celldetective 1.3.9.post5__py3-none-any.whl → 1.4.1__py3-none-any.whl

celldetective-1.4.1.dist-info/RECORD

@@ -0,0 +1,123 @@
+celldetective/__init__.py,sha256=ZygAIkX6Nbjag1czWdQa-yP-GM1mBE_9ss21Xh__JFc,34
+celldetective/__main__.py,sha256=bxTlSvbKhqn3LW_azd2baDCnDsgb37PAP9DfuAJ1_5M,1844
+celldetective/_version.py,sha256=BqOI5y46o1G1RWC9bF1DPL-YM68lGYPmZt1pn6FZFZs,22
+celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
+celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
+celldetective/extra_properties.py,sha256=QxXl-zug3NyxZMNTJUsDxo8PHLIRt0AwOFUkTyYBv7E,19987
+celldetective/filters.py,sha256=RhgwDBZ1wcpu1syQikjdVgkH7ln_fVv14IGNRhaAMLM,4637
+celldetective/io.py,sha256=7vCUprvmPa68Vp5BWHqYIJ46MHqamrF74Dc9MvqBXzg,124208
+celldetective/measure.py,sha256=VZibDPYgMtMqIPItoPq1Hhkl6R5gAAHfOpAnUHMe88E,59541
+celldetective/neighborhood.py,sha256=av7fzW3CjK7A5xO9AA1h36S50HzfM-aF9aaXb-uCrV4,60493
+celldetective/preprocessing.py,sha256=YpffYSYZxnd8A0KLfVANEQGWb2I9JW663_aSvZbt3nI,45005
+celldetective/relative_measurements.py,sha256=vQhgkHokUtt2xBpZbR-MHWUukfJ02WbiBsBJqV9A_90,30964
+celldetective/segmentation.py,sha256=WApzoU1s3Ntvp0eIw_pRZXNwCA8LDKC9YoyR52tioz4,30943
+celldetective/signals.py,sha256=-AnJOwU4S4T7y-xaH5vjrau2ZJgYDwFf3JjakdHJMog,112236
+celldetective/tracking.py,sha256=4ngFo5-slTmmOdYCqIjH3gqzQ4e3Zovk_X5P3uFAifQ,40567
+celldetective/utils.py,sha256=R2S1_lAoxhlSgEjuebr9Zs8NiQGwvehTdrzozQYoX7Q,105316
+celldetective/datasets/segmentation_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/datasets/signal_annotations/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/gui/InitWindow.py,sha256=2TUHJbT6qfPvzN63Nx8ld2Dr2StgKY-jWDykeGvNzac,14767
+celldetective/gui/__init__.py,sha256=AWNdszogNhpl0Fn7a6TYGNC11E2T-ZAemORqxyUk3B8,708
+celldetective/gui/about.py,sha256=TaPAAiOrDcyaYQMEZQLQmhNfZH3QKoasIV1gbbPc8iU,1801
+celldetective/gui/analyze_block.py,sha256=ukLlqqooP6UkJG00tZGnNWe3vqjVKj4zhtXcUnjOJj8,3048
+celldetective/gui/base_annotator.py,sha256=hDeYhppFAuRb-h2GkbfQMpUv077rCPzQ3B3a2Y18jRM,25898
+celldetective/gui/base_components.py,sha256=gYC0Gc3axDC241RpjNCXe7UKYG2uCDnMLx7at0kHKjA,768
+celldetective/gui/classifier_widget.py,sha256=J6FBgwa_P5Sw_40Ruh6uQ6Z1-aBwDduOH07E5CxcWoU,20548
+celldetective/gui/configure_new_exp.py,sha256=kYmWCqMK7F4yflS9b05gWvMEAoS1PoNV0siNNITNY1Y,24742
+celldetective/gui/control_panel.py,sha256=GDJaEmE9sWP8dfepvVw8sS1D9oWWMdBAEWVaAb6YFVM,18104
+celldetective/gui/event_annotator.py,sha256=SwX5s98UIzsh-nIvNLBXRfsiLqXHKOjzM37-9Yl76BQ,57110
+celldetective/gui/generic_signal_plot.py,sha256=9IYFKychgjCDeBRJUqyiAZ0bflOBWxk0S1aTQK8R99w,36459
+celldetective/gui/gui_utils.py,sha256=Uf9Qu0aPrbt1GEo0qw_RJCLtR79-R9zUekYYTXXKSs8,40253
+celldetective/gui/json_readers.py,sha256=gDE9ly8x8oMR1id5U--JsOylGPMSmu9xw9wCfxH1stA,3719
