Test Report Ci Ubuntu-Latest 3.11

Environnement

Python	3.11.15
Platform	Linux-6.17.0-1010-azure-x86_64-with-glibc2.39
CI	true
System	Linux
CPU	AMD EPYC 7763 64-Core Processor (3.02 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 07:31:59

Monitoring

Test Cases

Palmtracer

Test Name	Status	Duration
Reset Result	✅	63ms
Getter Localization	✅	48ms
Getter Beads	✅	44ms
Getter Tracks	✅	57ms
Getter Tracks Compute	✅	42ms
Get Status	✅	44ms
Getter Path	✅	47ms
Getter Stack	✅	48ms
Getter Suffix	✅	44ms
Load Bad Dll	✅	74ms
Load Nothing	✅	42ms
Load	✅	108ms
Process No Input	✅	42ms
Process Nothing	✅	156ms
Process Bad Dll	✅	67ms
Process Multiple Stack	✅	73ms
Process Localization	✅	85ms
Process Localization Z	✅	195ms
Process Localization Spline Bad	✅	55ms
Process Localization Spline	✅	122ms
Process Beads Extraction No Beads	✅	98ms
Process Plane Discontinuous	✅	46ms
Process Beads Extraction	✅	140ms
Process Tracking	✅	336ms
Process Tracking Blinking	✅	116ms
Process Tracks Compute	✅	2.37s
Process Gallery	✅	133ms
Process Visualization Graph	✅	5.47s
Process Visualization Hr	✅	1.32s
Process All	✅	5.59s
Reset Filtered	✅	50ms
Update Filtered	✅	124ms
Save Filtered	✅	56ms
Filter Localization	✅	1.24s
Filter Tracks Compute	✅	2.32s
Add Color	✅	91ms
Get Astigmatism Model	✅	50ms

Log Test : Update Filtered

[05-05-2026 07:30:33] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073033.log
[05-05-2026 07:30:33] Start Processing.
[05-05-2026 07:30:33] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 07:30:33] Meta file saved.
[05-05-2026 07:30:33] Settings saved.
[05-05-2026 07:30:33] Localization load previous result (Timestamp : 20260101_000000).
[05-05-2026 07:30:33]        File 'localizations-20260101_000000.csv' loaded successfully, 451 row(s) found.
[05-05-2026 07:30:33] Beads Extraction disabled.
[05-05-2026 07:30:33] Tracking disabled.
[05-05-2026 07:30:33] Blinking Reconnection disabled.
[05-05-2026 07:30:33] Tracks Compute disabled.
[05-05-2026 07:30:33] Gallery generation disabled.
[05-05-2026 07:30:33] Graphical visualization disabled.
[05-05-2026 07:30:33] High-resolution visualization disabled.
[05-05-2026 07:30:33] Processing complete.
[05-05-2026 07:30:33] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073033.log

Processing Astigmatism3D

Test Name	Status	Duration
Get Z From Planes	✅	1ms
Get Z From Step	✅	1ms
Remove Multi Loc	✅	12ms
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	✅	5ms
Extract Beads No Match Returns Empty	✅	5ms
Assign Tracks No Pairs	✅	1ms
Assign Tracks Skip Used Track	✅	1ms
Extract Beads	✅	56ms
Remove Beads	✅	9ms
Get Drift Bad Input	✅	6ms
Get Drift	✅	26ms
Apply Drift Bad Input	✅	2ms
Remove Drift	✅	17ms
Chain Drift	✅	27ms
Drift Correction	✅	29ms
Median Filter Centered	✅	6ms

Processing Filtering

Test Name	Status	Duration
Filter Bad	✅	34ms
Localization	✅	43ms
Tracking	✅	32ms
Tracks Compute	✅	48ms

Processing Gallery

Test Name	Status	Duration
Make Gallery	✅	7ms

Processing Grapher

Test Name	Status	Duration
Blank	✅	319ms
Histogram	✅	625ms
Scatter	✅	370ms
Cloud	✅	791ms
Astigmatism3D	✅	360ms

Processing Palm

Test Name	Status	Duration
Palm Dll Valid	✅	2ms
Palm Cpu Empty Result	✅	6ms
Palm Cpu Image	✅	1.19s
Palm Cpu Stack	✅	4.77s
Palm Cpu Stack Plane Selection	✅	268ms
Palm Cpu Stack Dll Check Quadrant	✅	350ms
Cpu Auto Threshold	✅	58ms
Tracking	✅	7.29s
Blinking Reconnection	✅	250ms
Tracks Compute	✅	73ms
Align	✅	94ms
Wavelett	✅	62ms
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	✅	4ms
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	✅	31ms
Draw Line	✅	1ms
Draw Gaussian	✅	2ms
Localizations	✅	1ms
Localizations Gaussian	✅	3ms
Tracks	✅	2ms

Processing Step

Test Name	Status	Duration
Object Creation	✅	1ms
Prepare Action	✅	18ms

Log Test : Object Creation

Step : Step(group_name='name', keys=['key'], process_func=<function test_object_creation.<locals>.f at 0x7f3f827de980>, filter_func=<function test_object_creation.<locals>.f at 0x7f3f827de980>, 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	✅	16ms
Render Hr Image Bad Input	✅	2ms
Render Tracks Image	✅	19ms
Render Tracks Image Bad Input	✅	5ms
Render Roi	✅	41ms
Render Roi Bad Input	✅	2ms
Plot Histogram	✅	939ms
Plot Histogram Bad Input	✅	168ms
Plot Violin	✅	749ms
Plot Violin Bad Input	✅	88ms
Plot Heatmap	✅	470ms
Plot Heatmap Bad Input	✅	84ms

