Test Report Ci Ubuntu-Latest 3.12

Environnement

Python

3.12.13

Platform

Linux-6.17.0-1010-azure-x86_64-with-glibc2.39

CI

true

System

Linux

CPU

AMD EPYC 7763 64-Core Processor (3.24 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 0:01:49s on 05/05/2026 at 07:30:53

Monitoring

Test Cases

Palmtracer

Test Name

Status

Duration

Reset Result

✅

70ms

Getter Localization

✅

50ms

Getter Beads

✅

48ms

Getter Tracks

✅

51ms

Getter Tracks Compute

✅

69ms

Get Status

✅

62ms

Getter Path

✅

53ms

Getter Stack

✅

50ms

Getter Suffix

✅

49ms

Load Bad Dll

✅

75ms

Load Nothing

✅

57ms

Load

✅

136ms

Process No Input

✅

47ms

Process Nothing

✅

223ms

Process Bad Dll

✅

73ms

Process Multiple Stack

✅

109ms

Process Localization

✅

97ms

Process Localization Z

✅

229ms

Process Localization Spline Bad

✅

65ms

Process Localization Spline

✅

138ms

Process Beads Extraction No Beads

✅

110ms

Process Plane Discontinuous

✅

51ms

Process Beads Extraction

✅

167ms

Process Tracking

✅

385ms

Process Tracking Blinking

✅

143ms

Process Tracks Compute

✅

2.38s

Process Gallery

✅

155ms

Process Visualization Graph

✅

5.63s

Process Visualization Hr

✅

1.38s

Process All

✅

5.85s

Reset Filtered

✅

48ms

Update Filtered

✅

139ms

Save Filtered

✅

60ms

Filter Localization

✅

1.28s

Filter Tracks Compute

✅

2.35s

Add Color

✅

86ms

Get Astigmatism Model

✅

59ms
Log Test : Update Filtered 
[05-05-2026 07:29:23] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_072923.log
[05-05-2026 07:29:23] Start Processing.
[05-05-2026 07:29:23] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 07:29:23] Meta file saved.
[05-05-2026 07:29:23] Settings saved.
[05-05-2026 07:29:23] Localization load previous result (Timestamp : 20260101_000000).
[05-05-2026 07:29:23]        File 'localizations-20260101_000000.csv' loaded successfully, 451 row(s) found.
[05-05-2026 07:29:23] Beads Extraction disabled.
[05-05-2026 07:29:23] Tracking disabled.
[05-05-2026 07:29:23] Blinking Reconnection disabled.
[05-05-2026 07:29:23] Tracks Compute disabled.
[05-05-2026 07:29:23] Gallery generation disabled.
[05-05-2026 07:29:23] Graphical visualization disabled.
[05-05-2026 07:29:23] High-resolution visualization disabled.
[05-05-2026 07:29:23] Processing complete.
[05-05-2026 07:29:23] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_072923.log

