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OME-TIFF IO in python

License: GNU General Public License v3.0

Python 99.40% Dockerfile 0.60%

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arkwave anntzer safahai zhenligod

pyometiff's Issues

Writing multi-series OME-TIFF

Hi, I was wondering if it would be possible to implement writing multi-series OME-TIFFs?

The underlying tifffile.TiffWriter class actually supports this natively (example here), and it would be really nice to have this alongside the XML validation that the OMETIFFWriter class does.

Happy to make a PR that does this, if that would help!

use pyproject.toml instead of setup.py

setup.py is dated, just use pyproject.toml

parse_metadata for user-supplied xml string

I try to parse an OME XML string read outside the OMETIFFReader object, using the OMETIFFReader.parse_metadata(s) function. However, this function always parses the internal attribute "self.omexml_string" instead of the argument string ("omexml_string"). I suggest modifying line 54 from pyometiff/omereader.py by dropping "self." from "self.omexml_string".

Thanks a lot for this nice package!

export pyramidal image

Hello,

I am currently trying to save an ome.tiff image pyramidalized with scikit image. Currently I have it as an array of multiple images, this is how scikit image returns it.

Is there a way to do it with pyometiff ? I cannot find it in the documentation.

Thank you !

install fails on python 3.10

version string direct import from package no longer supported and raises metadata-generation-failed
Possible workaround: read data from file instead of import.

Error while reading

Hello,

Thank you for this really nice package.
I was trying to read one of my files and I get a "list index out of range error".

These data have been saved in TIFF using ImSpector Pro 7.0.

Thank you for your help.
Arnaud

PS: I can also share some data if needed.

img_array, metadata, xml_metadata = reader.read()
Key not found: list index out of range
Key not found: list index out of range
key not found list index out of range
Key not found: list index out of range
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[8], line 1
----> 1 img_array, metadata, xml_metadata = reader.read()

File ~/.virtualenvs/microscopy/lib/python3.10/site-packages/pyometiff/omereader.py:40, in OMETIFFReader.read(self)
     38 def read(self) -> (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

File ~/.virtualenvs/microscopy/lib/python3.10/site-packages/pyometiff/omereader.py:166, in OMETIFFReader.parse_metadata(self, omexml_string)
    163     metadata["ObjMag"] = None
    165 # get channel names
--> 166 metadata["Channels"] = self._parse_channels(metadata["SizeC"], self.ox, self.imageseries)
    167 # for c in range(metadata["SizeC"]):
    168 #     channel_names.append(
    169 #         self.ox.image(self.imageseries).Pixels.Channel(c).Name
    170 #     )
    171 
    172 #     self.ox.image(self.imageseries).Pixels.Channel(c).
    173 metadata = self._remove_none_or_empty_dict(metadata)

File ~/.virtualenvs/microscopy/lib/python3.10/site-packages/pyometiff/omereader.py:180, in OMETIFFReader._parse_channels(cls, sizeC, ox, imageseries)
    178 channels_dict = {}
    179 for c in range(sizeC):
--> 180     channel_obj = ox.image(imageseries).Pixels.Channel(c)
    181     channel_name = channel_obj.Name
    182     channel_dict = {}

File ~/.virtualenvs/microscopy/lib/python3.10/site-packages/pyometiff/omexml.py:1032, in OMEXML.Pixels.Channel(self, index)
   1030 def Channel(self, index=0):
   1031     """Get the indexed channel from the Pixels element"""
-> 1032     channel = self.node.findall(qn(self.ns['ome'], "Channel"))[index]
   1033     return OMEXML.Channel(channel)

IndexError: list index out of range

TiffFrame 1: missing required tags OME series: expected 1 frames, got 2

Hello,

Thank you very much for providing a smooth interface to open OME TIF.

When I try and open the .OME.TIFF file that I have, I get the following error:
TiffFrame 1: missing required tags
OME series: expected 1 frames, got 2

import pathlib
from pyometiff import OMETIFFReader

img_fpath = pathlib.Path("/path_to_file/file.ome.tiff")

reader = OMETIFFReader(fpath=img_fpath)

img_array, metadata, xml_metadata = reader.read()

Your thoughts on this would be greatly appreciated!