Settings Groups

Test Name	Status	Duration
Base Group	✅	2ms
Batch	✅	206ms
Batch Get Path	✅	6ms
Batch Get Stacks	✅	13ms
Calibration	✅	8ms
Localization	✅	26ms
Gaussian Fit	✅	12ms
Spline Fit	✅	7ms
Beads	✅	5ms
Tracking	✅	4ms
Tracks Blinking Reconnection	✅	7ms
Tracks Computes	✅	9ms
Gallery	✅	6ms
Visualization Hr	✅	10ms
Visualization Graph	✅	6ms
Filters	✅	64ms
Filters L	✅	33ms
Filters T	✅	21ms

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	✅	113ms
Settings Group Getter	✅	52ms
Settings Signal	✅	73ms

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	✅	7ms
Create Setting From Dict Fail	✅	1ms
Spin Int	✅	3ms
Spin Float	✅	3ms
Check Box	✅	3ms
Combo	✅	3ms
Browse File	✅	4ms
File List	✅	6ms
Check Range Int	✅	6ms
Check Range Float	✅	7ms
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	✅	2ms
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	✅	8ms
Save Png Color	✅	13ms
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_073058
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	✅	4ms
Migrate	✅	290ms

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	✅	6.63s

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 : [661.1640625, 661.1796875, 661.18359375, 661.1953125, 661.203125, 661.19921875]
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	✅	3ms
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	✅	8ms
Bad Load Tif	✅	6ms
Bad Load Coef	✅	87ms
Bad Compute	✅	6ms
Compute	✅	7ms
Bad Align	✅	7ms
Align	✅	31ms

Ui Astigmatism3Dwidget

Test Name	Status	Duration
Widget Creation	✅	1.28s
Bad Load Loc	✅	134ms
Bad Load Model	✅	131ms
Bad Compute	✅	128ms
Check Loc	✅	178ms
Compute	✅	363ms
Compute Mean Beads	✅	369ms
Compute Remove Bead Col	✅	351ms
Compute Remove Multi	✅	346ms
Compute Z	✅	683ms
Compute Center Z	✅	361ms
Compute Bad Model	✅	368ms
Bad Estimate	✅	130ms
Estimate	✅	193ms
Estimate Backup	✅	217ms
Sync Spin	✅	168ms
Download	✅	184ms

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	✅	44ms
Update Plotly No Js	✅	44ms
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	✅	8ms
Bad Load	✅	7ms
Mirgate	✅	32ms

Ui Graphviewer

Test Name	Status	Duration
Widget Creation	✅	191ms
Add Stack	✅	258ms
Actualize	✅	370ms
Reset Filtered	✅	247ms
Update Filtered	✅	312ms
Update Plot	✅	598ms
Dual Source	✅	394ms
Get Plot Data	✅	757ms
Tracks Source	✅	196ms

Log Test : Add Stack

No valid settings file to load.

Ui Viewerhrwidget

Test Name	Status	Duration
Widget Creation	✅	1.66s
Add Stack	✅	1.42s
Change Source	✅	1.42s
Actualize	✅	1.41s
Reset Filtered	✅	1.46s
Update Filtered	✅	1.47s
Save	✅	1.46s
Screenshot	✅	1.46s
Crop	✅	1.46s
Generate Bad	✅	1.49s
Generate	✅	1.53s
Generate Drift	✅	1.52s

Log Test : Save

INFO: Image file saved successfully.

Log Test : Screenshot

INFO: Screenshot saved successfully.

Log Test : Generate

[05-05-2026 07:31:31] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073131.log
[05-05-2026 07:31:31] Start Processing.
[05-05-2026 07:31:31] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 07:31:31] Meta file saved.
[05-05-2026 07:31:31] Settings saved.
[05-05-2026 07:31:31] Localization disabled.
[05-05-2026 07:31:31] Beads Extraction disabled.
[05-05-2026 07:31:31] Tracking disabled.
[05-05-2026 07:31:31] Blinking Reconnection disabled.
[05-05-2026 07:31:31] Tracks Compute disabled.
[05-05-2026 07:31:31] Gallery generation disabled.
[05-05-2026 07:31:31] Graphical visualization disabled.
[05-05-2026 07:31:31] High-resolution visualization disabled.
[05-05-2026 07:31:31] Processing complete.
[05-05-2026 07:31:31] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073131.log
Loading setting file '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/settings-20260505_073131.json'.
   Loading files from the '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer' folder with the timestamp 20260505_073131.
    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	✅	1.43s
Widget On Load Setting	✅	1.43s
Widget Reset Setting	✅	1.44s
Widget Reset Layer	✅	2.09s
Widget Get Actual Image	✅	1.69s
Widget Add Detection Layers	✅	4.45s
Widget Preview	✅	2.52s
Widget Roi Filter Layer	✅	2.00s
Widget Auto Threshold	✅	1.76s
Widget Thread Process	✅	1.87s
Widget Keyblocker	✅	1.78s
Viewer3D	✅	1.85s

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 07:31:53] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073153.log
[05-05-2026 07:31:53] Start Processing.
[05-05-2026 07:31:53] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 07:31:53] Meta file saved.
[05-05-2026 07:31:53] Settings saved.
[05-05-2026 07:31:53] Localization disabled.
[05-05-2026 07:31:53] Beads Extraction disabled.
[05-05-2026 07:31:53] Tracking disabled.
[05-05-2026 07:31:53] Blinking Reconnection disabled.
[05-05-2026 07:31:53] Tracks Compute disabled.
[05-05-2026 07:31:53] Gallery generation disabled.
[05-05-2026 07:31:53] Graphical visualization disabled.
[05-05-2026 07:31:53] High-resolution visualization disabled.
[05-05-2026 07:31:53] Processing complete.
[05-05-2026 07:31:53] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073153.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.