DataWriterClass .put_Image() doesnt work below python version 3.9

[BenjaminSchaar]

my_dataset.put_image(
image=img,
position=p,
time=t,
channel=c,
z=z,
image_metadata=image_metadata.
)

problematic line:

image_metadata = basic_metadata | image_metadata

Fixes:

Python 3.9+

merged_dict = basic_metadata | image_metadata

Python 3.8 and earlier alternatives

Option 1: Using dictionary unpacking

merged_dict = {**basic_metadata, **image_metadata}

Option 2: Using dict.update() (modifies the first dictionary)

merged_dict = basic_metadata.copy()
merged_dict.update(image_metadata)

[BenjaminSchaar]

same problem in class init :

def get_summary_metadata(self) -> dict:
"""
Returns the summary metadata of the data set

Returns:
    dict: metadata
"""
if self._is_ndtiff:
    return self._data_store.summary_metadata
return None

File "/lisc/scratch/neurobiology/zimmer/schaar/code/tool_scripts/ndtiff-processing-script.py", line 98, in
main()
File "/lisc/scratch/neurobiology/zimmer/schaar/code/tool_scripts/ndtiff-processing-script.py", line 59, in main
my_dataset = MicroscopeDataWriter(
File "/lisc/scratch/neurobiology/zimmer/autoscope/code/imutils/imutils/scopedatamanager/microscope_data_writer.py", line 55, in init
self._check_metadata_format(summary_metadata)
File "/lisc/scratch/neurobiology/zimmer/autoscope/code/imutils/imutils/scopedatamanager/microscope_data_writer.py", line 102, in _check_metadata_format
if not isinstance(value, (str, int, float, bool, None)):
TypeError: isinstance() arg 2 must be a type or tuple of types
[schaar@login01 ~]$ <autoscope_behaviour_shared>

def __init__(self, dataset_path: Union[Path,str], dataset_name: str, add_date_time: bool = True, summary_metadata: dict = None, verbose: int = 1, **kwargs):
    """
    Writes data for microscope data sets as ndtiff.
    Metadata is stored in a header and as seperate files (_Metadata.json).
    Trys to keep the micromanager metadata schema.
    
    Args:
        dataset_path (Path or str): Path to the file or directory writing the data
        dataset_name (str): Name of the dataset (folder name)
        add_date_time (bool, optional): Add date and time to the dataset name. Defaults to True.
        summary_metadata (dict, optional): Summary metadata for the dataset. Defaults to None.
        verbose (int, optional): Verbosity level of logger messages. Defaults to 1.
        **kwargs: Additional arguments for the NDTiffDataset class
    """
    self.verbose = verbose # set the verbosity level
    self.logger = logger.bind(classname=self.__class__.__name__) # create a logger for the class
    self.init_date_time = datetime.now() # keep the time when the class was initialized
    
    # add date and time to the dataset name
    if add_date_time:
        dataset_name = f"{self.init_date_time.strftime('%Y-%m-%d_%H-%M')}_{dataset_name}"
    
    # add basic metadata
    basic_metadata = {'MicroscopeDataWriter': 'metadata provided', 'Package': 'imutils',
                      'Library': 'ndstorage', 'Date': self.init_date_time.strftime("%d.%m.%Y"),
                      'TimeCreated': self.init_date_time.strftime("%H:%M:%S")}
    if summary_metadata is None:
        if self.verbose >= 1:
            self.logger.warning("No metadata provided!")
        basic_metadata['MicroscopeDataWriter'] = 'no metadata provided!'
        self._summary_metadata = basic_metadata
    else:
        self._check_metadata_format(summary_metadata)
        self._summary_metadata = basic_metadata | summary_metadata
    
    # call the NDTiffDataset class constructor
    self._data_store = NDTiffDataset(dataset_path=dataset_path, name=dataset_name,
                                     summary_metadata=self._summary_metadata, writable=True, **kwargs)

self._summary_metadata = basic_metadata | summary_metadata -> ony python 3.9 +

[BenjaminSchaar]

I changed the dict merge line in the put image class and writing metadata now works also on python 3.8

self._summary_metadata = basic_metadata | summary_metadata

-> self._summary_metadata = {**basic_metadata, **summary_metadata}

what i couldnt solve is writing summary metadata :

Create dataset with metadata

my_dataset = MicroscopeDataWriter(
    dataset_path=dst_path, 
    dataset_name=dataset_name,
    summary_metadata = reader_obj.get_summary_metadata() -> doesnt work with 3.8
)