celldetective 1.5.0b8__py3-none-any.whl → 1.5.0b9__py3-none-any.whl

{celldetective-1.5.0b8.dist-info → celldetective-1.5.0b9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: celldetective
-Version: 1.5.0b8
+Version: 1.5.0b9
 Summary: description
 Home-page: http://github.com/remyeltorro/celldetective
 Author: Rémy Torro

{celldetective-1.5.0b8.dist-info → celldetective-1.5.0b9.dist-info}/RECORD

@@ -1,6 +1,6 @@
 celldetective/__init__.py,sha256=LfnOyfUnYPGDc8xcsF_PfYEL7-CqAb7BMBPBIWGv84o,666
 celldetective/__main__.py,sha256=Rzzu9ArxZSgfBVjV-lyn-3oanQB2MumQR6itK5ZaRpA,2597
-celldetective/_version.py,sha256=_aQC8i0kOHSYGEkfpTecn4OzPtL_z-LVXk1dtkjlJtQ,24
+celldetective/_version.py,sha256=C-mBr40Do8xTMcYdWQX-DapmWmTsr2JSmIPIRtYIXUU,24
 celldetective/event_detection_models.py,sha256=A7ZJFhJwfdhzfxJ-YZIj6IoI9Gc1hyAodFkKt8kNxDk,93549
 celldetective/events.py,sha256=n15R53c7QZ2wT8gjb0oeNikQbuRBrVVbyNsRCqXjzXA,8166
 celldetective/exceptions.py,sha256=f3VmIYOthWTiqMEV5xQCox2rw5c5e7yog88h-CcV4oI,356
@@ -26,28 +26,28 @@ celldetective/gui/configure_new_exp.py,sha256=vgT6ozRIGDvT3R0qENlqvDn17BpKnwyJRh
 celldetective/gui/control_panel.py,sha256=dMNzgivt6GdYROPlYpEY5TTNcANenm9ifUI3W3OcpOo,24337
 celldetective/gui/dynamic_progress.py,sha256=wjTmDPy62qssY0zdteP3T9umIGGQk0UvebFIdn54CIc,16676
 celldetective/gui/event_annotator.py,sha256=JVd64Gch_qzXv29VJGAa2Ytk-WhxifZVgMK-hAxnGu4,41262
-celldetective/gui/generic_signal_plot.py,sha256=D3b6pG1yrSi8C2PPyYzK2yA6711CBBPRp5_OIrjayqs,49348
-celldetective/gui/gui_utils.py,sha256=t6SjEfjcaRH9a0TlbTGEiVRpCgocaCh4lgkIvRgRRwE,33497
+celldetective/gui/generic_signal_plot.py,sha256=47kXIuMcnQXjeNEdzM_G1WbW9TL5eMSjHC9XgWXMly4,49492
+celldetective/gui/gui_utils.py,sha256=l7P6emKVEciCRdmnbfYvJAhl0MnbT3QkL2zpSPuHRoY,34120
 celldetective/gui/interactions_block.py,sha256=34VaHFrdKsq1hYuXrosmpP15JU26dSfbyx4lyt1jxNg,28440
 celldetective/gui/interactive_timeseries_viewer.py,sha256=u_amAhLdEHRpYSRwPDtVm5v-JZIz0ANTcG4YGksX1Vo,16079
 celldetective/gui/json_readers.py,sha256=t5rhtIxACj0pdwLrnPs-QjyhQo3P25UGWGgOCIBhQxs,4572
 celldetective/gui/measure_annotator.py,sha256=ljNbsKmFXQk0R9zEfBZ6XfBHzFmlL7Gt6QyPHyqh08g,38357
 celldetective/gui/pair_event_annotator.py,sha256=9PT67-8FJxcL7lSDIAZcZmrW75G_R-fpRellMOsgets,128788
 celldetective/gui/plot_measurements.py,sha256=a_Mks-5XUTn2QEYih0PlXGp2lX3C34zuhK9ozzE1guM,56593
-celldetective/gui/plot_signals_ui.py,sha256=9VmA1yaTcNf1jY7drtK41R1q87dhEk7bXBCq_cQ94fs,28133
+celldetective/gui/plot_signals_ui.py,sha256=fxgkUZ_m7jFTXOwdzfJdl8wt3n8RECny3n4Tpk-GE6w,29016
 celldetective/gui/preprocessing_block.py,sha256=cgUBv-eQBwfidK48-cTWJi0PS62wlXhsNLnsKhy6MQY,14967
