Test Report Ci Ubuntu-Latest 3.13

Environnement

Python	3.13.13
Platform	Linux-6.17.0-1010-azure-x86_64-with-glibc2.39
CI	true
System	Linux
CPU	AMD EPYC 9V74 80-Core Processor (2.79 GHz - 2 Cores (4 Logical))
RAM	15.61 GB
GPU	Error detecting GPU: NVML Shared Library Not Found

Summary

263 tests collected, 263 passed ✅, 0 failed ❌, 0 skipped ⏭️ in 0:01:44s on 05/05/2026 at 13:56:34

Monitoring

Test Cases

Palmtracer

Test Name	Status	Duration
Reset Result	✅	62ms
Getter Localization	✅	43ms
Getter Beads	✅	43ms
Getter Tracks	✅	43ms
Getter Tracks Compute	✅	41ms
Get Status	✅	47ms
Getter Path	✅	54ms
Getter Stack	✅	48ms
Getter Suffix	✅	41ms
Load Bad Dll	✅	46ms
Load Nothing	✅	42ms
Load	✅	107ms
Process No Input	✅	105ms
Process Nothing	✅	130ms
Process Bad Dll	✅	39ms
Process Multiple Stack	✅	71ms
Process Localization	✅	81ms
Process Localization Z	✅	198ms
Process Localization Spline Bad	✅	50ms
Process Localization Spline	✅	94ms
Process Beads Extraction No Beads	✅	87ms
Process Plane Discontinuous	✅	46ms
Process Beads Extraction	✅	131ms
Process Tracking	✅	346ms
Process Tracking Blinking	✅	112ms
Process Tracks Compute	✅	2.37s
Process Gallery	✅	112ms
Process Visualization Graph	✅	5.22s
Process Visualization Hr	✅	1.31s
Process All	✅	5.39s
Reset Filtered	✅	43ms
Update Filtered	✅	109ms
Save Filtered	✅	52ms
Filter Localization	✅	1.19s
Filter Tracks Compute	✅	2.29s
Add Color	✅	68ms
Get Astigmatism Model	✅	52ms

Log Test : Update Filtered

[05-05-2026 13:55:08] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_135508.log
[05-05-2026 13:55:08] Start Processing.
[05-05-2026 13:55:08] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 13:55:08] Meta file saved.
[05-05-2026 13:55:08] Settings saved.
[05-05-2026 13:55:08] Localization load previous result (Timestamp : 20260101_000000).
[05-05-2026 13:55:08]        File 'localizations-20260101_000000.csv' loaded successfully, 451 row(s) found.
[05-05-2026 13:55:08] Beads Extraction disabled.
[05-05-2026 13:55:08] Tracking disabled.
[05-05-2026 13:55:08] Blinking Reconnection disabled.
[05-05-2026 13:55:08] Tracks Compute disabled.
[05-05-2026 13:55:08] Gallery generation disabled.
[05-05-2026 13:55:08] Graphical visualization disabled.
[05-05-2026 13:55:08] High-resolution visualization disabled.
[05-05-2026 13:55:08] Processing complete.
[05-05-2026 13:55:08] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_135508.log

Processing Astigmatism3D

Test Name	Status	Duration
Get Z From Planes	✅	2ms
Get Z From Step	✅	1ms
Remove Multi Loc	✅	13ms
Sigma Model	✅	1ms
Model Validity	✅	3ms
Model Projection Validity	✅	15ms
Find Model Center	✅	3ms

Log Test : Remove Multi Loc

Not all valid columns in localizations. Unable to remove ambiguous localizations reliably.
All planes contain multiple localizations. Unable to remove ambiguous localizations reliably.

