Test Report Ci Ubuntu-Latest 3.10

Environnement

Python	3.10.20
Platform	Linux-6.17.0-1010-azure-x86_64-with-glibc2.39
CI	true
System	Linux
CPU	AMD EPYC 9V74 80-Core Processor (2.78 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 0:01:39s on 04/05/2026 at 14:27:24

Monitoring

Test Cases

Palmtracer

Test Name	Status	Duration
Reset Result	✅	64ms
Getter Localization	✅	55ms
Getter Beads	✅	41ms
Getter Tracks	✅	45ms
Getter Tracks Compute	✅	42ms
Get Status	✅	45ms
Getter Path	✅	66ms
Getter Stack	✅	39ms
Getter Suffix	✅	40ms
Load Bad Dll	✅	41ms
Load Nothing	✅	43ms
Load	✅	144ms
Process No Input	✅	41ms
Process Nothing	✅	165ms
Process Bad Dll	✅	43ms
Process Multiple Stack	✅	100ms
Process Localization	✅	83ms
Process Localization Z	✅	195ms
Process Localization Spline Bad	✅	54ms
Process Localization Spline	✅	117ms
Process Beads Extraction No Beads	✅	94ms
Process Plane Discontinuous	✅	45ms
Process Beads Extraction	✅	125ms
Process Tracking	✅	304ms
Process Tracking Blinking	✅	114ms
Process Tracks Compute	✅	2.29s
Process Gallery	✅	122ms
Process Visualization Graph	✅	5.11s
Process Visualization Hr	✅	1.31s
Process All	✅	5.15s
Reset Filtered	✅	51ms
Update Filtered	✅	124ms
Save Filtered	✅	65ms
Filter Localization	✅	1.24s
Filter Tracks Compute	✅	2.30s
Add Color	✅	66ms
Get Astigmatism Model	✅	59ms

Log Test : Update Filtered

[04-05-2026 14:26:01] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_142601.log
[04-05-2026 14:26:01] Start Processing.
[04-05-2026 14:26:01] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[04-05-2026 14:26:01] Meta file saved.
[04-05-2026 14:26:01] Settings saved.
[04-05-2026 14:26:01] Localization load previous result (Timestamp : 20260101_000000).
[04-05-2026 14:26:01]        File 'localizations-20260101_000000.csv' loaded successfully, 451 row(s) found.
[04-05-2026 14:26:01] Beads Extraction disabled.
[04-05-2026 14:26:01] Tracking disabled.
[04-05-2026 14:26:01] Blinking Reconnection disabled.
[04-05-2026 14:26:01] Tracks Compute disabled.
[04-05-2026 14:26:01] Gallery generation disabled.
[04-05-2026 14:26:01] Graphical visualization disabled.
[04-05-2026 14:26:01] High-resolution visualization disabled.
[04-05-2026 14:26:01] Processing complete.
[04-05-2026 14:26:01] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_142601.log

Processing Astigmatism3D

Test Name	Status	Duration
Get Z From Planes	✅	1ms
Get Z From Step	✅	2ms
Remove Multi Loc	✅	13ms
Sigma Model	✅	1ms
Model Validity	✅	2ms
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	✅	5ms
Extract Beads No Match Returns Empty	✅	5ms
Assign Tracks No Pairs	✅	1ms
Assign Tracks Skip Used Track	✅	1ms
Extract Beads	✅	48ms
Remove Beads	✅	9ms
Get Drift Bad Input	✅	5ms
Get Drift	✅	21ms
Apply Drift Bad Input	✅	2ms
Remove Drift	✅	13ms
Chain Drift	✅	20ms
Drift Correction	✅	25ms
Median Filter Centered	✅	5ms

Processing Filtering

Test Name	Status	Duration
Filter Bad	✅	31ms
Localization	✅	58ms
Tracking	✅	28ms
Tracks Compute	✅	40ms

Processing Gallery

Test Name	Status	Duration
Make Gallery	✅	8ms

Processing Grapher

Test Name	Status	Duration
Blank	✅	224ms
Histogram	✅	605ms
Scatter	✅	376ms
Cloud	✅	786ms
Astigmatism3D	✅	367ms