Best,

OME-TIFF compatible RGB images - metadata issues

I have an RGB image with shape (15840, 28800, 3) (i.e. axis order YXS) - I'm attempting to generate the ome-xml for this file by passing in the following parameters - note that this is after reshaping the array to be in dimension order SYX (as anything else raises an error with OMETIFFWriter):

metadata = {
    'Pixels BigEndian': False, 
    'DimensionOrdering': 'SYX', 
    'SizeY': 15840, 
    'SizeX': 28800, 
    'SizeC': 1, 
    'SizeZ': 1, 
    'SizeT': 1, 
    'PlaneCount': 1, 
    'PhysicalSizeX': 4.991469905942555e-05, 
    'PhysicalSizeXUnit': 'cm', 
    'PhysicalSizeY': 4.991469905942555e-05, 
    'PhysicalSizeYUnit': 'cm', 
    'Name': 'WholeSlideHnE', 
    'Type': 'uint8', 
    'Interleaved': True, 
    'Channels': {
        'RGB': {
            'SamplesPerPixel': 3, 
            'BitsPerSample': (8, 8, 8)
        }
    }
}

params = {
    "fpath"             : destination,
    "dimension_order"   : metadata['DimensionOrdering'],
    "array"             : pixels, 
    "metadata"          : metadata, 
    "explicit_tiffdata" : False,
    "photometric"       : "RGB"
}


xml = OMETIFFWriter(**params)._xml

This outputs the following XML:

<OME xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
       xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
    <Image ID="Image:0" Name="WholeSlideHnE">
            <AcquisitionDate>2022-07-08T16:01:50.130775</AcquisitionDate>
                    <Pixels BigEndian="false" 
                            DimensionOrder="XYS" 
                            ID="Pixels:0" 
                            Interleaved="false" 
                            PhysicalSizeX="4.991469905942555e-05" 
                            PhysicalSizeXUnit="cm" 
                            PhysicalSizeY="4.991469905942555e-05" 
                            PhysicalSizeYUnit="cm" 
                            SizeC="1" 
                            SizeT="1" 
                            SizeX="3" 
                            SizeY="1" 
                            SizeZ="1" 
                            Type="uint8">
            <Channel ID="Channel:00" Name="RGB" SamplesPerPixel="3">
                <LightPath/>
          </Channel>
        <TiffData IFD="0" PlaneCount="1"/></Pixels>
            </Image>\n</OME>

Questions:

Why does the dimension order flip from SYX to XYS?
Why are the SizeX, SizeY and Interleaved parameters not properly parsed?
Is Interleaved = True even a correct value to be passing in when trying to write out an RGB image as one single channel? I understand it affects the order in which the bytes representing each pixel are stored in memory, but I'm unclear as to whether or not this makes any other difference (say with trying to load the written image into viewers, etc).
Am I doing something wrong in general when trying to generate the metadata for an OME-TIFF compliant RGB file?

Any help would be much appreciated. Thank you!

EDIT:

It seems like it might not actually be possible to generate OME-XML compliant metadata for RGB images with this package - as seen here, the OMETIFFWriter object expects the Channels key within the passed in metadata dictionary to contain as many keys as there are channels (inferred from the shape of the image) - however, in the case of RGB images, we only want 1 channel with a SamplesPerPixel value of 3, rather than wanting each channel to be parsed as its own channel with SamplesPerPixel = 1.