Log Test : Model Projection Validity

{'rmse_z': 5.777646505663858, 'mae_z': 4.527265453090619, 'p95_abs_z': 11.402280456091262, 'bias_z': 0.034926985397079696, 'std_z': 5.777540934524036, 'mean_dist': 0.015979049334594875, 'p95_dist': 0.03907161488826703, 'slope_mean': 0.003993454737472619}
{'rmse_z': 577.3147040352493, 'mae_z': 499.9443888777755, 'p95_abs_z': 950.0000000000001, 'bias_z': 7.395319063812727, 'std_z': 577.2673356004581, 'mean_dist': 0.02749131099862401, 'p95_dist': 0.09899871427527444, 'slope_mean': 0.003993454737472619}
{'rmse_z': 763.5196346175319, 'mae_z': 749.5955591118224, 'p95_abs_z': 975.0050010002001, 'bias_z': 20.59999999999995, 'std_z': 763.2416867850505, 'mean_dist': 1.592075248599287, 'p95_dist': 2.2654090960555444, 'slope_mean': 0.00156321987547227}

Processing Drift

Test Name	Status	Duration
Extract Bead Bad Input	✅	16ms
Extract Beads No Match Returns Empty	✅	5ms
Assign Tracks No Pairs	✅	1ms
Assign Tracks Skip Used Track	✅	1ms
Extract Beads	✅	59ms
Remove Beads	✅	10ms
Get Drift Bad Input	✅	6ms
Get Drift	✅	27ms
Apply Drift Bad Input	✅	2ms
Remove Drift	✅	18ms
Chain Drift	✅	26ms
Drift Correction	✅	30ms
Median Filter Centered	✅	6ms

Processing Filtering

Test Name	Status	Duration
Filter Bad	✅	31ms
Localization	✅	41ms
Tracking	✅	29ms
Tracks Compute	✅	46ms

Processing Gallery

Test Name	Status	Duration
Make Gallery	✅	7ms

Processing Grapher

Test Name	Status	Duration
Blank	✅	295ms
Histogram	✅	963ms
Scatter	✅	389ms
Cloud	✅	805ms
Astigmatism3D	✅	374ms

Processing Palm

Test Name	Status	Duration
Palm Dll Valid	✅	1ms
Palm Cpu Empty Result	✅	6ms
Palm Cpu Image	✅	1.17s
Palm Cpu Stack	✅	4.38s
Palm Cpu Stack Plane Selection	✅	247ms
Palm Cpu Stack Dll Check Quadrant	✅	324ms
Cpu Auto Threshold	✅	63ms
Tracking	✅	7.41s
Blinking Reconnection	✅	279ms
Tracks Compute	✅	73ms
Align	✅	96ms
Wavelett	✅	61ms
Astigmatism 3D Calibration	✅	11ms
Astigmatism 3D Estimation	✅	6ms

Log Test : Palm Cpu Image

Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-0_103.6_True_0_1.0_0.0_7.csv'
Comparaison terminée : 51 Points comparés, 51 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-0_103.6_True_1_1.0_0.0_7.csv'
Comparaison terminée : 51 Points comparés, 51 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-0_103.6_True_2_1.0_0.0_7.csv'
Comparaison terminée : 51 Points comparés, 51 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-0_103.6_True_3_1.0_0.0_7.csv'
Comparaison terminée : 51 Points comparés, 51 Points identiques (100.00%)
Theta mean: 4.11°, Theta median (robust) : 0.52°, Concentration R: 0.923
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-0_103.6_True_4_1.0_0.0_7.csv'
Comparaison terminée : 51 Points comparés, 51 Points identiques (100.00%)
Theta mean: -5.05°, Theta median (robust) : -1.63°, Concentration R: 0.892
Theta mean: -7.82°, Theta median (robust) : -0.76°, Concentration R: 0.858
Theta mean: 3.99°, Theta median (robust) : -0.59°, Concentration R: 0.900
Theta mean: 1.57°, Theta median (robust) : -0.23°, Concentration R: 0.851
Theta mean: -0.87°, Theta median (robust) : 0.07°, Concentration R: 0.848
Theta mean: -1.38°, Theta median (robust) : 0.78°, Concentration R: 0.933
Theta mean: 3.27°, Theta median (robust) : 0.13°, Concentration R: 0.813
Theta mean: 1.46°, Theta median (robust) : 0.43°, Concentration R: 0.917
Theta mean: 0.58°, Theta median (robust) : 0.03°, Concentration R: 0.896

