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Merge pull request #938 from TheDeanLab/2024-07-11
Restful unit tests.
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‎src/navigate/model/features/restful_features.py‎

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# Copyright (c) 2021-2022 The University of Texas Southwestern Medical Center.
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# Copyright (c) 2021-2024 The University of Texas Southwestern Medical Center.
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# All rights reserved.
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# Redistribution and use in source and binary forms, with or without
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# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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# POSSIBILITY OF SUCH DAMAGE.
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#
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# Standard Library Imports
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import base64
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import requests
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import numpy
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import json
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from io import BytesIO
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from math import ceil
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import logging
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# Third Party Imports
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# Local Imports
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# Logger Setup
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p = __name__.split(".")[1]
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logger = logging.getLogger(p)
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)
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except (KeyError, AttributeError):
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return
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self.resolution = self.model.configuration["experiment"]["MicroscopeState"][
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"microscope_name"
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]

‎test/model/features/test_restful_features.py‎

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# Copyright (c) 2021-2024 The University of Texas Southwestern Medical Center.
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# All rights reserved.
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted for academic and research use only
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# (subject to the limitations in the disclaimer below)
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# provided that the following conditions are met:
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# * Redistributions of source code must retain the above copyright notice,
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# this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of the copyright holders nor the names of its
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# contributors may be used to endorse or promote products derived from this
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# software without specific prior written permission.
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# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
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# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
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# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
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# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
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# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
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# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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# POSSIBILITY OF SUCH DAMAGE.
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# Standard Library Import
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import base64
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import unittest
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import json
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import logging
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from unittest.mock import patch, Mock, MagicMock
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from io import BytesIO
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# Third Party Imports
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import numpy as np
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# Local Imports
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from navigate.model.features.restful_features import (
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prepare_service,
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IlastikSegmentation,
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)
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class TestPrepareService(unittest.TestCase):
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def setUp(self):
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self.service_url = "http://example.com/ilastik"
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self.project_file = "path/to/project.ilp"
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self.expected_url = f"{self.service_url}/load?project={self.project_file}"
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logging.basicConfig(level=logging.INFO)
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self.logger = logging.getLogger(
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"mymodule"
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) # Replace with the actual logger name used
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@patch("navigate.model.features.restful_features.requests.get")
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def test_prepare_service_success(self, mock_get):
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expected_response = {"status": "success", "data": "segmentation data"}
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mock_response = Mock()
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mock_response.status_code = 200
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mock_response.content = json.dumps(expected_response)
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mock_get.return_value = mock_response
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response = prepare_service(self.service_url, project_file=self.project_file)
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self.assertEqual(response, expected_response)
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mock_get.assert_called_once_with(self.expected_url)
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@patch("navigate.model.features.restful_features.requests.get")
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def test_prepare_service_failure(self, mock_get):
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mock_response = Mock()
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mock_response.status_code = 404
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mock_response.content = "Error"
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mock_get.return_value = mock_response
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response = prepare_service(self.service_url, project_file=self.project_file)
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self.assertIsNone(response)
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mock_get.assert_called_once_with(self.expected_url)
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def test_prepare_service_non_ilastik_url(self):
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non_ilastik_url = "http://example.com/not_ilastik"
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response = prepare_service(non_ilastik_url, project_file=self.project_file)
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self.assertIsNone(response)
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class TestIlastikSegmentation(unittest.TestCase):
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def setUp(self):
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# Set up a mock model object
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shape = (2048, 2048)
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self.mock_model = Mock()
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self.mock_model.configuration = {
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"rest_api_config": {"Ilastik": {"url": "http://example.com/ilastik"}},
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"experiment": {
