polo.widgets package

Submodules

polo.widgets.file_browser module

class polo.widgets.file_browser.fileBrowser(parent=None)

Bases: PyQt5.QtWidgets.QTreeWidget

DATA_INDEX = 5

DIR_ICON = '/home/ethan/Documents/github/HWI/Marco_Polo/src/data/images/icons/dir.png'

FILE_ICON = '/home/ethan/Documents/github/HWI/Marco_Polo/src/data/images/icons/file.png'

get_checked_files(home_dir)

Traverse the file tree and return the full paths to files that have been selected by the user.

Parameters

home_dir (str or Path) – User’s home directory. This path is the parent of all returned files.

Returns

List of checked Paths

Return type

list

grow_tree_using_mlsd(ftp, home_dir, set_checkable=True)

Rescursively add child nodes to the tree by traversing a user’s home directory at a remote ftp server. Filepaths are read using mlsd formating.

Parameters

• ftp (FTP) – FTP object with valid connection

• home_dir (str or Path) – Path to the user’s home directory

• set_checkable (bool, optional) – Set files and dirs to checkable, defaults to True

polo.widgets.map_box module

class polo.widgets.map_box.MapBox

Bases: PyQt5.QtWidgets.QComboBox

_MapBox__init(parent=None, mapping={}, sorter=<function MapBox.<lambda>>)

current_value()

property mapping

polo.widgets.optimize_widget module

class polo.widgets.optimize_widget.OptimizeWidget(parent, run=None)

Bases: PyQt5.QtWidgets.QWidget

GRID_ICON = '/home/ethan/Documents/github/HWI/Marco_Polo/src/data/images/icons/grid.png'

The OptimizeWidget class is a primary run interface widget that allows users to create optimization screens around the crystallization conditions that yielded xtal hits. The concept is very similar to the program MakeTray available from Hampton Research. Currently, users cannot specify their own conditions and are limited to the predetermined conditions of the Menu that was selected when the run was originally imported into Polo. Additionally, the OptimizeWidget is only available to HWIRun instances as the cocktail to well mapping cannot be inferred for other more general Run types.

Parameters

• parent (QWidget) – Parent Widget

• run (HWIRun, optional) – Run to screen for hits from, defaults to None

HTML_ICON = '/home/ethan/Documents/github/HWI/Marco_Polo/src/data/images/icons/html.png'

_check_for_overflow(volume_list)

Private method to check if the volume of Reagent instancess in a given well exceeds the total well volume. If an overflow is detected, return False otherwise return the volume of H20 that should be added to the well as a UnitValue instance.

Parameters

volume_list (list) – List of UnitValues that consitute the contents of a well in the optimization plate

Returns

UnitValue describing the volume of water that should be added to the well if it does not overflow in liters, False otherwise

Return type

UnitValue or False

_error_checker()

Private method to check if all widgets and attributes have allowed values before calculating the actual grid screen. Show error message if there is a conflict.

_export_screen()

Private method to write the current optimization screen to a html file.

_gradient(reagent, num_wells, step, stock=False)

Private method for calculating a concentration gradient for a given Reagent using a given step size as a proportion of the Reagent instance’s concentration attribute.

Parameters

• reagent (Reagent) – Reagent to vary concentration

• num_wells (int) – Number of wells to vary concentration across

• step (float < 1) – Proportion of hit concentration to vary each well by

• stock (bool, optional) – If True, vary the stock volume not the hit concentration unit, defaults to False

Returns

List of UnitValues that make up the _gradient

Return type

list

_handle_reagent_change(x=False, y=False, const=False)

Private method that handles when a Reagent is changed. The arguments indicate which Reagent has been changed.

Parameters

• x (bool, optional) – If True update the x reagent, defaults to False

• y (bool, optional) – If True update the y reagent, defaults to False

• const (bool, optional) – If True update the constant reagents, defaults to False

_make_plate_list()

Private method that converts the concents of the tableWidget UI (assuming that a optimization screen has been already rendered to the user) to a list of lists that is easier to write to html using the jinja2 template.

Returns

tableWidget contents converted to list

Return type

list

_make_well_html(x_con, x_stock, y_con, y_stock, constants, water)

Private method to format the information that describes the contents of an individual well into prettier html that can be displayed to the user in a textBrowser widget.

Parameters

• x_con (UnitValue) – Concentration of x reagent in this well

• x_stock (UnitValue) – Volume of x reagent stock in this well

• y_con (UnitValue) – Concentration of y reagent in this well

• y_stock (UnitValue) – Volume of y reagent stock in this well

• constants (list of tuples) – Tuples of constant reagents to be included in each well

• water (Signed Value) – Volume of water to be added to this well

Returns

Html string to be rendered to the user

Return type

str

_set_constant_reagents()

Private method that populates the listWidget with constant reagents to display to the user.

_set_hit_well_choices()

Private method that sets the hit well comboBox widget choices based on the images in the run attribute that are human classified as crystal. Wells are identified in the comboBox by their well number.

_set_reagent_choices()

Private method that sets Reagent choices for the x and y reagents based on the currently selected well. Reagents must come from the class:Cocktail instance associated with the selected well.

TODO: Add the option to vary pH instead of a Reagent along either axis. This would also mean that the constant reagents would need to be updated.

_set_reagent_stock_con()

Private method. If a Reagent has already been assigned a stock concentration this method displays that concentration to the user through the appropriate UnitCombobBox instance. Only displays concentrations for the x and y reagents.