Log Test : Palm Cpu Stack

Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_True_0_1.0_0.0_7.csv'
Comparaison terminée : 451 Points comparés, 451 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_True_1_1.0_0.0_7.csv'
Comparaison terminée : 451 Points comparés, 451 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_True_2_1.0_0.0_7.csv'
Comparaison terminée : 451 Points comparés, 451 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_True_3_1.0_0.0_7.csv'
Comparaison terminée : 451 Points comparés, 451 Points identiques (100.00%)
Theta mean: 0.04°, Theta median (robust) : 0.07°, Concentration R: 0.884
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_True_4_1.0_0.0_7.csv'
Comparaison terminée : 451 Points comparés, 451 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_False_0_1.0_0.0_7.csv'
Comparaison terminée : 429 Points comparés, 429 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_False_1_1.0_0.0_7.csv'
Comparaison terminée : 429 Points comparés, 429 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_False_2_1.0_0.0_7.csv'
Comparaison terminée : 429 Points comparés, 429 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_False_3_1.0_0.0_7.csv'
Comparaison terminée : 429 Points comparés, 429 Points identiques (100.00%)
Theta mean: -0.33°, Theta median (robust) : -0.04°, Concentration R: 0.887
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_False_4_1.0_0.0_7.csv'
Comparaison terminée : 429 Points comparés, 429 Points identiques (100.00%)

Log Test : Palm Cpu Stack Plane Selection

Theta mean: -0.53°, Theta median (robust) : -0.05°, Concentration R: 0.876
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-plane_select-103.6_True_4_1.0_0.0_7.csv'
Comparaison terminée : 227 Points comparés, 227 Points identiques (100.00%)

Log Test : Palm Cpu Stack Dll Check Quadrant

Theta mean: -1.19°, Theta median (robust) : -0.02°, Concentration R: 0.868
Comparaison terminée : 269 Points comparés, 269 Points identiques (100.00%)

Log Test : Tracking

Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_True_0_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 224 Points comparés, 224 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_True_1_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 223 Points comparés, 223 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_True_2_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 225 Points comparés, 225 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_True_3_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 222 Points comparés, 222 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_True_4_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 222 Points comparés, 222 Points identiques (100.00%)
Fichier de localisations '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_True_5_1.0_0.0_7.csv' indisponible.
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_False_0_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 214 Points comparés, 214 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_False_1_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 212 Points comparés, 212 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_False_2_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 217 Points comparés, 217 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_False_3_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 211 Points comparés, 211 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-tracking-103.6_False_4_1.0_0.0_7-5_2_10_0.5.csv'
Comparaison terminée : 214 Points comparés, 214 Points identiques (100.00%)
Fichier de localisations '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/stack-localizations-103.6_False_5_1.0_0.0_7.csv' indisponible.

Log Test : Blinking Reconnection

Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking-blinking-0.csv'
Comparaison terminée : 18 Points comparés, 18 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking-blinking-1.csv'
Comparaison terminée : 18 Points comparés, 18 Points identiques (100.00%)
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking-blinking-2.csv'
Comparaison terminée : 18 Points comparés, 18 Points identiques (100.00%)

Log Test : Tracks Compute

Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-MSD-True.csv'
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-Fit-True.csv'
Problem with trajectory identifiers, be careful with filtering
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-MSD-False.csv'
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-Fit-False.csv'
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-Fit-1.csv'
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-Fit-2.csv'
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Comparaison avec : '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-Fit-3.csv'
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering
Problem with trajectory identifiers, be careful with filtering

