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feat: init

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# Copyright (c) 2021-2025 The University of Texas Southwestern Medical Center.
# All rights reserved.
import tkinter
# Redistribution and use in source and binary forms, with or without
# modification, are permitted for academic and research use only
# (subject to the limitations in the disclaimer below)
# provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the copyright holders nor the names of its
# contributors may be used to endorse or promote products derived from this
# software without specific prior written permission.
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# Standard library imports
from unittest.mock import MagicMock
# Third party imports
import pytest
# Local imports
from navigate.controller.sub_controllers import AcquireBarController
from navigate.view.popups.acquire_popup import (
AcquirePopUp,
)
from navigate.model.data_sources import FILE_TYPES
class TestAcquireBarController:
"""Tests for the AcquireBarController class"""
@pytest.fixture(autouse=True)
def setup_class(self, dummy_controller):
"""Setup for the TestAcquireBarController class
Parameters
----------
dummy_controller : DummyController
Instance of the DummyController class
"""
c = dummy_controller
v = dummy_controller.view
self.acquire_bar_controller = AcquireBarController(
view=v.acquire_bar, parent_controller=c
)
self.acquire_bar_controller.populate_experiment_values()
c.channels_tab_controller.populate_experiment_values()
c.camera_setting_controller = MagicMock()
def test_init(self):
"""Tests the initialization of the AcquireBarController class
Raises
------
AssertionError
If the initialization of the AcquireBarController class is not correct
"""
assert isinstance(self.acquire_bar_controller, AcquireBarController)
def test_attr(self):
"""Tests the attributes of the AcquireBarController class
Raises
------
AssertionError
If the attributes of the AcquireBarController class are not correct
"""
# Listing off attributes to check existence
attrs = ["mode", "is_save", "mode_dict"]
for attr in attrs:
assert hasattr(self.acquire_bar_controller, attr)
@pytest.mark.parametrize(
"mode,mode_expected,value_expected",
[
("live", "indeterminate", None),
("single", "determinate", 0),
("customized", "indeterminate", None),
("z-stack", "determinate", 0),
],
)
def test_progress_bar(self, mode, mode_expected, value_expected):
"""Tests the progress bar of the AcquireBarController class
Parameters
----------
mode : str
Mode of the progress bar
mode_expected : str
Expected mode of the progress bar
value_expected : int
Expected value of the progress bar
Raises
------
AssertionError
If the progress bar of the AcquireBarController class is not correct
"""
# Startup progress bars
images_received = 0
mode = mode
stop = False
self.acquire_bar_controller.progress_bar(
images_received=images_received,
microscope_state=self.acquire_bar_controller.parent_controller.configuration[
"experiment"
][
"MicroscopeState"
],
mode=mode,
stop=stop,
)
progress_mode = str(self.acquire_bar_controller.view.CurAcq["mode"])
ovr_mode = str(self.acquire_bar_controller.view.OvrAcq["mode"])
assert progress_mode == mode_expected, (
f"Wrong progress bar mode ({progress_mode}) "
f"relative to microscope mode ({mode})"
)
assert ovr_mode == mode_expected, (
f"Wrong progress bar mode ({progress_mode}) "
f"relative to microscope mode ({mode})"
)
if value_expected is not None:
progress_start = int(self.acquire_bar_controller.view.CurAcq["value"])
ovr_start = int(self.acquire_bar_controller.view.OvrAcq["value"])
assert (
progress_start == value_expected
), "Wrong starting value for progress bar"
assert ovr_start == value_expected, "Wrong starting value for progress bar"
# Updating progress bar
images_received = 1
while images_received < 6:
self.acquire_bar_controller.progress_bar(
images_received=images_received,
microscope_state=self.acquire_bar_controller.parent_controller.configuration[
"experiment"
][
"MicroscopeState"
],
mode=mode,
stop=stop,
)
making_progress = float(self.acquire_bar_controller.view.CurAcq["value"])
