microscope_automation.util package

Submodules

microscope_automation.util.automation_exceptions module

Classes for exceptions Do not name module exceptions. It will conflict with system exceptions. Created on Jun 7, 2017

@author: winfriedw

exception microscope_automation.util.automation_exceptions.AutofocusError(message=None, error_component=None, focus_reference_obj_id=None)

Bases: microscope_automation.util.automation_exceptions.HardwareError

Exception if autofocus failed.

error_dialog()

Show error message to user.

Input:

none

Output:

none

get_focus_reference_obj_id()

Retrieve object (typcially plate) that is used as reference for autofocus

offset.

Input:

none

Output:

focus_reference_obj_id: Sample object used as reference for autofocus

set_focus_reference_obj_id(focus_reference_obj_id)

Set object (typcially plate) that is used as reference for autofocus offset.

Input:

focus_reference_obj_id: Sample object used as reference for autofocus

Output:

None

exception microscope_automation.util.automation_exceptions.AutofocusNoReferenceObjectError(message=None, error_component=None, focus_reference_obj_id=None)

Bases: microscope_automation.util.automation_exceptions.AutofocusError

Exception if no reference object was selected for autofocus

Input:

focus_reference_obj_id: Sample object used as reference for autofocus

message: Test to display as error message

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.AutofocusNotSetError(message=None, error_component=None, focus_reference_obj_id=None)

Bases: microscope_automation.util.automation_exceptions.AutofocusError

Exception if objective was changed since autofocus was initialized

Input:

focus_reference_obj_id: Sample object used as reference for autofocus

message: Test to display as error message

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.AutofocusObjectiveChangedError(message=None, error_component=None, focus_reference_obj_id=None)

Bases: microscope_automation.util.automation_exceptions.AutofocusError

Exception if objective was changed since autofocus was initialized

Input:

focus_reference_obj_id: Sample object used as reference for autofocus

message: Test to display as error message

Output:

none

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.AutomationError(message=None, error_component=None)

Bases: Exception

Base exception for all errors in package microscopeautomation

exception microscope_automation.util.automation_exceptions.CrashDangerError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception if danger for hardware was detected.

error_dialog(advice='')

Show error message to user.

Input:

advice: str with advice to user of how to avoid crash.

Output:

none

exception microscope_automation.util.automation_exceptions.ExperimentError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.HardwareError

Exception for failures experiment execution.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.ExperimentNotExistError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.ExperimentError

Exception for failures experiment execution.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.FileExistsError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception if file exists to prevent overriding it.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.HardwareCommandNotDefinedError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception if experiment is not defined for this microscope.

error_dialog(advice='')

Show error message to user.

Input:

advice: str with advice to user of how to avoid crash.

Output:

none

exception microscope_automation.util.automation_exceptions.HardwareDoesNotExistError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.HardwareError

Exception if hardware was not defined.

error_dialog(advice='')

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.HardwareError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception for failures in hardware.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.HardwareNotReadyError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception if hardware is not ready for experiment.

error_dialog(advice='')

Show error message to user.

Input:

advice: str with advice to user of how to avoid crash.

Output:

none

exception microscope_automation.util.automation_exceptions.IOError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception for I/O errors.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.LoadNotDefinedError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.HardwareError

Exception if load position for focus drive is not defined.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.MetaDataNotSavedError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Exception if data could not be saved to meta data file.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.ObjectiveNotDefinedError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.HardwareError

Exception if selected objective was not defined.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.StopCollectingError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.AutomationError

Stop collecting sample positions.

error_dialog()

Show error message to user.

Input:

none

Output:

none

exception microscope_automation.util.automation_exceptions.WorkNotDefinedError(message=None, error_component=None)

Bases: microscope_automation.util.automation_exceptions.HardwareError

Exception if work position for focus drive is not defined.

error_dialog()

Show error message to user.

Input:

none

Output:

none

microscope_automation.util.automation_exceptions.get_error_blocking()

Retrieve blocking behavior of error dialogs.

Input:

none

Output:

blocking: if True use modal dialog for error reporting, otherwise print message

Output:

None

microscope_automation.util.automation_exceptions.set_error_blocking(block)

Set blocking behavior of error dialogs.