Processing Parsing

Test Name	Status	Duration
Get Meta	✅	3ms
Rearrange Dataframe Columns	✅	4ms
Log10 Dataframe	✅	4ms
Degrees To Radians	✅	1ms
Radians To Degrees	✅	1ms
Wrap Angle	✅	1ms
Manage Theta	✅	1ms
Parse Irregular Array	✅	2ms
Parse Result	✅	19ms
Parse Localization For Tracking	✅	5ms

Log Test : Manage Theta

Theta mean: -16.32°, Theta median (robust) : 0.00°, Concentration R: 0.712

Processing Renderer

Test Name	Status	Duration
Set Size	✅	1ms
Get Localization Colors	✅	6ms
Get Tracks Colors	✅	32ms
Draw Line	✅	1ms
Draw Gaussian	✅	2ms
Localizations	✅	2ms
Localizations Gaussian	✅	2ms
Tracks	✅	2ms

Processing Step

Test Name	Status	Duration
Object Creation	✅	1ms
Prepare Action	✅	19ms

Log Test : Object Creation

Step : Step(group_name='name', keys=['key'], process_func=<function test_object_creation.<locals>.f at 0x7fc481c5a5c0>, filter_func=<function test_object_creation.<locals>.f at 0x7fc481c5a5c0>, allow_dirty=False, apply_filter=True)
Actions : StepAction.Compute,StepAction.Reuse,StepAction.Skip

Processing Visualization

Test Name	Status	Duration
Normalize Data	✅	1ms
Render Hr Image	✅	14ms
Render Hr Image Bad Input	✅	1ms
Render Tracks Image	✅	18ms
Render Tracks Image Bad Input	✅	5ms
Render Roi	✅	40ms
Render Roi Bad Input	✅	2ms
Plot Histogram	✅	927ms
Plot Histogram Bad Input	✅	163ms
Plot Violin	✅	737ms
Plot Violin Bad Input	✅	89ms
Plot Heatmap	✅	473ms
Plot Heatmap Bad Input	✅	82ms

Settings Groups

Test Name	Status	Duration
Base Group	✅	2ms
Batch	✅	204ms
Batch Get Path	✅	5ms
Batch Get Stacks	✅	13ms
Calibration	✅	7ms
Localization	✅	22ms
Gaussian Fit	✅	10ms
Spline Fit	✅	5ms
Beads	✅	5ms
Tracking	✅	4ms
Tracks Blinking Reconnection	✅	6ms
Tracks Computes	✅	7ms
Gallery	✅	5ms
Visualization Hr	✅	7ms
Visualization Graph	✅	5ms
Filters	✅	54ms
Filters L	✅	32ms
Filters T	✅	18ms

Log Test : Batch

- Activate : True
- Files : -1
- Mode : 0

{'Files': -1, 'Mode': 0}

Log Test : Batch Get Stacks

Error when concatenating stacks (they will be processed independently):
ValueError: all the input array dimensions except for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 128 and the array at index 1 has size 256

Log Test : Calibration

- Activate : True
- Pixel Size : 0.32
- Exposure : 0.05
- Intensity : 0.012

{'Pixel Size': 0.32, 'Exposure': 0.05, 'Intensity': 0.012}

Log Test : Localization

- Activate : True
- Preview : True
- Threshold : 90.0
- Auto Threshold : True
- ROI Shape : 0
- ROI Size : 7
- Watershed : True
- Fit : 0
- Gaussian Fit :
  - Activate : True
  - Mode : 0
  - Sigma : 1.0
  - Theta : 0.0
  - Z : False
  - Z max : 500
  - Model : 
- Spline Fit :
  - Activate : True
  - Sensor : 0
  - Variance Map : 
  - File : 

{'Preview': True, 'Threshold': 90.0, 'Auto Threshold': True, 'ROI Shape': 0, 'ROI Size': 7, 'Watershed': True, 'Fit': 0, 'Gaussian Fit Mode': 0, 'Gaussian Fit Sigma': 1.0, 'Gaussian Fit Theta': 0.0, 'Gaussian Fit Z': False, 'Gaussian Fit Z max': 500, 'Gaussian Fit Model': '', 'Spline Fit Sensor': 0, 'Spline Fit Variance Map': '', 'Spline Fit File': ''}