ovr_progress = float(self.acquire_bar_controller.view.OvrAcq["value"])
assert (
making_progress > 0
), f"Progress bar should be moving in {mode} mode (making_progress)"
assert (
ovr_progress > 0
), f"Progress bar should be moving in {mode} mode (ovr_progress)"
images_received += 1
# Stopping progress bar
self.acquire_bar_controller.progress_bar(
images_received=images_received,
microscope_state=self.acquire_bar_controller.parent_controller.configuration[
"experiment"
][
"MicroscopeState"
],
mode=mode,
stop=True,
)
after_stop = float(self.acquire_bar_controller.view.CurAcq["value"])
after_ovr = float(self.acquire_bar_controller.view.OvrAcq["value"])
assert after_stop == 0, "Progress Bar did not stop"
assert after_ovr == 0, "Progress Bar did not stop"
@pytest.mark.parametrize("mode", ["live", "single", "z-stack", "customized"])
def test_get_set_mode(self, mode):
"""Tests the get_mode and set_mode methods of the AcquireBarController class
Parameters
----------
mode : str
Mode of the progress bar
Raises
------
AssertionError
If the get_mode and set_mode methods of the
AcquireBarController class are not correct
"""
self.acquire_bar_controller.set_mode(mode)
test = self.acquire_bar_controller.get_mode()
assert test == mode, "Mode not set correctly"
# assert imaging mode is updated in the experiment
assert (
self.acquire_bar_controller.parent_controller.configuration["experiment"][
"MicroscopeState"
]["image_mode"]
== mode
)
def test_set_save(self):
"""Tests the set_save method of the AcquireBarController class
Raises
------
AssertionError
If the set_save method of the AcquireBarController class is not correct
"""
# Assuming save state starts as False
self.acquire_bar_controller.set_save_option(True)
assert self.acquire_bar_controller.is_save is True, "Save option not correct"
# Return value to False
self.acquire_bar_controller.set_save_option(False)
assert (
self.acquire_bar_controller.is_save is False
), "Save option did not return to original value"
def test_stop_acquire(self):
"""Tests the stop_acquire method of the AcquireBarController class
Raises
------
AssertionError
If the stop_acquire method of the AcquireBarController class is not correct
"""
# Stopping acquisition
self.acquire_bar_controller.stop_acquire()
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Acquire"
@pytest.mark.parametrize(
"user_mode,expected_mode",
[
("Continuous Scan", "live"),
("Z-Stack", "z-stack"),
("Single Acquisition", "single"),
("Customized", "customized"),
],
)
def test_update_microscope_mode(self, user_mode, expected_mode):
"""Tests the update_microscope_mode method of the AcquireBarController class
Parameters
----------
user_mode : str
Mode of the progress bar
expected_mode : str
Expected state of the progress bar
Raises
------
AssertionError
If the update_microscope_mode method of
the AcquireBarController class is not correct
"""
# Assuming mode starts on live
self.acquire_bar_controller.mode = "live"
# Setting to mode specified by user
self.acquire_bar_controller.view.pull_down.set(user_mode)
# Generate event that calls update microscope mode
self.acquire_bar_controller.view.pull_down.event_generate(
"<<ComboboxSelected>>"
)
# Checking that new mode gets set by function
assert self.acquire_bar_controller.mode == expected_mode
assert (
self.acquire_bar_controller.parent_controller.configuration["experiment"][
"MicroscopeState"
]["image_mode"]
== expected_mode
)
# Resetting to live
self.acquire_bar_controller.view.pull_down.set("Continuous Scan")
self.acquire_bar_controller.view.pull_down.event_generate(
"<<ComboboxSelected>>"
)
assert self.acquire_bar_controller.mode == "live"
def test_populate_experiment_values(self):
"""Tests the populate_experiment_values method of the AcquireBarController class
Raises
------
AssertionError
If the populate_experiment_values method
of the AcquireBarController class is not correct
"""
# Calling function to populate values
self.acquire_bar_controller.populate_experiment_values()
# Checking values are what we expect
for key, value in self.acquire_bar_controller.saving_settings.items():
assert (
self.acquire_bar_controller.saving_settings[key]
== self.acquire_bar_controller.parent_controller.configuration[
"experiment"