Processing Palm

Test Name	Status	Duration
Palm Dll Valid	✅	2ms
Palm Cpu Empty Result	✅	5ms
Palm Cpu Image	✅	1.04s
Palm Cpu Stack	✅	3.01s
Palm Cpu Stack Plane Selection	✅	179ms
Palm Cpu Stack Dll Check Quadrant	✅	236ms
Cpu Auto Threshold	✅	59ms
Tracking	✅	5.86s
Blinking Reconnection	✅	239ms
Tracks Compute	✅	71ms
Align	✅	92ms
Wavelett	✅	62ms
Astigmatism 3D Calibration	✅	10ms
Astigmatism 3D Estimation	✅	8ms

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	✅	3ms
Log10 Dataframe	✅	3ms
Degrees To Radians	✅	1ms
Radians To Degrees	✅	1ms
Wrap Angle	✅	1ms
Manage Theta	✅	1ms
Parse Irregular Array	✅	2ms
Parse Result	✅	17ms
Parse Localization For Tracking	✅	4ms

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	✅	5ms
Get Tracks Colors	✅	28ms
Draw Line	✅	1ms
Draw Gaussian	✅	2ms
Localizations	✅	1ms
Localizations Gaussian	✅	2ms
Tracks	✅	1ms

Processing Step

Test Name	Status	Duration
Object Creation	✅	1ms
Prepare Action	✅	16ms

Log Test : Object Creation

Step : Step(group_name='name', keys=['key'], process_func=<function test_object_creation.<locals>.f at 0x7fb2da052290>, filter_func=<function test_object_creation.<locals>.f at 0x7fb2da052290>, 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	✅	19ms
Render Tracks Image Bad Input	✅	4ms
Render Roi	✅	39ms
Render Roi Bad Input	✅	2ms
Plot Histogram	✅	846ms
Plot Histogram Bad Input	✅	160ms
Plot Violin	✅	709ms
Plot Violin Bad Input	✅	79ms
Plot Heatmap	✅	449ms
Plot Heatmap Bad Input	✅	79ms

Settings Groups

Test Name	Status	Duration
Base Group	✅	2ms
Batch	✅	208ms
Batch Get Path	✅	5ms
Batch Get Stacks	✅	14ms
Calibration	✅	6ms
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	✅	55ms
Filters L	✅	28ms
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	✅	95ms
Settings Group Getter	✅	44ms
Settings Signal	✅	71ms

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	✅	4ms
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	✅	4ms
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	✅	3ms

Log Test : Get Timestamp For Files

Timestamp with hour : 20260504_142622
Timestamp without hour : 20260504

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	✅	3ms
Column Migrator	✅	3ms
Analyze	✅	3ms
Migrate	✅	236ms

Log Test : Analyze

.

Tools Logger

Test Name	Status	Duration
Logger	✅	7ms
Logger Bad Use	✅	2ms
Logger With Use	✅	3ms

Tools Monitoring

Test Name	Status	Duration
Monitoring	✅	1.19s
Monitoring Save	✅	6.89s

Log Test : Monitoring

6 entrées.
Timestamps : [0.0, 0.21, 0.41, 0.62, 0.83, 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 : [660.8203125, 660.82421875, 660.8359375, 660.84375, 660.85546875, 660.85546875]
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	✅	31ms
Bad Load Tif	✅	6ms
Bad Load Coef	✅	53ms
Bad Compute	✅	5ms
Compute	✅	7ms
Bad Align	✅	6ms
Align	✅	31ms

Ui Astigmatism3Dwidget

Test Name	Status	Duration
Widget Creation	✅	1.11s
Bad Load Loc	✅	139ms
Bad Load Model	✅	134ms
Bad Compute	✅	131ms
Check Loc	✅	185ms
Compute	✅	362ms
Compute Mean Beads	✅	365ms
Compute Remove Bead Col	✅	342ms
Compute Remove Multi	✅	705ms
Compute Z	✅	364ms
Compute Center Z	✅	358ms
Compute Bad Model	✅	366ms
Bad Estimate	✅	133ms
Estimate	✅	200ms
Estimate Backup	✅	214ms
Sync Spin	✅	170ms
Download	✅	188ms