_set_reagent_stock_con_values(x=False, y=False, const=False)

Private method to update the stock concentations of current reagents through their stock_con attribute. The Reagent to update is indicated by the flag set to True at the time the method is called. The stock concentration value is pulled from each reagent’s respective unitComboBox instance.

Parameters

• x (bool, optional) – If True, set x_reagent stock con, defaults to False

• y (bool, optional) – If True, set the y_reagent stock con, defaults to False

• const (bool, optional) – If True, sets the constant reagents stock con, defaults to False

_set_up_unit_comboboxes()

Private method that sets the base unit and the scalers of all unitComboBox instances that are apart of the UI.

_update_current_reagents(image_index=None)

Private method that updates x and y Reagent comboBox widgets to reflect what Reagent instances are contained in the currently selected well.

Parameters

image_index (int, optional) – Index of the Image to set Reagent choices from, defaults to None.

_write_optimization_screen()

Private method to write the current optimization screen to the tableWidget UI for display to the user.

adjust_unit(signed_value, new_unit, ndigits=4)

property constant_reagents

Retrieve a set of Reagents that are not included as either the attr:x_reagent or the attr:y_reagent but are still part of the crystallization cocktail and therefore need to be included in the screen. Unlike either the x or y reagents, constant reagents do not change their concentration across the screening plate.

property hit_images

Retrieves a list of Image object instances that have human classification == ‘Crystals’. Used to determine what wells to allow the user to optimize. Currently, only allow the user to optimize wells they have marked as crystal.

property run

property selected_constant

Return the constant Reagent that is currently selected by the user.

Returns

Currently selected constant Reagent if exists and selected, None otherwise

Return type

Reagent or None

update_interface()

Method to update reagents and selectable wells to the user after they have made additional classifications that would increase or decrease the pool of crystal classified images.

property well_volume

Returns the well volume set by the user modifed by whatever well volume unit is currently selected.

property x_reagent

Used to retrieve the Reagent object that is to be varied along the x axis of the screen.

property x_step

The percent variance between x_reagent wells.

property x_wells

Returns spinBox value that representing the number wells on the x axis of the screen.

property y_reagent

Used to retreive the Reagent object that is to be varied along the y axis of the optimization plate

property y_step

The percent variance between y_reagent wells.

property y_wells

Returns spinBox value representing the number of wells on the y axis of the screen.

polo.widgets.plate_inspector_widget module

class polo.widgets.plate_inspector_widget.PlateInspectorWidget(parent, run=None)

Bases: PyQt5.QtWidgets.QWidget

_apply_color_mapping()

Applies the current color mapping to displayed images. Images are colored based on either their human or marco classification.

_apply_image_filters()

Wrapper function around plateViewer deemphasize_filtered_images() which changes the opacity of currently displayed images based on their classifications.

_parse_label_checkboxes()

Private method that reads values from QCheckBox instances related to image filtering. Returns a dictionary where keys are the labels of the QCheckBox instances which should also be the possible image classifications and values are the state of the QCheckBox (True or False).

Returned dictionary will have following structure.

{
'Crystals': True,
'Clear': False,
'Precipitate': True,
'Other': False
}

Returns

Dict of QCheckBox states.

Return type

dict

_set_alt_spectrum_buttons()

Private helper function similar to _set_time_resolved_buttons() that determines if the navigation button that allows users to view alt spectrum images should be enabled. If conditions are not met then the button is disabled.

_set_color_comboboxs()

Private method that sets the label text associated with each color selector QComboBox. Should be called in the __init__ method before the widget is shown to the user.

_set_color_options()

Private methods that uses the COLORS constant to set the color options for each color selector QComboBox instance in the image coloring tab.

_set_current_page(page_number)

Set the current page number and show the view for that page by calling show_current_page()

Parameters

page_number (int) – The new page number

_set_image_count_options()

Private method to be called in the __init__ method that sets the allowed number of images per page.

_set_images_per_page()

Private method that tells the plateViewer UI widget to set its images_per_page atttribute to the value specified in the images per page QComboBox.

_set_plate_label()

Private method to change the plate label to tell the user what view or “page” they are currently looking at.

_set_spin_box_range()

Set the allowed range for the page navigation spinbox.

_set_time_resolved_buttons()

Private helper function that determines if navigation buttons that display alt spectrum images, previous and next date images can be used.

apply_plate_settings()

Parses QCheckBox instances in the Plate View tab to determine what behavior of the plateViewer widget is requested by the user.

property color_mapping

Creates a color mapping dictionary that reflects the currently selected color selector QComboBox instances. The dictionary maps each image classification to a QColor instance that can then be used to color images in the plate viewer.

export_current_view()

property favorite

Status of the favorite QCheckBox filter.

Returns

State of the favorite QCheckBox

Return type

bool

property human

Status of human image classification QCheckBox.

Returns

State of the human filter QCheckBox

Return type

bool

images_per_page = [16, 64, 96]

property marco

Status of marco image classification QCheckBox.

Returns

State of the marco filter QCheckBox

Return type

bool

reset_all()

Method to un-check all user selected settings.

property run

property selected_classifications

Image classifications that are selected via the image filtering QCheckBox instances. Also see the image_type_checkboxes property.

Returns

List of currently selected image classifications. Images who’s classification is in this list should be shown / emphasized to the user.

Return type

list

set_aspect_ratio_mode()

Sets the preserve_aspect attribute based on the status of the preserve aspect ratio QCheckBox. Preserving the aspect ratio results in displaying undistorted crystallization images but utilizes available display space less efficiently.

show_current_plate(next_view=False, prev_view=False, next_date=False, prev_date=False, alt_spec=False)

Show the images belonging to the current plate view to the user.

