Test Report Ci Macos-Latest 3.12
Environnement
Python |
3.12.10 |
Platform |
macOS-15.7.4-arm64-arm-64bit |
CI |
true |
System |
Darwin |
CPU |
Apple M1 (Virtual) (Unknown frequency - 3 Cores (3 Logical)) |
RAM |
7.00 GB |
GPU |
Error detecting GPU: NVML Shared Library Not Found |
Summary
263 tests collected, 263 passed ✅, 0 failed ❌, 0 skipped ⏭️ in 0:00:57s on 04/05/2026 at 13:55:28
Monitoring
Test Cases
Palmtracer
Test Name |
Status |
Duration |
|---|---|---|
Reset Result |
✅ |
415ms |
Getter Localization |
✅ |
21ms |
Getter Beads |
✅ |
21ms |
Getter Tracks |
✅ |
27ms |
Getter Tracks Compute |
✅ |
20ms |
Get Status |
✅ |
20ms |
Getter Path |
✅ |
20ms |
Getter Stack |
✅ |
24ms |
Getter Suffix |
✅ |
20ms |
Load Bad Dll |
✅ |
29ms |
Load Nothing |
✅ |
19ms |
Load |
✅ |
86ms |
Process No Input |
✅ |
23ms |
Process Nothing |
✅ |
107ms |
Process Bad Dll |
✅ |
20ms |
Process Multiple Stack |
✅ |
43ms |
Process Localization |
✅ |
45ms |
Process Localization Z |
✅ |
108ms |
Process Localization Spline Bad |
✅ |
37ms |
Process Localization Spline |
✅ |
49ms |
Process Beads Extraction No Beads |
✅ |
48ms |
Process Plane Discontinuous |
✅ |
25ms |
Process Beads Extraction |
✅ |
76ms |
Process Tracking |
✅ |
142ms |
Process Tracking Blinking |
✅ |
63ms |
Process Tracks Compute |
✅ |
2.28s |
Process Gallery |
✅ |
72ms |
Process Visualization Graph |
✅ |
2.04s |
Process Visualization Hr |
✅ |
1.27s |
Process All |
✅ |
2.13s |
Reset Filtered |
✅ |
24ms |
Update Filtered |
✅ |
65ms |
Save Filtered |
✅ |
29ms |
Filter Localization |
✅ |
1.29s |
Filter Tracks Compute |
✅ |
2.44s |
Add Color |
✅ |
40ms |
Get Astigmatism Model |
✅ |
38ms |
Log Test : Update Filtered
[04-05-2026 13:54:41] Log opened : /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_135441.log
[04-05-2026 13:54:41] Start Processing.
[04-05-2026 13:54:41] Output folder: /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[04-05-2026 13:54:41] Meta file saved.
[04-05-2026 13:54:41] Settings saved.
[04-05-2026 13:54:41] Localization load previous result (Timestamp : 20260101_000000).
[04-05-2026 13:54:41] File 'localizations-20260101_000000.csv' loaded successfully, 451 row(s) found.
[04-05-2026 13:54:41] Beads Extraction disabled.
[04-05-2026 13:54:41] Tracking disabled.
[04-05-2026 13:54:41] Blinking Reconnection disabled.
[04-05-2026 13:54:41] Tracks Compute disabled.
[04-05-2026 13:54:41] Gallery generation disabled.
[04-05-2026 13:54:41] Graphical visualization disabled.
[04-05-2026 13:54:41] High-resolution visualization disabled.
[04-05-2026 13:54:41] Processing complete.