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"MicroscopeState": {"microscope_name": "Nanoscale", "zoom": "1.0"},
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"CameraParameters": {"x_pixels": "2048", "y_pixels": "2048"},
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"StageParameters": {
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"x": "100",
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"y": "100",
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"z": "50",
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"theta": "0",
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"f": "1.0",
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},
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},
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"configuration": {
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"microscopes": {
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"Nanoscale": {"zoom": {"pixel_size": {"N/A": "1.0", "1.0": "1.0"}}}
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}
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},
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}
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self.mock_model.data_buffer = {
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0: np.random.randint(0, 65536, size=shape, dtype=np.uint16),
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1: np.random.randint(0, 65536, size=shape, dtype=np.uint16),
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}
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self.mock_model.img_height = shape[0]
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self.mock_model.img_width = shape[1]
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self.mock_model.display_ilastik_segmentation = True
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self.mock_model.mark_ilastik_position = False
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self.mock_model.event_queue = MagicMock()
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self.ilastik_segmentation = IlastikSegmentation(self.mock_model)
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@patch("requests.post")
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def test_data_func_success(self, mock_post):
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frame_ids = [0, 1]
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expected_json_data = {
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"dtype": "uint16",
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"shape": (self.mock_model.img_height, self.mock_model.img_width),
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"image": [
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base64.b64encode(self.mock_model.data_buffer[0]).decode("utf-8"),
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base64.b64encode(self.mock_model.data_buffer[1]).decode("utf-8"),
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],
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}
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# Create a valid numpy array to simulate the response
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array_data = np.array([np.zeros((2048, 2048, 1), dtype=np.uint16)])
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buffer = BytesIO()
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np.savez(buffer, *array_data)
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buffer.seek(0)
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mock_response = Mock()
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mock_response.status_code = 200
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mock_response.raw.read.return_value = buffer.read()
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mock_post.return_value = mock_response
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self.ilastik_segmentation.data_func(frame_ids)
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mock_post.assert_called_once_with(
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"http://example.com/ilastik/segmentation",
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json=expected_json_data,
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stream=True,
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)
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self.mock_model.event_queue.put.assert_called()
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# Test with self.model.mark_ilastik_position set to True
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self.mock_model.mark_ilastik_position = True
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self.mock_model.event_queue.reset_mock()
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self.mock_model.ilastik_target_labels = range(1)
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self.ilastik_segmentation.update_setting()
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self.ilastik_segmentation.data_func(frame_ids)
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assert self.mock_model.event_queue.put.call_count == 2
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# self.mock_model.event_queue.put.assert_called_with(("multiposition"))
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called_args, _ = self.mock_model.event_queue.put.call_args
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assert "multiposition" in called_args[0]
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@patch("requests.post")
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def test_data_func_failure(self, mock_post):
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frame_ids = [0, 1]
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mock_response = Mock()
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mock_response.status_code = 404
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mock_response.content = "Error"
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mock_post.return_value = mock_response
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with patch("builtins.print") as mocked_print:
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self.ilastik_segmentation.data_func(frame_ids)
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mocked_print.assert_called_once_with("There is something wrong!")
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def test_update_setting(self):
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self.ilastik_segmentation.update_setting()
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self.assertEqual(self.ilastik_segmentation.resolution, "Nanoscale")
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self.assertEqual(self.ilastik_segmentation.zoom, "1.0")
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self.assertEqual(self.ilastik_segmentation.pieces_num, 1)
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self.assertEqual(self.ilastik_segmentation.pieces_size, 2048)
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self.assertEqual(self.ilastik_segmentation.posistion_step_size, 2048)
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self.assertEqual(self.ilastik_segmentation.x_start, -924)
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self.assertEqual(self.ilastik_segmentation.y_start, -924)
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def test_init_func_update_settings(self):
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with patch.object(
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self.ilastik_segmentation, "update_setting"
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) as mock_update_setting:
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self.ilastik_segmentation.resolution = "DifferentResolution"
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self.ilastik_segmentation.zoom = "DifferentZoom"
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self.ilastik_segmentation.init_func()
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mock_update_setting.assert_called_once()
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def test_mark_position(self):
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mask = np.zeros((2048, 2048, 1), dtype=np.uint16)
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mask[0:1024, 0:1024, 0] = 1 # Mock some segmentation data
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self.mock_model.ilastik_target_labels = [1]
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self.ilastik_segmentation.update_setting()
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self.ilastik_segmentation.mark_position(mask)
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self.mock_model.event_queue.put.assert_called()
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if __name__ == "__main__":
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unittest.main()

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