Parameters

• next_date (bool, optional) – Flag, if True show equivalent images from future date, defaults to False

• prev_date (bool, optional) – Flag, if True shows equivalent images from past date, defaults to False

• alt_spec (bool, optional) – Flag if True shows equivalent images in alternative imaging spectrum, defaults to False

polo.widgets.plate_viewer module

class polo.widgets.plate_viewer.PlateGraphicsItem(pixmap, parent=None)

Bases: PyQt5.QtWidgets.QGraphicsPixmapItem

contextMenuEvent(self, QGraphicsSceneContextMenuEvent)

class polo.widgets.plate_viewer.plateViewer(parent, run=None, images_per_page=24)

Bases: PyQt5.QtWidgets.QGraphicsView

_get_visible_wells(page=None)

Return indices of images that should be shown in the current page. A page is equivalent to a subsection of a larger screening plate.

Parameters

page (int, optional) – Page number to find images for, defaults to None

Yield

image index

Return type

int

_make_image_label(image, label_dict, font_size=35)

Private helper method for creating label strings to overlay onto each image in the view.

Parameters

• image (Image) – Image to create label from

• label_dict (dict) – Dictionary of image attributes to include in the label

• font_size (int, optional) – Font size for the label, defaults to 35

Returns

QGraphicsTextItem with label text set

Return type

QGraphicsTextItem

_set_prerender_info(item, image)

Private helper method that sets flags and the tooltip for QGraphicsItems before they are added to the GraphicsScene.

Parameters

• item (QGraphicsItem) – GraphicsItem that is to be added to the scene

• image (Image) – Image who’s data will be used to label the GraphicsItem

Returns

QGraphicsItem

Return type

QGraphicsItem

property aspect_ratio

Current “best” aspect ratio for the view given the size of the view and the number of images that need to be fit into the view.

Returns

Dimensions of the image grid, in images

Return type

tuple

changed_images_per_page_signal

changed_page_signal

property current_page

Current page

Returns

Current page

Return type

int

decolor_all_images()

Removes all coloring from images in the _scene attribute.

emphasize_all_images()

Returns the opacity of all images in the _scene attribute to 1, or fully opaque.

export_current_view(save_path=None)

Exports the current content of the _scene attribute to a png file.

Parameters

save_path (str or Path, optional) – Path to save the image to, defaults to None. If kept as None opens a QFileDialog to get a save file path.

fitInView(scene, preserve_aspect=False)

Fit items added to _scene attribute into the available display space.

Parameters

• scene (QGraphicsScene) – QGraphicsScene to fit

• preserve_aspect (bool, optional) – If True, preserves the aspect ratio of item is the scene, defaults to False

property images_per_page

Number of images in the current page.

Returns

Number of images

Return type

int

pop_out_selected_well()

Helper method to handle image selection and open an ImagePopDialog that displays the selected image in a pop out view.

property run

The current run being displayed.

Returns

The current run

Return type

HWIRun

set_scene_colors_from_filters(color_mapping, strength=0.5, human=False)

Set the color of images based on their current classifications. Very similar to set_opacity_from_filters(). Images can be colored by their MARCO or human classification.

Parameters

• color_mapping (dict) – Dictionary that maps image classifications to QColors

• strength (float, optional) – Image color strength, defaults to 0.5

• human (bool, optional) – If True, use the human classification to color images, defaults to False

set_scene_opacity_from_filters(image_types, human=False, marco=False, favorite=False, filtered_opacity=0.2)

Sets the opacity of all items in the _scene attribute based on image filtering criteria. Allows for highlighting images that meet specific qualifications such has having a MARCO classification of crystals. Images that do not meet the set filter requirements will have their opacity set to the value specificed by the filtered_opacity argument.

Parameters

• image_types (set of list) – Image classifications to select for.

• human (bool, optional) – If True, use human classification to determine image classification, defaults to False

• marco (bool, optional) – If True, use MARCO classification to determine image classification , defaults to False

• favorite (bool, optional) – If True, image must be favorited to be selected, defaults to False

• filtered_opacity (float, optional) – Set the opacity for images that do not need the filtering requirements, defaults to 0.2

subgrid_dict = {16: (4, 4), 64: (8, 8), 96: (8, 12), 1536: (32, 48)}

tile_images_onto_scene(label_dict={})

Calculates images that should be shown based on the current page and the number of images per page. Then tiles these images into a grid, adding them to _scene attribute.

Parameters

label_dict (dict, optional) – Dictionary of Image attributes to pass along to _make_image_label() to create image labels, defaults to {}

property total_pages

Total number of pages based on the number of images per page and the number of images in the current run.

Returns

Number of pages

Return type

int

property view_dims

Current view dimensions in pixels.

Returns

Width and height of the view

Return type

tuple

static well_index_to_subgrid(i, c_r, c_c, p_r, p_c)

Find the linear index of the subgrid that a particular index belongs to within a larger grid. For example, ou are given a list of length 16. The list is reshaped into a 4 x 4 2D list. We divide the new grid into 4 quadrants each 2 X 2 and label them with an index (0, 1, 2, 3). Given an index of the original list we want to find the subgrid it belongs to.

Parameters

• i (int) – Index of point to locate in the 1D list

• c_r (int) – Number of rows in each subgrid

• c_c (int) – Number of columns in each subgrid

• p_r (int) – Number or rows in the entire grid

• p_c (int) – Number of columns in the entire grid

Returns

Index of the subgrid the index i belongs to

Return type

int

wheelEvent(event)

Handle Qt wheelEvents by setting the _zoom attribute. Allows users to zoom in and out of the current view.