Log Test : Gaussian Fit

- Activate : True
- Mode : 2
- Sigma : 1.0
- Theta : 0.0
- Z : False
- Z max : 500
- Model : 

{'Mode': 2, 'Sigma': 1.0, 'Theta': 0.0, 'Z': False, 'Z max': 500, 'Model': ''}

Log Test : Spline Fit

- Activate : True
- Sensor : 1
- Variance Map : 
- File : 

{'Sensor': 1, 'Variance Map': '', 'File': ''}

Log Test : Beads

- Activate : True
- Max Distance : 2.0
- 3D : False

{'Max Distance': 2.0, '3D': False}

Log Test : Tracking

- Activate : True
- Max Distance : 2.0

{'Max Distance': 2.0}

Log Test : Tracks Blinking Reconnection

- Activate : True
- Mode : 1
- Max Duration : 1
- Max Distance : 1.0

{'Mode': 1, 'Max Duration': 1, 'Max Distance': 1.0}

Log Test : Tracks Computes

- Activate : True
- MSD : True
- Instant Diffusion : False
- Fit Length : 4
- 3D : False
- Log Scale : False
- Fit : 0

{'MSD': True, 'Instant Diffusion': False, 'Fit Length': 4, '3D': False, 'Log Scale': False, 'Fit': 0}

Log Test : Gallery

- Activate : True
- ROI Size : 11
- ROIs Per Line : 30

{'ROI Size': 11, 'ROIs Per Line': 30}

Log Test : Visualization Hr

- Activate : True
- Ratio : 1
- Type : 0
- Source L : 1
- Source T : 1

{'Ratio': 1, 'Type': 0, 'Source L': 1, 'Source T': 1}

Log Test : Visualization Graph

- Activate : True
- Mode : 1
- Source : 0

{'Mode': 1, 'Source': 0}

Log Test : Filters

- Activate : True
- Save : True
- Plane : [1, 100000]
- Localization :
  - Activate : True
  - X : [0, 100000]
  - Y : [0, 100000]
  - Z : [-2000, 2000]
  - Intensity : [0, 10000000]
  - Sigma X : [0.0, 10.0]
  - Sigma Y : [0.0, 10.0]
  - Circularity : [0.0, 1.0]
  - Theta : [-90.0, 90.0]
  - MSE XY : [0.0, 1.0]
  - MSE Z : [0.0, 1.0]
- Tracks :
  - Activate : True
  - Length : [1, 10000]
  - Instant D : [-5.0, 5.0]
  - D Coeff : [-5.0, 5.0]
  - Alpha : [-10.0, 10.0]
  - Speed : [0.0, 1.0]
  - Confinement : [-10.0, 10.0]

{'Save': True, 'Plane': [1, 100000], 'Localization X': [0, 100000], 'Localization Y': [0, 100000], 'Localization Z': [-2000, 2000], 'Localization Intensity': [0, 10000000], 'Localization Sigma X': [0.0, 10.0], 'Localization Sigma Y': [0.0, 10.0], 'Localization Circularity': [0.0, 1.0], 'Localization Theta': [-90.0, 90.0], 'Localization MSE XY': [0.0, 1.0], 'Localization MSE Z': [0.0, 1.0], 'Tracks Length': [1, 10000], 'Tracks Instant D': [-5.0, 5.0], 'Tracks D Coeff': [-5.0, 5.0], 'Tracks Alpha': [-10.0, 10.0], 'Tracks Speed': [0.0, 1.0], 'Tracks Confinement': [-10.0, 10.0]}