+celldetective/gui/layouts.py,sha256=h3xzfPRHM2Zos5v4m9yUl9ah4icrbpTJrdhUQVSF_Ug,60890
+celldetective/gui/pair_event_annotator.py,sha256=fdCqoOtrRFnduPJ_H-xn3s6jNE0iyNt4ikitTGzpzXs,94503
+celldetective/gui/plot_measurements.py,sha256=TQAFIOud8Tzrgm37EFKGd8Aj4rRYOjFk5BeiVstBheQ,51058
+celldetective/gui/plot_signals_ui.py,sha256=op5vMKJ4nV_Hoys4SRlTJhCHb-HXnQYCAFhtIhxGOC4,21060
+celldetective/gui/process_block.py,sha256=od5I_ZM1_GE_H5ApDB_l9_o4nWbWOhk5pZ1VGsNGLIw,75103
+celldetective/gui/seg_model_loader.py,sha256=xTzJ02DJxBoyqeanmEybheVbn8uoxP1eay2odZbGH04,18108
+celldetective/gui/styles.py,sha256=3yYr2-fMxGczsjPqlZ7VRfLRoWypWhsHimPALMvbKSU,5138
+celldetective/gui/survival_ui.py,sha256=e5SqthRgylqwD9EZjJQ1pnJ0CAMwuW8VrMtgnUDdgOE,12296
+celldetective/gui/tableUI.py,sha256=LWfq63N1sdTUjYaCKhZQbjJiqAOhliRnf8v4LytYBek,59249
+celldetective/gui/thresholds_gui.py,sha256=d_vncQO837yPw9OMTJmrT0zl02G3___ynUHh1uU8k7A,29235
+celldetective/gui/viewers.py,sha256=ZMbgVeVXGnYJHlYpiCzHoToB_HowpSnMc6za9f3C2n4,50019
+celldetective/gui/workers.py,sha256=1sdRDwBsGJjjTNsf8YqnKuf2m6Fa5E7YFLnncFWqbjU,4298
+celldetective/gui/help/DL-segmentation-strategy.json,sha256=PZD9xXjrwbX3TiudHJPuvcyZD28o4k-fVgeTd7dBKzI,1583
+celldetective/gui/help/Threshold-vs-DL.json,sha256=rrFnZT2DhyS7g1nIDWeUV8-HH7M2Sv8D7sDCGBU1M_0,934
+celldetective/gui/help/cell-populations.json,sha256=e5yJp75rKsYkGVuO8stXxU1TznkADw71djdMUs21gd8,1200
+celldetective/gui/help/exp-structure.json,sha256=61zZAHms7se4Vtuma904xKMsNlWuTOIeF24cbwQiYQg,1973
+celldetective/gui/help/feature-btrack.json,sha256=wvKFiM38AvfQ2QsePDjTflOovqq04CWYcK2QXZhHs-A,693
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+celldetective/gui/help/prefilter-for-segmentation.json,sha256=NEL6O2nj_l8ImjMzzX6qqg7U9QV01sgZMFvkGHUiG4E,791
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+celldetective/gui/help/propagate-classification.json,sha256=F7Ir1mtgRVTXWLN7n3ny3vrU01LFNeDh5dN2QBIXHqE,1227
+celldetective/gui/help/track-postprocessing.json,sha256=VaGd8EEkA33OL-EI3NXWZ8yHeWWyUeImDF5yAjsVYGA,3990
+celldetective/gui/help/tracking.json,sha256=yIAoOToqCSQ_XF4gwEZCcyXcvQ3mROju263ZPDvlUyY,776
+celldetective/gui/processes/compute_neighborhood.py,sha256=J0T1DaG58p1nB0_WseVbl3AL5jb76W0hzFaSNci5EDU,29181
+celldetective/gui/processes/downloader.py,sha256=jnNitmQ9xUCGJHSvr3Myts5soe6rdYDBx_AGJKr1AWk,3406
+celldetective/gui/processes/measure_cells.py,sha256=XAw6SnT14EXfJXZ01bQ2FmPLGYWJHnX9Nko25RH0ZIo,13388
+celldetective/gui/processes/segment_cells.py,sha256=nhoeOQ8YbIWpFZl-I6Ig8oFQpupvufwUAXXhDXTfLNE,12668
+celldetective/gui/processes/track_cells.py,sha256=4t6UZE_dyiryDH9e-G6jdINzdXHXi8BTta2v1gI0w3Q,10165
+celldetective/gui/processes/train_segmentation_model.py,sha256=bvcPG19hBjhNY9hd6Ch5_wk2FOJYQg97Azoz4RKeP-0,10776
