time point is stored in a separate TIFF file. An OME.tif typically contains a single plane or a Z-stack.
About tiles and 5D in Bioformats:
In the context of Bioformats, 5D typically refers to a dataset with dimensions T-Z-C-Y-X, where T is time, Z is the z-stack, C is the channel, and Y and X are spatial dimensions. Tiles may refer to sub-images or chunks of the larger image, which can be useful for efficiently working with large datasets.
The 6D, 7D, and 8D configurations in Bioformats likely involve additional dimensions or parameters specific to certain types of microscopy data.
To understand the exact definition of 5D in Bioformats, you should refer to the Bioformats documentation or OME data model specifications for detailed information on how these dimensions are interpreted and utilized in the context of microscopy data.
1.1. Data Path Assignment and Imports#
To begin our analysis, we first need to import the necessary libraries and assign the path to our data files. This step ensures that we have access to the tools and resources required for the subsequent tasks.
Let’s get started by executing the following code:
[1]:
%load_ext autoreload
%autoreload 2
from pathlib import Path
import skimage.io
import tifffile
import nima_io.read as ir
tdata = Path("../../tests/data/")
lif = tdata / "2015Aug28_TransHXB2_50min+DMSO.lif"
img_tile = tdata / "t4_1.tif" # C=3 T=4 S=15
img_void_tile = tdata / "tile6_1.tif" # C=4 T=3 S=14 scattered
# imgsingle = tdata / "exp2_2.tif" # C=2 T=81
# mcts = tdata / "multi-channel-time-series.ome.tif" # C=3 T=7
# bigtiff = tdata / "LC26GFP_1.tf8" # bigtiff
slif = str(lif)
simg_tile = str(img_tile)
simg_void_tile = str(img_void_tile)
# simgsingle = str(imgsingle)
# smcts = str(mcts)
# sbigtiff = str(bigtiff)
1.2. Skimage and Tifffile#
scikit-image serves as a versatile option for general image reading, encompassing various formats, including TIFF. Meanwhile tifffile stands out for its capabilities in managing sequences, OME metadata, memory mapping, and Zarr arrays specifically for TIFF data files.
Memory mapping
memmapenables efficient work with large files by mapping portions into memory as needed, without loading the entire file.Zarrstorage format, known for its handling of chunked, compressed, and n-dimensional arrays. This provides flexibility in reading and writing Zarr arrays, contributing to the library’s versatility in managing microscopy datasets, especially those with large or complex structures.
[2]:
t1 = skimage.io.imread(img_tile, plugin="tifffile")
t2 = skimage.io.imread(img_void_tile, plugin="tifffile")
t1.shape, t2.shape
/tmp/ipykernel_4307/3133617244.py:1: FutureWarning: The plugin infrastructure in `skimage.io` and the parameter `plugin` are deprecated since version 0.25 and will be removed in 0.27 (or later). To avoid this warning, please do not use the parameter `plugin`. Instead, use `imageio` or other I/O packages directly. See also `imread`.
t1 = skimage.io.imread(img_tile, plugin="tifffile")
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
/tmp/ipykernel_4307/3133617244.py in ?()
----> 1 t1 = skimage.io.imread(img_tile, plugin="tifffile")
2 t2 = skimage.io.imread(img_void_tile, plugin="tifffile")
3 t1.shape, t2.shape
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/skimage/_shared/utils.py in ?(*args, **kwargs)
324 elif self.new_name is not None:
325 # Assign old value to new one
326 kwargs[self.new_name] = deprecated_value
327
--> 328 return func(*args, **kwargs)
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/skimage/io/_io.py in ?(fname, as_gray, plugin, **plugin_args)
78 if fname.lower().endswith(('.tiff', '.tif')):
79 plugin = 'tifffile'
80
81 with file_or_url_context(fname) as fname, _hide_plugin_deprecation_warnings():
---> 82 img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
83
84 if not hasattr(img, 'ndim'):
85 return img
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/skimage/_shared/utils.py in ?(*args, **kwargs)
534 @functools.wraps(func)
535 def wrapped(*args, **kwargs):
536 stacklevel = 1 + self.get_stack_length(func) - stack_rank
537 warnings.warn(message, category=FutureWarning, stacklevel=stacklevel)
--> 538 return func(*args, **kwargs)
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/skimage/io/manage_plugins.py in ?(kind, *args, **kwargs)
250 func = [f for (p, f) in plugin_funcs if p == plugin][0]
251 except IndexError:
252 raise RuntimeError(f'Could not find the plugin "{plugin}" for {kind}.')