Log Test : Filters L

- Activate : True
- X : [2, 9]
- Y : [0, 100000]
- Z : [-2000, 2000]
- Intensity : [0, 10000000]
- Sigma X : [0.0, 10.0]
- Sigma Y : [0.0, 10.0]
- Circularity : [0.0, 1.0]
- Theta : [-90.0, 90.0]
- MSE XY : [0.0, 1.0]
- MSE Z : [0.0, 1.0]

{'X': [2, 9], 'Y': [0, 100000], 'Z': [-2000, 2000], 'Intensity': [0, 10000000], 'Sigma X': [0.0, 10.0], 'Sigma Y': [0.0, 10.0], 'Circularity': [0.0, 1.0], 'Theta': [-90.0, 90.0], 'MSE XY': [0.0, 1.0], 'MSE Z': [0.0, 1.0]}

Log Test : Filters T

- Activate : True
- Length : [2, 3]
- Instant D : [-5.0, 5.0]
- D Coeff : [-5.0, 5.0]
- Alpha : [-10.0, 10.0]
- Speed : [0.0, 1.0]
- Confinement : [-10.0, 10.0]

{'Length': [2, 3], 'Instant D': [-5.0, 5.0], 'D Coeff': [-5.0, 5.0], 'Alpha': [-10.0, 10.0], 'Speed': [0.0, 1.0], 'Confinement': [-10.0, 10.0]}

Settings Settings

Test Name	Status	Duration
Settings	✅	94ms
Settings Group Getter	✅	45ms
Settings Signal	✅	66ms

Settings Signal

Test Name	Status	Duration
Connect And Emit Direct	✅	1ms
Disconnect	✅	1ms
Block Simple Coalescence Last Value	✅	1ms
Block Without Emits No Output	✅	1ms
Nested Blocks Emit Once At Outer Exit	✅	1ms
Emit Default None Coalesced	✅	1ms
Block Flags Reset After Flush	✅	1ms
Blocked Returns Context Manager Instance	✅	1ms
Internal Block Begin End Paths	✅	1ms
Coalescence Overwrite Multiple Times	✅	1ms
Emit Direct After Previous Block	✅	1ms

Settings Types

Test Name	Status	Duration
Base Setting	✅	2ms
Create Setting From Dict	✅	6ms
Create Setting From Dict Fail	✅	1ms
Spin Int	✅	3ms
Spin Float	✅	3ms
Check Box	✅	2ms
Combo	✅	3ms
Browse File	✅	3ms
File List	✅	4ms
Check Range Int	✅	5ms
Check Range Float	✅	5ms
Button	✅	2ms

Tools Fileio

Test Name	Status	Duration
Add Extension	✅	1ms
Add Suffix	✅	1ms
Get Timestamp For Files	✅	1ms
Get Last File	✅	2ms
Extract Suffix	✅	1ms
Cleanup Process	✅	2ms
Load Dll	✅	1ms
Save Json	✅	1ms
Open Json	✅	1ms
Open Json Bad File	✅	1ms
Save Tif	✅	2ms
Save Tif 2D	✅	2ms
Save Tif Bad Stack	✅	1ms
Open Tif	✅	5ms
Open Tif Bad File	✅	1ms
Save Png	✅	6ms
Save Png Color	✅	11ms
Save Png Bad Sample	✅	1ms
Open Calibration Mat Bad File	✅	1ms
Open Calibration Mat	✅	4ms

Log Test : Get Timestamp For Files

Timestamp with hour : 20260505_135533
Timestamp without hour : 20260505

Log Test : Get Last File

/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/File-03.txt
/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/File-03.txt

Log Test : Load Dll

Unable to load the DLL 'PALMTracer_File.so':
 /home/runner/work/palm-tracer/palm-tracer/palm_tracer/DLL/PALMTracer_File.so: cannot open shared object file: No such file or directory

Tools Filemigrator

Test Name	Status	Duration
Open	✅	3ms
Update Meta	✅	4ms
Open Old File	✅	4ms
Open Old Irregular File	✅	4ms
Column Migrator	✅	3ms
Analyze	✅	3ms
Migrate	✅	299ms

Log Test : Analyze

.