]["Saving"][key]
)
# Assuming default value in exp file,
# can be altered TODO maybe set default to current date
assert self.acquire_bar_controller.saving_settings["date"] == "2022-06-07"
assert (
self.acquire_bar_controller.mode
== self.acquire_bar_controller.parent_controller.configuration[
"experiment"
]["MicroscopeState"]["image_mode"]
)
@pytest.mark.parametrize(
"text,is_acquiring, save,mode,file_types,choice",
[
("Stop", False, None, "live", [], None),
("Stop", True, None, "live", [], None),
("Acquire", True, True, "live", [], None),
("Acquire", False, True, "live", [], None),
("Acquire", False, False, "z-stack", [], None),
("Acquire", False, True, "z-stack", FILE_TYPES, "Done"),
("Acquire", False, True, "z-stack", FILE_TYPES, "Cancel"),
],
)
def test_launch_popup_window(
self, text, is_acquiring, save, mode, file_types, choice
):
"""Tests the launch_popup_window method of the AcquireBarController class
This is the largest test for this controller.
It will test multiple functions that are all used together
and difficult to isolate.
Funcs Tested:
launch_popup_window
update_file_type
launch_acquisition
update_experiment_values
acquire_pop.popup.dismiss # This will be double tested in view
Parameters
----------
text : str
Text of the button that is clicked
save : bool
Whether or not to save the image
mode : str
Mode of the progress bar
file_types : list
List of file types to save as
choice : str
Choice of the user in the popup window
Raises
------
AssertionError
If the launch_popup_window method of the
AcquireBarController class is not correct
"""
# Setup Gui for test
self.acquire_bar_controller.view.acquire_btn.configure(state="normal")
self.acquire_bar_controller.view.acquire_btn.configure(text=text)
self.acquire_bar_controller.is_save = save
self.acquire_bar_controller.set_mode(mode)
self.acquire_bar_controller.is_acquiring = is_acquiring
# Test based on setup, launches popup
self.acquire_bar_controller.view.acquire_btn.invoke()
# Checking things are what we expect
if text == "Stop":
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Stop"
if is_acquiring:
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "disabled"
)
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "stop_acquire"
else:
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "normal"
)
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"
if text == "Acquire":
if is_acquiring:
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "normal"
)
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"
return
# First scenario Save is on and in live mode
if save is True and mode == "live":
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Acquire"
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "disabled"
)
res = self.acquire_bar_controller.parent_controller.pop()
print(res)
print(self.acquire_bar_controller.parent_controller.pop())
assert res == "acquire"
# Second scenario Save is off and mode is not live
if save is False and mode != "live":
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Acquire"
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "disabled"
)
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "acquire"
# Third and final scenario Save is on and mode is not live
if save is True and mode != "live":
# Checking if popup created
assert isinstance(self.acquire_bar_controller.acquire_pop, AcquirePopUp)
assert self.acquire_bar_controller.acquire_pop.popup.winfo_exists() == 1
# Testing update_file_type if list exists
widgets = self.acquire_bar_controller.acquire_pop.get_widgets()
if len(file_types) > 0:
for file in file_types:
widgets["file_type"].set(file)
assert (
self.acquire_bar_controller.saving_settings["file_type"]
== file
)
# Resetting file type back to orginal
widgets["file_type"].set("TIFF")
assert (
self.acquire_bar_controller.saving_settings["file_type"]
== "TIFF"
)
# Check that loop thru saving settings is correct
for k, v in self.acquire_bar_controller.saving_settings.items():
if widgets.get(k, None):
value = widgets[k].get().strip()
assert value == v
# Grabbing buttons to test
buttons = self.acquire_bar_controller.acquire_pop.get_buttons()
if choice == "Cancel":