 celldetective/gui/process_block.py,sha256=KVfXnC55EYGlgKVDXDSMGu_MZbxjbQaQz4Ulyl5iqSE,76881
 celldetective/gui/seg_model_loader.py,sha256=CqcyT1ZeQ27R54RmOHjAt1pfRwjtvS-Psw29PpFsT5A,23549
-celldetective/gui/survival_ui.py,sha256=IwdRm1gRvhkWdMtrQk04OIKKksW3NZSGYtZO_2GptrA,16034
-celldetective/gui/tableUI.py,sha256=kZP2lp9NwHtbWEqIyaDwohX42tRkhI0Hlf_8O5w5BD0,61267
-celldetective/gui/thresholds_gui.py,sha256=w6ke2TyIEi71LxbuFGz0UrwH8h21N_ESU-o6xq_NNKo,33346
+celldetective/gui/survival_ui.py,sha256=YBtbkjXgJW4KLpRaFysJc_po4OjVcLyCmGSWKtMbjdk,17353
+celldetective/gui/tableUI.py,sha256=8cHVKMgTHMWLf_2yxYo003FQ0TaN7Cf13rBKBZQtefQ,58989
+celldetective/gui/thresholds_gui.py,sha256=KxPmCmoMGGwwHFwPWHCOr1wPTyOPR2d-zucuAvZfSqk,34783
 celldetective/gui/workers.py,sha256=WAtVxFEvHApBSAZMVyYsya_DHL_bYo8b57dbgUJQHc4,14890
 celldetective/gui/base/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/gui/base/channel_norm_generator.py,sha256=HJ57wBMdBIvca92V477T-aPuxvvC2aC5BDMssKSQKCQ,14592
 celldetective/gui/base/components.py,sha256=jNUsCU_QE7QUFR0_xEvEPFEBYolMJt7YXGUKMjF7uOE,8155
 celldetective/gui/base/feature_choice.py,sha256=n1T2fPoNLiTDS_6fa_GuGReDhBW11HdUrKy2RywotF8,2800
 celldetective/gui/base/figure_canvas.py,sha256=mSiIYvEfz7MYMgdPDf6RKSMpKN8FkeZL7lugDNnDpnM,2245
-celldetective/gui/base/list_widget.py,sha256=_WU3ZRU7UcJZIxm8qx_5HF7IK7dUu8IU1FY2AaW_qgo,4694
+celldetective/gui/base/list_widget.py,sha256=APt7rCfMRRlFnHUwvwrwZGMTYM6M10zgu6uoHHsmmuA,4694
 celldetective/gui/base/styles.py,sha256=3Kz1eXw6OLr90wtErhK0KPJyJbyhAlqkniqm0JNGwFc,7407
 celldetective/gui/base/utils.py,sha256=KojauRKGM9XKNhaWn211p6mJNZWIHLH75yeLpDd7pvA,1103
 celldetective/gui/help/DL-segmentation-strategy.json,sha256=PZD9xXjrwbX3TiudHJPuvcyZD28o4k-fVgeTd7dBKzI,1583
@@ -92,7 +92,7 @@ celldetective/gui/viewers/base_viewer.py,sha256=Wn4na79xRL1R6PSXIoE_UabxJNtNQ-Y5
 celldetective/gui/viewers/channel_offset_viewer.py,sha256=cywBkxyMPyKIuwZTGA03DBSS4a-H1SAohMJYOPISLEE,16289
 celldetective/gui/viewers/contour_viewer.py,sha256=riHj03LKXLoa-Ys2o2EhCE5nULfcHMohx9LFoXbI6zU,14720
 celldetective/gui/viewers/size_viewer.py,sha256=uXITjaxg5dhQ09Q6TNUxwLxi-ZglyGFcxEH1RtGIZWw,6020
-celldetective/gui/viewers/spot_detection_viewer.py,sha256=JO7kcqATHXR91lLvo8aQ5xVYdtxkMxV-xx36s01VlNQ,12545
+celldetective/gui/viewers/spot_detection_viewer.py,sha256=IsSqbdJ7Fuzc7CSIt5U8LoeHuq-GLgg-igqlw5NRn7g,16502
 celldetective/gui/viewers/threshold_viewer.py,sha256=F-13JF2wFhyvvKfUvgRcSjWL3leAliOXy5yUergndnE,12000
 celldetective/icons/logo-large.png,sha256=FXSwV3u6zEKcfpuSn4unnqB0oUnN9cHqQ9BCKWytrpg,36631
 celldetective/icons/logo.png,sha256=wV2OS8_dU5Td5cgdPbCOU3JpMpTwNuYLnfVcnQX0tJA,2437