Tools Logger

Test Name	Status	Duration
Logger	✅	6ms
Logger Bad Use	✅	2ms
Logger With Use	✅	2ms

Tools Monitoring

Test Name	Status	Duration
Monitoring	✅	1.20s
Monitoring Save	✅	6.74s

Log Test : Monitoring

6 entrées.
Timestamps : [0.0, 0.2, 0.41, 0.61, 0.82, 1.0]
CPU Usage : [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
GPU Usage : [0, 0, 0, 0, 0, 0]
Memory Usage : [669.5390625, 669.54296875, 669.5546875, 669.5625, 669.57421875, 669.5703125]
Disk Usage : [0, 0.0, 0.0, 0.0, 0.0, 0.0]

Log Test : Monitoring Save

Simulating high CPU usage for 2 seconds...
CPU simulation complete.
Allocating 50 MB of memory...
Memory allocated. Holding for 2 seconds...
Releasing memory.
Writing a file of size 1 MB...
File written. Holding for 2 seconds...
Deleting the file...
Disk I/O simulation complete.
Kaleido doesn't work so well need update. No Image Saved.

Tools Ui

Test Name	Status	Duration
Builders	✅	5ms
Builders Spin	✅	2ms
Sync Spin	✅	2ms
Sync Button Group	✅	2ms
Print Error	✅	1ms
Print Warning	✅	1ms
Print Success	✅	1ms
Format Time	✅	1ms

Log Test : Print Error

Message d'erreur

Log Test : Print Warning

Message d'avertissement

Log Test : Print Success

Message de succes

Ui Alignmentwidget

Test Name	Status	Duration
Widget Creation	✅	28ms
Bad Load Tif	✅	6ms
Bad Load Coef	✅	38ms
Bad Compute	✅	5ms
Compute	✅	7ms
Bad Align	✅	6ms
Align	✅	31ms

Ui Astigmatism3Dwidget

Test Name	Status	Duration
Widget Creation	✅	1.51s
Bad Load Loc	✅	138ms
Bad Load Model	✅	134ms
Bad Compute	✅	133ms
Check Loc	✅	188ms
Compute	✅	380ms
Compute Mean Beads	✅	381ms
Compute Remove Bead Col	✅	354ms
Compute Remove Multi	✅	367ms
Compute Z	✅	377ms
Compute Center Z	✅	387ms
Compute Bad Model	✅	376ms
Bad Estimate	✅	133ms
Estimate	✅	209ms
Estimate Backup	✅	212ms
Sync Spin	✅	173ms
Download	✅	193ms

Log Test : Download

/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref

Ui Baseplotlywidget

Test Name	Status	Duration
Creation	✅	39ms
Update Plotly	✅	46ms
Update Plotly No Js	✅	50ms
Download Plotly	✅	46ms
Export Plotly	✅	47ms

Log Test : Download Plotly

/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/output
/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/output

Log Test : Export Plotly

No figures to export.

Ui Filemigratorwidget

Test Name	Status	Duration
Widget Creation	✅	7ms
Bad Load	✅	7ms
Mirgate	✅	31ms

Ui Graphviewer

Test Name	Status	Duration
Widget Creation	✅	190ms
Add Stack	✅	259ms
Actualize	✅	359ms
Reset Filtered	✅	251ms
Update Filtered	✅	307ms
Update Plot	✅	630ms
Dual Source	✅	402ms
Get Plot Data	✅	793ms
Tracks Source	✅	197ms

Log Test : Add Stack

No valid settings file to load.

Ui Viewerhrwidget

Test Name	Status	Duration
Widget Creation	✅	1.78s
Add Stack	✅	1.40s
Change Source	✅	1.43s
Actualize	✅	1.43s
Reset Filtered	✅	1.47s
Update Filtered	✅	1.50s
Save	✅	1.51s
Screenshot	✅	1.47s
Crop	✅	1.48s
Generate Bad	✅	1.48s
Generate	✅	1.53s
Generate Drift	✅	1.55s

Log Test : Save

INFO: Image file saved successfully.

