scripts.helpers#

Classes#

Stain

Functions#

`apply_gating`(data_df[, stain1, stain2, extra_stains])
`button_style`([font_size, padding, color, bck_col, ...])
`create_file_path`(output_dir, sample, name, extension)	Helper function to create file paths.
`get_abs_path`(relative_path)	Get absolute path to a resource, relative to the base directory.
`get_app_dir`()	Get absolute path relative to the executable location.
`get_stains_from_panel`(Panel)	Build Stain instances for the two main stain types of living/dead and cells/not cells cases.
`load_model_from_files`(trained_model_dir)
`save_gating_results`(gated_data_df, output_dir, sample, ...)
`stain_sannity_check`(df, label, channel, sign, threshold)	Checks if gating applied for a stain returns both True and False cases.
`time_based_dir`(prefix, base_path[, multiple_cocultures])

Module Contents#

class scripts.helpers.Stain#

channel: str#

label: str | None = None#

sign: str#

value: float#

scripts.helpers.apply_gating(data_df, stain1=None, stain2=None, extra_stains=None)#

scripts.helpers.button_style(font_size=12, padding=5, color='black', bck_col='#90EE90', bck_col_hov='#7FCF7F', bck_col_clicked='#72B572', radius=5)#

scripts.helpers.create_file_path(output_dir, sample, name, extension)#: Helper function to create file paths.

scripts.helpers.get_abs_path(relative_path)#: Get absolute path to a resource, relative to the base directory.

scripts.helpers.get_app_dir()#: Get absolute path relative to the executable location.

scripts.helpers.get_stains_from_panel(Panel)#

Build Stain instances for the two main stain types of living/dead and cells/not cells cases. In this case, no label is part of the Stain instance. Function to be used only in the GUI framework.

Arguments:: PredictionPanel:
Returns:: stain1 (Stain) stain2 (Stain)

scripts.helpers.load_model_from_files(trained_model_dir)#

scripts.helpers.save_gating_results(gated_data_df, output_dir, sample, x_axis, y_axis, z_axis, all_labels)#

scripts.helpers.stain_sannity_check(df, label, channel, sign, threshold)#: Checks if gating applied for a stain returns both True and False cases. If not, raises an error so the user refines their thresholds.

scripts.helpers.time_based_dir(prefix, base_path, multiple_cocultures=False)#