[04-05-2026 13:54:41] Log closed : /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_135441.log
Processing Astigmatism3D
Test Name |
Status |
Duration |
|---|---|---|
Get Z From Planes |
✅ |
1ms |
Get Z From Step |
✅ |
1ms |
Remove Multi Loc |
✅ |
8ms |
Sigma Model |
✅ |
1ms |
Model Validity |
✅ |
2ms |
Model Projection Validity |
✅ |
12ms |
Find Model Center |
✅ |
2ms |
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': 2.265409096055544, 'slope_mean': 0.00156321987547227}
Processing Drift
Test Name |
Status |
Duration |
|---|---|---|
Extract Bead Bad Input |
✅ |
3ms |
Extract Beads No Match Returns Empty |
✅ |
4ms |
Assign Tracks No Pairs |
✅ |
1ms |
Assign Tracks Skip Used Track |
✅ |
1ms |
Extract Beads |
✅ |
30ms |
Remove Beads |
✅ |
8ms |
Get Drift Bad Input |
✅ |
3ms |
Get Drift |
✅ |
15ms |
Apply Drift Bad Input |
✅ |
1ms |
Remove Drift |
✅ |
11ms |
Chain Drift |
✅ |
10ms |
Drift Correction |
✅ |
11ms |
Median Filter Centered |
✅ |
2ms |
Processing Filtering
Test Name |
Status |
Duration |
|---|---|---|
Filter Bad |
✅ |
13ms |
Localization |
✅ |
19ms |
Tracking |
✅ |
14ms |
Tracks Compute |
✅ |
20ms |
Processing Gallery
Test Name |
Status |
Duration |
|---|---|---|
Make Gallery |
✅ |
13ms |
Processing Grapher
Test Name |
Status |
Duration |
|---|---|---|
Blank |
✅ |
252ms |
Histogram |
✅ |
381ms |
Scatter |
✅ |
218ms |
Cloud |
✅ |
403ms |
Astigmatism3D |
✅ |
223ms |
Processing Palm
Test Name |
Status |
Duration |
|---|---|---|
Palm Dll Valid |
✅ |
1ms |
Palm Cpu Empty Result |
✅ |
3ms |
Palm Cpu Image |
✅ |
453ms |
Palm Cpu Stack |
✅ |
1.85s |
Palm Cpu Stack Plane Selection |
✅ |
109ms |
Palm Cpu Stack Dll Check Quadrant |
✅ |
136ms |
Cpu Auto Threshold |
✅ |
26ms |
Tracking |
✅ |
2.73s |
Blinking Reconnection |
✅ |
97ms |
Tracks Compute |
✅ |
26ms |
Align |
✅ |
115ms |
Wavelett |
✅ |
62ms |
Astigmatism 3D Calibration |
✅ |
5ms |
Astigmatism 3D Estimation |
✅ |
3ms |
Log Test : Palm Cpu Image
Comparaison avec : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-MSD-True.csv'
Comparaison avec : '/Users/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 : '/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref/tracking2-MSD-False.csv'
Comparaison avec : '/Users/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 : '/Users/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 : '/Users/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 : '/Users/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 |
✅ |
1ms |
Rearrange Dataframe Columns |
✅ |
2ms |
Log10 Dataframe |
✅ |
2ms |
Degrees To Radians |
✅ |
1ms |
Radians To Degrees |
✅ |
1ms |
Wrap Angle |
✅ |
1ms |
Manage Theta |
✅ |
1ms |
Parse Irregular Array |
✅ |
1ms |
Parse Result |
✅ |
8ms |
Parse Localization For Tracking |
✅ |
2ms |
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 |
✅ |
2ms |
Get Tracks Colors |
✅ |
16ms |
Draw Line |
✅ |
1ms |
Draw Gaussian |
✅ |
1ms |
Localizations |
✅ |
1ms |
Localizations Gaussian |
✅ |
1ms |
Tracks |
✅ |
1ms |
Processing Step
Test Name |
Status |
Duration |
|---|---|---|
Object Creation |
✅ |
1ms |
Prepare Action |
✅ |
8ms |
Log Test : Object Creation
Step : Step(group_name='name', keys=['key'], process_func=<function test_object_creation.<locals>.f at 0x13b1ebce0>, filter_func=<function test_object_creation.<locals>.f at 0x13b1ebce0>, 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 |
✅ |
9ms |
Render Hr Image Bad Input |
✅ |
1ms |
Render Tracks Image |
✅ |
11ms |
Render Tracks Image Bad Input |
✅ |
2ms |
Render Roi |
✅ |
22ms |
Render Roi Bad Input |
✅ |
1ms |
Plot Histogram |
✅ |
336ms |
Plot Histogram Bad Input |
✅ |
62ms |
Plot Violin |
✅ |
219ms |
Plot Violin Bad Input |
✅ |
36ms |
Plot Heatmap |
✅ |
265ms |
Plot Heatmap Bad Input |
✅ |
33ms |
Settings Groups
Test Name |
Status |
Duration |
|---|---|---|
Base Group |
✅ |
1ms |
Batch |
✅ |
72ms |
Batch Get Path |
✅ |
2ms |
Batch Get Stacks |
✅ |
9ms |
Calibration |
✅ |
4ms |
Localization |
✅ |
11ms |
Gaussian Fit |
✅ |
5ms |
Spline Fit |
✅ |
2ms |
Beads |
✅ |
2ms |
Tracking |
✅ |
2ms |
Tracks Blinking Reconnection |
✅ |
3ms |
Tracks Computes |
✅ |
3ms |
Gallery |
✅ |
2ms |
Visualization Hr |
✅ |
3ms |
Visualization Graph |
✅ |
3ms |
Filters |
✅ |
24ms |
Filters L |
✅ |
13ms |
Filters T |
✅ |
9ms |
