microscope_automation.settings package

Submodules

microscope_automation.settings.meta_data_file module

Write meta data to file. Created on Oct 17, 2016

@author: winfriedw

class microscope_automation.settings.meta_data_file.MetaDataFile(file_path, format='csv')

Bases: object

Class to save meta data associated with samples and images.

write_csv(meta, file_path)

Write meta data to .csv file.

Input:

meta: dictionary with meta data

file_path: path and name of .csv file. If file does not exist, create new file.

Output:

none

write_meta(meta)

Write meta data to .csv file.

Input:

meta: dictionary or pandas DataFrame with meta data

Output:

none

microscope_automation.settings.preferences module

Created on Jun 7, 2016 Part of microscope_automation Will read and return values for different configuration files

@author: winfriedw

class microscope_automation.settings.preferences.Preferences(pref_path=None, pref_dict=None, parent_prefs=None)

Bases: object

Reads configuration files and will return Values

get_parent_prefs()

preferences objects that are created from a subset of preferences, keep a reference to the original preferences set.

Input:

none

Output:

parent_prefs: Object of class preferences of preferences that were source for current subset of preferences.

get_pref(name, valid_values=None)

Return value for key ‘name’ in preferences.

Input:

name: string with key name

valid_values: list with allowed values. Throw exception if value is not valid. Default: do not check.

Output:

pref: value for key ‘name’ in preferences

get_pref_as_meta(name)

Return subset of preferences as preferences object.

Input:

name: name of meta data dictionary

Output:

prefsObject: preferences dictionary as preferences object

print_prefs()

set_pref(name, value)

microscope_automation.settings.slidebook_experiment_info module

class microscope_automation.settings.slidebook_experiment_info.SlidebookExperiment(experiment_path, experiment_name)

Bases: object

experiment_exists()

Function to check if the experiment name provided in the preference file exists in the Slidebook software

Input:

none

Output:

a boolean indicating if the experiment exists or not

microscope_automation.settings.test_zen_experiment module

Test settings in ZEN experiment Created on Aug 17, 2018

@author: winfriedw

microscope_automation.settings.test_zen_experiment.current_z_set(settings)

Test if Focus Strategy for z-stack acquisition is set to CurrentZ. Input:

settings: FocusSetup part of ZEN XML settings tree.

Output:

is_valid: True if all instances FocusZStackMode are set to CurrentZ

microscope_automation.settings.test_zen_experiment.test_FocusSetup(experiment_object, verbose=True)

Test if all focus settings are correct.

Input:

experiment_object: object of class hardware.Experiment

verbose: if verbose == True print debug messages

Output:

is_valid: True, if focus settings are valid

microscope_automation.settings.zen_experiment_info module

class microscope_automation.settings.zen_experiment_info.ZenExperiment(experiment_path, experiment_name)

Bases: object

TAG_PATH_TILE_CENTER_XY = '/HardwareExperiment/ExperimentBlocks/AcquisitionBlock/SubDimensionSetups/RegionsSetup/SampleHolder/TileRegions/TileRegion/CenterPosition'

TAG_PATH_TILE_CENTER_Z = '/HardwareExperiment/ExperimentBlocks/AcquisitionBlock/SubDimensionSetups/RegionsSetup/SampleHolder/TileRegions/TileRegion/Z'

experiment_exists()

Function to check if the experiment name provided in the preference file exists in the Zen software

Input:

none

Output:

a boolean indicating if the experiment exists or not

get_focus_settings()

Function to get all the instances of focus settings in the experiment file

Input:

none

Output:

focus_settings: All instances of focus settings in experiment file

get_objective_position()

Return position of objective used in experiment. Method assumes that only one objective is used in experiment.

Input:

None

Output:

position: integer with position of objective used in experiment

get_tag_value(tag_path)

Function to find the value of a tag in the Zen Experiment file.

Input:

experiment_name: Name of the experiment file

Output:

tag_value: string value of the tag

is_tile_scan()

Test if experiment is tile scan.

Input:

none

Output:

is_tile_scan: True if experiment contains z-stack

is_z_stack()

Test if experiment is z-stack.

Input:

none

Output:

is_z_stack: True if experiment contains z-stack

update_tag_value(tag_path, new_value)

Function to update the value of a tag in the experiment xml file.

Input:

tag_path: Path where the tag is loacted in the xml tree

new_value: The value that needs to be assigned to the tag (string)

Output:

none

update_tile_positions(x_value, y_value, z_value)

In the tile function, correct the hard coded values of the tile region using the values from the automation software

Input:

x_value: float (x - coordinate)

y_value: float (y - coordinate)

z_value: float (z - coordinate)

Output:

none

z_stack_range()

Return range of first z-stack in experiment. Returns 0 if z-stack is not activated.

Input:

none

Output:

z_stack_range: True if experiment contains z-stack

Module contents

Settings package for Microscope Automation.