Parameters

event (QEvent) – event

polo.widgets.plate_visualizer module

class polo.widgets.plate_visualizer.PlateVisualizer(parent=None)

Bases: PyQt5.QtWidgets.QGraphicsView

The PlateVisualizer is a small widget to assist users understand what part of the screening plate they are currently viewing. It renders a grid of rectangles (blocks) that each represent one view (page) in the PlateInspector widget. The page that is currently being viewed is highlighted to show the user what part of the plate they are looking at.

Parameters

parent (QWidget, optional) – Parent widget, defaults to None

_block_size(x, y)

Private method to calculate the size of individual blocks to render in the QGraphicsView.

Parameters

• x (int) – Length of x-axis in blocks

• y (int) – Length of y-axis in blocks

Returns

tuple, length of block x-axis in pixels, length of block y-axis in pixels

Return type

tuple

_handle_block_selection()

Private helper method to handle when a user selects a block. In theory should open the view that the selected block corresponds to but currently having some issues with this causing segmentation faults so it is disabled for now.

_highlight_block(block)

Private method that highlights a block in the QGraphicsScene.

Parameters

block (QGraphicsRectItem) – Block to highlight

static block_dims(plate_x, plate_y, grid_x, grid_y)

Helper method to calculate the size of plate section blocks

Parameters

• plate_x (int) – Number of wells plate has on its x axis

• plate_y (int) – Number of wells plate has on it s y axis

• grid_x (int) – Number of wells in the subgrid on its x axis

• grid_y (int) – Number of wells in the subgrid on its y axis

Returns

tuple, first item being length of x axis in blocks and second being length of y axis in blocks

Return type

tuple

default_brush = <PyQt5.QtGui.QBrush object>

default_pen = <PyQt5.QtGui.QPen object>

plate_size = (32, 48)

plate_view_requested

selected_brush = <PyQt5.QtGui.QBrush object>

set_selected_block(block_id)

Sets the currently selected block based on its ID.

Parameters

block_id (int) – Block ID

setup_view(grid_cords, plate_size=None)

set up the intail view based on the current plate size (normally 32 * 48 wells for 1536 well plate) and the subgrid size in wells.

Parameters

• grid_cords (tuple) – Subgrid size tuple (x, y) in wells

• plate_size (tuple, optional) – Size of entire plate (x, y) in wells, defaults to None. If None used the default 1536 well plate size of 32 * 48.

polo.widgets.run_organizer module

class polo.widgets.run_organizer.RunOrganizer(parent=None, auto_link_runs=True)

Bases: PyQt5.QtWidgets.QWidget

Widget for organizing and importing runs into Polo.

Parameters

• parent (QWidget, optional) – Parent widget, defaults to None

• auto_link_runs (bool, optional) – If True runs are automatically linked as they are loaded in, defaults to True

_add_runs_to_tree(runs)

Private method to add a set of runs to the runTree.

Parameters

runs (list) – List of runs to add to the runTree

_check_for_existing_backup(run)

Check the directory specified by the BACKUP_DIR constant for a backup mso file that matches the run passed through the run argument. Run’s are matched to mso backups by their run name so it the user has renamed their run after the backup is saved it will not be found.

See backup_classifications() for details on how the mso files are written.

Parameters

run (HWIRun) – Run to search for mso backup with

Returns

Path to mso backup if one exists that matches the run, else return None

Return type

str or None

_classification_cleanup()

“Cleanup” the UI after a classification thread has completed.

_classify_multiple_runs(runs)

Run the MARCO model on a list of runs. Recursively creates ClassificationThreads for each Run until all Run instances have been classified.

Parameters

runs (list) – List of Run instance to classify using MARCO

_clear_current_run(run_list)

Clear out the current run from other widgets by emiting a opening_run signal with a list that does not contain a Run or HWIRun object.

Parameters

run_list (list) – List of runs

_finished_ftp_download()

Private method that cleans up after all queued FTP downloads have been completed and shows a message box to the user to inform them of the status of their downloads.

_handle_classification_request()

Private method to open a classification thread of the currently selected run. Calls _open_classification_thread() to start the classification thread.

_handle_ftp_download(file_path)

Private method that handles when an individual file in the FTP download queue has finished downloading. Attempts to import the run by calling import_runs() and then increments the FTP download counter by one.

Parameters

file_path (str or Path) – Path to file that was just downloaded

_handle_opening_run(*args)

Private method that signal to other widgets that the current run should be opened for analysis and viewing by emiting the opening_run signal containing the selected run.

_import_runs(file_paths)

Import Run objects from a list of file and directory paths. Runs that are imported successfully will be added to the sample browser.

Parameters

file_paths (list) – List of paths to files and directories to be imported as runs

_open_classification_thread(run)

Private method to create and run a classification thread which will run the MARCO model on all images in the run passed to run argument. Does not actually start the classification thread, just stores the newly created classification thread in classification_thread attribute.

Parameters

run (Run or HWIRun) – Run or HWIRun instance to run MARCO on

_set_estimated_classification_time(time, num_images_remain)

Display the estimated classification time to the user. Time remaining is calculated by multiplying the time it took to classify a representative image by the number of images that remain to be classified.

Parameters

• time (int) – Time to classify latest image

• num_images_remain (int) – Number of images that still require classification

_set_progress_value(val)

Private helper method to increment the classification progress bar.

Parameters

val (int) – Value to set progress bar to

property all_runs

Get all runs currently listed in the runTree.

