ome-types

ome-types

A pure-python implementation of the OME data model

ome_types provides a set of python dataclasses and utility functions for parsing the OME-XML format into fully-typed python objects for interactive or programmatic access in python. It can also take these python objects and output them into valid OME-XML. ome_types is a pure python library and does not require a Java virtual machine.

Note: The generated python code can be seen in the built branch. (Read the code generation section for details).

📖   documentation

Installation

from pip

pip install ome-types

With all optional dependencies:

# lxml => if you ...
#           - want to use lxml as the XML parser
#           - want to validate XML against the ome.xsd schema
#           - want to use XML documents older than the 2016-06 schema
# pint      => if you want to use object.<field>_quantity properties
# xmlschema => if you want to validate XML but DON'T want lxml

pip install ome-types[lxml,pint]

from conda

conda install -c conda-forge ome-types

from github (bleeding edge dev version)

pip install git+https://github.com/tlambert03/ome-types.git

Usage

convert an XML string or filepath into an instance of ome_types.model.OME

(The XML string/file will be validated against the ome.xsd schema)

from ome_types import from_xml

ome = from_xml('tests/data/hcs.ome.xml')

extract OME metadata from an OME-TIFF

from ome_types import from_tiff

ome2 = from_tiff('tests/data/ome.tiff')

manipulate the metadata via python objects

Both from_xml and from_tiff return an instance of ome_types.model.OME. All classes in ome_types.model follow the naming conventions of the OME data model, but use snake_case attribute names instead of CamelCase, to be consistent with the python ecosystem.

In [2]: ome = from_xml('tests/data/hcs.ome.xml')

In [3]: ome
Out[3]:
OME(
    images=[<1 Images>],
    plates=[<1 Plates>],
)

In [4]: ome.plates[0]
Out[4]:
Plate(
    id='Plate:1',
    name='Control Plate',
    column_naming_convention='letter',
    columns=12,
    row_naming_convention='number',
    rows=8,
    wells=[<1 Wells>],
)


In [5]: ome.images[0]
Out[5]:
Image(
    id='Image:0',
    name='Series 1',
    pixels=Pixels(
        id='Pixels:0',
        dimension_order='XYCZT',
        size_c=3,
        size_t=16,
        size_x=1024,
        size_y=1024,
        size_z=1,
        type='uint16',
        bin_data=[<1 Bin_Data>],
        channels=[<3 Channels>],
        physical_size_x=0.207,
        physical_size_y=0.207,
        time_increment=120.1302,
    ),
    acquisition_date=datetime.fromisoformat('2008-02-06T13:43:19'),
    description='An example OME compliant file, based on Olympus.oib',
)

Objects can be removed, or changed

In [6]: from ome_types.model.simple_types import UnitsLength

In [7]: from ome_types.model.channel import AcquisitionMode

In [8]: ome.images[0].description = "This is the new description."

In [9]: ome.images[0].pixels.physical_size_x = 350.0

In [10]: ome.images[0].pixels.physical_size_x_unit = UnitsLength.NANOMETER

In [11]: for c in ome.images[0].pixels.channels:
             c.acquisition_mode = AcquisitionMode.SPINNING_DISK_CONFOCAL

Elements can be added by constructing new OME model objects

In [12]: from ome_types.model import Instrument, Microscope, Objective, InstrumentRef

In [13]: microscope_mk4 = Microscope(
             manufacturer='OME Instruments',
             model='Lab Mk4',
             serial_number='L4-5678',
         )

In [14]: objective_40x = Objective(
             manufacturer='OME Objectives',
             model='40xAir',
             nominal_magnification=40.0,
         )

In [15]: instrument = Instrument(
             microscope=microscope_mk4,
             objectives=[objective_40x],
         )

In [16]: ome.instruments.append(instrument)

In [17]: ome.images[0].instrument_ref = InstrumentRef(id=instrument.id)

In [18]: ome.instruments
Out[18]:
[Instrument(
    id='Instrument:1',
    microscope=Microscope(
       manufacturer='OME Instruments',
       model='Lab Mk4',
       serial_number='L4-5678',
    ),
    objectives=[<1 Objectives>],
 )]

export to an OME-XML string

Finally, you can generate the OME-XML representation of the OME model object, for writing to a standalone .ome.xml file or inserting into the header of an OME-TIFF file:

In [19]: from ome_types import to_xml

In [20]: print(to_xml(ome))
<OME ...>
    <Plate ColumnNamingConvention="letter" Columns="12" ID="Plate:1" ...>
        ...
    </Plate>
    <Instrument ID="Instrument:1">
        <Microscope Manufacturer="OME Instruments" Model="Lab Mk4" SerialNumber="L4-5678" />
        <Objective Manufacturer="OME Objectives" Model="40xAir" ID="Objective:1"
        NominalMagnification="40.0" />
    </Instrument>
    <Image ID="Image:0" Name="Series 1">
        <AcquisitionDate>2008-02-06T13:43:19</AcquisitionDate>
        <Description>This is the new description.</Description>
        <InstrumentRef ID="Instrument:1" />
        <Pixels ... PhysicalSizeX="350.0" PhysicalSizeXUnit="nm" ...>
            <Channel AcquisitionMode="SpinningDiskConfocal" ...>
             ...
        </Pixels>
    </Image>
</OME>

Code generation

The bulk of this library (namely, modules inside ome_types._autogenerated) is generated at install time, and is therefore not checked into source (or visible in the main branch of this repo).

You can see the code generated by the main branch in the built branch

The package at src/ome_autogen converts the ome.xsd schema into valid python code. To run the code generation script in a development environment, clone this repository and run:

python -m src.ome_autogen

The documentation and types for the full model can be in the API Reference

Contributing

To clone and install this repository locally:

git clone https://github.com/tlambert03/ome-types.git
cd ome-types
pip install -e .[test,dev]

We use pre-commit to run various code-quality checks during continuous integration. If you'd like to make sure that your code will pass these checks before you commit your code, you should install pre-commit after cloning this repository:

pre-commit install

regenerating the models

If you modify anything in src/ome_autogen, you may need to regenerate the model with:

python -m src.ome_autogen

Running tests

To run tests:

pytest