Input:

block: if True use modal dialog for error reporting, otherwise print message

Output:

None

microscope_automation.util.automation_messages_form_layout module

QDialog boxes and other messages for Microscope Automation package based on formlayout https://pypi.python.org/pypi/formlayout http://pythonhosted.org/formlayout/index.html# https://github.com/PierreRaybaut/formlayout http://pyqt.sourceforge.net/Docs/PyQt4/ https://wiki.qt.io/PySide

Requires PyQt4 or PyQt5, set installed API below

Created on Jun 23, 2016

@author: winfriedw

microscope_automation.util.automation_messages_form_layout.check_box_message(message, checkBoxList, return_code=False)

Ask user to operate microscope manually and allows option to abort script.

Input:

message: Message that will be displayed

checkBoxList: list with check box names and settings in form:

[(‘Choice 1’, True), (‘Choice 2’, False)

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

new_check_box_list: User pressed ok result is updated checkBoxList

microscope_automation.util.automation_messages_form_layout.error_message(message, return_code=False, blocking=True)

Show error message and allows option to abort script.

Input:

message: Message that will be displayed

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

blocking: if True use modal dialog for error reporting, otherwise print(message)

Return:

0: User selected to abort script

1: User pressed ok

-1: User pressed ok and selected ‘Ignore’

microscope_automation.util.automation_messages_form_layout.file_select_dialog(directory, file_pattern=None, comment=None, return_code=False)

List all files in directory and select one.

Input:

directory: path to directory with files

file_pattern: string with regular expression. If file matches expression it will be pre-selected.

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Output:

file_path: path to selected file

microscope_automation.util.automation_messages_form_layout.information_message(title, message, return_code=False)

Displays information to user and allows option to abort script.

Input:

title: Title of dialog box

message: Message that will be displayed

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

1: User pressed ok

microscope_automation.util.automation_messages_form_layout.operate_message(message, return_code=False)

Ask user to operate microscope manually and allows option to abort script.

Input:

message: Message that will be displayed

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

1: User pressed ok

microscope_automation.util.automation_messages_form_layout.pull_down_select_dialog(item_list, message)

Show all items from itemList in pulldown menu and allow user to select one item.

Input:

itemList: list of strings to display in pull down menu

message: string with instructions to user

Output:

selected_item: item selected by user

microscope_automation.util.automation_messages_form_layout.read_string(title, label, default, return_code=False)

Ask for user input and allows option to abort script.

Input:

title: Title of dialog box

label: Text to display in front of sting input field

default: default input

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

1: User pressed ok

microscope_automation.util.automation_messages_form_layout.select_message(message, count=None, return_code=False)

Interrupt script and wait for user to continue.

Input:

message: Message that will be displayed

count: number of collected positions

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

resultDict: dictionary of form {‘Include’: True/False, ‘Continue’: True/False}

microscope_automation.util.automation_messages_form_layout.setup_message(message, return_code=False)

Displays information about setup error and allows option to abort script.

Input:

message: Message that will be displayed

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

1: User pressed ok

microscope_automation.util.automation_messages_form_layout.stop_script(message_text=None, allow_continue=False)

Script will stop all Microscope action immediately and ask user to stop execution of script or to continue.

Input:

message_text: Message to user explaining why processing should be stopped.

allow_continue: if True, allow user to continue. Default: False

Output:

none if user selects ‘Continue’, otherwise calls sys.exit()

microscope_automation.util.automation_messages_form_layout.value_calibration_form(title, comment, default, *form_fields)

Attribute selection dialog for value calibration Last result value will always be True or False for whether the value(s) were acceptable

Input:

title: title for the form

comment: comment for the form

form_fields: variable length argument list for all fields to be changed

Output:

result: contents of the calibration form

microscope_automation.util.automation_messages_form_layout.wait_message(message, return_code=False)

Interrupt script and wait for user to continue.

Input:

message: Message that will be displayed

return_code: if True, will return after cancel with code 0, otherwise will call sys.exit()

Return:

0: User selected to abort script

True: User pressed ok and want’s to continue to wait after each image

False: User pressed ok and want’s to cancel wait times

microscope_automation.util.error_handling module

Tools for error handling and logging Created on Jul 31, 2016

@author: winfriedw

microscope_automation.util.error_handling.setup_logger(prefs, log_level='DEBUG')

Initialize logger. Will work over multiple modules

see https://docs.python.org/2/howto/logging-cookbook.html#using-logging-in-multiple-modules

microscope_automation.util.get_path module

Collection of functions to return path for settings, logfile, and data Created on Aug 8, 2016

@author: winfriedw

microscope_automation.util.get_path.add_suffix(file_path, suffix)

Add suffix to end of file name.

