pycziutils package

Module contents

pycziutils

A tiny utility module to parse Zeiss CZI files in Python through python-bioformats. Parse tiled images, organize planes into pandas.DataFrame, get some hard-to-get metadata.

pycziutils.get_tiled_omexml_metadata(path=None, url=None, *, group_file=True)[source]

Read tiled czi image and get ZeissCZIReader without stitching

Parameters

  • path (str, default None) – path to the czi file

  • url (str, default None) – url to the czi file (optional)

  • groupfiles (bool, default True) – utilize the groupfiles option to take the directory structure into account.

Returns

xml – the OME-XML string

Return type

str

Notes

Copied & modified from bioformats.get_omexml_metadata

pycziutils.get_tiled_reader(path)[source]

Read tiled czi image and get ZeissCZIReader without stitching

Parameters

path (str) – path to the czi file

Returns

reader – tiled reader

Return type

ZeissCZIReader

pycziutils.parse_binning(ome_xml)[source]

parse OME-XML and get binning

Parameters

ome_xml (str) – the input OME-XML string

Returns

binning – the binning as [x,y]

Return type

list

Note

uses ‘HardwareSetting|ParameterCollection|Binning’

pycziutils.parse_camera_LUT(ome_xml)[source]

parse OME-XML and get camera LUT

Parameters

ome_xml (str) – the input OME-XML string

Returns

lut – the LUT as [lut1,lut2]. If the key is not found, returns (np.nan,np.nan)

Return type

list

Note

uses ‘HardwareSetting|ParameterCollection|CameraLUT1’ and

‘HardwareSetting|ParameterCollection|CameraLUT2’

pycziutils.parse_camera_bits(ome_xml)[source]

parse OME-XML and get camera bits

Parameters

ome_xml (str) – the input OME-XML string

Returns

bit_depth – the camera valid bits

Return type

int

Note

uses ‘HardwareSetting|ParameterCollection|ValidBits’

pycziutils.parse_camera_roi(ome_xml)[source]

parse OME-XML and get ROI

Parameters

ome_xml (str) – the input OME-XML string

Returns

roi – the camera ROI (x0,y0,x1,y1) as a list

Return type

list

Note

uses ‘HardwareSetting|ParameterCollection|ImageFrame’

pycziutils.parse_camera_roi_slice(ome_xml)[source]

parse OME-XML and get ROI as slices

Parameters

ome_xml (str) – the input OME-XML string

Returns

roi – the camera ROI as slices; slice(x0,x0),slice(y0,y1)

Return type

slice

Note

uses ‘HardwareSetting|ParameterCollection|ImageFrame’

pycziutils.parse_channels(ome_xml, assume_all_equal=True)[source]

parse OME-XML and get the channel list

Parameters

  • ome_xml (str) – the input OME-XML string

  • assume_all_equal (bool, default True) – if True, assume the channels are the same for all the planes

Returns

a list of channels if assume_all_equal==True, otherwise a list of lists of channels for each planes

Return type

channels

pycziutils.parse_pixel_size(ome_xml, assume_all_equal=True)[source]

parse OME-XML and get the pixel sizes

Parameters

  • ome_xml (str) – the input OME-XML string

  • assume_all_equal (bool, default True) – if True, assume the pixel sizes are the same for all the planes

Returns

a list of pixel sizes if assume_all_equal==True, otherwise a list of lists of pixel sizes for each planes

Return type

pixel sizes

pycziutils.parse_planes(ome_xml, acquisition_timezone=0)[source]

parse OME-XML and get pandas dataframe for each planes

Parameters

  • ome_xml (str) – the input OME-XML string

  • acquisition_timezone (Union[datetime.timezone, int]) – timezone to use. if int is given, datetime.timezone(datetime.timedelta(timezone)) is used

Returns

planes_df – dataframe for all planes, containing X,Y,Z positions and time

Return type

pandas.DataFrame

Note

absolute_T is T + AcquisitionDate, not sure if it is absolutely correct for now

pycziutils.parse_properties(ome_xml, keys, domain='pixels')[source]

parse OME-XML and get properties of the specified domain

Parameters

  • ome_xml (str) – the input OME-XML string

  • keys – the keys for the properties

  • domain (str) – the domain level to get properties, should be “image”, “pixels” or “plane”

Returns

the properties as a list

Return type

properties

pycziutils.parse_structured_annotation_dict(ome_xml)[source]

parse OME-XML and get structured annotation as a dict

Parameters

ome_xml (str) – the input OME-XML string

Returns

structured_annotation_dict – OriginalMetadata.key : OriginalMetadata.value pairs as a dict

Return type

dict

pycziutils.summarize_image_size(reader, print_summary=True)[source]

get image size and summarize from reader

Parameters

  • reader – the bioformat reader

  • print_summary (bool, default True) – wheather to print the size summary

Returns

  • seriesCount (int) – the count for series

  • sizeT (int) – the count for time

  • sizeC (int) – the count for channels

  • sizeX (int) – the count for X

  • sizeY (int) – the count for Y

  • sizeZ (int) – the count for Z

pycziutils.with_javabridge(func)[source]

runs function with javabridge, with the loglevel error https://forum.image.sc/t/python-bioformats-and-javabridge-debug-messages/12578/11