+celldetective/gui/processes/train_signal_model.py,sha256=qqqkq9gdvNyvycYkmzWgRXWvsbEozyzNWP_POGvnlIs,3816
+celldetective/gui/settings/__init__.py,sha256=sW3VeD5sWpHz7cN5-jLI7N10TaamEJuHI95gC9lkMDk,448
+celldetective/gui/settings/_settings_base.py,sha256=Y7kjMyAZyjVoPFxvlBjOR1fpKWRqej1rsPMyHtN8Sb8,2281
+celldetective/gui/settings/_settings_event_model_training.py,sha256=TSmd6_Oxw5qKtbawV2U-eG2IYu3HW2NRgXEfe-7cpRE,20219
+celldetective/gui/settings/_settings_measurements.py,sha256=fV9nYi1IMQmHLDgZznjtg0OQGCZAKp0Pd6eNYIT0gdw,38482
+celldetective/gui/settings/_settings_neighborhood.py,sha256=8ef6bmJblHFK68HUITxaKuyeMmdT59rx8fDvZQ3wqBo,19647
+celldetective/gui/settings/_settings_segmentation.py,sha256=6DihD1mk-dN4Sstdth1iJ-0HR34rTVlTHP-pXUh_rY0,1901
+celldetective/gui/settings/_settings_segmentation_model_training.py,sha256=dPcRjIkJTob-F7_FOIjDKVChPkot3ACJ2MLEKTfuTn8,21837
+celldetective/gui/settings/_settings_signal_annotator.py,sha256=s-csxb2JAJoUO9QTHSkt-XyNf3yk0ubW4yQm5eSdv8U,10223
+celldetective/gui/settings/_settings_tracking.py,sha256=pOdShRqHuq84woVuCf_6D4K9Xv4vcHdOUORuipZiU_g,42898
+celldetective/gui/table_ops/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/gui/table_ops/merge_groups.py,sha256=rWwmPBuUeLeAkJcI9ISW5lhmM1L6oQo5lAVc0-D05B4,4059
+celldetective/icons/logo-large.png,sha256=FXSwV3u6zEKcfpuSn4unnqB0oUnN9cHqQ9BCKWytrpg,36631
+celldetective/icons/logo.png,sha256=wV2OS8_dU5Td5cgdPbCOU3JpMpTwNuYLnfVcnQX0tJA,2437
+celldetective/icons/signals_icon.png,sha256=vEiKoqWTtN0-uJgVqtAlwCuP-f4QeWYOlO3sdp2tg2w,3969
+celldetective/icons/splash-test.png,sha256=W9smcuuwJUF9DU-rz4aACx7_rCmGRsxYUGPBDlDnrJk,17523
+celldetective/icons/splash.png,sha256=J_1jPJylxwHGzGF1xCGocc-BmylHtHTII9VJSLKnezY,17895
+celldetective/icons/splash0.png,sha256=qVXsrYUinm5g6-vbHcqwyjh8SIqs9lEqPWnPa1WijaQ,14233
+celldetective/icons/survival2.png,sha256=8zsualD7d9VPAecoFA4Om9TFARErqpJzMg6U7XANXf4,4479
+celldetective/icons/vignette_signals2.png,sha256=hsVOdQDpEfMGM45aaSeacEm3lvxbquRKKYutiS9qoS0,20743
+celldetective/icons/vignette_signals2.svg,sha256=muGNcQudV1jG-bmFd9FwV-Wb8PcrRV5osdZ7pHR7Ekk,5947
+celldetective/links/zenodo.json,sha256=3OSml-j5FbCY5B24t7LZ7raXyVA1834osurmaEckIP8,34511
+celldetective/models/pair_signal_detection/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/models/segmentation_effectors/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/models/segmentation_generic/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/models/segmentation_targets/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/models/signal_detection/blank,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+celldetective/models/tracking_configs/biased_motion.json,sha256=RZa-ZCP4jbFtMVz-M4lf1LtqmAvBrUxIhhudNiU1jtY,1782