Returns

List of Run objects

Return type

list

backup_classifications(run)

Write the human classifications of the images in the run argument to an mso file and store it in the directory specified by the BACKUP_DIR constant. Does not store MARCO classifications because these can be much more easily recreated than human classifications. Additionally, when a run is loaded back in and a backup mso exists for it Polo assumes the classifications in that mso file are human classifications.

Currently only HWIRun instances can be written as mso files because of mso’s integration with cocktail data and well assignments. Need a different format for non-HWI runs that would map filenames to classifications and ignore cocktail data / well assignments.

Parameters

run (HWIRun) – HWIRun to backup human classifications

backup_classifications_on_thread(run)

Does the exact same thing as backup_classifications() except excutes the job on a QuickThread instance to avoid slow computers complaining about the GUI being frozen. This has been especially prevelant on Windows machines.

Parameters

run (HWIRun) – Run to save as mso file

classify_run

ftp_download_status

import_run_from_dialog()

Import a run from a file dialog.

import_run_from_ftp()

Import runs from an FTP server. If an FTP download thread is not already running creates an FTPDialog instances and opens it to the user. FTP functions are then taken over by the FTPDialog until it is closed.

import_saved_runs(xtal_files=[])

Import runs saved to xtal files.

Parameters

xtal_files (list, optional) – List of xtal files to import runs from, defaults to []

opening_run

property recent_files

Return recently accessed imports.

Returns

List of recently accessed imports

Return type

list

refresh_run_after_update(run)

remove_run()

save_recent_import_paths()

Save the recently used import paths to the path specified by the RECENT_FILES path. Polo will attempt to open and read this file the next time the program is run in order to allow users to open recently opened runs.

polo.widgets.run_tree module

class polo.widgets.run_tree.RunTree(parent=None, auto_link=True)

Bases: PyQt5.QtWidgets.QTreeWidget

Inherits the QTreeWidget class and acts as the sample and run display. The User uses the RunTree to open and classify runs they load into Polo.

Parameters

• parent (QWidget, optional) – Parent widget, defaults to None

• auto_link (bool, optional) – If True automatically link runs together, defaults to True

_add_classifications_from_mso_slot(event=None)

Add classifications to an existing Run from the contents of an MSO file. Intended to be connected to the classify_from_mso QAction that is defined in the : contextMenuEvent() method.

Parameters

event (QEvent, optional) – QEvent, defaults to None

_add_run_node(run, tree=None)

Private method that adds a new run node.

Parameters

• run (Run or HWIRun) – Run to add to the tree

• tree (QTreeWidgetItem, optional) – QTreeWidgetItem to act as parent node, defaults to None. If None uses the root as the parent node.

Returns

Node added to the tree

Return type

QTreeWidgetItem

_classify_all_runs_slot(sample_name)

Classify all the unclassified runs belonging to a the selected sample.

_display_name_setter(run)

Private method that creates a display name for a run that also avoids collisions with existing display names. Currently the process of translating a display name to a Run object involves first looking up the display name in the formated_name_to_name dictionary to get the run name and then looking up the run name in the loaded_runs dictionary to get the Run object. This means that currently run names and display names need to be unique to avoid collisions.

Parameters

run (Run or HWIRun) – Run to create a display name for

_edit_data_slot(event=None)

Private method used to update the data in a Run after it has been modified by the user through the RunUpdater dialog.

Parameters

event (QEvent, optional) – QEvent, defaults to None

_get_run_node(run)

Private helper method that returns the QTreeWidgetItem corresponding to a given Run. Returns None if a node cannot be found.

Parameters

run (Run or HWIRun) – Run to search for

Returns

Given run’s corresponding QTreeWidgetItem if it exists

Return type

QTreeWidgetItem

_open_run_slot(event=None)

Private method that emits the opening_run signal when called. This signal can be connected to other widgets to communicate that the user has selected a run and wants to open it for analysis.

Parameters

event (QEvent, optional) – QEvent, defaults to None

_remove_run_slot(event=None)

Slot to connect to contextMenu popup to remove the selected run.

add_classified_run(run)

Marks a Run instance as classified by adding it to the classified_status dictionary.

Parameters

run (Run or HWIRun) – Run to mark as classified

add_run_to_tree(new_run)

Add a new Run instance to the tree. Uses the Run instance’s sampleName attribute to determine what sample node the Run instance should be added to. If the sample name does not exist in the tree a new sample node is added. If the Run instance lacks the sampleName attribute as is the case for non-HWIRuns the sampleName attribute is set to “Non-HWI Runs”. If the Run instance is an HWIRun and lacks the sampleName attribute sampleName is set to “Sampleless Runs”.

Parameters

new_run (Run or HWIRun) – Run to add to the tree

add_sample(sample_name, *args)

Adds a new sample to the tree. Samples are the highest level node in the RunTree.

Parameters

sample_name (str) – Name of sample to add, acts as key so should be unique.

classify_sample_signal

contextMenuEvent(event)

Handle left click events by creating a popup context menu.

Parameters

event (QEvent) – QEvent

property current_run_names

List of all currently loaded Run names.

Returns

List of :class:Run` names

Return type

list

dragEnterEvent(self, QDragEnterEvent)

dragMoveEvent(self, QDragMoveEvent)

dropEvent(self, QDropEvent)

dropped_links_signal

link_sample(sample_name)

Links all Run instances in a given sample together by both date and spectrum using the the_big_link() method.