253
--> 254 return func(*args, **kwargs)
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/skimage/io/_plugins/tifffile_plugin.py in ?(fname, **kwargs)
70 """
71 if 'img_num' in kwargs:
72 kwargs['key'] = kwargs.pop('img_num')
73
---> 74 return tifffile_imread(fname, **kwargs)
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(files, selection, aszarr, key, series, level, squeeze, maxworkers, buffersize, mode, name, offset, size, pattern, axesorder, categories, imread, imreadargs, sort, container, chunkshape, chunkdtype, axestiled, ioworkers, chunkmode, fillvalue, zattrs, multiscales, omexml, out, out_inplace, _multifile, _useframes, **kwargs)
1203 ):
1204 files = files[0]
1205
1206 if isinstance(files, str) or not isinstance(files, Sequence):
-> 1207 with TiffFile(
1208 files,
1209 mode=mode,
1210 name=name,
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size, omexml, _multifile, _useframes, _parent, **is_flags)
4278 raise ValueError('invalid OME-XML')
4279 self._omexml = omexml
4280 self.is_ome = True
4281
-> 4282 fh = FileHandle(file, mode=mode, name=name, offset=offset, size=size)
4283 self._fh = fh
4284 self._multifile = True if _multifile is None else bool(_multifile)
4285 self._files = {fh.name: self}
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size)
13323 self._offset = -1 if offset is None else offset
13324 self._size = -1 if size is None else size
13325 self._close = True
13326 self._lock = NullContext()
> 13327 self.open()
13328 assert self._fh is not None
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self)
13342 if self._mode not in {'rb', 'r+b', 'wb', 'xb'}:
13343 raise ValueError(f'invalid mode {self._mode}')
13344 self._file = os.path.realpath(self._file)
13345 self._dir, self._name = os.path.split(self._file)
> 13346 self._fh = open(self._file, self._mode, encoding=None)
13347 self._close = True
13348 self._offset = max(0, self._offset)
13349 elif isinstance(self._file, FileHandle):
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/nima_io/nima_io/tests/data/t4_1.tif'
[3]:
tf1 = tifffile.imread(img_tile)
tf2 = tifffile.imread(img_void_tile)
tf1.shape, tf2.shape
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
/tmp/ipykernel_4307/3090132194.py in ?()
----> 1 tf1 = tifffile.imread(img_tile)
2 tf2 = tifffile.imread(img_void_tile)
3 tf1.shape, tf2.shape
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(files, selection, aszarr, key, series, level, squeeze, maxworkers, buffersize, mode, name, offset, size, pattern, axesorder, categories, imread, imreadargs, sort, container, chunkshape, chunkdtype, axestiled, ioworkers, chunkmode, fillvalue, zattrs, multiscales, omexml, out, out_inplace, _multifile, _useframes, **kwargs)
1203 ):
1204 files = files[0]
1205
1206 if isinstance(files, str) or not isinstance(files, Sequence):
-> 1207 with TiffFile(
1208 files,
1209 mode=mode,
1210 name=name,
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size, omexml, _multifile, _useframes, _parent, **is_flags)
4278 raise ValueError('invalid OME-XML')
4279 self._omexml = omexml
4280 self.is_ome = True
4281
-> 4282 fh = FileHandle(file, mode=mode, name=name, offset=offset, size=size)
4283 self._fh = fh
4284 self._multifile = True if _multifile is None else bool(_multifile)
4285 self._files = {fh.name: self}
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size)
13323 self._offset = -1 if offset is None else offset
13324 self._size = -1 if size is None else size
13325 self._close = True
13326 self._lock = NullContext()
> 13327 self.open()
13328 assert self._fh is not None
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self)
13342 if self._mode not in {'rb', 'r+b', 'wb', 'xb'}:
13343 raise ValueError(f'invalid mode {self._mode}')
13344 self._file = os.path.realpath(self._file)
13345 self._dir, self._name = os.path.split(self._file)
> 13346 self._fh = open(self._file, self._mode, encoding=None)
13347 self._close = True
13348 self._offset = max(0, self._offset)
13349 elif isinstance(self._file, FileHandle):
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/nima_io/nima_io/tests/data/t4_1.tif'
[4]:
fp1glob = str(tdata / "im1s1z3c5t_?.ome.tif")
tifs = tifffile.TiffSequence(fp1glob)
d = tifs.asarray()
print(d.shape)
print(tifs.shape)
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/tmp/ipykernel_4307/2832391936.py in ?()
1 fp1glob = str(tdata / "im1s1z3c5t_?.ome.tif")
2
----> 3 tifs = tifffile.TiffSequence(fp1glob)
4 d = tifs.asarray()
5 print(d.shape)
6 print(tifs.shape)
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, files, imread, **kwargs)
13039 *,
13040 imread: Callable[..., NDArray[Any]] = imread,
13041 **kwargs: Any,
13042 ) -> None:
> 13043 super().__init__(imread, '*.tif' if files is None else files, **kwargs)
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, imread, files, container, sort, parse, **kwargs)
12757 files = sort_func(files)
12758
12759 files = [os.fspath(f) for f in files] # type: ignore[union-attr]
12760 if not files:
> 12761 raise ValueError('no files found')
12762
12763 if not callable(imread):
12764 raise ValueError('invalid imread function')
ValueError: no files found
[5]:
with tifffile.TiffFile(img_tile) as tif:
tag = tif.pages[0].tags["ImageDescription"]
tag.value[:1000]
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
/tmp/ipykernel_4307/3879889513.py in ?()
----> 1 with tifffile.TiffFile(img_tile) as tif:
2 tag = tif.pages[0].tags["ImageDescription"]
3
4 tag.value[:1000]
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size, omexml, _multifile, _useframes, _parent, **is_flags)
4278 raise ValueError('invalid OME-XML')
4279 self._omexml = omexml
4280 self.is_ome = True
4281
-> 4282 fh = FileHandle(file, mode=mode, name=name, offset=offset, size=size)
4283 self._fh = fh
4284 self._multifile = True if _multifile is None else bool(_multifile)
4285 self._files = {fh.name: self}
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size)
13323 self._offset = -1 if offset is None else offset
13324 self._size = -1 if size is None else size
13325 self._close = True
13326 self._lock = NullContext()
> 13327 self.open()
13328 assert self._fh is not None
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self)
13342 if self._mode not in {'rb', 'r+b', 'wb', 'xb'}:
13343 raise ValueError(f'invalid mode {self._mode}')
13344 self._file = os.path.realpath(self._file)
13345 self._dir, self._name = os.path.split(self._file)
> 13346 self._fh = open(self._file, self._mode, encoding=None)
13347 self._close = True
13348 self._offset = max(0, self._offset)
13349 elif isinstance(self._file, FileHandle):
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/nima_io/nima_io/tests/data/t4_1.tif'
1.3. nima_io#
1.3.1. read#
[6]:
md, wr = ir.read(simg_void_tile)
md.core, wr
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[6], line 1
----> 1 md, wr = ir.read(simg_void_tile)
2 md.core, wr
File ~/work/nima_io/nima_io/src/nima_io/read.py:428, in read(filepath)
426 if not Path(filepath).is_file():