+celldetective/models/tracking_configs/mcf7.json,sha256=iDjb8i6yxs0GleW39dvY3Ld5bZJatlXJrwI8PG3vCT0,1780
+celldetective/models/tracking_configs/no_z_motion.json,sha256=b4RWOJ0w6Y2e0vJYwKMyOexedeL2eA8fEDbSzbNmB4A,2702
+celldetective/models/tracking_configs/ricm.json,sha256=L-vmwCR1f89U-qnH2Ms0cBfPFR_dxIWoe2ccH8V-QBA,2727
+celldetective/models/tracking_configs/ricm2.json,sha256=DDjJ6ScYcDWvlsy7ujPID8v8H28vcNcMuZmNR8XmGxo,2718
+celldetective/regionprops/__init__.py,sha256=ohe9vC7j4lnpKnGXidVo1PVfoQfC8TqCuHTNo8rXmdg,44
+celldetective/regionprops/_regionprops.py,sha256=sNa8Wdvq8lL1VLxmTIH-AJdJqJY3ia7g1EdT8IXINwM,10288
+celldetective/regionprops/props.json,sha256=sCwACmbh0n-JAw9eve9yV85REukoMBJLsRjxCwTRMm8,2424
+celldetective/scripts/analyze_signals.py,sha256=WfBqWFKzPpJNkkgLSWwpmpqFO67ZSewdxe2NCIXxEyQ,2190
+celldetective/scripts/measure_cells.py,sha256=db6K0wO_uPbBDNlqK-9OOe1YMGTQe0eolWcoDyMKyh0,11803
+celldetective/scripts/measure_relative.py,sha256=Tv0tagL07l4P6_0YNLN5-1hVw2Qq--FgAM2XfSLvR-Q,4091
+celldetective/scripts/segment_cells.py,sha256=odadT16C4z3NIrTyiAz3DA5547VLJqhJax0xWmV05T8,6949
+celldetective/scripts/segment_cells_thresholds.py,sha256=JanfXVbekgxDosKJDU9SejMcXiLkxnRwFTsA6gyeY8U,5141
+celldetective/scripts/track_cells.py,sha256=GfCqXHsuS8k5jizY4tGye2l6Vwkoenb4_VjBq_dMDyI,8892
+celldetective/scripts/train_segmentation_model.py,sha256=8QXyhQtxBhdYBNleqCbkP3II1AztfrtpyeVyx0Ijy6s,9710
+celldetective/scripts/train_signal_model.py,sha256=D643wKVYg-LWHF2VU9FWKSuazXrpCpQK0YjGqoIimD0,3167
+celldetective-1.4.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
+tests/test_filters.py,sha256=iJksl_HgquqGzPPv46qpNtlD4rkBpZ5eVtIotgZ7LDs,656
+tests/test_io.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
+tests/test_measure.py,sha256=FEUAs1rVHylvIvubCb0bJDNGZLVmkgXNgI3NaGQ1dA8,4542
+tests/test_neighborhood.py,sha256=gk5FmoI7ANEczUtNXYRxc48KzkfYzemwS_eYaLq4_NI,2093
+tests/test_preprocessing.py,sha256=c0rKS9d5h37uDcV7fVOTnn5GMVbEB84b8ZTCTdRmvFs,1422
+tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
+tests/test_signals.py,sha256=No4cah6KxplhDcKXnU8RrA7eDla4hWw6ccf7xGnBokU,3599
+tests/test_tracking.py,sha256=8hebWSqEIuttD1ABn-6dKCT7EXKRR7-4RwyFWi1WPFo,8800
+tests/test_utils.py,sha256=NKRCAC1d89aBK5cWjTb7-pInYow901RrT-uBlIdz4KI,3692
+tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/gui/test_new_project.py,sha256=D3166GefxQeOBw3Uc2nC_wzklF6b_86xrPiLC46jbUk,8228
+tests/gui/test_project.py,sha256=scDr50WAZybTkeTPPphGvor1VL9nHQXUIjvScdxmAmI,4146
+celldetective-1.4.1.dist-info/METADATA,sha256=uy2o-Y7v7jvhCq5wYIAHNYj5N-FNkeCbf1Ui_duW1js,10945
+celldetective-1.4.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+celldetective-1.4.1.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.4.1.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.4.1.dist-info/RECORD,,