Log Test : Screenshot

INFO: Screenshot saved successfully.

Log Test : Generate

[05-05-2026 13:56:07] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_135607.log
[05-05-2026 13:56:07] Start Processing.
[05-05-2026 13:56:07] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 13:56:07] Meta file saved.
[05-05-2026 13:56:07] Settings saved.
[05-05-2026 13:56:07] Localization disabled.
[05-05-2026 13:56:07] Beads Extraction disabled.
[05-05-2026 13:56:07] Tracking disabled.
[05-05-2026 13:56:07] Blinking Reconnection disabled.
[05-05-2026 13:56:07] Tracks Compute disabled.
[05-05-2026 13:56:07] Gallery generation disabled.
[05-05-2026 13:56:07] Graphical visualization disabled.
[05-05-2026 13:56:07] High-resolution visualization disabled.
[05-05-2026 13:56:07] Processing complete.
[05-05-2026 13:56:07] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_135607.log
Loading setting file '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/settings-20260505_135607.json'.
   Loading files from the '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer' folder with the timestamp 20260505_135607.
    File 'localizations' loaded successfully.
   File 'localizations_filtered' not found.
    File 'localizations_corrected' not found.
   File 'localizations_corrected_filtered' not found.
  File 'beads' loaded successfully.
   File 'tracking' loaded successfully.
        File 'tracking_filtered' not found.
 File 'tracking_reconnected' not found.
      File 'tracking_reconnected_filtered' not found.
     File 'tracking_MSD' not found.
      File 'tracking_MSD_filtered' not found.
     File 'tracking_InstantD' not found.
 File 'tracking_InstantD_filtered' not found.
        File 'tracking_Fit' not found.
      File 'tracking_Fit_filtered' not found.
     Stack loaded successfully (size: (10, 128, 256)).

Ui Widget

Test Name	Status	Duration
Widget Creation	✅	1.47s
Widget On Load Setting	✅	1.50s
Widget Reset Setting	✅	1.48s
Widget Reset Layer	✅	2.04s
Widget Get Actual Image	✅	1.73s
Widget Add Detection Layers	✅	4.26s
Widget Preview	✅	2.39s
Widget Roi Filter Layer	✅	2.03s
Widget Auto Threshold	✅	1.76s
Widget Thread Process	✅	1.91s
Widget Keyblocker	✅	1.78s
Viewer3D	✅	1.92s

Log Test : Widget Get Actual Image

INFO: Loaded /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.

Log Test : Widget Roi Filter Layer

INFO: Loaded /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.

Log Test : Widget Thread Process

INFO: Loaded /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.
[05-05-2026 13:56:29] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_135629.log
[05-05-2026 13:56:29] Start Processing.
[05-05-2026 13:56:29] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 13:56:29] Meta file saved.
[05-05-2026 13:56:29] Settings saved.
[05-05-2026 13:56:29] Localization disabled.
[05-05-2026 13:56:29] Beads Extraction disabled.
[05-05-2026 13:56:29] Tracking disabled.
[05-05-2026 13:56:29] Blinking Reconnection disabled.
[05-05-2026 13:56:29] Tracks Compute disabled.
[05-05-2026 13:56:29] Gallery generation disabled.
[05-05-2026 13:56:29] Graphical visualization disabled.
[05-05-2026 13:56:29] High-resolution visualization disabled.
[05-05-2026 13:56:29] Processing complete.
[05-05-2026 13:56:29] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_135629.log
Auto Threshold: 63.95

Log Test : Widget Keyblocker

INFO: Loading the setting file '/home/runner/.palm_tracer/settings.json'.
INFO: Loaded /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.

Log Test : Viewer3D

WARNING: The file must contain the columns X, Y, Z, and Integrated Intensity.