427 msg = f"File not found: {filepath}"
--> 428 raise FileNotFoundError(msg)
429 ensure_jvm()
430 channel_separator = jimport("loci.formats.ChannelSeparator")
FileNotFoundError: File not found: ../../tests/data/tile6_1.tif
[7]:
md.core.voxel_size
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[7], line 1
----> 1 md.core.voxel_size
NameError: name 'md' is not defined
[8]:
root = wr.rdr.getMetadataStoreRoot()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[8], line 1
----> 1 root = wr.rdr.getMetadataStoreRoot()
NameError: name 'wr' is not defined
[9]:
ome_store = wr.rdr.getMetadataStore()
ome_store
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[9], line 1
----> 1 ome_store = wr.rdr.getMetadataStore()
2 ome_store
NameError: name 'wr' is not defined
[10]:
get_power = ome_store.getArcPower(0, 4)
get_power
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[10], line 1
----> 1 get_power = ome_store.getArcPower(0, 4)
2 get_power
NameError: name 'ome_store' is not defined
[11]:
att = ome_store.getChannelLightSourceSettingsAttenuation(0, 0)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[11], line 1
----> 1 att = ome_store.getChannelLightSourceSettingsAttenuation(0, 0)
NameError: name 'ome_store' is not defined
[12]:
nmax = 7
(
len([md for md in md.full.items() if len(md[1][0][0]) == nmax]),
[md for md in md.full.items() if len(md[1][0][0]) == nmax],
)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[12], line 3
1 nmax = 7
2 (
----> 3 len([md for md in md.full.items() if len(md[1][0][0]) == nmax]),
4 [md for md in md.full.items() if len(md[1][0][0]) == nmax],
5 )
NameError: name 'md' is not defined
[13]:
list(range(4))
[13]:
[0, 1, 2, 3]
[14]:
[(0,) * n for n in range(3 + 1)]
[14]:
[(), (0,), (0, 0), (0, 0, 0)]
[15]:
ir.convert_java_numeric_field(att), ir.convert_java_numeric_field(get_power)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[15], line 1
----> 1 ir.convert_java_numeric_field(att), ir.convert_java_numeric_field(get_power)
AttributeError: module 'nima_io.read' has no attribute 'convert_java_numeric_field'
[16]:
{md.full.get(k)[0][0] for k in md.full}
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[16], line 1
----> 1 {md.full.get(k)[0][0] for k in md.full}
NameError: name 'md' is not defined
[17]:
[(k, md.full.get(k)[0]) for k in md.full if not md.full.get(k)[0][1]]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[17], line 1
----> 1 [(k, md.full.get(k)[0]) for k in md.full if not md.full.get(k)[0][1]]
NameError: name 'md' is not defined
[18]:
ome_store.getRoot() == root
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[18], line 1
----> 1 ome_store.getRoot() == root
NameError: name 'ome_store' is not defined
[19]:
ome_store.getPlaneCount(4), ome_store.getPlaneTheC(4, 11), ome_store.getPixelsSizeZ(4)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[19], line 1
----> 1 ome_store.getPlaneCount(4), ome_store.getPlaneTheC(4, 11), ome_store.getPixelsSizeZ(4)
NameError: name 'ome_store' is not defined
[20]:
wr.rdr.getDimensionOrder(), ir.read(slif)[1].rdr.getDimensionOrder()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[20], line 1
----> 1 wr.rdr.getDimensionOrder(), ir.read(slif)[1].rdr.getDimensionOrder()
NameError: name 'wr' is not defined
Mind the difference between img_void_tile and lif files.
[21]:
md.full["PixelsDimensionOrder"]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[21], line 1
----> 1 md.full["PixelsDimensionOrder"]
NameError: name 'md' is not defined
[22]:
root.getImage(0)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[22], line 1
----> 1 root.getImage(0)
NameError: name 'root' is not defined
[23]:
root.getImage(13).getPixels().getPlane(11).getTheC().getValue()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[23], line 1
----> 1 root.getImage(13).getPixels().getPlane(11).getTheC().getValue()
NameError: name 'root' is not defined
[24]:
(
root.getImage(13).getName(),
ir.read(slif)[1].rdr.getMetadataStoreRoot().getImage(2).getName(),
)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[24], line 2
1 (
----> 2 root.getImage(13).getName(),
3 ir.read(slif)[1].rdr.getMetadataStoreRoot().getImage(2).getName(),
4 )
NameError: name 'root' is not defined
[25]:
md.core.__dict__
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[25], line 1
----> 1 md.core.__dict__
NameError: name 'md' is not defined
[26]:
vars(md.core)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[26], line 1
----> 1 vars(md.core)
NameError: name 'md' is not defined
1.3.2. Stitch#
[27]:
f = ir.stitch(md.core, wr, c=2, t=2)
skimage.io.imshow(f)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[27], line 1
----> 1 f = ir.stitch(md.core, wr, c=2, t=2)
2 skimage.io.imshow(f)
NameError: name 'md' is not defined
[28]:
md.core.stage_position[2]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[28], line 1
----> 1 md.core.stage_position[2]
NameError: name 'md' is not defined
1.4. nima_io.read#
function |
time (ms) |
note |
|---|---|---|
read |
169 |
|
read_pims |
195 |
extra pims DIMS |
Metadata is now uniform across different reading functions.
In the following sections, various bioformats implementations are explored. None of the explored libraries return the numerous metadata linked to individual planes. Consequently, I have developed a small library to handle additional (often neglected) metadata, such as acquisition stage position (essential for reconstructing tiled images) and illumination and emission settings.
1.4.1. PIMS#
Which is currently unable to download loci_tools.jar.
I really like the frame metadata t_s, x_um, y_um and z_um. Every array (2D, 3D, …, n-D) having those metadata in common are contained in the Frame obj: a numpy array with metadata(dict) and frame_no(int).
Are fs.bundle_axes (fs.frame_shape), fs.iter_axes and fs.default_coords overcomplicated?
Anyway: iter=0 == iter=n which is at least unexpected.
[29]:
md_pims, wr_pims = ir.read_pims(img_void_tile)
md_pims.core.__dict__
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
Cell In[29], line 1
----> 1 md_pims, wr_pims = ir.read_pims(img_void_tile)
2 md_pims.core.__dict__
File ~/work/nima_io/nima_io/src/nima_io/read.py:479, in read_pims(filepath)
442 def read_pims(filepath: str) -> tuple[Metadata, ImageReaderWrapper]:
443 """Read metadata and initialize Bioformats reader using the pims library.
444
445 Parameters
(...) 477 (series, plane) where plane combines z, t and c?
478 """
--> 479 fs = pims.Bioformats(filepath)
480 core_md = CoreMetadata(fs.rdr)
481 md = Metadata(core_md, {}, {})
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/pims/bioformats.py:330, in BioformatsReader.__init__(self, filename, meta, java_memory, read_mode, series)
328 # Make sure that file exists before starting java
329 if not os.path.isfile(filename):
--> 330 raise IOError('The file "{}" does not exist.'.format(filename))
332 # Start java VM and initialize logger (globally)
333 if not jpype.isJVMStarted():
OSError: The file "../../tests/data/tile6_1.tif" does not exist.