Input:

file_path: path to file name

suffix: suffix to put between end of filename and file extension

Output:

new_file_path: file_path with suffix

microscope_automation.util.get_path.get_calibration_path(prefs)

Return path to calibration information e.g. blackreference images

Input:

prefs: Preferences object created from YAML file

Output:

calibration_path: path to calibration directory

microscope_automation.util.get_path.get_colony_dir_path(prefs, barcode=None)

Return path to directory with .csv file with colony positions and features.

Input:

prefs: Preferences object created from YAML file

barcode: Use the plate barcode to make the folder

Output:

colonyDir: path to log file

microscope_automation.util.get_path.get_colony_file_path(prefs, colony_file, barcode=None)

Return path to file with colony information typically produced by CellProfiler based on Celigo platescanner data.

Input:

prefs: Preferences object created from YAML file

colony_file: path to .csv file with colony data

barcode: Use the plate barcode to make the folder

Output:

colony_file_path: complete path to colony file

microscope_automation.util.get_path.get_colony_remote_dir_path(prefs)

Return path to directory with .csv file with colony positions and features on network.

Input:

prefs: Preferences object created from YAML file

Output:

colony_dir_path: path to log file

microscope_automation.util.get_path.get_daily_folder(prefs, barcode=None)

Find folder for daily settings and results. Create folder if not existing.

Input:

prefs: Preferences object created from YAML file

barcode: Use the plate barcode to make the folder

Output:

daily_path: path to daily folder. No ‘/’ at end.

microscope_automation.util.get_path.get_experiment_path(prefs, dir=False)

Return path to experiment.

Input:

prefs: Preferences object created from YAML file

dir: if true return path to experiments directory, otherwise to experiment file. Default: False

Output:

experiment_path: path to experiment

microscope_automation.util.get_path.get_hardware_settings_path(prefs)

Return path to .yml file with microscope specifications from preferences file.

Input:

prefs: Preferences object created from YAML file

Output:

hardwarePath: path to layout file

microscope_automation.util.get_path.get_images_path(prefs, sub_dir=None, barcode=None)

Return path to directory for images. Create directory if not available

Input:

prefs: Preferences object created from YAML file

sub_dir: Sub-directory for images. Will create folder with this name

barcode: Use the plate barcode to make the folder

Output:

references_path: path to directory for reference images for specific well

microscope_automation.util.get_path.get_log_file_path(prefs)

Return path to log file.

Input:

prefs: Preferences object created from YAML file

Output:

log_file_path: path to log file

microscope_automation.util.get_path.get_meta_data_path(prefs, barcode=None)

Return path for meta data.

Input:

prefs: Preferences object created from YAML file

barcode: Use the plate barcode to make the folder

Output:

meta_data_file: path to log file

microscope_automation.util.get_path.get_position_csv_path(prefs, barcode=None)

Function to get the file path for the csv files where all the positions are stored after segmentation.

Input:

prefs: preferences

barcode: Use the plate barcode to make the folder

Output:

paths: file paths for the files

microscope_automation.util.get_path.get_recovery_settings_path(prefs)

Returns the file path to save the pickled dictionary after interruption

Input:

prefs: Preferences object created from YAML file

Output:

file_path: path to recovery settings

microscope_automation.util.get_path.get_references_path(prefs, barcode=None)

Return path to directory for reference images. Create directory if not available

Input:

prefs: Preferences object created from YAML file

barcode: Use the plate barcode to make the folder

Output:

references_path: path to directory for reference images for specific well

microscope_automation.util.get_path.get_valid_path_from_prefs(prefs, key, search_dir=True, validate=False)

Read list of paths from prefs and return first valid match.

Input:

prefs: Preferences object created from YAML file

key: key for pathlist in preferences.yml

search_dir: if True search for directory, otherwise for file

Output:

return_path: path to valid file or directory

microscope_automation.util.get_path.get_well_edge_path(prefs, barcode=None)

Return path to folder where well edge images are saved. Used to determine the well’s center.