@@ -167,7 +167,7 @@ celldetective/utils/event_detection/__init__.py,sha256=GvsdyQLMTXJj1S_FfRXjrpOxE
 celldetective/utils/plots/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 celldetective/utils/plots/regression.py,sha256=oUCn29-hp7PxMqC-R0yoL60KMw5ZWpZAIoCDh2ErlcY,1764
 celldetective/utils/stardist_utils/__init__.py,sha256=SY2kxFNXSRjXN4ncs3heDdXT3UNk8M3dELJQySysAf4,4231
-celldetective-1.5.0b8.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+celldetective-1.5.0b9.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_cellpose_fallback.py,sha256=BJZTDFF8sFR1x7rDbvZQ2RQOB1OP6wuFBRfc8zbl5zw,3513
 tests/test_events.py,sha256=eLFwwEEJfQAdwhews3-fn1HSvzozcNNFN_Qn0gOvQkE,685
@@ -179,7 +179,7 @@ tests/test_notebooks.py,sha256=7HVmYiytsz0QIJ11iRkGGs4_hzNjofXAUs_OZou3Gm0,301
 tests/test_partial_install.py,sha256=G69-GNcJ9YNgs6K2bVTEZO0Jpb14xMRQWTm8A6VuIco,2841
 tests/test_preprocessing.py,sha256=c0rKS9d5h37uDcV7fVOTnn5GMVbEB84b8ZTCTdRmvFs,1422
 tests/test_segmentation.py,sha256=k1b_zIZdlytEdJcHjAUQEO3gTBAHtv5WvrwQN2xD4kc,3470
-tests/test_signals.py,sha256=DWDRGpw_k2VE5pWnqJexsa313YEi8c2KzC51DFzykco,3641
+tests/test_signals.py,sha256=upfhDyQMquOOKuYf7a34TglimHK74oYWQ9RyuK7Mg7c,4285
 tests/test_tracking.py,sha256=_YLjwQ3EChQssoHDfEnUJ7fI1yC5KEcJsFnAVR64L70,18909
 tests/test_utils.py,sha256=aSB_eMw9fzTsnxxdYoNmdQQRrXkWqBXB7Uv4TGU6kYE,4778
 tests/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -187,8 +187,9 @@ tests/gui/test_enhancements.py,sha256=3x9au_rkQtMZ94DRj3OaEHKPr511RrWqBAUAcNQn1y
 tests/gui/test_measure_annotator_bugfix.py,sha256=tPfgWNKC0UkvrVssSrUcVDC1qgpzx6l2yCqvKtKYkM4,4544
 tests/gui/test_new_project.py,sha256=wRjW2vEaZb0LWT-f8G8-Ptk8CW9z8-FDPLpV5uqj6ck,8778
 tests/gui/test_project.py,sha256=KzAnodIc0Ovta0ARL5Kr5PkOR5euA6qczT_GhEZpyE4,4710
-celldetective-1.5.0b8.dist-info/METADATA,sha256=hUsQY-GrHvD70Htr2XKBXkJlHwv3B4dBe5hQ9sFQonw,11523
-celldetective-1.5.0b8.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-celldetective-1.5.0b8.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
-celldetective-1.5.0b8.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
-celldetective-1.5.0b8.dist-info/RECORD,,
+tests/gui/test_spot_detection_viewer.py,sha256=g-Lyi1sJNWCDy3gPkRU0RlP1BJaOJ6Gg3Ouy0cX_F3Y,6415
+celldetective-1.5.0b9.dist-info/METADATA,sha256=-Vdw3UnjUJDidGKCCb8Z_5EcQ9Z4TUj35w5KYx6z1x4,11523
+celldetective-1.5.0b9.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+celldetective-1.5.0b9.dist-info/entry_points.txt,sha256=2NU6_EOByvPxqBbCvjwxlVlvnQreqZ3BKRCVIKEv3dg,62
+celldetective-1.5.0b9.dist-info/top_level.txt,sha256=6rsIKKfGMKgud7HPuATcpq6EhdXwcg_yknBVWn9x4C4,20
+celldetective-1.5.0b9.dist-info/RECORD,,