[30]:
mdata = wr.rdr.getMetadataStore()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[30], line 1
----> 1 mdata = wr.rdr.getMetadataStore()
NameError: name 'wr' is not defined
[31]:
root = mdata.getRoot()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[31], line 1
----> 1 root = mdata.getRoot()
NameError: name 'mdata' is not defined
[32]:
im0 = root.getImage(0)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[32], line 1
----> 1 im0 = root.getImage(0)
NameError: name 'root' is not defined
[33]:
pixels = im0.getPixels()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[33], line 1
----> 1 pixels = im0.getPixels()
NameError: name 'im0' is not defined
[34]:
for idx in range(pixels.sizeOfTiffDataList()):
tiffData = pixels.getTiffData(idx)
c = tiffData.getFirstC().getValue().intValue()
t = tiffData.getFirstT().getValue().intValue()
print(f"TiffData: c={c}, t={t}")
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[34], line 1
----> 1 for idx in range(pixels.sizeOfTiffDataList()):
2 tiffData = pixels.getTiffData(idx)
3 c = tiffData.getFirstC().getValue().intValue()
NameError: name 'pixels' is not defined
1.5. ImageIO#
[35]:
from imageio.v3 import imread
%timeit imread(img_void_tile, index=13)
i = imread(img_void_tile, index=13)
i.shape
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[35], line 3
1 from imageio.v3 import imread
----> 3 get_ipython().run_line_magic('timeit', 'imread(img_void_tile, index=13)')
4 i = imread(img_void_tile, index=13)
5 i.shape
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/IPython/core/interactiveshell.py:2488, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
2486 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2487 with self.builtin_trap:
-> 2488 result = fn(*args, **kwargs)
2490 # The code below prevents the output from being displayed
2491 # when using magics with decorator @output_can_be_silenced
2492 # when the last Python token in the expression is a ';'.
2493 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/IPython/core/magics/execution.py:1225, in ExecutionMagics.timeit(self, line, cell, local_ns)
1223 for index in range(0, 10):
1224 number = 10 ** index
-> 1225 time_number = timer.timeit(number)
1226 if time_number >= 0.2:
1227 break
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/IPython/core/magics/execution.py:183, in Timer.timeit(self, number)
181 gc.disable()
182 try:
--> 183 timing = self.inner(it, self.timer)
184 finally:
185 if gcold:
File <magic-timeit>:1, in inner(_it, _timer)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/imageio/v3.py:53, in imread(uri, index, plugin, extension, format_hint, **kwargs)
50 if index is not None:
51 call_kwargs["index"] = index
---> 53 with imopen(uri, "r", **plugin_kwargs) as img_file:
54 return np.asarray(img_file.read(**call_kwargs))
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/imageio/core/imopen.py:113, in imopen(uri, io_mode, plugin, extension, format_hint, legacy_mode, **kwargs)
111 request.format_hint = format_hint
112 else:
--> 113 request = Request(uri, io_mode, format_hint=format_hint, extension=extension)
115 source = "<bytes>" if isinstance(uri, bytes) else uri
117 # fast-path based on plugin
118 # (except in legacy mode)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/imageio/core/request.py:249, in Request.__init__(self, uri, mode, extension, format_hint, **kwargs)
246 raise ValueError(f"Invalid Request.Mode: {mode}")
248 # Parse what was given
--> 249 self._parse_uri(uri)
251 # Set extension
252 if extension is not None:
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/imageio/core/request.py:409, in Request._parse_uri(self, uri)
406 if is_read_request:
407 # Reading: check that the file exists (but is allowed a dir)
408 if not os.path.exists(fn):
--> 409 raise FileNotFoundError("No such file: '%s'" % fn)
410 else:
411 # Writing: check that the directory to write to does exist
412 dn = os.path.dirname(fn)
FileNotFoundError: No such file: '/home/runner/work/nima_io/nima_io/tests/data/tile6_1.tif'
[36]:
i.nbytes, 512**2 * 3 * 4 * 2
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[36], line 1
----> 1 i.nbytes, 512**2 * 3 * 4 * 2
NameError: name 'i' is not defined
It can read tif (tf8) files. Series might be passed using index (you need to know in advance).
1.6. AICSImageIO#
[37]:
from aicsimageio import AICSImage
i = AICSImage(img_void_tile)
# i = AICSImage(img_void_tile, reconstruct_mosaic=True)
# i_lif = AICSImage(lif)
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Cell In[37], line 1
----> 1 from aicsimageio import AICSImage
3 i = AICSImage(img_void_tile)
4 # i = AICSImage(img_void_tile, reconstruct_mosaic=True)
5 # i_lif = AICSImage(lif)
ModuleNotFoundError: No module named 'aicsimageio'
[38]:
i.ome_metadata.instruments[0].arcs[0]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[38], line 1
----> 1 i.ome_metadata.instruments[0].arcs[0]
NameError: name 'i' is not defined
[39]:
lif_aics = AICSImage(slif)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[39], line 1
----> 1 lif_aics = AICSImage(slif)
NameError: name 'AICSImage' is not defined
[40]:
lif_aics.metadata
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[40], line 1
----> 1 lif_aics.metadata
NameError: name 'lif_aics' is not defined
[41]:
i.ome_metadata
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[41], line 1
----> 1 i.ome_metadata
NameError: name 'i' is not defined
[42]:
i.metadata.images[0].pixels.channels[0].light_source_settings.attenuation
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[42], line 1
----> 1 i.metadata.images[0].pixels.channels[0].light_source_settings.attenuation
NameError: name 'i' is not defined
[43]:
i.scenes
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[43], line 1
----> 1 i.scenes
NameError: name 'i' is not defined
[44]:
i.get_dask_stack()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[44], line 1
----> 1 i.get_dask_stack()
NameError: name 'i' is not defined
Mosaic stitch is not supported on tif files; so I will use my function relying on the PositionXYZ metadata.