Input:

prefs: Preferences object created from YAML file

Output:

well_edge_path: path to calibration directory

microscope_automation.util.get_path.set_up_settings_folders(prefs, keys=['PathCalibration', 'RecoverySettingsFilePath', 'LogFilePath', 'PathDailyFolder'])

Checks if the folders specified in preferences exist and makes them if not

Input:

prefs: Preferences object created from YAML file

Output:

none

microscope_automation.util.get_path.set_up_subfolders(parent_folder_path, subfolder)

Set the Subfolders for imaging folder - e.g. TapeOnly and Failed QC

Input:

parent_folder_path: Image Folder Path

subfolder: folder to create, can be list of multiple folders

Output:

subfolders: list of full path of subfolders created

microscope_automation.util.image_AICS module

Module with class ImageAICS to wrap image data as numpy arrays and meta data as dictionaries. Add display methods Created on Jul 11, 2016

@author: winfriedw

class microscope_automation.util.image_AICS.ImageAICS(data=None, meta=None)

Bases: object

store and display image data

add_data(data)

add image data

Input:

data: numpy array with image data

Output:

none

add_meta(meta)

Add meta data. Use keys as defined in OME-XML.

Input:

meta: dictionary with meta data

Output:

none

create_file_name(template)

Create file name based on meta data and template.

Input:

template: string with filename with path for saved image in original format or tuple with path to directory and template for file name

Output:

filePath: file name and path for image

get_data()

retrieve image data as numpy array.

Input:

none

Output:

data: numpy array with image data

get_meta(key=None)

Retrieve meta data. Use keys as defined in OME-XML.

Input:

none

Output:

meta: dictionary with meta data

parse_file_template(template)

Create file name based on meta data and template.

Input:

template: string with filename

Output:

fileName: file name for image

save_as_tiff(path, bits=16)

Save data portion of image as .tif file.

Input:

path: file path with extension .tif as string

bits: bit depth of image. Default: 16

Output:

none

show(title='ImageAICS', channel=0, z=0, t=0)

display image data

Input:

title: string with title for window. Default=’ImageAICS’

channel: channel for display. Default = 0

z: z slice. Default = 0

t: time point. Default = 0

Output:

none

microscope_automation.util.load_image_czi module

class microscope_automation.util.load_image_czi.LoadImageCzi

Bases: object

load_image(image, get_meta_data)

Parameters

• image – ImageAICS object

• get_meta_data – Flag if the user wants the meta data

Returns

ImageAICS object with full pixel data and relevant meta data

microscope_automation.util.software_state module

File to keep track of the state of the software.

@author: winfriedw

class microscope_automation.util.software_state.DiagnosticPickler(file, protocol=None, fix_imports=True, buffer_callback=None)

Bases: _pickle.Pickler

save(obj)

class microscope_automation.util.software_state.State(recovery_file_path=None)

Bases: object

add_last_experiment_object(exp_object_name)

Add objects to the list for last experiment objects to keep track of which cells have already been imaged. To be able to pick up exactly where we left off

Input:

exp_object_list: list of experiment objects to add for the next experiment

Output:

none

add_next_experiment_object(experiment_name, exp_object_list)

Add objects to the list for next experiment objects.

Input:

experiment_name: name of experiment to add

exp_object_list: list of experiment objects to add for the next experiment

Output:

none

add_unpickled_objects(base_object)

Function to add Zen object back

Input

base_object: The reference object or next experiment object to rehydrate

Output:

none

eliminate_unpickled_objects(base_object)

Remove unpickled objects from given object

Input:

base_object: Object that needs to be pruned

Output:

none

prune_object_dict()

Function to strip away the Zen microscope object from each level of the sample object tree.

Reason - there are some objects in microscope class (communication object) that can’t be pickled.

Input:

object_dict: The dictionary that needs to be filtered.

Output:

object_dict: The filtered dictionary.

recover_objects(file_path)

Function to return next objects dictionary and the reference object by unpickling the file.

Input:

filepath: path to the pickled file

Output:

tuple of recovered objects in the form (next_experiment_objects, reference_object, last_experiment_objects, hardware_status_dict)

rehydrate_removed_references()

In case of auto save, we need the Zen object to be added back (it was removed before pickling)

Input:

none

Output:

none

save_state()

Function to process the objects and save them by pickling.

Input:

none

Output:

none

save_state_and_exit()

Function to process the objects and save them by pickling and exiting the software.

Input:

none

Output:

none

Module contents

Utility package for Microscope Automation.