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 |
✅ |
43ms |
Settings Group Getter |
✅ |
21ms |
Settings Signal |
✅ |
26ms |
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 |
✅ |
1ms |
Create Setting From Dict |
✅ |
3ms |
Create Setting From Dict Fail |
✅ |
1ms |
Spin Int |
✅ |
12ms |
Spin Float |
✅ |
2ms |
Check Box |
✅ |
1ms |
Combo |
✅ |
1ms |
Browse File |
✅ |
3ms |
File List |
✅ |
2ms |
Check Range Int |
✅ |
2ms |
Check Range Float |
✅ |
3ms |
Button |
✅ |
1ms |
Tools Fileio
Test Name |
Status |
Duration |
|---|---|---|
Add Extension |
✅ |
1ms |
Add Suffix |
✅ |
1ms |
Get Timestamp For Files |
✅ |
1ms |
Get Last File |
✅ |
1ms |
Extract Suffix |
✅ |
1ms |
Cleanup Process |
✅ |
1ms |
Load Dll |
✅ |
2ms |
Save Json |
✅ |
1ms |
Open Json |
✅ |
1ms |
Open Json Bad File |
✅ |
1ms |
Save Tif |
✅ |
11ms |
Save Tif 2D |
✅ |
9ms |
Save Tif Bad Stack |
✅ |
1ms |
Open Tif |
✅ |
4ms |
Open Tif Bad File |
✅ |
1ms |
Save Png |
✅ |
3ms |
Save Png Color |
✅ |
6ms |
Save Png Bad Sample |
✅ |
1ms |
Open Calibration Mat Bad File |
✅ |
1ms |
Open Calibration Mat |
✅ |
2ms |
Log Test : Get Timestamp For Files
Timestamp with hour : 20260504_135454
Timestamp without hour : 20260504
Log Test : Get Last File
/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/File-03.txt
/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/File-03.txt
Log Test : Load Dll
Unable to load the DLL 'PALMTracer_File.dylib':
dlopen(/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/DLL/PALMTracer_File.dylib, 0x0006): tried: '/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/DLL/PALMTracer_File.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/DLL/PALMTracer_File.dylib' (no such file), '/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/DLL/PALMTracer_File.dylib' (no such file)
Tools Filemigrator
Test Name |
Status |
Duration |
|---|---|---|
Open |
✅ |
2ms |
Update Meta |
✅ |
2ms |
Open Old File |
✅ |
2ms |
Open Old Irregular File |
✅ |
2ms |
Column Migrator |
✅ |
2ms |
Analyze |
✅ |
2ms |
Migrate |
✅ |
132ms |
Log Test : Analyze
.
Tools Logger
Test Name |
Status |
Duration |
|---|---|---|
Logger |
✅ |
9ms |
Logger Bad Use |
✅ |
3ms |
Logger With Use |
✅ |
2ms |
Tools Monitoring
Test Name |
Status |
Duration |
|---|---|---|
Monitoring |
✅ |
1.38s |
Monitoring Save |
✅ |
6.87s |
Log Test : Monitoring
4 entrées.
Timestamps : [0.0, 0.47, 0.91, 1.02]
CPU Usage : [0.03333333333333333, 0.06666666666666667, 2.6999999999999997, 2.5]
GPU Usage : [0, 0, 0, 0]
Memory Usage : [729.140625, 729.140625, 729.140625, 729.140625]
Disk Usage : [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 |
✅ |
3ms |
Builders Spin |
✅ |
1ms |
Sync Spin |
✅ |
1ms |
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 |
✅ |
9ms |
Bad Load Tif |
✅ |
4ms |
Bad Load Coef |
✅ |
5ms |
Bad Compute |
✅ |
3ms |
Compute |
✅ |
4ms |
Bad Align |
✅ |
4ms |
Align |
✅ |
31ms |
Ui Astigmatism3Dwidget
Test Name |
Status |
Duration |
|---|---|---|
Widget Creation |
✅ |
883ms |
Bad Load Loc |
✅ |
144ms |
Bad Load Model |
✅ |
84ms |
Bad Compute |
✅ |
79ms |
Check Loc |
✅ |
113ms |
Compute |
✅ |
225ms |
Compute Mean Beads |
✅ |
212ms |
Compute Remove Bead Col |
✅ |
203ms |
Compute Remove Multi |
✅ |
197ms |
Compute Z |
✅ |
348ms |
Compute Center Z |
✅ |
204ms |
Compute Bad Model |
✅ |
217ms |
Bad Estimate |
✅ |
82ms |
Estimate |
✅ |
122ms |
Estimate Backup |
✅ |
131ms |
Sync Spin |
✅ |
105ms |
Download |
✅ |
119ms |
Log Test : Download
/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/ref
Ui Baseplotlywidget
Test Name |
Status |
Duration |
|---|---|---|
Creation |
✅ |
27ms |
Update Plotly |
✅ |
31ms |
Update Plotly No Js |
✅ |
30ms |
Download Plotly |
✅ |
31ms |
Export Plotly |
✅ |
34ms |
Log Test : Download Plotly
/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/output
/Users/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 |
✅ |
4ms |
Bad Load |
✅ |
4ms |
Mirgate |
✅ |
19ms |
Ui Graphviewer
Test Name |
Status |
Duration |
|---|---|---|
Widget Creation |
✅ |
131ms |
Add Stack |
✅ |
172ms |
Actualize |
✅ |
216ms |
Reset Filtered |
✅ |
159ms |
Update Filtered |
✅ |
198ms |
Update Plot |
✅ |
341ms |
Dual Source |
✅ |
237ms |
Get Plot Data |
✅ |
431ms |
Tracks Source |
✅ |
110ms |
Log Test : Add Stack
No valid settings file to load.