tests/gui/test_spot_detection_viewer.py

@@ -0,0 +1,187 @@
+import pytest
+import numpy as np
+import logging
+from PyQt5.QtWidgets import QApplication
+from celldetective.gui.viewers.spot_detection_viewer import SpotDetectionVisualizer
+from celldetective.gui.gui_utils import PreprocessingLayout2
+from unittest.mock import MagicMock, patch
+
+
+@pytest.fixture(autouse=True)
+def disable_logging():
+    """Disable all logging to avoid Windows OSError with pytest capture."""
+    logger = logging.getLogger()
+    try:
+        logging.disable(logging.CRITICAL)
+        yield
+    finally:
+        logging.disable(logging.NOTSET)
+
+
+@pytest.fixture
+def dummy_data():
+    """
+    Create a dummy stack: 5 frames, 100x100 pixels, 2 channels.
+    Channel 0: Clean background (zeros)
+    Channel 1: Two Gaussian spots with high intensity
+    """
+    frames = 5
+    y, x = 100, 100
+    channels = 2
+
+    stack = np.zeros((frames, y, x, channels), dtype=np.float32)
+
+    # Create coordinate grids
+    Y, X = np.ogrid[:y, :x]
+
+    # Gaussian spot 1 at (22, 22) - center of mask 1
+    center_y1, center_x1 = 22, 22
+    sigma = 2.0
+    gaussian1 = np.exp(-((Y - center_y1) ** 2 + (X - center_x1) ** 2) / (2 * sigma**2))
+
+    # Gaussian spot 2 at (62, 62) - center of mask 2
+    center_y2, center_x2 = 62, 62
+    gaussian2 = np.exp(-((Y - center_y2) ** 2 + (X - center_x2) ** 2) / (2 * sigma**2))
+
+    # Add to stack with high intensity (1000 for spot 1, 800 for spot 2)
+    spots_frame = (gaussian1 * 1000 + gaussian2 * 800).astype(np.float32)
+    for f in range(frames):
+        stack[f, :, :, 1] = spots_frame
+
+    # Channel 0 stays at zero (clean background)
+
+    # Create dummy masks (labels) - each spot is inside its own cell
+    masks = np.zeros((frames, y, x), dtype=np.uint16)
+    masks[:, 15:30, 15:30] = 1  # Mask around Spot 1 (22, 22)
+    masks[:, 55:70, 55:70] = 2  # Mask around Spot 2 (62, 62)
+
+    return stack, masks
+
+
+def test_spot_detection_visualizer_interactions(qtbot, dummy_data):
+    """
+    Test interactions with SpotDetectionVisualizer.
+    """
+    stack, labels = dummy_data
+    channel_names = ["Background", "Spots"]
+
+    # Mock parent widgets that might be updated by the visualizer
+    parent_channel_cb = MagicMock()
+    parent_diameter_le = MagicMock()
+    parent_threshold_le = MagicMock()
+    parent_preprocessing_list = MagicMock()
+
+    viewer = SpotDetectionVisualizer(
+        stack=stack,
+        labels=labels,
+        channel_names=channel_names,
+        n_channels=2,
+        parent_channel_cb=parent_channel_cb,
+        parent_diameter_le=parent_diameter_le,
+        parent_threshold_le=parent_threshold_le,
+        parent_preprocessing_list=parent_preprocessing_list,
+        window_title="Test Spot Detective",
+        channel_cb=True,
+        contrast_slider=False,
+        frame_slider=False,
+    )
+
+    qtbot.addWidget(viewer)
+    viewer.show()
+    qtbot.waitForWindowShown(viewer)
+
+    # 1. Test Channel Selection
+    # Default is target_channel=0 (Background)
+    assert viewer.detection_channel == 0
+
+    # Switch to Spots channel (Index 1)
+    viewer.detection_channel_cb.setCurrentIndex(1)
+    assert viewer.detection_channel == 1
+
+    # Force frame update to ensure target_img is correct for channel 1
+    viewer.change_frame(0)
+
+    # Verify image updated to Channel 1, Frame 0