1.7. dask_image#
[45]:
from dask_image.imread import imread
i = imread(img_void_tile)
---------------------------------------------------------------------------
UnknownFormatError Traceback (most recent call last)
Cell In[45], line 3
1 from dask_image.imread import imread
----> 3 i = imread(img_void_tile)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/dask_image/imread/__init__.py:48, in imread(fname, nframes, arraytype)
45 import cupy
46 arrayfunc = cupy.asanyarray
---> 48 with pims.open(sfname) as imgs:
49 shape = (len(imgs),) + imgs.frame_shape
50 dtype = np.dtype(imgs.pixel_type)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/pims/api.py:199, in open(sequence, **kwargs)
197 except Exception as e:
198 messages.append('{} errored: {}'.format(str(handler), str(e)))
--> 199 raise UnknownFormatError(
200 "All handlers returned exceptions:\n" + "\n".join(messages))
UnknownFormatError: All handlers returned exceptions:
<class 'pims.tiff_stack.TiffStack_tifffile'> errored: [Errno 2] No such file or directory: '/home/runner/work/nima_io/nima_io/tests/data/tile6_1.tif'
<class 'pims.imageio_reader.ImageIOReader'> errored: No such file: '/home/runner/work/nima_io/nima_io/tests/data/tile6_1.tif'
<class 'pims.bioformats.BioformatsReader'> errored: The file "../../tests/data/tile6_1.tif" does not exist.
[46]:
i
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[46], line 1
----> 1 i
NameError: name 'i' is not defined
Somehow it uses bioformats and can handle lif. No mosaic, no metadata though.
Pycroscopy https://pypi.org/project/pycroscopy/ is not reading lif nor ome-tif at the moment.
large-image[all] failed to install.
pyimagej need conda?
1.8. bioio-bioformats#
import bioio_ome_tiled_tiff
bioio_ome_tiled_tiff.Reader(str(img_void_tile))
TypeError: tile6_1.tif is not a tiled tiff. The python backend of the BioReader only supports OME tiled tiffs.
[47]:
import bioio_bioformats
im = bioio_bioformats.Reader(img_void_tile)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[47], line 3
1 import bioio_bioformats
----> 3 im = bioio_bioformats.Reader(img_void_tile)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bioio_bioformats/reader.py:110, in Reader.__init__(self, image, original_meta, memoize, options, dask_tiles, tile_size, fs_kwargs)
99 def __init__(
100 self,
101 image: types.PathLike,
(...) 108 fs_kwargs: Dict[str, Any] = {},
109 ):
--> 110 self._fs, self._path = io.pathlike_to_fs(
111 image,
112 enforce_exists=True,
113 fs_kwargs=fs_kwargs,
114 )
115 # Catch non-local file system
116 if not isinstance(self._fs, LocalFileSystem):
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bioio_base/io.py:58, in pathlike_to_fs(uri, enforce_exists, fs_kwargs)
56 if enforce_exists:
57 if not fs.exists(path):
---> 58 raise FileNotFoundError(f"{fs.protocol}://{path}")
60 # Get and store details
61 # We do not return an AbstractBufferedFile (i.e. fs.open) as we do not want to have
62 # any open file buffers _after_ any API call. API calls must themselves call
63 # fs.open and complete their function during the context of the opened buffer.
64 return fs, path
FileNotFoundError: ('file', 'local'):///home/runner/work/nima_io/nima_io/docs/tutorials/../../tests/data/tile6_1.tif
[48]:
im.ome_metadata.images[0].pixels.channels[2].light_source_settings
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[48], line 1
----> 1 im.ome_metadata.images[0].pixels.channels[2].light_source_settings
NameError: name 'im' is not defined
[49]:
lif_bioio = bioio_bioformats.Reader(lif)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[49], line 1
----> 1 lif_bioio = bioio_bioformats.Reader(lif)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bioio_bioformats/reader.py:110, in Reader.__init__(self, image, original_meta, memoize, options, dask_tiles, tile_size, fs_kwargs)
99 def __init__(
100 self,
101 image: types.PathLike,
(...) 108 fs_kwargs: Dict[str, Any] = {},
109 ):
--> 110 self._fs, self._path = io.pathlike_to_fs(
111 image,
112 enforce_exists=True,
113 fs_kwargs=fs_kwargs,
114 )
115 # Catch non-local file system
116 if not isinstance(self._fs, LocalFileSystem):
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bioio_base/io.py:58, in pathlike_to_fs(uri, enforce_exists, fs_kwargs)
56 if enforce_exists:
57 if not fs.exists(path):
---> 58 raise FileNotFoundError(f"{fs.protocol}://{path}")
60 # Get and store details
61 # We do not return an AbstractBufferedFile (i.e. fs.open) as we do not want to have
62 # any open file buffers _after_ any API call. API calls must themselves call
63 # fs.open and complete their function during the context of the opened buffer.
64 return fs, path
FileNotFoundError: ('file', 'local'):///home/runner/work/nima_io/nima_io/docs/tutorials/../../tests/data/2015Aug28_TransHXB2_50min+DMSO.lif
[50]:
lif_bioio.physical_pixel_sizes
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[50], line 1
----> 1 lif_bioio.physical_pixel_sizes
NameError: name 'lif_bioio' is not defined
[51]:
im.get_dask_stack()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[51], line 1
----> 1 im.get_dask_stack()
NameError: name 'im' is not defined
[52]:
im.ome_metadata.plates[0].wells[0]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[52], line 1
----> 1 im.ome_metadata.plates[0].wells[0]
NameError: name 'im' is not defined
[53]:
i = bioio_bioformats.Reader(img_tile)
i.data.shape, i.dims
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[53], line 1
----> 1 i = bioio_bioformats.Reader(img_tile)
2 i.data.shape, i.dims
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bioio_bioformats/reader.py:110, in Reader.__init__(self, image, original_meta, memoize, options, dask_tiles, tile_size, fs_kwargs)
99 def __init__(
100 self,
101 image: types.PathLike,
(...) 108 fs_kwargs: Dict[str, Any] = {},
109 ):
--> 110 self._fs, self._path = io.pathlike_to_fs(
111 image,
112 enforce_exists=True,
113 fs_kwargs=fs_kwargs,
114 )
115 # Catch non-local file system
116 if not isinstance(self._fs, LocalFileSystem):
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bioio_base/io.py:58, in pathlike_to_fs(uri, enforce_exists, fs_kwargs)
56 if enforce_exists:
57 if not fs.exists(path):
---> 58 raise FileNotFoundError(f"{fs.protocol}://{path}")
60 # Get and store details
61 # We do not return an AbstractBufferedFile (i.e. fs.open) as we do not want to have
62 # any open file buffers _after_ any API call. API calls must themselves call
63 # fs.open and complete their function during the context of the opened buffer.