# Testing cancel button
buttons["Cancel"].invoke() # Call to dismiss popup
# Check toplevel gone
assert (
self.acquire_bar_controller.acquire_pop.popup.winfo_exists()
== 0
)
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "normal"
)
elif choice == "Done":
# Testing done button
# Update experiment values test
# Changing popup vals to test update
# experiment values inside launch acquisition
widgets["user"].set("John")
widgets["tissue"].set("Heart")
widgets["celltype"].set("34T")
widgets["label"].set("BCB")
widgets["solvent"].set("uDISCO")
widgets["file_type"].set("OME-TIFF")
# Tab frame
for i in range(100):
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"misc"
].insert(tkinter.END, f"L{i}")
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"shear_data"
].set(True)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"shear_dimension"
].set("XZ")
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"shear_angle"
].set(45)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"rotate_data"
].set(True)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"rotate_angle_x"
].set(90)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"rotate_angle_y"
].set(90)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"rotate_angle_z"
].set(90)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"down_sample_data"
].set(True)
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"lateral_down_sample"
].set("2x")
self.acquire_bar_controller.acquire_pop.tab_frame.inputs[
"axial_down_sample"
].set("2x")
# Launch acquisition start/test
buttons["Done"].invoke() # Call to launch acquisition
# Check if update experiment values works correctly
pop_vals = self.acquire_bar_controller.acquire_pop.get_variables()
for k, v in self.acquire_bar_controller.saving_settings.items():
if pop_vals.get(k, None):
value = pop_vals[k].strip()
assert value == v
# Check command sent to controller
# and if acquire button changed to Stop
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "acquire_and_save"
assert (
str(self.acquire_bar_controller.view.acquire_btn["state"])
== "disabled"
)
assert (
self.acquire_bar_controller.acquire_pop.popup.winfo_exists()
== 0
)
def test_frequent_start_and_stop_acquisition(self):
# set up
self.acquire_bar_controller.view.acquire_btn.configure(state="normal")
self.acquire_bar_controller.view.acquire_btn.configure(text="Acquire")
self.acquire_bar_controller.is_save = False
self.acquire_bar_controller.set_mode("live")
self.acquire_bar_controller.is_acquiring = False
# start acquisition
self.acquire_bar_controller.view.acquire_btn.invoke()
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Acquire"
assert str(self.acquire_bar_controller.view.acquire_btn["state"]) == "disabled"
assert self.acquire_bar_controller.is_acquiring is True
# assert dummy_controller_to_test_acquire_bar.acquisition_count == 1
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "acquire"
# not in acquisition, click the "Acquire" button several times
self.acquire_bar_controller.view.acquire_btn.invoke()
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Acquire"
assert str(self.acquire_bar_controller.view.acquire_btn["state"]) == "disabled"
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"
self.acquire_bar_controller.view.acquire_btn.invoke()
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"
# in acquisition, click "Stop" button several times
self.acquire_bar_controller.view.acquire_btn.configure(state="normal")
self.acquire_bar_controller.view.acquire_btn.configure(text="Stop")
self.acquire_bar_controller.is_acquiring = True
self.acquire_bar_controller.view.acquire_btn.invoke()
assert self.acquire_bar_controller.view.acquire_btn["text"] == "Stop"
assert str(self.acquire_bar_controller.view.acquire_btn["state"]) == "disabled"
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "stop_acquire"
self.acquire_bar_controller.view.acquire_btn.invoke()
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"
self.acquire_bar_controller.view.acquire_btn.invoke()
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"
self.acquire_bar_controller.view.acquire_btn.invoke()
res = self.acquire_bar_controller.parent_controller.pop()
assert res == "Empty command list"