Log Test : Download

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

Ui Baseplotlywidget

Test Name	Status	Duration
Creation	✅	38ms
Update Plotly	✅	45ms
Update Plotly No Js	✅	44ms
Download Plotly	✅	46ms
Export Plotly	✅	48ms

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	✅	6ms
Mirgate	✅	27ms

Ui Graphviewer

Test Name	Status	Duration
Widget Creation	✅	191ms
Add Stack	✅	247ms
Actualize	✅	346ms
Reset Filtered	✅	243ms
Update Filtered	✅	311ms
Update Plot	✅	617ms
Dual Source	✅	406ms
Get Plot Data	✅	766ms
Tracks Source	✅	190ms

Log Test : Add Stack

No valid settings file to load.

Ui Viewerhrwidget

Test Name	Status	Duration
Widget Creation	✅	1.63s
Add Stack	✅	1.40s
Change Source	✅	1.41s
Actualize	✅	1.40s
Reset Filtered	✅	1.43s
Update Filtered	✅	1.42s
Save	✅	1.47s
Screenshot	✅	1.53s
Crop	✅	1.46s
Generate Bad	✅	1.47s
Generate	✅	1.52s
Generate Drift	✅	1.52s

Log Test : Save

INFO: Image file saved successfully.

Log Test : Screenshot

INFO: Screenshot saved successfully.

Log Test : Generate

[04-05-2026 14:26:55] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_142655.log
[04-05-2026 14:26:55] Start Processing.
[04-05-2026 14:26:55] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[04-05-2026 14:26:55] Meta file saved.
[04-05-2026 14:26:55] Settings saved.
[04-05-2026 14:26:55] Localization disabled.
[04-05-2026 14:26:55] Beads Extraction disabled.
[04-05-2026 14:26:55] Tracking disabled.
[04-05-2026 14:26:55] Blinking Reconnection disabled.
[04-05-2026 14:26:55] Tracks Compute disabled.
[04-05-2026 14:26:55] Gallery generation disabled.
[04-05-2026 14:26:55] Graphical visualization disabled.
[04-05-2026 14:26:55] High-resolution visualization disabled.
[04-05-2026 14:26:55] Processing complete.
[04-05-2026 14:26:55] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_142655.log
Loading setting file '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/settings-20260504_142655.json'.
   Loading files from the '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer' folder with the timestamp 20260504_142655.
    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	✅	1.44s
Widget On Load Setting	✅	1.55s
Widget Reset Setting	✅	1.57s
Widget Reset Layer	✅	2.14s
Widget Get Actual Image	✅	1.75s
Widget Add Detection Layers	✅	4.13s
Widget Preview	✅	2.35s
Widget Roi Filter Layer	✅	1.99s
Widget Auto Threshold	✅	1.76s
Widget Thread Process	✅	1.88s
Widget Keyblocker	✅	1.79s
Viewer3D	✅	1.88s

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.
[04-05-2026 14:27:17] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_142717.log
[04-05-2026 14:27:17] Start Processing.
[04-05-2026 14:27:17] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[04-05-2026 14:27:17] Meta file saved.
[04-05-2026 14:27:17] Settings saved.
[04-05-2026 14:27:17] Localization disabled.
[04-05-2026 14:27:17] Beads Extraction disabled.
[04-05-2026 14:27:17] Tracking disabled.
[04-05-2026 14:27:17] Blinking Reconnection disabled.
[04-05-2026 14:27:17] Tracks Compute disabled.
[04-05-2026 14:27:17] Gallery generation disabled.
[04-05-2026 14:27:17] Graphical visualization disabled.
[04-05-2026 14:27:17] High-resolution visualization disabled.
[04-05-2026 14:27:17] Processing complete.
[04-05-2026 14:27:17] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_142717.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.