64 return fs, path
FileNotFoundError: ('file', 'local'):///home/runner/work/nima_io/nima_io/docs/tutorials/../../tests/data/t4_1.tif
[54]:
i.xarray_dask_data.attrs["processed"]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[54], line 1
----> 1 i.xarray_dask_data.attrs["processed"]
NameError: name 'i' is not defined
[55]:
unp = i.xarray_dask_data.attrs["unprocessed"]
unp[:1000]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[55], line 1
----> 1 unp = i.xarray_dask_data.attrs["unprocessed"]
2 unp[:1000]
NameError: name 'i' is not defined
[56]:
stk = i.get_dask_stack()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[56], line 1
----> 1 stk = i.get_dask_stack()
NameError: name 'i' is not defined
[57]:
stk.A
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[57], line 1
----> 1 stk.A
NameError: name 'stk' is not defined
1.9. bfio#
[58]:
import bfio
bfio.BioReader(img_void_tile)
18-Jun-25 07:21:10 - jgo - ERROR - Failed to bootstrap the artifact.
18-Jun-25 07:21:10 - jgo - ERROR -
18-Jun-25 07:21:10 - jgo - ERROR - Possible solutions:
18-Jun-25 07:21:10 - jgo - ERROR - * Double check the endpoint for correctness (https://search.maven.org/).
18-Jun-25 07:21:10 - jgo - ERROR - * Add needed repositories to ~/.jgorc [repositories] block (see README).
18-Jun-25 07:21:10 - jgo - ERROR - * Try with an explicit version number (release metadata might be wrong).
18-Jun-25 07:21:10 - jgo - ERROR -
18-Jun-25 07:21:10 - jgo - ERROR - Full Maven error output:
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] [ERROR] Some problems were encountered while processing the POMs:
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] Non-resolvable import POM: The following artifacts could not be resolved: ome:formats-gpl:pom:8.0.1 (absent): Could not transfer artifact ome:formats-gpl:pom:8.0.1 from/to scijava.public (https://maven.scijava.org/content/groups/public): status code: 503, reason phrase: Service Unavailable (503) @ line 8, column 29
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] The build could not read 1 project -> [Help 1]
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR]
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] The project ome-BOOTSTRAPPER:formats-gpl-BOOTSTRAPPER:0 (/home/runner/.jgo/ome/formats-gpl/8.0.1/344539b25396a9fec73bbca83cd544ca093643095ca71d7225ef568cd60ef13a/pom.xml) has 1 error
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] Non-resolvable import POM: The following artifacts could not be resolved: ome:formats-gpl:pom:8.0.1 (absent): Could not transfer artifact ome:formats-gpl:pom:8.0.1 from/to scijava.public (https://maven.scijava.org/content/groups/public): status code: 503, reason phrase: Service Unavailable (503) @ line 8, column 29 -> [Help 2]
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR]
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] Re-run Maven using the -X switch to enable full debug logging.
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR]
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] For more information about the errors and possible solutions, please read the following articles:
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
18-Jun-25 07:21:10 - jgo - ERROR - [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
18-Jun-25 07:21:10 - jgo - ERROR -
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
Cell In[58], line 3
1 import bfio
----> 3 bfio.BioReader(img_void_tile)
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/bfio.py:98, in BioReader.__init__(self, file_path, max_workers, backend, clean_metadata, level)
96 elif self._backend_name == "bioformats":
97 try:
---> 98 self._backend = backends.JavaReader(self)
99 if max_workers is not None:
100 self.logger.warning(
101 "The max_workers keyword was present, but bioformats backend "
102 + "only operates with a single worker. Setting max_workers=1."
103 )
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/backends.py:951, in JavaReader.__init__(self, frontend)
949 def __init__(self, frontend):
950 if not JavaReader._classes_loaded:
--> 951 self._load_java_classes()
953 super().__init__(frontend)
955 factory = ServiceFactory()
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/backends.py:933, in JavaReader._load_java_classes(self)
931 def _load_java_classes(self):
932 if not jpype.isJVMStarted():
--> 933 start()
935 global ImageReader
936 from loci.formats import ImageReader
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/utils.py:43, in start()
41 global JAR_VERSION
42 scyjava.config.endpoints.append("ome:formats-gpl:8.0.1")
---> 43 scyjava.start_jvm()
44 import loci
46 loci.common.DebugTools.setRootLevel("ERROR")
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/scyjava/_jvm.py:146, in start_jvm(options)
144 endpoints = endpoints[:1] + sorted(endpoints[1:])
145 _logger.debug("Using endpoints %s", endpoints)
--> 146 _, workspace = jgo.resolve_dependencies(
147 "+".join(endpoints),
148 m2_repo=scyjava.config.get_m2_repo(),
149 cache_dir=scyjava.config.get_cache_dir(),
150 manage_dependencies=scyjava.config.get_manage_deps(),
151 repositories=repositories,
152 verbose=scyjava.config.get_verbose(),
153 shortcuts=scyjava.config.get_shortcuts(),
154 )
155 jpype.addClassPath(os.path.join(workspace, "*"))
157 # HACK: Try to set JAVA_HOME if it isn't already.
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/jgo/jgo.py:667, in resolve_dependencies(endpoint_string, cache_dir, m2_repo, link_type, update_cache, force_update, manage_dependencies, repositories, shortcuts, verbose)
664 _logger.debug("\t%s", line)
665 _logger.error("")
--> 667 raise e
669 info_regex = re.compile("^.*\\[[A-Z]+\\] *")
670 relevant_jars = []
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/jgo/jgo.py:638, in resolve_dependencies(endpoint_string, cache_dir, m2_repo, link_type, update_cache, force_update, manage_dependencies, repositories, shortcuts, verbose)
636 try:
637 mvn = executable_path_or_raise("mvn")
--> 638 mvn_out = run_and_combine_outputs(mvn, *mvn_args)
639 except subprocess.CalledProcessError as e:
640 _logger.error("Failed to bootstrap the artifact.")
