pyview/synthetic_data/06_PROGS/export_movies_synthetic.py

import view
import pathlib as pl
# this tells view all settings including the folder structure of your project
# On Windows, if you copy paths from the file explorer, make sure the string below is always of the form r"......"

# insert your current directory 
#moaf = r"/Users/galizia/Documents/DATA/synthetic_data/"
# or detect your directory, skipping the last folder
moaf = pl.Path(__file__).parents[1]

print('working in directory: ', moaf)

# this tells view all settings including the folder structure of your project
# On Windows, if you copy paths from the file explorer, make sure the string below is always of the form r"......"
ymlfile = moaf / r"view_synthetic_666.yml"


# any  manual changes to flags, add to dictionary as required
# i.e. flags that should have a different value from the project .yml file above
flags_to_update = {
    "RM_ROITrace": 3,  # set to 0 for .coor files, 3 for .roi files and 4 for .roi.tif
    # Other flag changes can be included, for example:
    # CTV_scalebar: True,
    # mv_individualScale: 2,
    # .....
}

# list of animals for which moview are to be exported
animals = [
    "Synthetic_data_strip"#,
    #""
]


Analyze_column_values_to_use = (-1,1)



if __name__ == '__main__':

    # create a view object
    view_obj = view.VIEW()

    # load flags from yml file
    view_obj.update_flags_from_ymlfile(ymlfile)

    # update flags specified locally
    view_obj.update_flags(flags_to_update)

    # iterate over animals
    for animal in animals:

        # initialize view object with animal
        view_obj.initialize_animal(animal=animal)

        # iterate over measurements of the animal
        for measu in view_obj.get_measus_for_current_animal(analyze_values_to_use=Analyze_column_values_to_use):

            # load a measurement for the animal
            view_obj.load_measurement_data_from_current_animal(measu)

            # calculate signals
            view_obj.calculate_signals()

            # save movie for the loaded data
            view_obj.export_movie_for_current_measurement()

    # backup this script and the yml file used next to the created GDMs
    view_obj.backup_script_flags_configs_for_movies(files=[__file__, ymlfile])