{celldetective-1.3.9.post5.dist-info → celldetective-1.4.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (76.0.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tests/gui/test_new_project.py

@@ -0,0 +1,228 @@
+import pytest
+from PyQt5 import QtCore
+from PyQt5.QtWidgets import QApplication
+from celldetective.gui.InitWindow import AppInitWindow
+from celldetective.utils import get_software_location
+import os
+from unittest.mock import patch
+import shutil
+from pathlib import Path
+
+abs_path = os.sep.join([os.path.split(os.path.dirname(os.path.realpath(__file__)))[0]])
+print(abs_path)
+
+@pytest.fixture
+def app(qtbot):
+	software_location = get_software_location()
+	test_app = AppInitWindow(software_location=software_location)
+	qtbot.addWidget(test_app)
+	return test_app
+
+def test_new_project(app, qtbot):
+	# app.newExpAction.trigger()
+	# qtbot.wait(1000)
+	interaction_time = 500
+	test_directory = os.path.dirname(os.path.abspath(__file__))
+	parent_directory = str(Path(test_directory).parent)
+
+	# Patch QFileDialog.getExistingDirectory to return test_directory
+	with patch('PyQt5.QtWidgets.QFileDialog.getExistingDirectory', return_value=parent_directory):
+		
+		if os.path.exists(os.sep.join([parent_directory, "ExperimentTest"])):
+			shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
+		
+		app.newExpAction.trigger()
+		qtbot.wait(interaction_time*3)
+
+		app.new_exp_window.expName.setText('ExperimentTest')
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.SliderWells.setValue(10)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.SliderPos.setValue(3)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.MovieLengthSlider.setValue(1)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.PxToUm_field.setText("0,3112")
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.shape_x_field.setText("660")
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.shape_y_field.setText('682')
+		qtbot.wait(interaction_time)
+
+		# set first channel
+		app.new_exp_window.checkBoxes[0].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[0].setValue(0)
+		qtbot.wait(interaction_time)
+
+		# set second with channel index of 1
+		app.new_exp_window.checkBoxes[1].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[1].setValue(3)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.checkBoxes[2].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[2].setValue(1)
+		qtbot.wait(interaction_time)
+
+		# add extra custom channel
+		qtbot.mouseClick(app.new_exp_window.addChannelBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.name_le.setText('empty_channel')
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.createBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.checkBoxes[-1].setChecked(True)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.sliders[-1].setValue(2)
+		qtbot.wait(interaction_time)
+
+		# Untick populations and create new one
+		for box in app.new_exp_window.population_checkboxes:
+			if box.text() == 'targets':
+				box.setChecked(True)
+			else:
+				box.setChecked(False)
+		
+		qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+
+		app.new_exp_window.name_le.setText('more_cells')
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.addPopBtn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.validate_button, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		qtbot.mouseClick(app.new_exp_window.w.submit_btn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		shutil.copy(os.sep.join([parent_directory, "assets", "sample.tif"]), os.sep.join([parent_directory, "ExperimentTest", "W1", "100", "movie", "sample.tif"]))
+		qtbot.wait(interaction_time)
+
+		qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+		qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
+		qtbot.wait(interaction_time)
+		
+		app.control_panel.viewer.channels_cb.setCurrentIndex(1)
