sarcasm.export

Classes

`MultiStructureAnalysis`	Class for multi-tif-file comparison of structure.
`MultiLOIAnalysis`	Class for multi-LOI comparison.
`Export`	A class used to export structure and motion data from SarcAsM and Motion objects.

Module Contents

class sarcasm.export.MultiStructureAnalysis(list_files: list, folder: str, experiment: str = None, load_data: bool = False, **conditions)[source]

Class for multi-tif-file comparison of structure.

Parameters:

list_files (list) – List of tif files.
folder (str) – Path to a folder to store data and results.
experiment (str, optional) – Name of the experiment (default is None).
load_data (bool, optional) – Whether to load the dataframe from previous analysis from the data folder (default is False).
**conditions (dict) – Keyword arguments with regex functions to extract information from the filename.

folder

Path to the folder with data and results.

Type:: str

experiment

Name of the experiment.

Type:: str

files

List of tif files.

Type:: list

conditions

Keyword arguments with regex functions to extract information from the filename.

Type:: dict

data

DataFrame to store the structure data.

Type:: pandas.DataFrame

folder

experiment = None

files

conditions

data = None

get_data(structure_keys=None, meta_keys=None)[source]

Iterate files and get structure data.

Parameters:

structure_keys (list, optional) – List of keys to extract structure data (default is None).
meta_keys (list, optional) – List of keys to extract metadata (default is None).

Return type:

None

save_data()[source]

Save the DataFrame to the data folder.

Return type:: None

load_data()[source]

Load the DataFrame from the data folder.

Return type:: None
Raises:: FileExistsError – If the data file does not exist in the specified folder.

export_data(filepath, format='.xlsx')[source]

Export the DataFrame to .xlsx or .csv format.

Parameters:

filepath (str) – Path to the output file.
format (str, optional) – Format of the output file (‘.xlsx’ or ‘.csv’) (default is ‘.xlsx’).

Return type:

None

class sarcasm.export.MultiLOIAnalysis(list_lois, folder, load_data=False, **conditions)[source]

Class for multi-LOI comparison.

Parameters:

list_lois (list) – List of tuples containing tif file paths and LOI names.
folder (str) – Path to a folder to store data and results.
load_data (bool, optional) – Whether to load the dataframe from previous analysis from the folder (default is False).
**conditions (dict) – Keyword arguments with regex functions to extract information from the filename.

folder

Path to the folder with data and results.

Type:: str

lois

List of tuples containing tif file paths and LOI names.

Type:: list

conditions

Keyword arguments with regex functions to extract information from the filename.

Type:: dict

data

DataFrame to store the motion data.

Type:: pandas.DataFrame

folder

lois

conditions

data = None

get_data(loi_keys=None, meta_keys=None)[source]

Iterate files and get motion data.

Parameters:

loi_keys (list, optional) – List of keys to extract motion data (default is None).
meta_keys (list, optional) – List of keys to extract metadata (default is None).

Return type:

None

save_data()[source]

Save the DataFrame to the data folder as a pandas DataFrame.

Return type:: None

load_data()[source]

Load the DataFrame from the data folder.

Return type:: None
Raises:: FileExistsError – If the data file does not exist in the specified folder.

export_data(filepath, format='.xlsx')[source]

Export the DataFrame to .xlsx or .csv format.

Parameters:

filepath (str) – Path to the output file.
format (str, optional) – Format of the output file (‘.xlsx’ or ‘.csv’) (default is ‘.xlsx’).

Return type:

None

class sarcasm.export.Export[source]

A class used to export structure and motion data from SarcAsM and Motion objects.

meta_keys_default

Default metadata keys.

Type:: list

structure_keys_default

Default structure keys.

Type:: list

motion_keys_default

Default motion keys.

Type:: list

meta_keys_default = ['file_name', 'file_path', 'frames', 'size', 'pixelsize', 'timestamps', 'time', 'frametime']

structure_keys_default = ['cell_mask_area', 'cell_mask_area_ratio', 'cell_mask_intensity', 'domain_area_mean',...

motion_keys_default = ['beating_rate', 'beating_rate_variability', 'contr_max', 'contr_max_avg', 'elong_max',...

static get_structure_dict(sarc_obj, meta_keys=None, structure_keys=None, **conditions)[source]

Create a dictionary of structure and metadata features from a SarcAsM object.

Parameters:

sarc_obj (SarcAsM) – Object of SarcAsM class or Motion class.
meta_keys (list, optional) – List of metadata keys (default is None).
structure_keys (list, optional) – List of structure keys (default is None).
conditions (kwargs) – Keyword arguments to add information to the dictionary (e.g., “cell_line”= “wt”, “info_xyz”=42).

Returns:

Dictionary containing selected metadata and structure features.

Return type:

dict

static export_structure_data(filepath, sarc_obj: sarcasm.structure.Structure | sarcasm.motion.Motion, meta_keys=None, structure_keys=None, remove_arrays=True, fileformat='.xlsx')[source]

Export structure data to a file.

Parameters:

filepath (str) – Path to the output file.
sarc_obj (SarcAsM) – Object of SarcAsM class.
meta_keys (list, optional) – List of metadata keys (default is None).
structure_keys (list, optional) – List of structure keys (default is None).
remove_arrays (bool, optional) – If True, removes columns with array data (default is True).
fileformat (str, optional) – Format of the output file (default is ‘.xlsx’).

static remove_arrays_dataframe(df)[source]

Remove columns with array data from a DataFrame.

Parameters:: df (pandas.DataFrame) – Input DataFrame.
Returns:: DataFrame with array columns removed.
Return type:: pandas.DataFrame

static get_motion_dict(motion_obj, meta_keys=None, loi_keys=None, concat=False, **conditions)[source]

Create a dictionary of motion features and metadata from a Motion object.

Parameters:

motion_obj (Motion) – Object of Motion class for LOI analysis.
meta_keys (list, optional) – List of metadata keys (default is None).
loi_keys (list, optional) – List of LOI keys (default is None).
concat (bool, optional) – If True, all 2D arrays will be concatenated to 1D arrays (default is False).
conditions (kwargs) – Keyword arguments to add to the dictionary, can be any information, e.g., drug=’ABC’.

Returns:

Dictionary containing selected metadata and motion features.

Return type:

dict

static export_motion_data(mot_obj: sarcasm.motion.Motion, filepath, meta_keys=None, motion_keys=None, remove_arrays=True, fileformat='.xlsx')[source]

Export motion data to a file.

Parameters:

mot_obj (Motion) – Object of Motion class.
filepath (str) – Path to the output file.
meta_keys (list, optional) – List of metadata keys (default is None).
motion_keys (list, optional) – List of motion keys (default is None).
remove_arrays (bool, optional) – If True, removes columns with array data (default is True).
fileformat (str, optional) – Format of the output file (default is ‘.xlsx’).