Parameters

sample_name (str) – Name of the sample who’s runs should be linked

opening_run

remove_run(display_name)

Private method to remove a Run completely from the

Polo interface.

Parameters

display_name – Display name being shown to the user to represent the run to be removed.

remove_run_from_view(display_name, sample_name)

Remove a Run instance using its run_name attribute. Does not effect any other widgets. Calling this method only removes the Run instance from the display. If a Run instance is removed from successfully it is returned.

TODO UPDATE

Parameters

run_name (str) – Name of run to remove

Returns

Removed run

Return type

Run or HWIRun

remove_run_signal

save_run_signal

property selected_run

The: class:Run that is currently selected. If no Run is selected returns False.

Returns

The currently selected run, if one exists, otherwise returns False

Return type

Run, HWIRun or False

class polo.widgets.run_tree.RunTreeItem(date, parent)

Bases: PyQt5.QtWidgets.QTreeWidgetItem

polo.widgets.slideshow_inspector module

class polo.widgets.slideshow_inspector.slideshowInspector(parent, run=None)

Bases: PyQt5.QtWidgets.QWidget

The slideshowInspector widget is a primary run interface that allows users to view their screening images in a standard slideshow format. If multiple imaging runs of the sample sample exist it also allows the user to navigate between or simultaneously view these images.

Parameters

• parent (QtWidget) – Parent widget

• run (Run or HWIRun, optional) – Run to show to the user, defaults to None

_classify_image(classification)

Private method to change the human classification of the current image.

Parameters

classification (str) – Image classification

_display_current_image()

Private method that displays the current image as determined by the current_image attribute of the slideshowViewer widget and populates any widgets that display current image metadata.

_mark_current_image_as_favorite()

Private method that sets the favorite label on the current image to the current value of the favorite QCheckBox.

Parameters

favorite_status (bool) – Whether this image is a favorite or not

_navigate_carousel(next_image=False, prev_image=False)

Private method to control the carousel using boolean flags. Calls carousel_controls().

Parameters

• next_image (bool, optional) – If True navigates to next image in carousel, defaults to False

• prev_image (bool, optional) – If True navigates to previous image in carousel, defaults to False

_set_alt_image(next_date=False, prev_date=False, alt_spec=False)

Display an image linked to the current image based on boolean flags.

Parameters

• next_date (bool, optional) – If True show the current image’s next image by date, defaults to False

• prev_date (bool, optional) – If True, show the current image’s previous image by date, defaults to False

• alt_spec (bool, optional) – If True, show the current image’s alt spectrum image, defaults to False

_set_alt_spectrum_buttons()

Turns alt spectrum functions on or off depending on contents of the Run instance referenced by the run attribute. Alt spectrum buttons will be enabled if the run is a part of an alt spectrum linked list. This means another Run instance is referenced by it’s alt_spectrum attribute.

_set_classification_button_labels()

Private method that sets the labels of image classification buttons based on the IMAGE_CLASSIFICATIONS constant. Should be called in the __init__ method.

_set_favorite_checkbox()

Private method that sets the value of the favorite QCheckBox based on whether the current image is marked as a favorite or not. Should be used when loading an image into the view.

An image is considered a favorite if it’s favorite attribute == True.

_set_image_class_checkbox_labels()

Private method to the QCheckBox labels for imaging filtering from the IMAGE_CLASSIFICATIONS constant. Should be called in the __init__ method.

_set_image_name()

Private method that sets current image label to the image’s filepath basename.

_set_slide_number_label()

_set_slideshow_mode(show_all_dates=False, show_all_specs=False)

Private method to set the slideshowViewer mode. Either to display a single image, all dates or all spectrums.

Parameters

• show_all_dates (bool, optional) – If True sets slideshowViewer to show all dates, defaults to False

• show_all_specs (bool, optional) – If True sets slideshowViewer to show all spectrums, defaults to False

_set_time_resolved_functions()

Private method that turns time resolved functions on or off depending on contents of the Run instance referenced by the run attribute. Time resolved functions are enabled when the run is part of a time resolved linked list. This means another Run instance is referenced by it’s next_run and / or previous_run attributes.

_show_image_from_well_number(well_number)

Private method to display an image by well number.

Parameters

well_number (int) – Well number of image to display

_submit_filters()

Private method that passes the current user selected image filters to the slideshowViewer so the current slideshow contents can be adjusted to reflect the new filters. Displays the current image after filtering.

property current_image

Current Image object being displayed in the slideshowViewer widget.

Returns

The current image

Return type

Image

property current_sort_function

Return a function to use for image sorting based on current user radiobutton sort selections.

Returns

Sort function

Return type

func

export_current_view()

Export the current view to a png file. Show the user a message box to tell them if the export succeeded or failed.

property favorites

Returns the state of the favorite QCheckBox.

Returns

Favorite QCheckBox state

Return type

bool

property human

State of the human classifier QCheckBox. If True, assume the user wants their selected image classifications to be in reference to image’s human classification.

Returns

State of the QCheckBox

Return type

bool

property marco

State of the MARCO classifier QCheckBox. If True, assume the user wants their selected image classifications to be in reference to image’s MARCO classification.

Returns

State of the QCheckBox

Return type

bool

property run

property selected_classifications

Returns image classification keywords for any image classification QCheckBox instances that are checked.

Returns

List of selected images classifications

Return type

list

static sort_images_by_cocktail_number(images)

Helper method that sorts a collection of images by their cocktail number. Returns False if the images cannot be sorted by this parameter.