+		qtbot.wait(interaction_time*2)
+		
+		app.control_panel.viewer.contrast_slider.setValue([200,300])
+		qtbot.wait(interaction_time*2)
+	
+	# QApplication.closeAllWindows()
+	# try:
+	# 	shutil.rmtree(os.sep.join([parent_directory, "ExperimentTest"]))
+	# except:
+	# 	pass
+# def test_lauch_app(app, qtbot):
+# 	app.show()
+# 	qtbot.wait(1000)
+#
+# def test_open_project(app, qtbot):
+# 	app.experiment_path_selection.setText(abs_path + os.sep + 'examples/demo')
+# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+#
+# def test_launch_demo(app, qtbot):
+# 	app.experiment_path_selection.setText(abs_path + os.sep + 'examples/demo')
+# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+#
+# def test_preprocessing_panel(app, qtbot):
+#
+# 	app.experiment_path_selection.setText(abs_path + os.sep + 'examples/demo')
+# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+#
+# 	qtbot.mouseClick(app.control_panel.PreprocessingPanel.collapse_btn, QtCore.Qt.LeftButton)
+# 	qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
+# 	qtbot.mouseClick(app.control_panel.PreprocessingPanel.collapse_btn, QtCore.Qt.LeftButton)
+#
+# def test_app(app, qtbot):
+#
+# 	# Set an experiment folder and open
+# 	app.experiment_path_selection.setText(os.sep.join([abs_path,'examples','demo']))
+# 	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+#
+# 	# Set a position
+# 	#app.control_panel.position_list.setCurrentIndex(0)
+# 	#app.control_panel.update_position_options()
+#
+# 	# View stacl
+# 	qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
+# 	#qtbot.wait(1000)
+# 	app.control_panel.viewer.close()
+#
+# 	# Expand process block
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton)
+#
+# 	# Use Threshold Config Wizard
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].upload_model_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].SegModelLoader.threshold_config_button, QtCore.Qt.LeftButton)
+# 	app.control_panel.ProcessPopulations[0].SegModelLoader.ThreshWizard.close()
+# 	app.control_panel.ProcessPopulations[0].SegModelLoader.close()
+#
+# 	# Check segmentation with napari
+# 	#qtbot.mouseClick(app.control_panel.ProcessEffectors.check_seg_btn, QtCore.Qt.LeftButton)
+# 	# close napari?
+#
+# 	# Train model
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].train_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigSegmentationTrain.close()
+#
+# 	# Config tracking
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].track_config_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigTracking.close()
+#
+# 	# Config measurements
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].measurements_config_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigMeasurements.close()
+#
+# 	# Classifier widget
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].classify_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ClassifierWidget.close()
+#
+# 	# Config signal annotator
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].config_signal_annotator_btn, QtCore.Qt.LeftButton)
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].ConfigSignalAnnotator.rgb_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].ConfigSignalAnnotator.close()
+#
+# 	# Signal annotator widget
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].check_signals_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].SignalAnnotator.close()
+#
+# 	# Table widget
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].view_tab_btn, QtCore.Qt.LeftButton)
+# 	qtbot.wait(1000)
+# 	app.control_panel.ProcessPopulations[0].tab_ui.close()
+#
+# 	#qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
+# 	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton)
+#
+#
+#
+# def test_click(app, qtbot):
+# 	qtbot.mouseClick(app.new_exp_button, QtCore.Qt.LeftButton)
+# 	qtbot.wait(10000)