Compression of a OME-TIFF file when writing

Hello again,
I want to write OME-TIFF from big arrays (23000 X 23000 for example). Following the example in the README, this is how I generate an OME-TIFF with random values:

import pyometiff
import numpy as np

data = np.random.randn(1, 1, 3, 23000, 23000).astype('uint8')

metadata_dict = {
    "PhysicalSizeX" : "0.88",
    "PhysicalSizeXUnit" : "µm",
    "PhysicalSizeY" : "0.88",
    "PhysicalSizeYUnit" : "µm",
    "PhysicalSizeZ" : "3.3",
    "PhysicalSizeZUnit" : "µm",
    "Channels" : {
        "405" : {
            "Name" : "405nm",
            "SamplesPerPixel": 1,
            "ExcitationWavelength": 405.,
            "ExcitationWavelengthUnit": "nm"
        },
        "488" : {
            "Name" : "488nm",
            "SamplesPerPixel": 1,
            "ExcitationWavelength": 488.,
            "ExcitationWavelengthUnit": "nm"
        },
        "638" : {
            "Name" : "638nm",
            "SamplesPerPixel": 1,
            "ExcitationWavelength": 638.,
            "ExcitationWavelengthUnit": "nm"
        },
    }
}

writer = pyometiff.OMETIFFWriter("test_out.ome.tiff", dimension_order="ZTCYX", array=data, metadata=metadata_dict)
writer.write()

It works, but the output file is 1.47 GB big. Is there a way to compress it, in JPEG, for example?

Thanks for your help,

Etienne

ValueError when reading a OME-TIFF file

Hello,
I'm trying to read 2D OME-TIFF sample files that I found on the OME website (https://downloads.openmicroscopy.org/images/OME-TIFF/2016-06/tubhiswt-2D/) with the package pyometiff. Here is my code:

import pyometiff
reader = pyometiff.OMETIFFReader('tubhiswt_C0.ome.tif')
img_array, metadata, xml_metadata = reader.read()

When I run it, I get this error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-10-bd3614b76a8e> in <module>
      1 reader = pyometiff.OMETIFFReader('tubhiswt_C0.ome.tif')
----> 2 img_array, metadata, xml_metadata = reader.read()

~\miniconda3\envs\tpGBM\lib\site-packages\pyometiff\omereader.py in read(self)
     37     def read(self) -> (np.ndarray, dict, str):
     38         self.array, self.omexml_string = self._open_tiff(self.fpath)
---> 39         self.metadata = self.parse_metadata(self.omexml_string)
     40         return self.array, self.metadata, self.omexml_string
     41 

~\miniconda3\envs\tpGBM\lib\site-packages\pyometiff\omereader.py in parse_metadata(self, omexml_string)
    131                 self.imageseries
    132             ).Detector.get_ID()
--> 133             metadata["DetectorType"] = self.ox.instrument(
    134                 self.imageseries
    135             ).Detector.get_Type()

~\miniconda3\envs\tpGBM\lib\site-packages\pyometiff\omexml.py in get_Type(self)
   1172 
   1173         def get_Type(self):
-> 1174             return get_int_attr(self.node, "Type")
   1175         def set_Type(self, value):
   1176             self.node.set("Type", str(value))

~\miniconda3\envs\tpGBM\lib\site-packages\pyometiff\omexml.py in get_int_attr(node, attribute)
    294     '''Cast an element attribute to an int or return None if not present'''
    295     attr = node.get(attribute)
--> 296     return None if attr is None else int(attr)
    297 
    298 def make_text_node(parent, namespace, tag_name, text):

ValueError: invalid literal for int() with base 10: 'PMT'

I also tried with another OME-TIFF file from https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/data.html, for example 00001_01.ome.tiff, and the reading works just fine.

Do you know why the first ones can't be read?

Thanks for your help,

Etienne

Meaning of Sizes BF, DimOrder BF, DimOrder BF Array, DimOrder

Dear all,

Could you clarify a bit exact meaning of Sizes BF, DimOrder BF, DimOrder BF Array, DimOrder fields in metadata?

Thank you for any input.

Support multi-scene OME-TIFF

The example dataset at https://docs.openmicroscopy.org/ome-model/6.0.0/ome-tiff/data.html#plate contains multiple (thousands of) scenes (think "plate positions"). aicsimageio allows accessing them via the scenes and current_scene attributes and set_scene method on the AICSImage object. On the other hand, AFAICT (but I may be wrong), pyometiff only lets one access the first scene. (My guess is that accessing the other scenes requires passing the series kwarg to TiffFile.asarray(...).)

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