Processing Astigmatism3D

Test Name

Status

Duration

Get Z From Planes

✅

2ms

Get Z From Step

✅

1ms

Remove Multi Loc

✅

14ms

Sigma Model

✅

1ms

Model Validity

✅

4ms

Model Projection Validity

✅

16ms

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

✅

6ms

Extract Beads No Match Returns Empty

✅

7ms

Assign Tracks No Pairs

✅

1ms

Assign Tracks Skip Used Track

✅

1ms

Extract Beads

✅

62ms

Remove Beads

✅

11ms

Get Drift Bad Input

✅

6ms

Get Drift

✅

30ms

Apply Drift Bad Input

✅

2ms

Remove Drift

✅

20ms

Chain Drift

✅

27ms

Drift Correction

✅

31ms

Median Filter Centered

✅

7ms

Processing Filtering

Test Name

Status

Duration

Filter Bad

✅

34ms

Localization

✅

47ms

Tracking

✅

34ms

Tracks Compute

✅

51ms

Processing Grapher

Test Name

Status

Duration

Blank

✅

323ms

Histogram

✅

717ms

Scatter

✅

413ms

Cloud

✅

862ms

Astigmatism3D

✅

424ms

Processing Palm

Test Name

Status

Duration

Palm Dll Valid

✅

2ms

Palm Cpu Empty Result

✅

7ms

Palm Cpu Image

✅

1.28s

Palm Cpu Stack

✅

5.03s

Palm Cpu Stack Plane Selection

✅

278ms

Palm Cpu Stack Dll Check Quadrant

✅

378ms

Cpu Auto Threshold

✅

60ms

Tracking

✅

8.02s

Blinking Reconnection

✅

275ms

Tracks Compute

✅

86ms

Align

✅

137ms

Wavelett

✅

130ms

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

✅

23ms

Parse Localization For Tracking

✅

6ms
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

✅

34ms

Draw Line

✅

1ms

Draw Gaussian

✅

2ms

Localizations

✅

2ms

Localizations Gaussian

✅

3ms

Tracks

✅

2ms

Processing Step

Test Name

Status

Duration

Object Creation

✅

1ms

Prepare Action

✅

20ms
Log Test : Object Creation 
Step : Step(group_name='name', keys=['key'], process_func=<function test_object_creation.<locals>.f at 0x7f6c72041120>, filter_func=<function test_object_creation.<locals>.f at 0x7f6c72041120>, 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

✅

20ms

Render Tracks Image Bad Input

✅

5ms

Render Roi

✅

45ms

Render Roi Bad Input

✅

2ms

Plot Histogram

✅

1.01s

Plot Histogram Bad Input

✅

178ms

Plot Violin

✅

782ms

Plot Violin Bad Input

✅

90ms

Plot Heatmap

✅

500ms

Plot Heatmap Bad Input

✅

87ms

Settings Groups

Test Name

Status

Duration

Base Group

✅

3ms

Batch

✅

208ms

Batch Get Path

✅

6ms

Batch Get Stacks

✅

17ms

Calibration

✅

8ms

Localization

✅

25ms

Gaussian Fit

✅

11ms

Spline Fit

✅

6ms

Beads

✅

6ms

Tracking

✅

5ms

Tracks Blinking Reconnection

✅

7ms

Tracks Computes

✅

10ms

Gallery

✅

7ms

Visualization Hr

✅

10ms

Visualization Graph

✅

6ms

Filters

✅

67ms

Filters L

✅

34ms

Filters T

✅

23ms
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

✅

116ms

Settings Group Getter

✅

54ms

Settings Signal

✅

76ms

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

✅

4ms

Spin Float

✅

4ms

Check Box

✅

4ms

Combo

✅

4ms

Browse File

✅

5ms

File List

✅

7ms

Check Range Int

✅

8ms

Check Range Float

✅

6ms

Button

✅

3ms

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

✅

14ms

Save Tif 2D

✅

14ms

Save Tif Bad Stack

✅

1ms

Open Tif

✅

5ms

Open Tif Bad File

✅

1ms

Save Png

✅

8ms

Save Png Color

✅

12ms

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_072949
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

✅

4ms

Update Meta

✅

5ms

Open Old File

✅

5ms

Open Old Irregular File

✅

4ms

Column Migrator

✅

4ms

Analyze

✅

4ms

Migrate

✅

345ms
Log Test : Analyze 
.

Tools Logger

Test Name

Status

Duration

Logger

✅

18ms

Logger Bad Use

✅

5ms

Logger With Use

✅

3ms

Tools Monitoring

Test Name

Status

Duration

Monitoring

✅

1.20s

Monitoring Save

✅

6.81s
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 : [657.7421875, 657.76171875, 657.7734375, 657.78125, 657.79296875, 657.7890625]
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

✅

7ms

Bad Load Tif

✅

6ms

Bad Load Coef

✅

27ms

Bad Compute

✅

6ms

Compute

✅

8ms

Bad Align

✅

8ms

Align

✅

47ms

Ui Astigmatism3Dwidget

Test Name

Status

Duration

Widget Creation

✅

625ms

Bad Load Loc

✅

160ms

Bad Load Model

✅

160ms

Bad Compute

✅

505ms

Check Loc

✅

212ms

Compute

✅

415ms

Compute Mean Beads

✅

429ms

Compute Remove Bead Col

✅

399ms

Compute Remove Multi

✅

399ms

Compute Z

✅

430ms

Compute Center Z

✅

413ms

Compute Bad Model

✅

427ms

Bad Estimate

✅

153ms

Estimate

✅

229ms

Estimate Backup

✅

248ms

Sync Spin

✅

198ms

Download

✅

217ms
Log Test : Download 
/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref