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/jgo/jgo.py:269, in run_and_combine_outputs(command, *args)
267 command_string = (command,) + args
268 _logger.debug(f"Executing: {command_string}")
--> 269 return subprocess.check_output(command_string, stderr=subprocess.STDOUT)
File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/subprocess.py:466, in check_output(timeout, *popenargs, **kwargs)
463 empty = b''
464 kwargs['input'] = empty
--> 466 return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
467 **kwargs).stdout
File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/subprocess.py:571, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
569 retcode = process.poll()
570 if check and retcode:
--> 571 raise CalledProcessError(retcode, process.args,
572 output=stdout, stderr=stderr)
573 return CompletedProcess(process.args, retcode, stdout, stderr)
CalledProcessError: Command '('/usr/bin/mvn', '-B', '-f', '/home/runner/.jgo/ome/formats-gpl/8.0.1/344539b25396a9fec73bbca83cd544ca093643095ca71d7225ef568cd60ef13a/pom.xml', 'dependency:resolve')' returned non-zero exit status 1.
[59]:
rdr = bfio.BioReader(img_void_tile)
%timeit i = rdr.read()
i = rdr.read()
i.shape
18-Jun-25 07:21:43 - jgo - ERROR - Failed to bootstrap the artifact.
18-Jun-25 07:21:43 - jgo - ERROR -
18-Jun-25 07:21:43 - jgo - ERROR - Possible solutions:
18-Jun-25 07:21:43 - jgo - ERROR - * Double check the endpoint for correctness (https://search.maven.org/).
18-Jun-25 07:21:43 - jgo - ERROR - * Add needed repositories to ~/.jgorc [repositories] block (see README).
18-Jun-25 07:21:43 - jgo - ERROR - * Try with an explicit version number (release metadata might be wrong).
18-Jun-25 07:21:43 - jgo - ERROR -
18-Jun-25 07:21:43 - jgo - ERROR - Full Maven error output:
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] [ERROR] Some problems were encountered while processing the POMs:
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] Non-resolvable import POM: The following artifacts could not be resolved: ome:formats-gpl:pom:8.0.1 (absent): Could not transfer artifact ome:formats-gpl:pom:8.0.1 from/to scijava.public (https://maven.scijava.org/content/groups/public): status code: 503, reason phrase: Service Unavailable (503) @ line 8, column 29
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] The build could not read 1 project -> [Help 1]
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR]
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] The project ome-BOOTSTRAPPER:formats-gpl-BOOTSTRAPPER:0 (/home/runner/.jgo/ome/formats-gpl/8.0.1/a15c5e3bb47cd22481cf59c89685740cd2f7b08fa54309173309300e97d04535/pom.xml) has 1 error
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] Non-resolvable import POM: The following artifacts could not be resolved: ome:formats-gpl:pom:8.0.1 (absent): Could not transfer artifact ome:formats-gpl:pom:8.0.1 from/to scijava.public (https://maven.scijava.org/content/groups/public): status code: 503, reason phrase: Service Unavailable (503) @ line 8, column 29 -> [Help 2]
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR]
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] Re-run Maven using the -X switch to enable full debug logging.
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR]
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] For more information about the errors and possible solutions, please read the following articles:
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
18-Jun-25 07:21:43 - jgo - ERROR - [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
18-Jun-25 07:21:43 - jgo - ERROR -
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
Cell In[59], line 1
----> 1 rdr = bfio.BioReader(img_void_tile)
2 get_ipython().run_line_magic('timeit', 'i = rdr.read()')
3 i = rdr.read()
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/bfio.py:98, in BioReader.__init__(self, file_path, max_workers, backend, clean_metadata, level)
96 elif self._backend_name == "bioformats":
97 try:
---> 98 self._backend = backends.JavaReader(self)
99 if max_workers is not None:
100 self.logger.warning(
101 "The max_workers keyword was present, but bioformats backend "
102 + "only operates with a single worker. Setting max_workers=1."
103 )
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/backends.py:951, in JavaReader.__init__(self, frontend)
949 def __init__(self, frontend):
950 if not JavaReader._classes_loaded:
--> 951 self._load_java_classes()
953 super().__init__(frontend)
955 factory = ServiceFactory()
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/backends.py:933, in JavaReader._load_java_classes(self)
931 def _load_java_classes(self):
932 if not jpype.isJVMStarted():
--> 933 start()
935 global ImageReader
936 from loci.formats import ImageReader
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/bfio/utils.py:43, in start()
41 global JAR_VERSION
42 scyjava.config.endpoints.append("ome:formats-gpl:8.0.1")
---> 43 scyjava.start_jvm()
44 import loci
46 loci.common.DebugTools.setRootLevel("ERROR")
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/scyjava/_jvm.py:146, in start_jvm(options)
144 endpoints = endpoints[:1] + sorted(endpoints[1:])
145 _logger.debug("Using endpoints %s", endpoints)
--> 146 _, workspace = jgo.resolve_dependencies(
147 "+".join(endpoints),
148 m2_repo=scyjava.config.get_m2_repo(),
149 cache_dir=scyjava.config.get_cache_dir(),
150 manage_dependencies=scyjava.config.get_manage_deps(),
151 repositories=repositories,
152 verbose=scyjava.config.get_verbose(),
153 shortcuts=scyjava.config.get_shortcuts(),
154 )
155 jpype.addClassPath(os.path.join(workspace, "*"))
157 # HACK: Try to set JAVA_HOME if it isn't already.
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/jgo/jgo.py:667, in resolve_dependencies(endpoint_string, cache_dir, m2_repo, link_type, update_cache, force_update, manage_dependencies, repositories, shortcuts, verbose)
664 _logger.debug("\t%s", line)
665 _logger.error("")
--> 667 raise e
669 info_regex = re.compile("^.*\\[[A-Z]+\\] *")
670 relevant_jars = []
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/jgo/jgo.py:638, in resolve_dependencies(endpoint_string, cache_dir, m2_repo, link_type, update_cache, force_update, manage_dependencies, repositories, shortcuts, verbose)
636 try:
637 mvn = executable_path_or_raise("mvn")
--> 638 mvn_out = run_and_combine_outputs(mvn, *mvn_args)
639 except subprocess.CalledProcessError as e:
640 _logger.error("Failed to bootstrap the artifact.")