tests/gui/test_project.py

@@ -0,0 +1,99 @@
+import pytest
+from PyQt5 import QtCore
+from celldetective.gui.InitWindow import AppInitWindow
+from celldetective.utils import get_software_location
+import os
+
+software_location = get_software_location()
+
+@pytest.fixture
+def app(qtbot):
+	test_app = AppInitWindow(software_location=software_location)
+	qtbot.addWidget(test_app)
+	return test_app
+
+def test_open_project(app, qtbot):
+	app.experiment_path_selection.setText(software_location + os.sep + 'examples/demo')
+	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+	qtbot.wait(10000)
+
+def test_launch_demo(app, qtbot):
+	app.experiment_path_selection.setText(software_location + os.sep + 'examples/demo')
+	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+
+def test_preprocessing_panel(app, qtbot):
+
+	app.experiment_path_selection.setText(software_location + os.sep + 'examples/demo')
+	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+
+	qtbot.mouseClick(app.control_panel.PreprocessingPanel.collapse_btn, QtCore.Qt.LeftButton)
+	qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
+	qtbot.mouseClick(app.control_panel.PreprocessingPanel.collapse_btn, QtCore.Qt.LeftButton)
+
+def test_app(app, qtbot):
+
+	# Set an experiment folder and open
+	app.experiment_path_selection.setText(os.sep.join([software_location,'examples','demo']))
+	qtbot.mouseClick(app.validate_button, QtCore.Qt.LeftButton)
+
+	# Set a position
+	#app.control_panel.position_list.setCurrentIndex(0)
+	#app.control_panel.update_position_options()
+
+	# View stacl
+	qtbot.mouseClick(app.control_panel.view_stack_btn, QtCore.Qt.LeftButton)
+	#qtbot.wait(1000)
+	app.control_panel.viewer.close()
+
+	# Expand process block
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton)
+
+	# Use Threshold Config Wizard
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].upload_model_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].SegModelLoader.threshold_config_button, QtCore.Qt.LeftButton)
+	app.control_panel.ProcessPopulations[0].SegModelLoader.ThreshWizard.close()
+	app.control_panel.ProcessPopulations[0].SegModelLoader.close()
+
+	# Check segmentation with napari
+	#qtbot.mouseClick(app.control_panel.ProcessEffectors.check_seg_btn, QtCore.Qt.LeftButton)
+	# close napari?
+
+	# Train model
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].train_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].settings_segmentation_training.close()
+
+	# Config tracking
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].track_config_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].settings_tracking.close()
+
+	# Config measurements
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].measurements_config_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].settings_measurements.close()
+
+	# Classifier widget
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].classify_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].ClassifierWidget.close()
+
+	# Config signal annotator
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].config_signal_annotator_btn, QtCore.Qt.LeftButton)
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].settings_signal_annotator.rgb_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].settings_signal_annotator.close()
+
+	# Signal annotator widget
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].check_signals_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].event_annotator.close()
+
+	# Table widget
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].view_tab_btn, QtCore.Qt.LeftButton)
+	qtbot.wait(1000)
+	app.control_panel.ProcessPopulations[0].tab_ui.close()
+
+	#qtbot.mouseClick(app.control_panel.PreprocessingPanel.fit_correction_layout.add_correction_btn, QtCore.Qt.LeftButton)
+	qtbot.mouseClick(app.control_panel.ProcessPopulations[0].collapse_btn, QtCore.Qt.LeftButton)

tests/test_preprocessing.py

@@ -20,11 +20,11 @@ class TestFitPlane(unittest.TestCase):
 		self.assertTrue(np.allclose(self.img, mat))
 
 	def test_plane_is_well_fit_and_applied_with_division(self):
-		result = field_correction(self.img, threshold_on_std=1.0E05, operation='divide', model='plane', clip=False, return_bg=False, activation_protocol=[])
+		result = field_correction(self.img, threshold=1.0E05, operation='divide', model='plane', clip=False, return_bg=False, activation_protocol=[])
 		self.assertTrue(np.allclose(result, np.full((100,100), 1.0)))
 
 	def test_plane_is_well_fit_and_applied_with_subtraction(self):
-		result = field_correction(self.img, threshold_on_std=1.0E05, operation='subtract', model='plane', clip=False, return_bg=False, activation_protocol=[])
+		result = field_correction(self.img, threshold=1.0E05, operation='subtract', model='plane', clip=False, return_bg=False, activation_protocol=[])
 		self.assertTrue(np.allclose(result, np.zeros((100,100))))
 