+    current_img = viewer.target_img
+    expected_img = stack[0, :, :, 1]
+    np.testing.assert_array_equal(current_img, expected_img)
+
+    # 2. Test Spot Detection Parameters
+    # Set Diameter (LoG works best with diameter ~ 2*sqrt(2)*sigma ~ 5.6 for sigma=2)
+    viewer.spot_diam_le.clear()
+    qtbot.keyClicks(viewer.spot_diam_le, "4")
+    assert viewer.spot_diam_le.text() == "4"
+
+    # Set Threshold (low threshold to ensure detection)
+    viewer.spot_thresh_le.clear()
+    qtbot.keyClicks(viewer.spot_thresh_le, "0.01")
+    assert viewer.spot_thresh_le.text() == "0.01"
+
+    # Manually trigger control_valid_parameters to update self.diameter and self.thresh
+    viewer.control_valid_parameters()
+
+    # Verify parameters were set
+    assert viewer.diameter == 4.0
+    assert viewer.thresh == 0.01
+
+    # Trigger detection by clicking apply button
+    qtbot.mouseClick(viewer.apply_diam_btn, 1)  # Qt.LeftButton = 1
+    qtbot.wait(200)  # Wait for detection to complete
+
+    # Check that we recovered 2 spots
+    # In dummy_data: Spot 1 at (22, 22), Spot 2 at (62, 62)
+    n_spots = (
+        len(viewer.spot_positions)
+        if hasattr(viewer, "spot_positions") and viewer.spot_positions is not None
+        else 0
+    )
+    assert (
+        n_spots == 2
+    ), f"Expected 2 spots, found {n_spots}. Positions: {viewer.spot_positions if hasattr(viewer, 'spot_positions') else 'N/A'}"
+
+    # Verify positions roughly match (22, 22) and (62, 62)
+    # spot_positions are (x, y) pairs
+    pos = viewer.spot_positions
+    has_spot_1 = np.any(np.all(np.abs(pos - [22, 22]) < 5, axis=1))
+    has_spot_2 = np.any(np.all(np.abs(pos - [62, 62]) < 5, axis=1))
+    assert has_spot_1, f"Spot 1 not found near (22, 22). Positions: {pos}"
+    assert has_spot_2, f"Spot 2 not found near (62, 62). Positions: {pos}"
+
+    # 3. Test Preprocessing and Preview
+    # Ensure preview is unchecked initially
+    assert not viewer.preview_cb.isChecked()
+
+    # Check "Preview" - should show original image if filter list is empty
+    viewer.preview_cb.setChecked(True)
+    assert viewer.preview_cb.isChecked()
+    # Image should still match original target since no filters
+    np.testing.assert_array_equal(viewer.im.get_array(), expected_img)
+
+    # Add a filter: "gauss" with sigma=2
+    # Directly manipulate the list since dialog interaction is complex
+    viewer.preprocessing.list.items.append(["gauss", 2])
+    viewer.preprocessing.list.list_widget.addItems(["gauss_filter"])
+
+    # Force preview update
+    viewer.update_preview_if_active()
+    qtbot.wait(200)
+
+    preview_img = viewer.im.get_array()
+    assert not np.array_equal(
+        preview_img, expected_img
+    ), "Preview image should differ after adding gaussian filter"
+
+    # 4. Remove Filter
+    # Select item 0
+    viewer.preprocessing.list.list_widget.setCurrentRow(0)
+    # Click remove button
+    viewer.preprocessing.delete_filter_btn.click()
+
+    qtbot.wait(200)
+
+    # Internal items should be empty
+    assert len(viewer.preprocessing.list.items) == 0
+
+    # Preview should revert to original
+    reverted_img = viewer.im.get_array()
+    np.testing.assert_array_equal(reverted_img, expected_img)

tests/test_signals.py

@@ -1,135 +1,154 @@
 import unittest
-import matplotlib.pyplot as plt
 import numpy as np
 import os
 import random
 import pandas as pd
 import shutil
 