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/jgo/jgo.py:269, in run_and_combine_outputs(command, *args)
267 command_string = (command,) + args
268 _logger.debug(f"Executing: {command_string}")
--> 269 return subprocess.check_output(command_string, stderr=subprocess.STDOUT)
File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/subprocess.py:466, in check_output(timeout, *popenargs, **kwargs)
463 empty = b''
464 kwargs['input'] = empty
--> 466 return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
467 **kwargs).stdout
File /opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/subprocess.py:571, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
569 retcode = process.poll()
570 if check and retcode:
--> 571 raise CalledProcessError(retcode, process.args,
572 output=stdout, stderr=stderr)
573 return CompletedProcess(process.args, retcode, stdout, stderr)
CalledProcessError: Command '('/usr/bin/mvn', '-B', '-f', '/home/runner/.jgo/ome/formats-gpl/8.0.1/a15c5e3bb47cd22481cf59c89685740cd2f7b08fa54309173309300e97d04535/pom.xml', 'dependency:resolve')' returned non-zero exit status 1.
[60]:
rdr.metadata
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[60], line 1
----> 1 rdr.metadata
NameError: name 'rdr' is not defined
[61]:
rdr.ps_x
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[61], line 1
----> 1 rdr.ps_x
NameError: name 'rdr' is not defined
[62]:
rdr.close()
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[62], line 1
----> 1 rdr.close()
NameError: name 'rdr' is not defined
1.10. PIMS#
[63]:
import pims
# %timeit fs = pims.Bioformats(img_void_tile)
fs = pims.Bioformats(img_void_tile)
fs.sizes
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
Cell In[63], line 4
1 import pims
3 # %timeit fs = pims.Bioformats(img_void_tile)
----> 4 fs = pims.Bioformats(img_void_tile)
5 fs.sizes
File ~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/pims/bioformats.py:330, in BioformatsReader.__init__(self, filename, meta, java_memory, read_mode, series)
328 # Make sure that file exists before starting java
329 if not os.path.isfile(filename):
--> 330 raise IOError('The file "{}" does not exist.'.format(filename))
332 # Start java VM and initialize logger (globally)
333 if not jpype.isJVMStarted():
OSError: The file "../../tests/data/tile6_1.tif" does not exist.
1.11. PyOMETiff#
[64]:
import pyometiff
%timeit rdr = pyometiff.OMETIFFReader(fpath=img_void_tile)
rdr = pyometiff.OMETIFFReader(fpath=img_void_tile)
1.32 μs ± 4.39 ns per loop (mean ± std. dev. of 7 runs, 1,000,000 loops each)
[65]:
%timeit r = rdr.read()
res = rdr.read()
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
/tmp/ipykernel_4307/1732195015.py in ?()
----> 1 get_ipython().run_line_magic('timeit', 'r = rdr.read()')
2 res = rdr.read()
<magic-timeit> in ?(_it, _timer)
----> 1 'Could not get source, probably due dynamically evaluated source code.'
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/pyometiff/omereader.py in ?(self)
38 def read(self) -> tuple[np.ndarray, dict, str]:
---> 39 self.array, self.omexml_string = self._open_tiff(self.fpath)
40 self.metadata = self.parse_metadata(self.omexml_string)
41 return self.array, self.metadata, self.omexml_string
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/pyometiff/omereader.py in ?(cls, fpath)
221 @classmethod
222 def _open_tiff(cls, fpath: pathlib.Path) -> tuple[np.ndarray, str]:
--> 223 with tifffile.TiffFile(str(fpath)) as tif:
224 omexml_string = tif.ome_metadata
225 array = tif.asarray()
226
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size, omexml, _multifile, _useframes, _parent, **is_flags)
4278 raise ValueError('invalid OME-XML')
4279 self._omexml = omexml
4280 self.is_ome = True
4281
-> 4282 fh = FileHandle(file, mode=mode, name=name, offset=offset, size=size)
4283 self._fh = fh
4284 self._multifile = True if _multifile is None else bool(_multifile)
4285 self._files = {fh.name: self}
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self, file, mode, name, offset, size)
13323 self._offset = -1 if offset is None else offset
13324 self._size = -1 if size is None else size
13325 self._close = True
13326 self._lock = NullContext()
> 13327 self.open()
13328 assert self._fh is not None
~/.local/share/hatch/env/virtual/nima-io/FLi94gtt/nima-io/lib/python3.12/site-packages/tifffile/tifffile.py in ?(self)
13342 if self._mode not in {'rb', 'r+b', 'wb', 'xb'}:
13343 raise ValueError(f'invalid mode {self._mode}')
13344 self._file = os.path.realpath(self._file)
13345 self._dir, self._name = os.path.split(self._file)
> 13346 self._fh = open(self._file, self._mode, encoding=None)
13347 self._close = True
13348 self._offset = max(0, self._offset)
13349 elif isinstance(self._file, FileHandle):
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/nima_io/nima_io/tests/data/tile6_1.tif'
[66]:
res[1]
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[66], line 1
----> 1 res[1]
NameError: name 'res' is not defined
[67]:
pyometiff.OMETIFFReader._get_metadata_template()
[67]:
{'Directory': None,
'Filename': None,
'Extension': None,
'ImageType': None,
'AcqDate': None,
'TotalSeries': None,
'SizeX': None,
'SizeY': None,
'SizeZ': 1,
'SizeC': 1,
'SizeT': 1,
'SizeS': 1,
'SizeB': 1,
'SizeM': 1,
'PhysicalSizeX': None,
'PhysicalSizeXUnit': None,
'PhysicalSizeY': None,
'PhysicalSizeYUnit': None,
'PhysicalSizeZ': None,
'PhysicalSizeZUnit': None,
'Sizes BF': None,
'DimOrder BF': None,
'DimOrder BF Array': None,
'ObjNA': [],
'ObjMag': [],
'ObjID': [],
'ObjName': [],
'ObjImmersion': [],
'TubelensMag': [],
'ObjNominalMag': [],
'DetectorModel': [],
'DetectorName': [],
'DetectorID': [],
'DetectorType': [],
'InstrumentID': [],
'MicroscopeType': [],
'Channels': [],
'ImageIDs': []}
1.12. Final Note#
I will keep
Read
stitch
md_grouping
impy
napari.read
pycromanager
microscope
python-microscopy