Ui Viewerhrwidget
Test Name |
Status |
Duration |
|---|---|---|
Widget Creation |
✅ |
886ms |
Add Stack |
✅ |
633ms |
Change Source |
✅ |
637ms |
Actualize |
✅ |
635ms |
Reset Filtered |
✅ |
655ms |
Update Filtered |
✅ |
648ms |
Save |
✅ |
649ms |
Screenshot |
✅ |
658ms |
Crop |
✅ |
661ms |
Generate Bad |
✅ |
671ms |
Generate |
✅ |
690ms |
Generate Drift |
✅ |
711ms |
Log Test : Save
INFO: Image file saved successfully.
Log Test : Screenshot
INFO: Screenshot saved successfully.
Log Test : Generate
[04-05-2026 13:55:15] Log opened : /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_135515.log
[04-05-2026 13:55:15] Start Processing.
[04-05-2026 13:55:15] Output folder: /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[04-05-2026 13:55:15] Meta file saved.
[04-05-2026 13:55:15] Settings saved.
[04-05-2026 13:55:15] Localization disabled.
[04-05-2026 13:55:15] Beads Extraction disabled.
[04-05-2026 13:55:15] Tracking disabled.
[04-05-2026 13:55:15] Blinking Reconnection disabled.
[04-05-2026 13:55:15] Tracks Compute disabled.
[04-05-2026 13:55:15] Gallery generation disabled.
[04-05-2026 13:55:15] Graphical visualization disabled.
[04-05-2026 13:55:15] High-resolution visualization disabled.
[04-05-2026 13:55:15] Processing complete.
[04-05-2026 13:55:15] Log closed : /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_135515.log
Loading setting file '/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/settings-20260504_135515.json'.
Loading files from the '/Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer' folder with the timestamp 20260504_135515.
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 |
✅ |
714ms |
Widget On Load Setting |
✅ |
708ms |
Widget Reset Setting |
✅ |
686ms |
Widget Reset Layer |
✅ |
1.16s |
Widget Get Actual Image |
✅ |
812ms |
Widget Add Detection Layers |
✅ |
1.86s |
Widget Preview |
✅ |
920ms |
Widget Roi Filter Layer |
✅ |
879ms |
Widget Auto Threshold |
✅ |
778ms |
Widget Thread Process |
✅ |
858ms |
Widget Keyblocker |
✅ |
805ms |
Viewer3D |
✅ |
891ms |
Log Test : Widget Get Actual Image
INFO: Loaded /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.
Log Test : Widget Roi Filter Layer
INFO: Loaded /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.
Log Test : Widget Thread Process
INFO: Loaded /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack.tif into Napari viewer.
[04-05-2026 13:55:25] Log opened : /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_135525.log
[04-05-2026 13:55:25] Start Processing.
[04-05-2026 13:55:25] Output folder: /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer
[04-05-2026 13:55:26] Meta file saved.
[04-05-2026 13:55:26] Settings saved.
[04-05-2026 13:55:26] Localization disabled.
[04-05-2026 13:55:26] Beads Extraction disabled.
[04-05-2026 13:55:26] Tracking disabled.
[04-05-2026 13:55:26] Blinking Reconnection disabled.
[04-05-2026 13:55:26] Tracks Compute disabled.
[04-05-2026 13:55:26] Gallery generation disabled.
[04-05-2026 13:55:26] Graphical visualization disabled.
[04-05-2026 13:55:26] High-resolution visualization disabled.
[04-05-2026 13:55:26] Processing complete.
[04-05-2026 13:55:26] Log closed : /Users/runner/work/palm-tracer/palm-tracer/palm_tracer/_tests/input/stack_PALM_Tracer/log-20260504_135525.log
Auto Threshold: 63.95
Log Test : Widget Keyblocker
INFO: Loading the setting file '/Users/runner/.palm_tracer/settings.json'.
INFO: Loaded /Users/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.