 	def test_plane_is_well_fit_with_cell(self):

celldetective/models/segmentation_effectors/ricm_bf_all_last/config_input.json

@@ -1,79 +0,0 @@
-{
-    "channels": [
-        "adhesion_channel",
-        "brightfield_channel"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        false,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.75,
-            1.25
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.2,
-    "dataset": {
-        "train": [
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_404_0066_roi_429_935_159_649.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_200_0003_roi_457_991_5_488.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_508_0008.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_305_0075.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_302_0063_roi_405_865_462_937.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_506_0066_roi_473_944_494_953.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_202_0027_roi_557_998_3_447.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_208_0027_roi_600_997_5_387.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_206_0023_roi_251_707_249_666.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_201_0017_roi_324_961_23_596.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_102_0053_roi_511_996_4_433.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_403_0009_roi_554_996_460_994.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_508_0066.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_507_0066_roi_492_998_9_474.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_202_0029_roi_177_746_4_533.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_203_0060_roi_369_906_119_648.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_304_0025.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0030_roi_152_661_531_998.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_105_0018_roi_510_954_13_422.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_507_0016_roi_29_585_462_996.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_504_0066_roi_305_866_382_909.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_605_0060_roi_6_479_351_847.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_403_0008.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_203_0029_roi_3_376_622_1000.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_102_0094.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_202_0055_roi_1_514_68_597.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_206_0000.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_302_0023_roi_295_768_6_437.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_805_0081.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_605_0010_roi_341_847_162_673.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_205_0002_roi_70_569_6_490.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_200_0055_roi_99_778_341_986.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_802_0040.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_206_0028_roi_2_426_487_995.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_706_0042_roi_99_515_11_394.tif"
-        ],
-        "validation": [
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_201_0003_roi_501_957_576_1000.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-11-23-analysis-2024_603_0032.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_706_0030_roi_323_824_488_995.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_202_0014_roi_258_711_504_959.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0007_roi_119_611_5_451.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_206_0030.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_207_0055_roi_519_989_6_429.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-03-03-analysis-2024_506_0053_roi_190_724_13_490.tif",
-            "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects/Marie-20-06-analysis-2024_300_0047_roi_416_985_436_972.tif"
-        ]
-    }
-}

celldetective/models/segmentation_effectors/ricm_bf_all_last/training_instructions.json

@@ -1,37 +0,0 @@
-{
-    "model_name": "ricm_bf_all_last",
-    "model_type": "cellpose",
-    "pretrained": null,
-    "spatial_calibration": 0.2,
-    "channel_option": [
-        "adhesion_channel",
-        "brightfield_channel"
-    ],
-    "normalization_percentile": [
-        false,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.75,
-            1.25
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "ds": [
-        "/home/limozin/Downloads/dataset-marie-all-objects(1)/dataset-marie-all-objects"
-    ],
-    "augmentation_factor": 3.0,
-    "validation_split": 0.2,
-    "learning_rate": 0.008,
-    "batch_size": 8,
-    "epochs": 3000,
-    "target_directory": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_effectors"
-}

celldetective/models/segmentation_effectors/test-transfer/config_input.json

@@ -1,39 +0,0 @@
-{
-    "channels": [
-        "brightfield_channel",
-        "None"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        true,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            1.0,
-            99.0
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.36666666666666664,
-    "dataset": {
-        "train": [
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_206_0028_roi_2_426_487_995.tif",
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_203_0029_roi_3_376_622_1000.tif",
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_208_0027_roi_600_997_5_387.tif"
-        ],
-        "validation": [
-            "/home/torro/Documents/Experiments/Marie-03-03-analysis-2024/annotations_effectors/Marie-03-03-analysis-2024_206_0023_roi_251_707_249_666.tif"
-        ]
-    }
-}

celldetective/models/signal_detection/NucCond/config_input.json

@@ -1 +0,0 @@
-{"channels": ["area"], "model_signal_length": 128, "label": "nucShrink", "normalize": true, "normalization_percentile": [true], "normalization_values": [[0.1, 99.99]], "normalization_clip": [true]}