Ui Baseplotlywidget

Test Name

Status

Duration

Creation

✅

46ms

Update Plotly

✅

54ms

Update Plotly No Js

✅

54ms

Download Plotly

✅

54ms

Export Plotly

✅

55ms
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

✅

34ms

Ui Graphviewer

Test Name

Status

Duration

Widget Creation

✅

220ms

Add Stack

✅

280ms

Actualize

✅

402ms

Reset Filtered

✅

285ms

Update Filtered

✅

336ms

Update Plot

✅

699ms

Dual Source

✅

463ms

Get Plot Data

✅

870ms

Tracks Source

✅

210ms
Log Test : Add Stack 
No valid settings file to load.

Ui Viewerhrwidget

Test Name

Status

Duration

Widget Creation

✅

1.68s

Add Stack

✅

1.39s

Change Source

✅

1.43s

Actualize

✅

1.41s

Reset Filtered

✅

1.47s

Update Filtered

✅

1.47s

Save

✅

1.47s

Screenshot

✅

1.46s

Crop

✅

1.47s

Generate Bad

✅

1.51s

Generate

✅

1.56s

Generate Drift

✅

1.56s
Log Test : Save 
INFO: Image file saved successfully.
Log Test : Screenshot 
INFO: Screenshot saved successfully.
Log Test : Generate 
[05-05-2026 07:30:24] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073024.log
[05-05-2026 07:30:24] Start Processing.
[05-05-2026 07:30:24] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 07:30:24] Meta file saved.
[05-05-2026 07:30:24] Settings saved.
[05-05-2026 07:30:24] Localization disabled.
[05-05-2026 07:30:24] Beads Extraction disabled.
[05-05-2026 07:30:24] Tracking disabled.
[05-05-2026 07:30:24] Blinking Reconnection disabled.
[05-05-2026 07:30:24] Tracks Compute disabled.
[05-05-2026 07:30:24] Gallery generation disabled.
[05-05-2026 07:30:24] Graphical visualization disabled.
[05-05-2026 07:30:24] High-resolution visualization disabled.
[05-05-2026 07:30:24] Processing complete.
[05-05-2026 07:30:24] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073024.log
Loading setting file '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/settings-20260505_073024.json'.
   Loading files from the '/home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer' folder with the timestamp 20260505_073024.
    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

✅

1.48s

Widget On Load Setting

✅

1.47s

Widget Reset Setting

✅

1.43s

Widget Reset Layer

✅

2.06s

Widget Get Actual Image

✅

1.77s

Widget Add Detection Layers

✅

4.60s

Widget Preview

✅

2.55s

Widget Roi Filter Layer

✅

2.12s

Widget Auto Threshold

✅

1.86s

Widget Thread Process

✅

1.96s

Widget Keyblocker

✅

1.87s

Viewer3D

✅

1.94s
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 07:30:46] Log opened : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073046.log
[05-05-2026 07:30:46] Start Processing.
[05-05-2026 07:30:46] Output folder: /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[05-05-2026 07:30:46] Meta file saved.
[05-05-2026 07:30:46] Settings saved.
[05-05-2026 07:30:46] Localization disabled.
[05-05-2026 07:30:46] Beads Extraction disabled.
[05-05-2026 07:30:46] Tracking disabled.
[05-05-2026 07:30:46] Blinking Reconnection disabled.
[05-05-2026 07:30:46] Tracks Compute disabled.
[05-05-2026 07:30:46] Gallery generation disabled.
[05-05-2026 07:30:46] Graphical visualization disabled.
[05-05-2026 07:30:46] High-resolution visualization disabled.
[05-05-2026 07:30:46] Processing complete.
[05-05-2026 07:30:46] Log closed : /home/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260505_073046.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.