Parameters

images (list) – List of images to be sorted

Returns

List of images sorted by cocktail number, False if cannot be sorted

Return type

list, bool

static sort_images_by_marco_confidence(images)

Helper method to sort a collection of images by their MARCO classification confidence. Does not descriminate based on image classification.

Parameters

images (list) – List of images to sort

Returns

List of images sorted by prediction confidence

Return type

list

static sort_images_by_well_number(images)

Helper method to sort a collection of images by their well number. If images cannot be sorted by well number (which in theory shouldn’t happen) returns False

Parameters

images (list) – List of images to be sorted

Returns

List os images sorted by well number

Return type

list

polo.widgets.slideshow_viewer module

class polo.widgets.slideshow_viewer.Carousel

Bases: object

The Carousel class handles navigation between Slide instances.

add_slides(ordered_images, sort_function=None)

Sets up linked list consisting of nodes of Slide instances. The list is circular and bi-directional. Sets self.current_slide to the first slide in the linked list. The order of the slides in the linked list will reflect the order of the images in the ordered_images argument.

Parameters

ordered_images – a list of Image objects to create the linked list from. The order of the images will be reflected by the linked list.

Returns

First slide in linked list

Return type

Slide

controls(next_slide=False, prev_slide=False)

Controls the navigation through the slides in the carousel. Does not control access to alternative images that may be available to the user.

Parameters

• next_slide (bool) – If set to True, tells the carousel to advance one Slide

• prev_slide (bool) – If set to True, tells the carousel to retreat by one Slide

property current_slide

Current slide, the slide that should be displayed to the user.

Returns

The current slide

Return type

Slide

class polo.widgets.slideshow_viewer.PhotoViewer(parent)

Bases: PyQt5.QtWidgets.QGraphicsView

add_pixmap(pixmap)

Adds a Pixmap instances to the current sene.

Parameters

pixmap (Pixmap) – Pixmap to add to the sene

fitInView(self, QRectF, mode: Qt.AspectRatioMode = Qt.IgnoreAspectRatio)

fitInView(self, QGraphicsItem, mode: Qt.AspectRatioMode = Qt.IgnoreAspectRatio) fitInView(self, float, float, float, float, mode: Qt.AspectRatioMode = Qt.IgnoreAspectRatio)

hasPhoto()

mousePressEvent(event)

Handles mouse press events.

Parameters

event (QEvent) – Mouse press event

photoClicked

toggleDragMode()

Turns drag mode on and off.

wheelEvent(event)

Handles mouse wheel events to allow for scaling for zooming in and out of the currently displayed image.

Parameters

event (QEvent) – Mouse scroll wheel event

class polo.widgets.slideshow_viewer.Slide(image, next_slide=None, prev_slide=None, slide_number=None)

Bases: object

Acts like a slide in a slideshow carousel. Holds an Image object instance as the contents of the slide. Forms a linked list with other slides through the next_slide and prev_slide attributes which act as the forwards and backwards pointers to other slides.

Parameters

• image (Image) – Image that this slide will display

• next_slide (Slide, optional) – Next slide in the slideshow, defaults to None

• prev_slide (Slide, optional) – Previous slide in the slideshow, defaults to None

• slide_number (int, optional) – Index of this slide in the slideshow, defaults to None

class polo.widgets.slideshow_viewer.SlideshowViewer(parent, run=None, current_image=None)

Bases: polo.widgets.slideshow_viewer.PhotoViewer

_add_text_to_scene(text, x, y, size=40)

Private method to add text on top of an image. Adds the text to the current scene at the position specified by the x and y arguments.

Parameters

• text (str) – Text to add to image

• x (int) – X cordinate of text

• y (int) – Y cordinate of text

• size (int, optional) – Size of text, defaults to 40

_set_all_dates_scene(image)

Private method that creates a time resolved view from the Image instance passed through the image argument.

Parameters

image (Image) – Image to create time resolved view from

_set_all_spectrums_scene(image)

Private method that creates a view that includes all alt spectrum images the Image instance is linked to.

Parameters

image (Image) – Image to create the view from

_set_single_image_scene(image)

Private method that creates a standard single image view from the Image instance passed to the image argument.

Parameters

image (Image) – Image to display

arrange_multi_image_scene(image_list, render_date=False)

Helper method to arrange multiple images into the same view.

Parameters

• image_list (list) – List of images to add to the view

• render_date (bool, optional) – If True adds a date label to each image, defaults to False

carousel_controls(next_image=False, previous_image=False)

Wrapper around the controls() method that allows image navigation. Does not actually display the image.

Parameters

• next_image (bool) – If True, tells carousel to advance by one slide.

• previous_image (bool) – If True, tells carousel to retreat by one slide.

:returns The current image. :rtype Image

classify_current_image(classification)

Changes the human classification of the current image.

property current_slide_number

display_current_image()

Renders the Image instance currently stored in the current_image attribute.

get_cur_img_cocktail_str()

Retruns the current_image cocktail information as a string.

Returns

Cocktail information string

Return type

str

get_cur_img_meta_str()

Returns the current_image metadata as a string.

Returns

Metadata string

Return type

str

photoClicked

Wrapper class around QGraphicsView and displays image to the user in the slideshow viewer tab of the main window.

Parameters

• run (Run) – Current run whose images are to be shown by the viewer.

• parent (QWidget) – Parent Widget of this instance.

• current_image (Image) – Image that is currently displayed by the viewer.

property run

set_alt_image(next_date=False, prev_date=False, alt_spec=False)

Sets the current_image attribute to a linked image specified by one of the three boolean flags.