-def sigmoid(t,t0,dt,A,offset):
-	return A/(1+np.exp(-(t-t0)/dt)) + offset
+
+def sigmoid(t, t0, dt, A, offset):
+    return A / (1 + np.exp(-(t - t0) / dt)) + offset
+
 
 def generate_fake_signal_data(n_signals):
-	
-	timeline = np.linspace(0,100,100)
-	amplitudes = list(np.linspace(2000,3000,100))
-	slopes = list(np.linspace(0.5,5,100))
-	means = list(np.linspace(-100,200,100))
-	random_cut = list(np.linspace(25,200,176,dtype=int))
-	noise_levels = list(np.linspace(1,100,100,dtype=int))
-
-	trajectories = []
-	for i in range(n_signals):
-		
-		a = random.sample(amplitudes,k=1)[0]
-		dt = random.sample(slopes,k=1)[0]
-		mu = random.sample(means,k=1)[0]
-		cut = random.sample(random_cut,k=1)[0]
-		n = random.sample(noise_levels,k=1)[0]
-		
-		if mu<=0.:
-			cclass=2
-			t0=-1
-		elif (mu>0)*(mu<=100):
-			cclass=0
-			t0=mu
-		else:
-			cclass=1
-			t0=-1
-		
-		noise = [random.random()*n for i in range(len(timeline))]
-		signal = sigmoid(timeline, mu, dt,a,0)+noise
-		signal = signal[:cut]
-		if mu>=cut:
-			cclass=1
-			t0=-1
-		
-		for j in range(len(signal)):
-			trajectories.append({'TRACK_ID': i, 'POSITION_X': 0., 'POSITION_Y': 0., 'FRAME': j,'signal': signal[j], 't0': t0, 'cclass': cclass})  
-
-	trajectories = pd.DataFrame(trajectories)
-
-	return trajectories
-
-def export_set(trajectories, name='set.npy', output_folder='.'):
-	
-	training_set = []
-	cols = trajectories.columns
-	tracks = np.unique(trajectories["TRACK_ID"].to_numpy())
-
-	for track in tracks:
-		signals = {}
-		for c in cols:
-			signals.update({c: trajectories.loc[trajectories["TRACK_ID"] == track, c].to_numpy()})
-		time_of_interest = trajectories.loc[trajectories["TRACK_ID"] == track, "t0"].to_numpy()[0]
-		cclass = trajectories.loc[trajectories["TRACK_ID"] == track, "cclass"].to_numpy()[0]
-		signals.update({"time_of_interest": time_of_interest, "class": cclass})
-		training_set.append(signals)
-		
-	np.save(os.sep.join([output_folder,name]), training_set)
+
+    timeline = np.linspace(0, 100, 100)
+    amplitudes = list(np.linspace(2000, 3000, 100))
+    slopes = list(np.linspace(0.5, 5, 100))
+    means = list(np.linspace(-100, 200, 100))
+    random_cut = list(np.linspace(25, 200, 176, dtype=int))
+    noise_levels = list(np.linspace(1, 100, 100, dtype=int))
+
+    trajectories = []
+    for i in range(n_signals):
+
+        a = random.sample(amplitudes, k=1)[0]
+        dt = random.sample(slopes, k=1)[0]
+        mu = random.sample(means, k=1)[0]
+        cut = random.sample(random_cut, k=1)[0]
+        n = random.sample(noise_levels, k=1)[0]
+
+        if mu <= 0.0:
+            cclass = 2
+            t0 = -1
+        elif (mu > 0) * (mu <= 100):
+            cclass = 0
+            t0 = mu
+        else:
+            cclass = 1
+            t0 = -1
+
+        noise = [random.random() * n for i in range(len(timeline))]
+        signal = sigmoid(timeline, mu, dt, a, 0) + noise
+        signal = signal[:cut]
+        if mu >= cut:
+            cclass = 1
+            t0 = -1
+
+        for j in range(len(signal)):
+            trajectories.append(
+                {
+                    "TRACK_ID": i,
+                    "POSITION_X": 0.0,
+                    "POSITION_Y": 0.0,
+                    "FRAME": j,
+                    "signal": signal[j],
+                    "t0": t0,
+                    "cclass": cclass,
+                }
+            )
+
+    trajectories = pd.DataFrame(trajectories)
+
+    return trajectories
+
+
+def export_set(trajectories, name="set.npy", output_folder="."):
+
+    training_set = []
+    cols = trajectories.columns
+    tracks = np.unique(trajectories["TRACK_ID"].to_numpy())
+
+    for track in tracks:
+        signals = {}
+        for c in cols:
+            signals.update(
+                {c: trajectories.loc[trajectories["TRACK_ID"] == track, c].to_numpy()}
+            )
+        time_of_interest = trajectories.loc[
+            trajectories["TRACK_ID"] == track, "t0"
+        ].to_numpy()[0]
+        cclass = trajectories.loc[
+            trajectories["TRACK_ID"] == track, "cclass"
+        ].to_numpy()[0]
+        signals.update({"time_of_interest": time_of_interest, "class": cclass})
+        training_set.append(signals)
+
+    np.save(os.sep.join([output_folder, name]), training_set)
 