Parameters

• next_date – If True, sets the current_image to the next image by date

• prev_date – If True, sets the current_image to the previous image by date

• alt_spec – If True, sets the current_image to an alt spectrum image

set_current_image_by_well_number(well_number)

Set the current image to the Image instance associated with a specific well number.

Parameters

well_number (int) – Well number to display

property total_slides

update_slides_from_filters(image_types, human, marco, favorite=False, sort_function=None)

Creates new Carousel slides based on selected image filters. Sets the current_image attribute to the Image instance at the the current slide attribute of _carousel attribute.

Parameters

• image_types (set or list) – Set of image classifications to include in results.

• human (bool) – If True, image_types refers to human classification of the image.

• marco (bool) – If True, image_types refers to the machine (MARCO) classification of the image.

polo.widgets.table_inspector module

class polo.widgets.table_inspector.TableInspector(parent=None, run=None)

Bases: PyQt5.QtWidgets.QWidget

TableInspector class displays a run’s data in a spreadsheet type view.

Parameters

• parent (QWidget, optional) – Parent widget, defaults to None

• run (Run or HWIRun, optional) – Run to display in the table, defaults to None

_assign_checkboxes_to_class()

Private method that assigns filtering checkboxs to an image classification from the IMAGE_CLASSIFICATION constant.

_set_column_options()

Private method that sets the availabe columns to display based on the attributes of the run stored in the run attribute. Adds a QCheckBox widget for each attribute.

TODO: formating for private attributes to make them prettier

property run

property selected_classifications

Return image classifications that are currently selected.

Returns

List of selected image classifications

Return type

set

property selected_headers

Return the headers that have been selected by the user.

Returns

Names of column headers that are currently selected

Return type

set

update_table_view()

Private method that updates the data being displayed in the tableViewer.

polo.widgets.table_viewer module

class polo.widgets.table_viewer.TableViewer(parent, run=None)

Bases: PyQt5.QtWidgets.QTableWidget

TableViewer instances override QTableWidget and provide a more convenient interface for translating the data in Run and HWIRun objects into a table format.

Parameters

• parent (QtWidget) – Parent widget

• run (Run, optional) – Run to show in this table view, defaults to None

_make_header_map(headers)

Private method to map header keywords to their index (order). This method is required as headers are delivered as a set and we want them to be presented in a consistent order to the user.

Parameters

headers (set) – Set of headers strings

Returns

Dictionary of header strings mapped to indices

Return type

dict

property fieldnames

Return the fieldnames for the current run. Should only be used when setting the values for the listWidget in a tableInspector instance as is expensive to call.

Returns

list of fieldnames

Return type

list

static filter(row, image_classes, human, marco)

Helper method to determine if a row should be included based on the image filters the user has selected

Parameters

• row (dict) – row data

• image_classes (set or list) – types of images to include, i.e Crystals, Clear

• human (Bool) – If image_classes should be in reference to human classifier

• marco (Bool) – If image_classes should be in reference to machine classifier

Returns

If image should be filtered, False means do not filter image

Return type

Bool

populate_table(image_classes, human, marco)

Populates the table and displays data to the user based on their header and image filtering selections.

Parameters

• image_classes (set or list) – types of images to include, i.e Crystals, Clear

• human (Bool) – If image_classes should be in reference to human classifier

• marco (Bool) – If image_classes should be in reference to machine classifier

Returns

If image should be filtered, False means do not filter image

property run

Return the run object

Returns

Run object

Return type

Run

property table_data

Property to retrieve the current table fieldnames and table data using get_csv_data function of the RunCsvWriter class.

Returns

fieldnames, table data

Return type

tuple

polo.widgets.unit_combo module

class polo.widgets.unit_combo.UnitComboBox(parent=None, base_unit=None, scalers={})

Bases: PyQt5.QtWidgets.QWidget

Widget that is a combination of a spinbox and a comboBox that allows a user to select a value using the spinBox and a unit using the comboBox.

Example:

Lets say we want to create a UnitComboBox that allows someone to select a Molar concentration using micro-molar, milli-molar, centi-molar or molar.

# create the scaler dictionary
s = {
    'u': 1e-6, 'm': 1e-3, 'c': 1e-2
}
# values are in reference to the base unit
unit_combo = UnitComboBox(
    parent=None, base_unit='M', scalers=s
    )

Parameters

• parent (QWidget, optional) – Parent widget, defaults to None

• base_unit (str, optional) – Base unit string, defaults to None

• scalers (dict, optional) – Dictionary of prefixes to apply to the baseunit. Keys should be string prefixes and values should be value that scales the baseunit, defaults to {}

_set_unit_combobox_text()

Private method to add units to the unit comboBox based on the base_unit and the scalers attributes.

Returns

Items added to the comboBox

Return type

list

get_value()

Return a UnitValue constructed from the value of the spinBox value and unit from the comboBox.

Returns

UnitValue constructed from current spinBox value and comboBox unit

Return type

UnitValue

saved_scalers = {'c': 0.01, 'm': 0.001, 'u': 1e-06}

property scalers

The current scalers.

Returns

List of scaler values

Return type

list

set_value(value, *args)

Set the spinBox value and the comboBox unit based on the value and unit of a UnitValue instance

Parameters

value (UnitValue) – UnitValue

set_zero()

Set the spinbox value to 0

property sorted_scalers

Scalers sorted by their magnitude.

Returns

List of scalers

Return type

list

property unit_combobox_text

The text in unit comboBox which corresponds to a specific scaler.

Returns

List of all scalers in the unit comboBox

Return type

list

unit_text_parser(unit_text=None)

Module contents