 
 class TestCreateSignalModel(unittest.TestCase):
 
-	def test_create_model(self):
+    def test_create_model(self):
 
-		from celldetective.event_detection_models import SignalDetectionModel
+        from celldetective.event_detection_models import SignalDetectionModel
 
         model = SignalDetectionModel(
-									 channel_option=["signal"], 
-									 model_signal_length=128,
-									 n_channels=1,
-									 n_conv=2,
-									 n_classes=3,
-									 dense_collection=512,
-									 dropout_rate=0.1,
-									 label='test',
-									 )
+            channel_option=["signal"],
+            model_signal_length=128,
+            n_channels=1,
+            n_conv=2,
+            n_classes=3,
+            dense_collection=512,
+            dropout_rate=0.1,
+            label="test",
+        )
 
 
 class TestTrainSignalModel(unittest.TestCase):
 
-	@classmethod
-	def setUpClass(self):
+    @classmethod
+    def setUpClass(self):
 
-		from celldetective.event_detection_models import SignalDetectionModel
+        from celldetective.event_detection_models import SignalDetectionModel
 
         self.trajectories = generate_fake_signal_data(300)
-		if not os.path.exists('temp'):
-			os.mkdir('temp')
-		export_set(self.trajectories, name='set.npy', output_folder='temp')
-		self.model = SignalDetectionModel(
-									 channel_option=["signal"], 
-									 model_signal_length=128,
-									 n_channels=1,
-									 n_conv=2,
-									 n_classes=3,
-									 dense_collection=512,
-									 dropout_rate=0.1,
-									 label='test',
-									 )
-
-	def test_train_signal_model(self):
-
-		self.model.fit_from_directory(
-									 ['temp'],
-									 normalize=True,
-									 normalization_percentile=None,
-									 normalization_values = None,
-									 normalization_clip = None,
-									 channel_option=["signal"],
-									 target_directory='temp',
-									 augment=False,
-									 model_name='None',
-									 validation_split=0.2,
-									 test_split=0.1,
-									 batch_size = 16,
-									 epochs=1,
-									 recompile_pretrained=False,
-									 learning_rate=0.01,
-									 show_plots=False,
-		                        )
-		shutil.rmtree('temp')
-
-if __name__=="__main__":
-	unittest.main()
+        if not os.path.exists("temp"):
+            os.mkdir("temp")
+        export_set(self.trajectories, name="set.npy", output_folder="temp")
+        self.model = SignalDetectionModel(
+            channel_option=["signal"],
+            model_signal_length=128,
+            n_channels=1,
+            n_conv=2,
+            n_classes=3,
+            dense_collection=512,
+            dropout_rate=0.1,
+            label="test",
+        )
+
+    def test_train_signal_model(self):
+
+        self.model.fit_from_directory(
+            ["temp"],
+            normalize=True,
+            normalization_percentile=None,
+            normalization_values=None,
+            normalization_clip=None,
+            channel_option=["signal"],
+            target_directory="temp",
+            augment=False,
+            model_name="None",
+            validation_split=0.2,
+            test_split=0.1,
+            batch_size=16,
+            epochs=1,
+            recompile_pretrained=False,
+            learning_rate=0.01,
+            show_plots=False,
+        )
+        shutil.rmtree("temp")
+
+
+if __name__ == "__main__":
+    unittest.main()